[bug#55424] [PATCH 001/602] packages: Fix typo in package-superseded doc.

[bug#55424] [PATCH 001/602] packages: Fix typo in package-superseded doc.

[Maxim Cournoyer]

* guix/packages.scm (package-superseded): Fix typo.
---
 guix/packages.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/guix/packages.scm b/guix/packages.scm
index a79b36d03d..18fa190c1d 100644
--- a/guix/packages.scm
+++ b/guix/packages.scm
@@ -662,7 +662,7 @@ (define (hidden-package? p)
   (assoc-ref (package-properties p) 'hidden?))
 
 (define (package-superseded p)
-  "Return the package the supersedes P, or #f if P is still current."
+  "Return the package that supersedes P, or #f if P is still current."
   (assoc-ref (package-properties p) 'superseded))
 
 (define (deprecated-package old-name p)
-- 
2.36.0

[bug#55424] [PATCH 002/602] etc/committer: Prefix (sxml xpath) symbols to avoid name conflict.

[Maxim Cournoyer]

This avoids a naming conflict for 'filter', provided by both (srfi srfi-1)
and (sxml xpath).

* etc/committer.scm.in: Use 'use-modules' instead of 'import', and use a
prefix for the (sxml xpath) module.
(new-sexp): Adjust accordingly.
(change-commit-message): Likewise.
---
 etc/committer.scm.in | 33 +++++++++++++++++----------------
 1 file changed, 17 insertions(+), 16 deletions(-)

diff --git a/etc/committer.scm.in b/etc/committer.scm.in
index 5a57d51577..3b37320e89 100755
--- a/etc/committer.scm.in
+++ b/etc/committer.scm.in
@@ -6,6 +6,7 @@
 ;;; Copyright © 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2021 Sarah Morgensen <iskarian@mgsn.dev>
 ;;; Copyright © 2021 Xinglu Chen <public@yoctocell.xyz>
+;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -28,19 +29,19 @@
 
 ;;; Code:
 
-(import (sxml xpath)
-        (srfi srfi-1)
-        (srfi srfi-2)
-        (srfi srfi-9)
-        (srfi srfi-11)
-        (srfi srfi-26)
-        (ice-9 format)
-        (ice-9 popen)
-        (ice-9 match)
-        (ice-9 rdelim)
-        (ice-9 regex)
-        (ice-9 textual-ports)
-        (guix gexp))
+(use-modules ((sxml xpath) #:prefix xpath:)
+             (srfi srfi-1)
+             (srfi srfi-2)
+             (srfi srfi-9)
+             (srfi srfi-11)
+             (srfi srfi-26)
+             (ice-9 format)
+             (ice-9 popen)
+             (ice-9 match)
+             (ice-9 rdelim)
+             (ice-9 regex)
+             (ice-9 textual-ports)
+             (guix gexp))
 
 (define* (break-string str #:optional (max-line-length 70))
   "Break the string STR into lines that are no longer than MAX-LINE-LENGTH.
@@ -214,10 +215,10 @@ (define (new-sexp hunk)
 (define* (change-commit-message file-name old new #:optional (port (current-output-port)))
   "Print ChangeLog commit message for changes between OLD and NEW."
   (define (get-values expr field)
-    (match ((sxpath `(// ,field quasiquote *)) expr)
+    (match ((xpath:sxpath `(// ,field quasiquote *)) expr)
       (()
        ;; New-style plain lists
-       (match ((sxpath `(// ,field list *)) expr)
+       (match ((xpath:sxpath `(// ,field list *)) expr)
          ((inner) inner)
          (_ '())))
       ;; Old-style labelled inputs
@@ -234,7 +235,7 @@ (define (listify items)
   (define variable-name
     (second old))
   (define version
-    (and=> ((sxpath '(// version *any*)) new)
+    (and=> ((xpath:sxpath '(// version *any*)) new)
            first))
   (format port
           "gnu: ~a: Update to ~a.~%~%* ~a (~a): Update to ~a.~%"
-- 
2.36.0

[bug#55424] [PATCH 003/602] etc/committer: Teach it how to commit package removal.

[Maxim Cournoyer]

* etc/committer.scm.in (hunk-types): New variable.
(<hunk>): Rename hunk-definition? getter to 'hunk-type'.
(diff-info): Mute a git warning by separating file names from arguments with
'--'.  Rename the 'definitions?' variable to 'type'.
Use the 'addition type when a new package addition is detected, 'removal when
removed else #f.
(add-commit-message): Re-indent.
(remove-commit-message): New procedure.
(main)[definitions]: Make commit message conditional depending on whether it
is an addition or removal.
[changes]: Adjust indentation.
---
 etc/committer.scm.in | 164 ++++++++++++++++++++++++-------------------
 1 file changed, 91 insertions(+), 73 deletions(-)

diff --git a/etc/committer.scm.in b/etc/committer.scm.in
index 3b37320e89..e7f1ca8c45 100755
--- a/etc/committer.scm.in
+++ b/etc/committer.scm.in
@@ -101,12 +101,16 @@ (define (surrounding-sexp port line-no)
            (read-line port)
            (loop (1- i) last-top-level-sexp))))))
 
+;;; Whether the hunk contains a newly added package (definition), a removed
+;;; package (removal) or something else (#false).
+(define hunk-types '(addition removal #false))
+
 (define-record-type <hunk>
   (make-hunk file-name
              old-line-number
              new-line-number
              diff-lines
-             definition?)
+             type)
   hunk?
   (file-name       hunk-file-name)
   ;; Line number before the change
@@ -115,8 +119,8 @@ (define-record-type <hunk>
   (new-line-number hunk-new-line-number)
   ;; The full diff to be used with "git apply --cached"
   (diff-lines hunk-diff-lines)
-  ;; Does this hunk add a definition?
-  (definition? hunk-definition?))
+  ;; Does this hunk add or remove a package?
+  (type hunk-type))                     ;one of 'hunk-types'
 
 (define* (hunk->patch hunk #:optional (port (current-output-port)))
   (let ((file-name (hunk-file-name hunk)))
@@ -134,25 +138,30 @@ (define (diff-info)
                           ;; new definitions with changes to existing
                           ;; definitions.
                           "--unified=1"
-                          "gnu")))
+                          "--" "gnu")))
     (define (extract-line-number line-tag)
       (abs (string->number
             (car (string-split line-tag #\,)))))
     (define (read-hunk)
       (let loop ((lines '())
-                 (definition? #false))
+                 (type #false))
         (let ((line (read-line port 'concat)))
           (cond
            ((eof-object? line)
-            (values (reverse lines) definition?))
+            (values (reverse lines) type))
            ((or (string-prefix? "@@ " line)
                 (string-prefix? "diff --git" line))
             (unget-string port line)
-            (values (reverse lines) definition?))
+            (values (reverse lines) type))
            (else
             (loop (cons line lines)
-                  (or definition?
-                      (string-prefix? "+(define" line))))))))
+                  (or type
+                      (cond
+                       ((string-prefix? "+(define" line)
+                        'addition)
+                       ((string-prefix? "-(define" line)
+                        'removal)
+                       (else #false)))))))))
     (define info
       (let loop ((acc '())
                  (file-name #f))
@@ -167,13 +176,13 @@ (define info
             (match (string-split line #\space)
               ((_ old-start new-start . _)
                (let-values
-                   (((diff-lines definition?) (read-hunk)))
+                   (((diff-lines type) (read-hunk)))
                  (loop (cons (make-hunk file-name
                                         (extract-line-number old-start)
                                         (extract-line-number new-start)
                                         (cons (string-append line "\n")
                                               diff-lines)
-                                        definition?) acc)
+                                        type) acc)
                        file-name)))))
            (else (loop acc file-name))))))
     (close-pipe port)
@@ -263,10 +272,18 @@ (define version
                                           (listify added))))))))))
             '(inputs propagated-inputs native-inputs)))
 
-(define* (add-commit-message file-name variable-name #:optional (port (current-output-port)))
-  "Print ChangeLog commit message for a change to FILE-NAME adding a definition."
-  (format port
-          "gnu: Add ~a.~%~%* ~a (~a): New variable.~%"
+(define* (add-commit-message file-name variable-name
+                             #:optional (port (current-output-port)))
+  "Print ChangeLog commit message for a change to FILE-NAME adding a
+definition."
+  (format port "gnu: Add ~a.~%~%* ~a (~a): New variable.~%"
+          variable-name file-name variable-name))
+
+(define* (remove-commit-message file-name variable-name
+                                #:optional (port (current-output-port)))
+  "Print ChangeLog commit message for a change to FILE-NAME removing a
+definition."
+  (format port "gnu: Remove ~a.~%~%* ~a (~a): Delete variable.~%"
           variable-name file-name variable-name))
 
 (define* (custom-commit-message file-name variable-name message changelog
@@ -345,66 +362,67 @@ (define* (change-commit-message* file-name old new #:rest rest)
     (()
      (display "Nothing to be done.\n" (current-error-port)))
     (hunks
-     (let-values
-         (((definitions changes)
-           (partition hunk-definition? hunks)))
+     (let-values (((definitions changes) (partition hunk-type hunks)))
+       ;; Additions/removals.
+       (for-each
+        (lambda (hunk)
+          (and-let* ((define-line (find (cut string-match "(\\+|-)\\(define" <>)
+                                        (hunk-diff-lines hunk)))
+                     (variable-name (and=> (string-tokenize define-line)
+                                           second))
+                     (commit-message-proc (match (hunk-type hunk)
+                                            ('addition add-commit-message)
+                                            ('removal remove-commit-message))))
+            (commit-message-proc (hunk-file-name hunk) variable-name)
+            (let ((port (open-pipe* OPEN_WRITE
+                                    "git" "apply"
+                                    "--cached"
+                                    "--unidiff-zero")))
+              (hunk->patch hunk port)
+              (unless (eqv? 0 (status:exit-val (close-pipe port)))
+                (error "Cannot apply")))
 
-       ;; Additions.
-       (for-each (lambda (hunk)
-                   (and-let*
-                       ((define-line (find (cut string-prefix? "+(define" <>)
-                                           (hunk-diff-lines hunk)))
-                        (variable-name (and=> (string-tokenize define-line) second)))
-                     (add-commit-message (hunk-file-name hunk) variable-name)
-                     (let ((port (open-pipe* OPEN_WRITE                   
-                                             "git" "apply"                
-                                             "--cached"                   
-                                             "--unidiff-zero")))          
-                       (hunk->patch hunk port)                            
-                       (unless (eqv? 0 (status:exit-val (close-pipe port))) 
-                         (error "Cannot apply")))
+            (let ((port (open-pipe* OPEN_WRITE "git" "commit" "-F" "-")))
+              (commit-message-proc (hunk-file-name hunk) variable-name port)
+              (usleep %delay)
+              (unless (eqv? 0 (status:exit-val (close-pipe port)))
+                (error "Cannot commit"))))
+          (usleep %delay))
+        definitions))
 
-                     (let ((port (open-pipe* OPEN_WRITE "git" "commit" "-F" "-")))
-                       (add-commit-message (hunk-file-name hunk)
-                                           variable-name port)
-                       (usleep %delay)
+     ;; Changes.
+     (for-each
+      (match-lambda
+        ((new old . hunks)
+         (for-each (lambda (hunk)
+                     (let ((port (open-pipe* OPEN_WRITE
+                                             "git" "apply"
+                                             "--cached"
+                                             "--unidiff-zero")))
+                       (hunk->patch hunk port)
                        (unless (eqv? 0 (status:exit-val (close-pipe port)))
-                         (error "Cannot commit"))))
-                   (usleep %delay))
-                 definitions)
-
-       ;; Changes.
-       (for-each (match-lambda
-                   ((new old . hunks)
-                    (for-each (lambda (hunk)
-                                (let ((port (open-pipe* OPEN_WRITE
-                                                        "git" "apply"
-                                                        "--cached"
-                                                        "--unidiff-zero")))
-                                  (hunk->patch hunk port)
-                                  (unless (eqv? 0 (status:exit-val (close-pipe port)))
-                                    (error "Cannot apply")))
-                                (usleep %delay))
-                              hunks)
-                    (define copyright-line
-                      (any (lambda (line) (and=> (string-prefix? "+;;; Copyright ©" line)
-                                              (const line)))
-                                (hunk-diff-lines (first hunks))))
-                    (cond
-                     (copyright-line
-                      (add-copyright-line copyright-line))
-                     (else
-                      (let ((port (open-pipe* OPEN_WRITE "git" "commit" "-F" "-")))
-                        (change-commit-message* (hunk-file-name (first hunks))
-                                                old new)
-                      (change-commit-message* (hunk-file-name (first hunks))
-                                              old new
-                                              port)
-                      (usleep %delay)
-                      (unless (eqv? 0 (status:exit-val (close-pipe port)))
-                        (error "Cannot commit")))))))
-                 ;; XXX: we recompute the hunks here because previous
-                 ;; insertions lead to offsets.
-                 (new+old+hunks (diff-info)))))))
+                         (error "Cannot apply")))
+                     (usleep %delay))
+                   hunks)
+         (define copyright-line
+           (any (lambda (line) (and=> (string-prefix? "+;;; Copyright ©" line)
+                                      (const line)))
+                (hunk-diff-lines (first hunks))))
+         (cond
+          (copyright-line
+           (add-copyright-line copyright-line))
+          (else
+           (let ((port (open-pipe* OPEN_WRITE "git" "commit" "-F" "-")))
+             (change-commit-message* (hunk-file-name (first hunks))
+                                     old new)
+             (change-commit-message* (hunk-file-name (first hunks))
+                                     old new
+                                     port)
+             (usleep %delay)
+             (unless (eqv? 0 (status:exit-val (close-pipe port)))
+               (error "Cannot commit")))))))
+      ;; XXX: we recompute the hunks here because previous
+      ;; insertions lead to offsets.
+      (new+old+hunks (diff-info))))))
 
 (apply main (cdr (command-line)))
-- 
2.36.0

[bug#55424] [PATCH 004/602] utils: Add a 'delete-expression' procedure.

[Maxim Cournoyer]

* guix/utils.scm: Fix copyright lines and order imports.
(edit-expression): Fix typo in doc.  Add a new 'include-trailing-newline?'
keyword argument.  Update doc.
(delete-expression): New procedure.
---
 guix/utils.scm | 32 +++++++++++++++++++++-----------
 1 file changed, 21 insertions(+), 11 deletions(-)

diff --git a/guix/utils.scm b/guix/utils.scm
index 44c46cb4a9..e169624ee6 100644
--- a/guix/utils.scm
+++ b/guix/utils.scm
@@ -8,12 +8,11 @@
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2018, 2020 Marius Bakke <marius@gnu.org>
 ;;; Copyright © 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2020, 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2021 Chris Marusich <cmmarusich@gmail.com>
 ;;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be>
 ;;; Copyright © 2018 Steve Sprang <scs@stevesprang.com>
-;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -38,7 +37,6 @@ (define-module (guix utils)
   #:use-module (srfi srfi-26)
   #:use-module (srfi srfi-39)
   #:use-module (srfi srfi-71)
-  #:use-module (ice-9 ftw)
   #:use-module (rnrs io ports)                    ;need 'port-position' etc.
   #:use-module ((rnrs bytevectors) #:select (bytevector-u8-set!))
   #:use-module (guix memoization)
@@ -49,10 +47,11 @@ (define-module (guix utils)
   #:use-module ((guix combinators) #:select (fold2))
   #:use-module (guix diagnostics)           ;<location>, &error-location, etc.
   #:use-module (ice-9 format)
-  #:use-module (ice-9 regex)
-  #:use-module (ice-9 match)
-  #:use-module (ice-9 format)
+  #:use-module (ice-9 ftw)
   #:use-module ((ice-9 iconv) #:prefix iconv:)
+  #:use-module (ice-9 match)
+  #:use-module (ice-9 regex)
+  #:use-module (ice-9 rdelim)
   #:use-module (ice-9 vlist)
   #:autoload   (zlib) (make-zlib-input-port make-zlib-output-port)
   #:use-module (system foreign)
@@ -133,6 +132,7 @@ (define-module (guix utils)
             readlink*
             go-to-location
             edit-expression
+            delete-expression
 
             filtered-port
             decompressed-port
@@ -433,11 +433,13 @@ (define (move-source-location-map! source target line)
          (hash-set! %source-location-map target-key
                     `(,@target-stamp ,source-map)))))))
 
-(define* (edit-expression source-properties proc #:key (encoding "UTF-8"))
+(define* (edit-expression source-properties proc #:key (encoding "UTF-8")
+                          include-trailing-newline?)
   "Edit the expression specified by SOURCE-PROPERTIES using PROC, which should
 be a procedure that takes the original expression in string and returns a new
-one.  ENCODING will be used to interpret all port I/O, it default to UTF-8.
-This procedure returns #t on success."
+one.  ENCODING will be used to interpret all port I/O, it defaults to UTF-8.
+This procedure returns #t on success.  When INCLUDE-TRAILING-NEWLINE? is true,
+the trailing line is included in the edited expression."
   (define file   (assq-ref source-properties 'filename))
   (define line   (assq-ref source-properties 'line))
   (define column (assq-ref source-properties 'column))
@@ -446,10 +448,14 @@ (define column (assq-ref source-properties 'column))
     (call-with-input-file file
       (lambda (in)
         (let* ( ;; The start byte position of the expression.
-               (start  (begin (go-to-location in (+ 1 line) (+ 1 column))
+               (start  (begin (go-to-location
+                               in (+ 1 line) (+ 1 column))
                               (ftell in)))
                ;; The end byte position of the expression.
-               (end    (begin (read in) (ftell in))))
+               (end    (begin (read in)
+                              (when include-trailing-newline?
+                                (read-line in))
+                              (ftell in))))
           (seek in 0 SEEK_SET)          ; read from the beginning of the file.
           (let* ((pre-bv  (get-bytevector-n in start))
                  ;; The expression in string form.
@@ -478,6 +484,10 @@ (define column (assq-ref source-properties 'column))
                 (move-source-location-map! (stat in) (stat file)
                                            (+ 1 line))))))))))
 
+(define (delete-expression source-properties)
+  "Delete the expression specified by SOURCE-PROPERTIES."
+  (edit-expression source-properties (const "") #:include-trailing-newline? #t))
+
 \f
 ;;;
 ;;; Keyword arguments.
-- 
2.36.0

[bug#55424] [PATCH 005/602] utils: Add a %guix-source-root-directory procedure.

[Maxim Cournoyer]

* guix/utils.scm (%guix-source-root-directory): New procedure.
---
 guix/utils.scm | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/guix/utils.scm b/guix/utils.scm
index e169624ee6..37b2e29800 100644
--- a/guix/utils.scm
+++ b/guix/utils.scm
@@ -78,6 +78,7 @@ (define-module (guix utils)
             substitute-keyword-arguments
             ensure-keyword-arguments
 
+            %guix-source-root-directory
             current-source-directory
 
             nix-system->gnu-triplet
@@ -1031,6 +1032,10 @@ (define (read! bv start n)
 ;;; Source location.
 ;;;
 
+(define (%guix-source-root-directory)
+  "Return the source root directory of the Guix found in %load-path."
+  (dirname (absolute-dirname "guix/packages.scm")))
+
 (define absolute-dirname
   ;; Memoize to avoid repeated 'stat' storms from 'search-path'.
   (mlambda (file)
-- 
2.36.0

[bug#55424] [PATCH 006/602] diagnostics: Fix typo about 0-indexed COL in location.

[Maxim Cournoyer]

* guix/diagnostics.scm (source-properties->location): The location column is
0-indexed, not 1-indexed (the same as in source-properties, so the code is
accurate).
---
 guix/diagnostics.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/guix/diagnostics.scm b/guix/diagnostics.scm
index bf1ced8140..9f0d558f2f 100644
--- a/guix/diagnostics.scm
+++ b/guix/diagnostics.scm
@@ -232,7 +232,7 @@ (define (source-properties->location loc)
 by Guile's `source-properties', `frame-source', `current-source-location',
 etc."
   ;; In accordance with the GCS, start line and column numbers at 1.  Note
-  ;; that unlike LINE and `port-column', COL is actually 1-indexed here...
+  ;; that unlike LINE and `port-column', COL is actually 0-indexed here...
   (match loc
     ((('line . line) ('column . col) ('filename . file)) ;common case
      (and file line col
-- 
2.36.0

[bug#55424] [PATCH 007/602] gnu: Remove python-pytest-runner-2.

[Maxim Cournoyer]

* gnu/packages/check.scm (python-pytest-runner-2): Delete variable.
(python2-pytest-runner): Likewise.
---
 gnu/packages/check.scm | 16 ----------------
 1 file changed, 16 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 8e6576208c..ef1c7edd13 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -1315,22 +1315,6 @@ (define-public python-pytest-runner
 (define-public python2-pytest-runner
   (package-with-python2 python-pytest-runner))
 
-;; python-bleach 3.1.0 requires this ancient version of pytest-runner.
-;; Remove once no longer needed.
-(define-public python-pytest-runner-2
-  (package
-    (inherit python-pytest-runner)
-   (version "2.12.2")
-   (source (origin
-             (method url-fetch)
-             (uri (pypi-uri "pytest-runner" version))
-             (sha256
-              (base32
-               "11ivjj9hfphkv4yfb2g74av4yy86y8gcbf7gbif0p1hcdfnxg3w6"))))))
-
-(define-public python2-pytest-runner-2
-  (package-with-python2 python-pytest-runner-2))
-
 (define-public python-pytest-lazy-fixture
   (package
     (name "python-pytest-lazy-fixture")
-- 
2.36.0

[bug#55424] [PATCH 008/602] gnu: Remove python2-langkit.

[Maxim Cournoyer]

* gnu/packages/ada.scm (python2-langkit): Delete variable.
---
 gnu/packages/ada.scm | 29 -----------------------------
 1 file changed, 29 deletions(-)

diff --git a/gnu/packages/ada.scm b/gnu/packages/ada.scm
index a3bba245ec..ea3e9c365b 100644
--- a/gnu/packages/ada.scm
+++ b/gnu/packages/ada.scm
@@ -149,32 +149,3 @@ (define-public ada/ed
 clauses, and thus does not support systems programming close to the machine
 level.")
     (license license:gpl2+)))
-
-(define-public python2-langkit
-  (let ((commit "fe0bc8bf60dbd2937759810df76ac420d99fc15f")
-        (revision "0"))
-    (package
-      (name "python2-langkit")
-      (version (git-version "0.0.0" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://github.com/AdaCore/langkit")
-                      (commit commit)))
-                (sha256
-                 (base32
-                  "1abqgw2p8pb1pm54my5kkbbixfhc6l0bwajdv1xlzyrh31xki3wx"))
-                (file-name (string-append name "-" version "-checkout"))))
-      (build-system python-build-system)
-      (propagated-inputs
-       (list python2-docutils python2-enum34 python2-funcy python2-mako))
-      (arguments
-       `(#:python ,python-2
-         #:tests? #f))           ; Tests would requite gprbuild (Ada).
-      (synopsis "Semantic analysis tool generator in Python")
-      (description "@code{Langkit} is a tool whose purpose is to make it easy
-to create syntactic and semantic analysis engines.  Write a language
-specification in our Python DSL and Langkit will generate for you an
-Ada library with bindings for the C and Python programming languages.")
-      (home-page "https://github.com/AdaCore/langkit/")
-      (license license:gpl3+))))   ; and gcc runtime library exception
-- 
2.36.0

[bug#55424] [PATCH 009/602] gnu: Remove graphios.

[Maxim Cournoyer]

* gnu/packages/admin.scm (graphios): Delete variable.
---
 gnu/packages/admin.scm | 36 ------------------------------------
 1 file changed, 36 deletions(-)

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 34e4a6e8ca..591899dc79 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -2567,42 +2567,6 @@ (define-public fdupes
 specified directories.")
     (license license:expat)))
 
-(define-public graphios
-  (package
-   (name "graphios")
-   (version "2.0.3")
-   (source
-    (origin
-      (method url-fetch)
-      (uri (pypi-uri "graphios" version))
-      (sha256
-       (base32
-        "1h87hvc315wg6lklbf4l7csd3n5pgljwrfli1p3nasdi0izgn66i"))))
-   (build-system python-build-system)
-   (arguments
-    ;; Be warned: Building with Python 3 succeeds, but the build process
-    ;; throws a syntax error that is ignored.
-    `(#:python ,python-2
-      #:phases
-      (modify-phases %standard-phases
-        (add-before 'build 'fix-setup.py
-          (lambda* (#:key outputs #:allow-other-keys)
-            ;; Fix hardcoded, unprefixed file names.
-            (let ((out (assoc-ref outputs "out")))
-              (substitute* '("setup.py")
-                (("/etc") (string-append out "/etc"))
-                (("/usr") out)
-                (("distro_ver = .*") "distro_ver = ''"))
-              #t))))))
-   (home-page "https://github.com/shawn-sterling/graphios")
-   (synopsis "Emit Nagios metrics to Graphite, Statsd, and Librato")
-   (description
-    "Graphios is a script to emit nagios perfdata to various upstream metrics
-processing and time-series systems.  It's currently compatible with Graphite,
-Statsd, Librato and InfluxDB.  Graphios can emit Nagios metrics to any number
-of supported upstream metrics systems simultaneously.")
-   (license license:gpl2+)))
-
 (define-public ansible-core
   (package
     (name "ansible-core")
-- 
2.36.0

[bug#55424] [PATCH 010/602] gnu: Remove python2-pyalsaaudio.

[Maxim Cournoyer]

* gnu/packages/audio.scm (python2-pyalsaaudio): Delete variable.
---
 gnu/packages/audio.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 6b16269670..402ec329c3 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -4347,9 +4347,6 @@ (define-public python-pyalsaaudio
 mixers.")
     (license license:psfl)))
 
-(define-public python2-pyalsaaudio
-  (package-with-python2 python-pyalsaaudio))
-
 (define-public ldacbt
   (package
     (name "ldacbt")
-- 
2.36.0

[bug#55424] [PATCH 011/602] gnu: Remove ingen.

[Maxim Cournoyer]

* gnu/packages/music.scm (ingen): Delete variable.
---
 gnu/packages/music.scm | 85 ------------------------------------------
 1 file changed, 85 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 210af3b166..0b76e57acf 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -4474,91 +4474,6 @@ (define-public mod-utilities
 plugins, a switch trigger, a toggle switch, and a peakmeter.")
       (license license:gpl2+))))
 
-(define-public ingen
-  (let ((commit "cc4a4db33f4d126a07a4a498e053c5fb9a883be3")
-        (revision "2"))
-    (package
-      (name "ingen")
-      (version (string-append "0.0.0-" revision "."
-                              (string-take commit 9)))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://git.drobilla.net/ingen.git")
-               (commit commit)))
-         (file-name (string-append name "-" version "-checkout"))
-         (sha256
-          (base32
-           "1wg47vjw9djn99gbnsl2bcwj4xhdid61m4wrbn2nlp797flj91ic"))))
-      (build-system waf-build-system)
-      (arguments
-       `(#:python ,python-2
-         #:tests? #f ; no "check" target
-         #:configure-flags (list "--no-webkit")
-         #:phases
-         (modify-phases %standard-phases
-           (add-after 'unpack 'patch-wscript
-             (lambda* (#:key outputs #:allow-other-keys)
-               (let ((out (assoc-ref outputs "out")))
-                 (substitute* "wscript"
-                   ;; FIXME: Our version of lv2specgen.py does not behave as
-                   ;; expected.  Maybe this requires a development version of
-                   ;; LV2.
-                   (("lv2specgen.py") "touch ingen.lv2/ingen.html; echo")
-                   ;; Add libraries to RUNPATH.
-                   (("^(.+)target.*= 'src/ingen/ingen'," line prefix)
-                    (string-append prefix
-                                   "linkflags=[\"-Wl,-rpath="
-                                   out "/lib" "\"]," line)))
-                 (substitute* '("src/wscript"
-                                "src/server/wscript")
-                   ;; Add libraries to RUNPATH.
-                   (("bld.env.PTHREAD_LINKFLAGS" line)
-                    (string-append line
-                                   " + [\"-Wl,-rpath=" out "/lib" "\"]")))
-                 (substitute* "src/client/wscript"
-                   ;; Add libraries to RUNPATH.
-                   (("^(.+)target.*= 'ingen_client'," line prefix)
-                    (string-append prefix
-                                   "linkflags=[\"-Wl,-rpath="
-                                   out "/lib" "\"]," line)))
-                 (substitute* "src/gui/wscript"
-                   ;; Add libraries to RUNPATH.
-                   (("^(.+)target.* = 'ingen_gui.*" line prefix)
-                    (string-append prefix
-                                   "linkflags=[\"-Wl,-rpath="
-                                   out "/lib" "\"]," line))))
-               #t)))))
-      (inputs
-       (list boost
-             python-rdflib
-             python
-             jack-1
-             lv2
-             lilv
-             raul-devel
-             ganv
-             suil
-             serd
-             sord
-             sratom
-             gtkmm-2))
-      (native-inputs
-       (list pkg-config python-pygments))
-      (home-page "https://drobilla.net/software/ingen")
-      (synopsis "Modular audio processing system")
-      (description "Ingen is a modular audio processing system for JACK and
-LV2 based systems.  Ingen is built around LV2 technology and a strict
-separation of engine from user interface.  The engine is controlled
-exclusively through a protocol, and can execute as a headless process, with an
-in-process GUI, or as an LV2 plugin.  The GUI can run as a program which
-communicates over a Unix or TCP/IP socket, or as an embeddable LV2 GUI which
-communicates via LV2 ports.  Any saved Ingen graph can be loaded as an LV2
-plugin on any system where Ingen is installed.  This allows users to visually
-develop custom plugins for use in other applications without programming.")
-      (license license:agpl3+))))
-
 (define-public qmidiarp
   (package
     (name "qmidiarp")
-- 
2.36.0

[bug#55424] [PATCH 012/602] gnu: Remove raul.

[Maxim Cournoyer]

* gnu/packages/audio.scm (raul): Delete variable.
---
 gnu/packages/audio.scm | 26 --------------------------
 1 file changed, 26 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 402ec329c3..6936a100df 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -3163,32 +3163,6 @@ (define-public libshout-idjc
     ;; GNU Library (not Lesser) General Public License.
     (license license:lgpl2.0+)))
 
-(define-public raul
-  (package
-    (name "raul")
-    (version "0.8.0")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://download.drobilla.net/raul-"
-                                  version ".tar.bz2"))
-              (sha256
-               (base32
-                "09ms40xc1x6qli6lxkwn5ibqh62nl9w7dq0b6jh1q2zvnrxwsd8b"))))
-    (build-system waf-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:tests? #f)) ; no check target
-    (inputs
-     (list glib boost))
-    (native-inputs
-     (list pkg-config))
-    (home-page "https://drobilla.net/software/raul/")
-    (synopsis "Real-time audio utility library")
-    (description
-     "Raul (Real-time Audio Utility Library) is a C++ utility library primarily
-aimed at audio/musical applications.")
-    (license license:gpl2+)))
-
 (define-public raul-devel
   (let ((commit "4db870b2b20b0a608ec0283139056b836c5b1624")
         (revision "1"))
-- 
2.36.0

[bug#55424] [PATCH 013/602] gnu: Remove raul-devel.

[Maxim Cournoyer]

* gnu/packages/audio.scm (raul-devel): Delete variable.
---
 gnu/packages/audio.scm | 17 -----------------
 1 file changed, 17 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 6936a100df..c07f9c3156 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -3163,23 +3163,6 @@ (define-public libshout-idjc
     ;; GNU Library (not Lesser) General Public License.
     (license license:lgpl2.0+)))
 
-(define-public raul-devel
-  (let ((commit "4db870b2b20b0a608ec0283139056b836c5b1624")
-        (revision "1"))
-    (package (inherit raul)
-      (name "raul")
-      (version (string-append "0.8.9-" revision "."
-                              (string-take commit 9)))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://git.drobilla.net/raul.git")
-                      (commit commit)))
-                (file-name (string-append name "-" version "-checkout"))
-                (sha256
-                 (base32
-                  "04fajrass3ymr72flx5js5vxc601ccrmx8ny8scp0rw7j0igyjdr")))))))
-
 (define-public resample
   (package
     (name "resample")
-- 
2.36.0

[bug#55424] [PATCH 014/602] gnu: Remove python2-pyaudio.

[Maxim Cournoyer]

* gnu/packages/audio.scm (python2-pyaudio): Delete variable.
---
 gnu/packages/audio.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index c07f9c3156..d2f8f2e5ce 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -2568,9 +2568,6 @@ (define-public python-pyaudio
 cross-platform audio input/output stream library.")
     (license license:expat)))
 
-(define-public python2-pyaudio
-  (package-with-python2 python-pyaudio))
-
 (define-public python-pyliblo
   (package
     (name "python-pyliblo")
-- 
2.36.0

[bug#55424] [PATCH 015/602] gnu: Remove python2-fastalite.

[Maxim Cournoyer]

* gnu/packages/bioinformatics.scm (python2-fastalite): Delete variable.
---
 gnu/packages/bioinformatics.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 33bf0921d1..6037a100aa 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1305,9 +1305,6 @@ (define-public python-fastalite
 relying on a complex dependency tree.")
     (license license:expat)))
 
-(define-public python2-fastalite
-  (package-with-python2 python-fastalite))
-
 (define-public biosoup
   (package
     (name "biosoup")
-- 
2.36.0

[bug#55424] [PATCH 016/602] gnu: Remove grit.

[Maxim Cournoyer]

* gnu/packages/bioinformatics.scm (grit): Delete variable.
---
 gnu/packages/bioinformatics.scm | 42 ---------------------------------
 1 file changed, 42 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6037a100aa..c754cdb176 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4024,48 +4024,6 @@ (define-public gemma
 genome-wide association studies}.")
     (license license:gpl3)))
 
-(define-public grit
-  (package
-    (name "grit")
-    (version "2.0.5")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/nboley/grit")
-                    (commit version)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1l5v8vfvfbrpmgnrvbrbv40d0arhxcnmxgv2f1mlcqfa3q6bkqm9"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'generate-from-cython-sources
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             ;; Delete these C files to force fresh generation from pyx sources.
-             (delete-file "grit/sparsify_support_fns.c")
-             (delete-file "grit/call_peaks_support_fns.c")
-             (substitute* "setup.py"
-               (("Cython.Setup") "Cython.Build"))
-             #t)))))
-    (inputs
-     (list python2-scipy python2-numpy python2-pysam python2-networkx))
-    (native-inputs
-     (list python2-cython))
-    ;; The canonical <http://grit-bio.org> home page times out as of 2020-01-21.
-    (home-page "https://github.com/nboley/grit")
-    (synopsis "Tool for integrative analysis of RNA-seq type assays")
-    (description
-     "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify
-full length transcript models.  When none of these data sources are available,
-GRIT can be run by providing a candidate set of TES or TSS sites.  In
-addition, GRIT can merge in reference junctions and gene boundaries.  GRIT can
-also be run in quantification mode, where it uses a provided GTF file and just
-estimates transcript expression.")
-    (license license:gpl3+)))
-
 (define-public hisat
   (package
     (name "hisat")
-- 
2.36.0

[bug#55424] [PATCH 017/602] gnu: Remove ribodiff.

[Maxim Cournoyer]

* gnu/packages/bioinformatics.scm (ribodiff): Delete variable.
---
 gnu/packages/bioinformatics.scm | 46 ---------------------------------
 1 file changed, 46 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c754cdb176..902e65394d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -839,52 +839,6 @@ (define-public ribotaper
 provides the Ribotaper pipeline.")
     (license license:gpl3+)))
 
-(define-public ribodiff
-  (package
-    (name "ribodiff")
-    (version "0.2.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/ratschlab/RiboDiff")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "0x75nlp7qnmm64jasbi6l21f2cy99r2cjyl6b4hr8zf2bq22drnz"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:phases
-       (modify-phases %standard-phases
-         ;; This test fails because of the matplotlib plotting backend.
-         (add-after 'unpack 'disable-plot-test
-           (lambda _
-             (substitute* "src/ribodiff/functional_test_te.py"
-               (("pl\\.make_plots\\(data, opts\\)") "#"))))
-         ;; Generate an installable executable script wrapper.
-         (add-after 'unpack 'patch-setup.py
-           (lambda _
-             (substitute* "setup.py"
-               (("^(.*)packages=.*" line prefix)
-                (string-append line "\n"
-                               prefix "scripts=['scripts/TE.py'],\n"))))))))
-    (inputs
-     (list python2-numpy python2-matplotlib python2-scipy
-           python2-statsmodels))
-    (native-inputs
-     (list python2-mock python2-nose))
-    (home-page "https://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/")
-    (synopsis "Detect translation efficiency changes from ribosome footprints")
-    (description "RiboDiff is a statistical tool that detects the protein
-translational efficiency change from Ribo-Seq (ribosome footprinting) and
-RNA-Seq data.  It uses a generalized linear model to detect genes showing
-difference in translational profile taking mRNA abundance into account.  It
-facilitates us to decipher the translational regulation that behave
-independently with transcriptional regulation.")
-    (license license:gpl3+)))
-
 (define-public bioawk
   (package
     (name "bioawk")
-- 
2.36.0

[bug#55424] [PATCH 018/602] gnu: Remove python2-pybigwig.

[Maxim Cournoyer]

* gnu/packages/bioinformatics.scm (python2-pybigwig): Delete variable.
---
 gnu/packages/bioinformatics.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 902e65394d..8b9c8c65c2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2853,9 +2853,6 @@ (define-public python-pybigwig
 accessing bigWig files.")
     (license license:expat)))
 
-(define-public python2-pybigwig
-  (package-with-python2 python-pybigwig))
-
 (define-public python-schema-salad
   (package
     (name "python-schema-salad")
-- 
2.36.0

[bug#55424] [PATCH 019/602] gnu: tetoolkit: Update to 2.2.1b.

[Maxim Cournoyer]

* gnu/packages/bioinformatics.scm (tetoolkit): Update to 2.2.1b.
[python]: Delete argument.
[phases]: Delete trailing #t.
{make-writable}: Delete phase.
{adjust-requirements}: New phase.
{patch-invocations}: Use search-input-file.
{wrap-program}: Use search-input-file.
[inputs]: Remove python2-argparse.  Replace python2-pysam with python-pysam.
[home-page]: Update URL.
---
 gnu/packages/bioinformatics.scm | 53 +++++++++++++++++----------------
 1 file changed, 27 insertions(+), 26 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8b9c8c65c2..72d033888f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2390,59 +2390,60 @@ (define-public python-plastid
 (define-public tetoolkit
   (package
     (name "tetoolkit")
-    (version "2.0.3")
+    (version "2.2.1b")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                    (url "https://github.com/mhammell-laboratory/tetoolkit")
+                    (url "https://github.com/mhammell-laboratory/TEtranscripts")
                     (commit version)))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1yzi0kfpzip8zpjb82x1ik6h22yzfyjiz2dv85v6as2awwqvk807"))))
+                "1m3xsydakhdan9gp9mfdz7llka5g6ak91d0mbl1cmmxq9qs6an4y"))))
     (build-system python-build-system)
     (arguments
-     `(#:python ,python-2               ; not guaranteed to work with Python 3
-       #:phases
+     `(#:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'make-writable
+         (add-after 'unpack 'adjust-requirements
            (lambda _
-             (for-each make-file-writable (find-files "."))
-             #t))
+             (substitute* "setup.py"
+               ;; This defunct dependency isn't required for Python 3 (see:
+               ;; https://github.com/mhammell-laboratory/TEtranscripts/issues/111).
+               ((".*'argparse'.*") ""))))
          (add-after 'unpack 'patch-invocations
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* '("bin/TEtranscripts"
                             "bin/TEcount")
                (("'sort ")
-                (string-append "'" (which "sort") " "))
+                (string-append "'" (search-input-file inputs "bin/sort") " "))
                (("'rm -f ")
-                (string-append "'" (which "rm") " -f "))
-               (("'Rscript'") (string-append "'" (which "Rscript") "'")))
+                (string-append "'" (search-input-file inputs "bin/rm") " -f "))
+               (("'Rscript'")
+                (string-append "'" (search-input-file inputs "bin/Rscript")
+                               "'")))
              (substitute* "TEToolkit/IO/ReadInputs.py"
-               (("BamToBED") (which "bamToBed")))
+               (("BamToBED")
+                (search-input-file inputs "bin/bamToBed")))
              (substitute* "TEToolkit/Normalization.py"
                (("\"Rscript\"")
-                (string-append "\"" (which "Rscript") "\"")))
-             #t))
+                (string-append "\"" (search-input-file inputs "bin/Rscript")
+                               "\"")))))
          (add-after 'install 'wrap-program
            (lambda* (#:key outputs #:allow-other-keys)
              ;; Make sure the executables find R packages.
-             (let ((out (assoc-ref outputs "out")))
-               (for-each
-                (lambda (script)
-                  (wrap-program (string-append out "/bin/" script)
-                    `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
-                '("TEtranscripts"
-                  "TEcount")))
-             #t)))))
+             (for-each (lambda (script)
+                         (wrap-program script
+                           `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
+                       (list (search-input-file outputs "bin/TEtranscripts")
+                             (search-input-file outputs "bin/TEcount"))))))))
     (inputs
-     (list coreutils
+     (list bash-minimal
+           coreutils
            bedtools
-           python2-argparse
-           python2-pysam
+           python-pysam
            r-minimal
            r-deseq2))
-    (home-page "https://github.com/mhammell-laboratory/tetoolkit")
+    (home-page "https://github.com/mhammell-laboratory/TEtranscripts")
     (synopsis "Transposable elements in differential enrichment analysis")
     (description
      "This is package for including transposable elements in differential
-- 
2.36.0

[bug#55424] [PATCH 020/602] gnu: Remove pepr.

[Maxim Cournoyer]

* gnu/packages/bioinformatics.scm (pepr): Delete variable.
---
 gnu/packages/bioinformatics.scm | 26 --------------------------
 1 file changed, 26 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 72d033888f..250d075b6e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8726,32 +8726,6 @@ (define-public piranha
 may optionally be provided to further inform the peak-calling process.")
       (license license:gpl3+))))
 
-(define-public pepr
-  (package
-    (name "pepr")
-    (version "1.0.9")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "PePr" version))
-              (sha256
-               (base32
-                "0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2 ; python2 only
-       #:tests? #f)) ; no tests included
-    (propagated-inputs
-     (list python2-numpy python2-scipy python2-pysam))
-    (home-page "https://github.com/shawnzhangyx/PePr")
-    (synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data")
-    (description
-     "PePr is a ChIP-Seq peak calling or differential binding analysis tool
-that is primarily designed for data with biological replicates.  It uses a
-negative binomial distribution to model the read counts among the samples in
-the same group, and look for consistent differences between ChIP and control
-group or two ChIP groups run under different conditions.")
-    (license license:gpl3+)))
-
 (define-public filevercmp
   (let ((commit "1a9b779b93d0b244040274794d402106907b71b7")
         (revision "1"))
-- 
2.36.0

[bug#55424] [PATCH 021/602] gnu: Remove python2-htseq.

[Maxim Cournoyer]

* gnu/packages/bioinformatics.scm (python2-htseq): Delete variable.
---
 gnu/packages/bioinformatics.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 250d075b6e..8e7615cef0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4156,9 +4156,6 @@ (define-public htseq
 from high-throughput sequencing assays.")
     (license license:gpl3+)))
 
-(define-public python2-htseq
-  (package-with-python2 htseq))
-
 (define-public java-htsjdk
   (package
     (name "java-htsjdk")
-- 
2.36.0

[bug#55424] [PATCH 022/602] gnu: Remove python2-pybedtools.

[Maxim Cournoyer]

* gnu/packages/bioinformatics.scm (python2-pybedtools): Delete variable.
---
 gnu/packages/bioinformatics.scm | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8e7615cef0..9d4fcbb188 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -980,14 +980,6 @@ (define (cythonized? c/c++-file)
 Python.")
     (license license:gpl2+)))
 
-(define-public python2-pybedtools
-  (let ((pybedtools (package-with-python2 python-pybedtools)))
-    (package
-      (inherit pybedtools)
-      (native-inputs
-       (modify-inputs (package-native-inputs pybedtools)
-         (prepend python2-pathlib))))))
-
 (define-public python-biom-format
   (package
     (name "python-biom-format")
-- 
2.36.0

[bug#55424] [PATCH 023/602] gnu: Remove bamm.

[Maxim Cournoyer]

* gnu/packages/bioinformatics.scm (bamm): Delete variable.
---
 gnu/packages/bioinformatics.scm | 79 ---------------------------------
 1 file changed, 79 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9d4fcbb188..5f637fe29a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -210,85 +210,6 @@ (define-public aragorn
 structure of the predicted RNA.")
     (license license:gpl2)))
 
-(define-public bamm
-  (package
-    (name "bamm")
-    (version "1.7.3")
-    (source (origin
-              (method git-fetch)
-              ;; BamM is not available on pypi.
-              (uri (git-reference
-                    (url "https://github.com/Ecogenomics/BamM")
-                    (commit version)
-                    (recursive? #t)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1p83ahi984ipslxlg4yqy1gdnya9rkn1v71z8djgxkm9d2chw4c5"))
-              (modules '((guix build utils)))
-              (snippet
-               `(begin
-                  ;; Delete bundled htslib.
-                  (delete-file-recursively "c/htslib-1.3.1")))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2 ; BamM is Python 2 only.
-       ;; Do not use bundled libhts.  Do use the bundled libcfu because it has
-       ;; been modified from its original form.
-       #:configure-flags
-       ,#~(let ((htslib #$(this-package-input "htslib")))
-            (list "--with-libhts-lib" (string-append htslib "/lib")
-                  "--with-libhts-inc" (string-append htslib "/include/htslib")))
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'autogen
-           (lambda _
-             (with-directory-excursion "c"
-               (let ((sh (which "sh")))
-                 (for-each make-file-writable (find-files "." ".*"))
-                 ;; Use autogen so that 'configure' works.
-                 (substitute* "autogen.sh" (("/bin/sh") sh))
-                 (setenv "CONFIG_SHELL" sh)
-                 (invoke "./autogen.sh")))))
-         (delete 'build)                ;the build loops otherwise
-         (replace 'check
-           (lambda _
-             ;; There are 2 errors printed, but they are safe to ignore:
-             ;; 1) [E::hts_open_format] fail to open file ...
-             ;; 2) samtools view: failed to open ...
-             (invoke "nosetests")))
-         (add-after 'install 'wrap-executable
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let* ((out  (assoc-ref outputs "out"))
-                    (path (getenv "PATH"))
-                    (pythonpath (getenv "GUIX_PYTHONPATH")))
-               (wrap-program (string-append out "/bin/bamm")
-                 `("PATH" ":" prefix (,path))
-                 `("GUIX_PYTHONPATH" ":" prefix (,pythonpath)))))))))
-    (native-inputs
-     (list autoconf
-           automake
-           libtool
-           zlib
-           python2-nose
-           python2-pysam))
-    (inputs
-     (list htslib-1.3 ; At least one test fails on htslib-1.4+.
-           samtools
-           bwa
-           grep
-           sed
-           coreutils))
-    (propagated-inputs
-     (list python2-numpy))
-    (home-page "https://ecogenomics.github.io/BamM/")
-    (synopsis "Metagenomics-focused BAM file manipulator")
-    (description
-     "BamM is a C library, wrapped in python, to efficiently generate and
-parse BAM files, specifically for the analysis of metagenomic data.  For
-instance, it implements several methods to assess contig-wise read coverage.")
-    (license license:lgpl3+)))
-
 (define-public bamtools
   (package
     (name "bamtools")
-- 
2.36.0

[bug#55424] [PATCH 024/602] gnu: Remove python2-dendropy.

[Maxim Cournoyer]

* gnu/packages/bioinformatics.scm (python2-dendropy): Delete variable.
---
 gnu/packages/bioinformatics.scm | 16 ----------------
 1 file changed, 16 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5f637fe29a..cb3328cc1c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2954,22 +2954,6 @@ (define-public python-dendropy
 trees (phylogenies) and characters.")
     (license license:bsd-3)))
 
-(define-public python2-dendropy
-  (let ((base (package-with-python2 python-dendropy)))
-    (package/inherit base
-      (arguments
-       `(#:phases
-         (modify-phases %standard-phases
-           (add-after 'unpack 'remove-failing-test
-             (lambda _
-               ;; This test fails when the full test suite is run, as documented
-               ;; at https://github.com/jeetsukumaran/DendroPy/issues/74
-               (substitute* "tests/test_dataio_nexml_reader_tree_list.py"
-                 (("test_collection_comments_and_annotations")
-                  "do_not_test_collection_comments_and_annotations"))
-               #t)))
-         ,@(package-arguments base))))))
-
 (define-public python-py2bit
   (package
     (name "python-py2bit")
-- 
2.36.0

[bug#55424] [PATCH 025/602] gnu: Remove poretools.

[Maxim Cournoyer]

* gnu/packages/bioinformatics.scm (poretools): Delete variable.
---
 gnu/packages/bioinformatics.scm | 36 ---------------------------------
 1 file changed, 36 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index cb3328cc1c..c70b9e3aa7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12855,42 +12855,6 @@ (define-public porechop
 Barcoding Kit or Rapid Barcoding Kit.")
       (license license:gpl3+))))
 
-(define-public poretools
-  ;; The latest release was in 2016 and the latest commit is from 2017
-  ;; the recommended way to install is to clone the git repository
-  ;; https://poretools.readthedocs.io/en/latest/content/installation.html
-  (let ((commit "e426b1f09e86ac259a00c261c79df91510777407")
-        (revision "1"))
-    (package
-      (name "poretools")
-      (version (git-version "0.6.0" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/arq5x/poretools")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32 "0bglj833wxpp3cq430p1d3xp085ls221js2y90w7ir2x5ay8l7am"))))
-      (build-system python-build-system)
-      ;; requires python >=2.7, <3.0, and the same for python dependencies
-      (arguments `(#:python ,python-2))
-      (inputs
-       (list hdf5))
-      (propagated-inputs
-       (list python2-dateutil python2-h5py python2-matplotlib
-             python2-pandas python2-seaborn))
-      (home-page "https://poretools.readthedocs.io")
-      (synopsis "Toolkit for working with nanopore sequencing data")
-      (description
-       "The MinION from Oxford Nanopore Technologies is a nanopore sequencer.
-This @code{poretools} package is a flexible toolkit for exploring datasets
-generated by nanopore sequencing devices for the purposes of quality control and
-downstream analysis.  Poretools operates directly on the native FAST5, a variant
-of the Hierarchical Data Format (HDF5) standard.")
-      (license license:expat))))
-
 (define-public jamm
   (package
     (name "jamm")
-- 
2.36.0

[bug#55424] [PATCH 026/602] gnu: Remove python2-warpedlmm.

[Maxim Cournoyer]

* gnu/packages/bioinformatics.scm (python2-warpedlmm): Delete variable.
---
 gnu/packages/bioinformatics.scm | 41 ---------------------------------
 1 file changed, 41 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c70b9e3aa7..b0ad03612e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5365,47 +5365,6 @@ (define-public python2-pbcore
 files and writing bioinformatics applications.")
     (license license:bsd-3)))
 
-(define-public python2-warpedlmm
-  (package
-    (name "python2-warpedlmm")
-    (version "0.21")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "WarpedLMM" version ".zip"))
-       (sha256
-        (base32
-         "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2  ; requires Python 2.7
-       #:tests? #f ; test data are not included
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'use-weave
-           (lambda _
-             (substitute* "warpedlmm/util/linalg.py"
-               (("from scipy import linalg, weave")
-                "from scipy import linalg\nimport weave"))
-             #t)))))
-    (propagated-inputs
-     (list python2-scipy
-           python2-numpy
-           python2-matplotlib
-           python2-fastlmm
-           python2-pandas
-           python2-pysnptools
-           python2-weave))
-    (native-inputs
-     (list python2-mock python2-nose unzip))
-    (home-page "https://github.com/PMBio/warpedLMM")
-    (synopsis "Implementation of warped linear mixed models")
-    (description
-     "WarpedLMM is a Python implementation of the warped linear mixed model,
-which automatically learns an optimal warping function (or transformation) for
-the phenotype as it models the data.")
-    (license license:asl2.0)))
-
 (define-public prank
   (package
     (name "prank")
-- 
2.36.0

[bug#55424] [PATCH 027/602] gnu: Remove miso.

[Maxim Cournoyer]

* gnu/packages/bioinformatics.scm (miso): Delete variable.
---
 gnu/packages/bioinformatics.scm | 48 ---------------------------------
 1 file changed, 48 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b0ad03612e..d4354e8ea8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5194,54 +5194,6 @@ (define-public minced
 assembled metagenomic sequence.")
     (license license:gpl3+)))
 
-(define-public miso
-  (let ((commit "b71402188000465e3430736a11ea118fd5639a4a")
-        (revision "1"))
-    (package
-      (name "miso")
-      (version (git-version "0.5.4" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://github.com/yarden/MISO/")
-                      (commit commit)))
-                (file-name (git-file-name name version))
-                (sha256
-                 (base32
-                  "0x37ipwwvpxbkrg17gmq3hp92c9cphch8acd6cj7fqgnrjwd47g5"))
-                (modules '((guix build utils)))
-                (snippet
-                 '(substitute* "setup.py"
-                    ;; Use "gcc" instead of "cc" for compilation.
-                    (("^defines")
-                     "cc.set_executables(
-compiler='gcc',
-compiler_so='gcc',
-linker_exe='gcc',
-linker_so='gcc -shared'); defines")))))
-      (build-system python-build-system)
-      (arguments
-       `(#:python ,python-2               ; only Python 2 is supported
-         #:tests? #f))                    ; no "test" target
-      (inputs
-       ;; Samtools must not be newer than 1.2.  See
-       ;; https://github.com/yarden/MISO/issues/135
-       (list samtools-1.2 python2-numpy python2-pysam python2-scipy
-             python2-matplotlib))
-      (native-inputs
-       (list python2-mock ; for tests
-             python2-pytz))  ; for tests
-      (home-page "https://miso.readthedocs.io/en/fastmiso/")
-      (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation")
-      (description
-       "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates
-the expression level of alternatively spliced genes from RNA-Seq data, and
-identifies differentially regulated isoforms or exons across samples.  By
-modeling the generative process by which reads are produced from isoforms in
-RNA-Seq, the MISO model uses Bayesian inference to compute the probability
-that a read originated from a particular isoform.")
-      (license license:gpl2))))
-
 (define-public muscle
   (package
     (name "muscle")
-- 
2.36.0

[bug#55424] [PATCH 028/602] gnu: Remove python2-screed.

[Maxim Cournoyer]

* gnu/packages/bioinformatics.scm (python2-screed): Delete variable.
---
 gnu/packages/bioinformatics.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d4354e8ea8..3debc32ea9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6544,9 +6544,6 @@ (define-public python-screed
 sequence itself can be retrieved from these databases.")
     (license license:bsd-3)))
 
-(define-public python2-screed
-  (package-with-python2 python-screed))
-
 (define-public sra-tools
   (package
     (name "sra-tools")
-- 
2.36.0

[bug#55424] [PATCH 029/602] gnu: Remove python2-pyfaidx.

[Maxim Cournoyer]

* gnu/packages/bioinformatics.scm (python2-pyfaidx): Delete variable.
---
 gnu/packages/bioinformatics.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3debc32ea9..dd811815e0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12316,9 +12316,6 @@ (define-public python-pyfaidx
 fasta subsequences.")
     (license license:bsd-3)))
 
-(define-public python2-pyfaidx
-  (package-with-python2 python-pyfaidx))
-
 (define-public python-cooler
   (package
     (name "python-cooler")
-- 
2.36.0

[bug#55424] [PATCH 030/602] gnu: Remove python2-pbcore.

[Maxim Cournoyer]

* gnu/packages/bioinformatics.scm (python2-pbcore): Delete variable.
---
 gnu/packages/bioinformatics.scm | 33 ---------------------------------
 1 file changed, 33 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index dd811815e0..bda958f6f5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5284,39 +5284,6 @@ (define-public orfm
     (home-page "https://github.com/wwood/OrfM")
     (license license:lgpl3+)))
 
-(define-public python2-pbcore
-  (package
-    (name "python2-pbcore")
-    (version "1.2.10")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "pbcore" version))
-              (sha256
-               (base32
-                "1kjmv891d6qbpp4shhhvkl02ff4q5xlpnls2513sm2cjcrs52f1i"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2               ;pbcore < 2.0 requires Python 2.7
-       #:phases (modify-phases %standard-phases
-                  (add-after 'unpack 'remove-sphinx-dependency
-                    (lambda _
-                      ;; Sphinx is only required for documentation tests, which
-                      ;; we do not run; furthermore it depends on python2-sphinx
-                      ;; which is no longer maintained.
-                      (substitute* "requirements-dev.txt"
-                        (("^sphinx") ""))
-                      #t)))))
-    (propagated-inputs
-     (list python2-cython python2-numpy python2-pysam python2-h5py))
-    (native-inputs
-     (list python2-nose python2-pyxb))
-    (home-page "https://pacificbiosciences.github.io/pbcore/")
-    (synopsis "Library for reading and writing PacBio data files")
-    (description
-     "The pbcore package provides Python APIs for interacting with PacBio data
-files and writing bioinformatics applications.")
-    (license license:bsd-3)))
-
 (define-public prank
   (package
     (name "prank")
-- 
2.36.0

[bug#55424] [PATCH 031/602] gnu: Remove pyicoteo.

[Maxim Cournoyer]

* gnu/packages/bioinformatics.scm (pyicoteo): Delete variable.
---
 gnu/packages/bioinformatics.scm | 39 ---------------------------------
 1 file changed, 39 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bda958f6f5..0fd7844a26 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5405,45 +5405,6 @@ (define-public proteinortho
 large-scale data and can be applied to hundreds of species at once.")
     (license license:gpl3+)))
 
-(define-public pyicoteo
-  (package
-    (name "pyicoteo")
-    (version "2.0.7")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://bitbucket.org/regulatorygenomicsupf/pyicoteo.git")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "0hz5g8d25lbjy1wpscr490l0lmyvaix893hhax4fxnh1h9w34w8p"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2 ; does not work with Python 3
-       #:tests? #f))      ; there are no tests
-    (inputs
-     (list python2-matplotlib))
-    (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo")
-    (synopsis "Analyze high-throughput genetic sequencing data")
-    (description
-     "Pyicoteo is a suite of tools for the analysis of high-throughput genetic
-sequencing data.  It works with genomic coordinates.  There are currently six
-different command-line tools:
-
-@enumerate
-@item pyicoregion: for generating exploratory regions automatically;
-@item pyicoenrich: for differential enrichment between two conditions;
-@item pyicoclip: for calling CLIP-Seq peaks without a control;
-@item pyicos: for genomic coordinates manipulation;
-@item pyicoller: for peak calling on punctuated ChIP-Seq;
-@item pyicount: to count how many reads from N experiment files overlap in a
-  region file;
-@item pyicotrocol: to combine operations from pyicoteo.
-@end enumerate\n")
-    (license license:gpl3+)))
-
 (define-public prodigal
   (package
     (name "prodigal")
-- 
2.36.0

[bug#55424] [PATCH 032/602] gnu: Remove transmission-remote-cli.

[Maxim Cournoyer]

* gnu/packages/bittorrent.scm (transmission-remote-cli): Delete variable.
---
 gnu/packages/bittorrent.scm | 43 -------------------------------------
 1 file changed, 43 deletions(-)

diff --git a/gnu/packages/bittorrent.scm b/gnu/packages/bittorrent.scm
index 0191bb8e1b..1c9358b896 100644
--- a/gnu/packages/bittorrent.scm
+++ b/gnu/packages/bittorrent.scm
@@ -255,49 +255,6 @@ (define-public tremc
     (home-page "https://github.com/tremc/tremc")
     (license l:gpl3+)))
 
-(define-public transmission-remote-cli
-  (package
-    (name "transmission-remote-cli")
-    (version "1.7.1")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/fagga/transmission-remote-cli")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "09w9f8vrm61lapin8fmq4rgahr95y3c6wss10g0fgd0kl16f895v"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2 ; only supports Python 2
-       #:tests? #f ; no test suite
-       #:phases (modify-phases %standard-phases
-                  ;; The software is just a Python script that must be
-                  ;; copied into place.
-                  (delete 'build)
-                  (replace 'install
-                    (lambda* (#:key outputs #:allow-other-keys)
-                      (let* ((out (assoc-ref outputs "out"))
-                             (bin (string-append out "/bin"))
-                             (man (string-append out "/share/man/man1"))
-                             ;; FIXME install zsh completions
-                             (completions (string-append out "/etc/bash_completion.d")))
-                        (install-file "transmission-remote-cli" bin)
-                        (install-file "transmission-remote-cli.1" man)
-                        (install-file
-                          (string-append
-                            "completion/bash/"
-                            "transmission-remote-cli-bash-completion.sh")
-                          completions)))))))
-    (synopsis "Console client for the Transmission BitTorrent daemon")
-    (description "Transmission-remote-cli is a console client, with a curses
-interface, for the Transmission BitTorrent daemon.  This package is no longer
-maintained upstream.")
-    (home-page "https://github.com/fagga/transmission-remote-cli")
-    (license l:gpl3+)
-    (properties `((superseded . ,tremc)))))
-
 (define-public aria2
   (package
     (name "aria2")
-- 
2.36.0

[bug#55424] [PATCH 033/602] gnu: Remove python2-nose-timer.

[Maxim Cournoyer]

* gnu/packages/check.scm (python2-nose-timer): Delete variable.
---
 gnu/packages/check.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index ef1c7edd13..59e9d16dd5 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2885,9 +2885,6 @@ (define-public python-nose-timer
     (description "Shows how much time was needed to run individual tests.")
     (license license:expat)))
 
-(define-public python2-nose-timer
-  (package-with-python2 python-nose-timer))
-
 (define-public python-freezegun
   (package
     (name "python-freezegun")
-- 
2.36.0

[bug#55424] [PATCH 034/602] gnu: Remove python2-pytest-catchlog.

[Maxim Cournoyer]

* gnu/packages/check.scm (python2-pytest-catchlog): Delete variable.
---
 gnu/packages/check.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 59e9d16dd5..ac680bdd62 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2659,9 +2659,6 @@ (define-public python-pytest-catchlog
 a fork of pytest-capturelog.")
     (license license:expat)))
 
-(define-public python2-pytest-catchlog
-  (package-with-python2 python-pytest-catchlog))
-
 (define-public python-nosexcover
   (package
     (name "python-nosexcover")
-- 
2.36.0

[bug#55424] [PATCH 035/602] gnu: Remove python2-testlib.

[Maxim Cournoyer]

* gnu/packages/check.scm (python2-testlib): Delete variable.
---
 gnu/packages/check.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index ac680bdd62..3f31243f1c 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2016,9 +2016,6 @@ (define-public python-testlib
     (home-page "https://github.com/trentm/testlib")
     (license license:expat)))
 
-(define-public python2-testlib
-  (package-with-python2 python-testlib))
-
 ;;; The software provided by this package was integrated into pytest 2.8.
 (define-public python-pytest-cache
   (package
-- 
2.36.0

[bug#55424] [PATCH 036/602] gnu: Remove python2-nose2.

[Maxim Cournoyer]

* gnu/packages/check.scm (python2-nose2): Delete variable.
---
 gnu/packages/check.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 3f31243f1c..5dec698fc3 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -947,9 +947,6 @@ (define-public python-nose2
 interfaces and processes.")
     (license license:bsd-2)))
 
-(define-public python2-nose2
-  (package-with-python2 python-nose2))
-
 (define-public python-unittest2
   (package
     (name "python-unittest2")
-- 
2.36.0

[bug#55424] [PATCH 037/602] gnu: Remove python2-pytest-capturelog.

[Maxim Cournoyer]

* gnu/packages/check.scm (python2-pytest-capturelog): Delete variable.
---
 gnu/packages/check.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 5dec698fc3..15929831e1 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2627,9 +2627,6 @@ (define-public python-pytest-capturelog
      "Python-pytest-catchlog is a pytest plugin to catch log messages.")
     (license license:expat)))
 
-(define-public python2-pytest-capturelog
-  (package-with-python2 python-pytest-capturelog))
-
 (define-public python-pytest-catchlog
   (package
     (name "python-pytest-catchlog")
-- 
2.36.0

[bug#55424] [PATCH 038/602] gnu: Remove python2-python-paramunittest.

[Maxim Cournoyer]

* gnu/packages/check.scm (python2-python-paramunittest): Delete variable.
---
 gnu/packages/check.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 15929831e1..2d0609b68c 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2575,9 +2575,6 @@ (define-public python-paramunittest
 recognize TestCases.")
     (license license:bsd-2)))
 
-(define-public python2-python-paramunittest
-  (package-with-python2 python-paramunittest))
-
 (define-public python-pytest-warnings
   (package
     (name "python-pytest-warnings")
-- 
2.36.0

[bug#55424] [PATCH 039/602] gnu: Remove python2-rednose.

[Maxim Cournoyer]

* gnu/packages/check.scm (python2-rednose): Delete variable.
---
 gnu/packages/check.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 2d0609b68c..e89e346532 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2796,9 +2796,6 @@ (define-public python-rednose
 @command{nosetests} command of the Python Nose unit test framework.")
     (license license:bsd-3)))
 
-(define-public python2-rednose
-  (package-with-python2 python-rednose))
-
 (define-public python-nose-random
   (package
     (name "python-nose-random")
-- 
2.36.0

[bug#55424] [PATCH 040/602] gnu: Remove python2-minimock.

[Maxim Cournoyer]

* gnu/packages/check.scm (python2-minimock): Delete variable.
---
 gnu/packages/check.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index e89e346532..a093fedfe8 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -849,9 +849,6 @@ (define-public python-minimock
 doctest.")
     (license license:expat)))
 
-(define-public python2-minimock
-  (package-with-python2 python-minimock))
-
 (define-public python-mock
   (package
     (name "python-mock")
-- 
2.36.0

[bug#55424] [PATCH 041/602] gnu: Remove python2-flexmock.

[Maxim Cournoyer]

* gnu/packages/check.scm (python2-flexmock): Delete variable.
---
 gnu/packages/check.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index a093fedfe8..7ddf424019 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2915,9 +2915,6 @@ (define-public python-flexmock
 mocks, stubs and fakes.")
     (license license:bsd-3)))
 
-(define-public python2-flexmock
-  (package-with-python2 python-flexmock))
-
 (define-public python-flaky
   (package
     (name "python-flaky")
-- 
2.36.0

[bug#55424] [PATCH 042/602] gnu: Remove python2-discover.

[Maxim Cournoyer]

* gnu/packages/check.scm (python2-discover): Delete variable.
---
 gnu/packages/check.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 7ddf424019..cd5401748b 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2690,9 +2690,6 @@ (define-public python-discover
 backported from Python 2.7 for Python 2.4+.")
     (license license:bsd-3)))
 
-(define-public python2-discover
-  (package-with-python2 python-discover))
-
 (define-public behave
   (package
     (name "behave")
-- 
2.36.0

[bug#55424] [PATCH 043/602] gnu: Remove python2-cov-core.

[Maxim Cournoyer]

* gnu/packages/check.scm (python2-cov-core): Delete variable.
---
 gnu/packages/check.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index cd5401748b..089f686c94 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -1919,9 +1919,6 @@ (define-public python-cov-core
 testing frameworks.")
     (license license:expat)))
 
-(define-public python2-cov-core
- (package-with-python2 python-cov-core))
-
 (define-public python-codecov
   (package
     (name "python-codecov")
-- 
2.36.0

[bug#55424] [PATCH 044/602] gnu: Remove python2-pytest-flakes.

[Maxim Cournoyer]

* gnu/packages/check.scm (python2-pytest-flakes): Delete variable.
---
 gnu/packages/check.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 089f686c94..c4884c72d3 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2462,9 +2462,6 @@ (define-public python-pytest-flakes
     (description "Pytest plugin for checking Python source code with pyflakes.")
     (license license:expat)))
 
-(define-public python2-pytest-flakes
-  (package-with-python2 python-pytest-flakes))
-
 (define-public python-coverage-test-runner
   (package
     (name "python-coverage-test-runner")
-- 
2.36.0

[bug#55424] [PATCH 045/602] gnu: Remove python2-pytest-subtesthack.

[Maxim Cournoyer]

* gnu/packages/check.scm (python2-pytest-subtesthack): Delete variable.
---
 gnu/packages/check.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index c4884c72d3..0cabbecbfa 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2100,9 +2100,6 @@ (define-public python-pytest-subtesthack
     (home-page "https://github.com/untitaker/pytest-subtesthack/")
     (license license:unlicense)))
 
-(define-public python2-pytest-subtesthack
-  (package-with-python2 python-pytest-subtesthack))
-
 (define-public python-pytest-sugar
   (package
     (name "python-pytest-sugar")
-- 
2.36.0

[bug#55424] [PATCH 046/602] gnu: Remove python2-nose-randomly.

[Maxim Cournoyer]

* gnu/packages/check.scm (python2-nose-randomly): Delete variable.
---
 gnu/packages/check.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 0cabbecbfa..805e8c2041 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2831,9 +2831,6 @@ (define-public python-nose-randomly
 create data based on random numbers and yet remain repeatable.")
     (license license:bsd-3)))
 
-(define-public python2-nose-randomly
-  (package-with-python2 python-nose-randomly))
-
 (define-public python-nose-timer
   (package
     (name "python-nose-timer")
-- 
2.36.0

[bug#55424] [PATCH 047/602] gnu: Remove domainfinder.

[Maxim Cournoyer]

* gnu/packages/chemistry.scm (domainfinder): Delete variable.
---
 gnu/packages/chemistry.scm | 29 -----------------------------
 1 file changed, 29 deletions(-)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 94803719ac..d94f3ec787 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -128,35 +128,6 @@ (define-public avogadro2
 powerful plugin architecture.")
     (license license:bsd-3)))
 
-(define-public domainfinder
-  (package
-    (name "domainfinder")
-    (version "2.0.5")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://bitbucket.org/khinsen/"
-                           "domainfinder/downloads/DomainFinder-"
-                           version ".tar.gz"))
-       (sha256
-        (base32
-         "1z26lsyf7xwnzwjvimmbla7ckipx6p734w7y0jk2a2fzci8fkdcr"))))
-    (build-system python-build-system)
-    (inputs
-     (list python2-mmtk))
-    (arguments
-     `(#:python ,python-2
-       ;; No test suite
-       #:tests? #f))
-    (home-page "http://dirac.cnrs-orleans.fr/DomainFinder.html")
-    (synopsis "Analysis of dynamical domains in proteins")
-    (description "DomainFinder is an interactive program for the determination
-and characterization of dynamical domains in proteins.  It can infer dynamical
-domains by comparing two protein structures, or from normal mode analysis on a
-single structure.  The software is currently not actively maintained and works
-only with Python 2 and NumPy < 1.9.")
-    (license license:cecill-c)))
-
 (define-public inchi
   (package
     (name "inchi")
-- 
2.36.0

[bug#55424] [PATCH 048/602] gnu: Remove nmoldyn.

[Maxim Cournoyer]

* gnu/packages/chemistry.scm (nmoldyn): Delete variable.
---
 gnu/packages/chemistry.scm | 60 --------------------------------------
 1 file changed, 60 deletions(-)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index d94f3ec787..e5b6309585 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -306,66 +306,6 @@ (define-public molequeue
 (define with-numpy-1.8
   (package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8))))
 
-(define-public nmoldyn
-  (package
-    (name "nmoldyn")
-    (version "3.0.11")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/khinsen/nMOLDYN3")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "016h4bqg419p6s7bcx55q5iik91gqmk26hbnfgj2j6zl0j36w51r"))))
-    (build-system python-build-system)
-    (inputs
-     (list (with-numpy-1.8 python2-matplotlib) python2-scientific netcdf
-           gv))
-    (propagated-inputs
-     (list python2-mmtk))
-    (arguments
-     `(#:python ,python-2
-       #:tests? #f  ; No test suite
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'build 'create-linux2-directory
-           (lambda _
-             (mkdir-p "nMOLDYN/linux2")))
-         (add-before 'build 'change-PDF-viewer
-           (lambda* (#:key inputs #:allow-other-keys)
-             (substitute* "nMOLDYN/Preferences.py"
-               ;; Set the paths for external executables, substituting
-               ;; gv for acroread.
-               ;; There is also vmd_path, but VMD is not free software
-               ;; and Guix contains currently no free molecular viewer that
-               ;; could be substituted.
-               (("PREFERENCES\\['acroread_path'\\] = ''")
-                (format #f "PREFERENCES['acroread_path'] = '~a'"
-                        (which "gv")))
-               (("PREFERENCES\\['ncdump_path'\\] = ''")
-                (format #f "PREFERENCES['ncdump_path'] = '~a'"
-                        (which "ncdump")))
-               (("PREFERENCES\\['ncgen_path'\\] = ''")
-                (format #f "PREFERENCES['ncgen_path'] = '~a'"
-                        (which "ncgen3")))
-               (("PREFERENCES\\['task_manager_path'\\] = ''")
-                (format #f "PREFERENCES['task_manager_path'] = '~a'"
-                        (which "task_manager")))
-               ;; Show documentation as PDF
-               (("PREFERENCES\\['documentation_style'\\] = 'html'")
-                "PREFERENCES['documentation_style'] = 'pdf'") ))))))
-    (home-page "http://dirac.cnrs-orleans.fr/nMOLDYN.html")
-    (synopsis "Analysis software for Molecular Dynamics trajectories")
-    (description "nMOLDYN is an interactive analysis program for Molecular Dynamics
-simulations.  It is especially designed for the computation and decomposition of
-neutron scattering spectra, but also computes other quantities.  The software
-is currently not actively maintained and works only with Python 2 and
-NumPy < 1.9.")
-    (license license:cecill)))
-
 (define-public tng
   (package
     (name "tng")
-- 
2.36.0

[bug#55424] [PATCH 049/602] gnu: Remove python2-neo4j-driver.

[Maxim Cournoyer]

* gnu/packages/databases.scm (python2-neo4j-driver): Delete variable.
---
 gnu/packages/databases.scm | 21 ---------------------
 1 file changed, 21 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index feedfe68e7..82ff9fc13c 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -3652,27 +3652,6 @@ (define-public python-databases
     (description "This package implements async database support for Python.")
     (license license:bsd-3)))
 
-(define-public python2-neo4j-driver
-  (package
-    (name "python2-neo4j-driver")
-    ;; NOTE: When upgrading to 1.5.0, please add a python3 variant.
-    (version "1.4.0")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "neo4j-driver" version))
-              (sha256
-               (base32
-                "011r1vh182p8mm83d8dz9rfnc3l7rf7fd00cyrbyfzi71jmc4g98"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2))
-    (home-page "https://neo4j.com/developer/python/")
-    (synopsis "Neo4j driver code written in Python")
-    (description "This package provides the Neo4j Python driver that connects
-to the database using Neo4j's binary protocol.  It aims to be minimal, while
-being idiomatic to Python.")
-    (license license:asl2.0)))
-
 (define-public python2-py2neo
   (package
     (name "python2-py2neo")
-- 
2.36.0

[bug#55424] [PATCH 050/602] gnu: Remove python2-redis.

[Maxim Cournoyer]

* gnu/packages/databases.scm (python2-redis): Delete variable.
---
 gnu/packages/databases.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 82ff9fc13c..717918ed0d 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -3998,9 +3998,6 @@ (define-public python-redis
      "This package provides a Python interface to the Redis key-value store.")
     (license license:expat)))
 
-(define-public python2-redis
-  (package-with-python2 python-redis))
-
 (define-public python-rq
   (package
     (name "python-rq")
-- 
2.36.0

[bug#55424] [PATCH 051/602] gnu: Remove python2-trollius-redis.

[Maxim Cournoyer]

* gnu/packages/databases.scm (python2-trollius-redis): Delete variable.
---
 gnu/packages/databases.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 717918ed0d..126c32725e 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -4095,9 +4095,6 @@ (define-public python-trollius-redis
   Redis protocol.")
     (license license:bsd-2)))
 
-(define-public python2-trollius-redis
-  (package-with-python2 python-trollius-redis))
-
 (define-public python-sqlparse
   (package
     (name "python-sqlparse")
-- 
2.36.0

[bug#55424] [PATCH 052/602] gnu: Remove python2-peewee.

[Maxim Cournoyer]

* gnu/packages/databases.scm (python2-peewee): Delete variable.
---
 gnu/packages/databases.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 126c32725e..e7693552f2 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -2876,9 +2876,6 @@ (define-public python-peewee
 can autogenerate peewee models using @code{pwiz}, a model generator.")
     (license license:expat)))
 
-(define-public python2-peewee
-  (package-with-python2 python-peewee))
-
 (define-public python-pypika-tortoise
   (package
     (name "python-pypika-tortoise")
-- 
2.36.0

[bug#55424] [PATCH 053/602] gnu: Remove python2-ccm.

[Maxim Cournoyer]

* gnu/packages/databases.scm (python2-ccm): Delete variable.
---
 gnu/packages/databases.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index e7693552f2..96bb05a486 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -3289,9 +3289,6 @@ (define-public python-ccm
 on localhost.")
     (license license:asl2.0)))
 
-(define-public python2-ccm
-  (package-with-python2 python-ccm))
-
 (define-public python2-pysqlite
   (package
     (name "python2-pysqlite")
-- 
2.36.0

[bug#55424] [PATCH 054/602] gnu: Remove python2-apsw.

[Maxim Cournoyer]

* gnu/packages/databases.scm (python2-apsw): Delete variable.
---
 gnu/packages/databases.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 96bb05a486..945525d791 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -3587,9 +3587,6 @@ (define-public python-apsw
 translate the complete SQLite API into Python.")
     (license license:zlib)))
 
-(define-public python2-apsw
-  (package-with-python2 python-apsw))
-
 (define-public python-aiosqlite
   (package
     (name "python-aiosqlite")
-- 
2.36.0

[bug#55424] [PATCH 055/602] gnu: Remove python2-py2neo.

[Maxim Cournoyer]

* gnu/packages/databases.scm (python2-py2neo): Delete variable.
---
 gnu/packages/databases.scm | 21 ---------------------
 1 file changed, 21 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 945525d791..b2c74a54ba 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -3643,27 +3643,6 @@ (define-public python-databases
     (description "This package implements async database support for Python.")
     (license license:bsd-3)))
 
-(define-public python2-py2neo
-  (package
-    (name "python2-py2neo")
-    (version "3.1.2")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "py2neo" version))
-              (sha256
-               (base32
-                "1f1q95vqcvlc3nsc33p841swnjdcjazddlq2dzi3qfnjqjrajxw1"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2))
-    (home-page "https://py2neo.org")
-    (synopsis "Library and toolkit for working with Neo4j in Python")
-    (description "This package provides a client library and toolkit for
-working with Neo4j from within Python applications and from the command
-line.  The core library has no external dependencies and has been carefully
-designed to be easy and intuitive to use.")
-    (license license:asl2.0)))
-
 (define-public python-psycopg2
   (package
     (name "python-psycopg2")
-- 
2.36.0

[bug#55424] [PATCH 056/602] gnu: Remove python2-pyodbc-c.

[Maxim Cournoyer]

* gnu/packages/databases.scm (python2-pyodbc-c): Delete variable.
---
 gnu/packages/databases.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index b2c74a54ba..cd3f92a855 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -3091,9 +3091,6 @@ (define-public python-pyodbc-c
 for ODBC.")
     (license (license:x11-style "file://LICENSE.TXT"))))
 
-(define-public python2-pyodbc-c
-  (package-with-python2 python-pyodbc-c))
-
 (define-public python-pyodbc
   (package
     (name "python-pyodbc")
-- 
2.36.0

[bug#55424] [PATCH 057/602] gnu: Remove python2-pymysql.

[Maxim Cournoyer]

* gnu/packages/databases.scm (python2-pymysql): Delete variable.
---
 gnu/packages/databases.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index cd3f92a855..03d8c64037 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -1525,9 +1525,6 @@ (define-public python-pymysql
 Most public APIs are compatible with @command{mysqlclient} and MySQLdb.")
     (license license:expat)))
 
-(define-public python2-pymysql
-  (package-with-python2 python-pymysql))
-
 (define-public qdbm
   (package
     (name "qdbm")
-- 
2.36.0

[bug#55424] [PATCH 058/602] gnu: Remove python2-hiredis.

[Maxim Cournoyer]

* gnu/packages/databases.scm (python2-hiredis): Delete variable.
---
 gnu/packages/databases.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 03d8c64037..56fef5ee13 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -3873,9 +3873,6 @@ (define-public python-hiredis
 parsing code in hiredis.  It primarily speeds up parsing of multi bulk replies.")
     (license license:bsd-3)))
 
-(define-public python2-hiredis
-  (package-with-python2 python-hiredis))
-
 (define-public python-aioredis
   (package
     (name "python-aioredis")
-- 
2.36.0

[bug#55424] [PATCH 059/602] gnu: Remove python2-pytest-pep8.

[Maxim Cournoyer]

* gnu/packages/check.scm (python2-pytest-pep8): Delete variable.
---
 gnu/packages/check.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 805e8c2041..ca8b744904 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2367,9 +2367,6 @@ (define-public python-pytest-pep8
     (description "Pytest plugin for checking PEP8 compliance.")
     (license license:expat)))
 
-(define-public python2-pytest-pep8
-  (package-with-python2 python-pytest-pep8))
-
 (define-public python-pytest-perf
   (package
     (name "python-pytest-perf")
-- 
2.36.0

[bug#55424] [PATCH 060/602] gnu: Remove python2-scikit-learn.

[Maxim Cournoyer]

* gnu/packages/machine-learning.scm (python2-scikit-learn): Delete variable.
(python-scikit-learn)[properties]: Remove the python2-variant property.
---
 gnu/packages/machine-learning.scm | 47 -------------------------------
 1 file changed, 47 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 3897342345..02cd6b31aa 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1128,55 +1128,8 @@ (define-public python-scikit-learn
     (description
      "Scikit-learn provides simple and efficient tools for data mining and
 data analysis.")
-    (properties `((python2-variant . ,(delay python2-scikit-learn))))
     (license license:bsd-3)))
 
-;; scikit-learn 0.22 and later only supports Python 3, so we stick with
-;; an older version here.
-(define-public python2-scikit-learn
-  (let ((base (package-with-python2 (strip-python2-variant python-scikit-learn))))
-    (package
-      (inherit base)
-      (version "0.20.4")
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://github.com/scikit-learn/scikit-learn")
-                      (commit version)))
-                (file-name (git-file-name "python-scikit-learn" version))
-                (sha256
-                 (base32
-                  "08zbzi8yx5wdlxfx9jap61vg1malc9ajf576w7a0liv6jvvrxlpj"))))
-      (arguments
-       `(#:python ,python-2
-         #:phases
-         (modify-phases %standard-phases
-           (add-after 'build 'build-ext
-             (lambda _ (invoke "python" "setup.py" "build_ext" "--inplace")))
-           (replace 'check
-             (lambda* (#:key tests? #:allow-other-keys)
-               (when tests?
-                 ;; Restrict OpenBLAS threads to prevent segfaults while testing!
-                 (setenv "OPENBLAS_NUM_THREADS" "1")
-
-                 ;; Some tests require write access to $HOME.
-                 (setenv "HOME" "/tmp")
-
-                 (invoke "pytest" "sklearn" "-m" "not network"
-                         "-k"
-                         (string-append
-                          ;; This test tries to access the internet.
-                          "not test_load_boston_alternative"
-                          ;; This test fails for unknown reasons
-                          " and not test_rank_deficient_design"))))))))
-      (inputs
-       (list openblas))
-      (native-inputs
-       (list python2-pytest python2-pandas ;for tests
-             python2-cython))
-      (propagated-inputs
-       (list python2-numpy python2-scipy python2-joblib)))))
-
 (define-public python-threadpoolctl
   (package
     (name "python-threadpoolctl")
-- 
2.36.0

[bug#55424] [PATCH 061/602] gnu: Remove ocrodjvu.

[Maxim Cournoyer]

This package still depends on Python 2, and upstream considers this issue as
"wontfix".

* gnu/packages/djvu.scm (ocrodjvu): Delete variable.
---
 gnu/packages/djvu.scm | 84 -------------------------------------------
 1 file changed, 84 deletions(-)

diff --git a/gnu/packages/djvu.scm b/gnu/packages/djvu.scm
index 07c77f318e..38e6278ce5 100644
--- a/gnu/packages/djvu.scm
+++ b/gnu/packages/djvu.scm
@@ -396,87 +396,3 @@ (define-public didjvu
 and background layers of images, which can then be encoded into a DjVu file.")
     (home-page "https://jwilk.net/software/didjvu")
     (license license:gpl2)))
-
-(define-public ocrodjvu
-  (package
-    (name "ocrodjvu")
-    (version "0.12")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://github.com/jwilk/ocrodjvu/releases/download/" version
-             "/ocrodjvu-" version ".tar.xz"))
-       (sha256
-        (base32 "09w9rqr7z2jd5kwp178zz2yrsc82mxs7gksipg92znxzgzhmw2ng"))))
-    (build-system gnu-build-system)
-    (native-inputs
-     (list libxml2 python2-nose python2-pillow))
-    (inputs
-     `(("djvulibre" ,djvulibre)
-       ("ocrad" ,ocrad)
-       ("python" ,python-2)
-       ("python2-djvulibre" ,python2-djvulibre)
-       ("python2-html5lib" ,python2-html5lib)
-       ("python2-lxml" ,python2-lxml)
-       ("python2-pyicu" ,python2-pyicu)
-       ("python2-subprocess32" ,python2-subprocess32)
-       ("tesseract-ocr" ,tesseract-ocr)))
-    (arguments
-     `(#:modules ((guix build gnu-build-system)
-                  ((guix build python-build-system) #:prefix python:)
-                  (guix build utils))
-       #:imported-modules (,@%gnu-build-system-modules
-                           (guix build python-build-system))
-       #:test-target "test"
-       #:phases
-       (modify-phases %standard-phases
-         (delete 'configure)
-         (add-before 'check 'disable-failing-test
-           (lambda _
-             (substitute* "tests/test_ipc.py"
-               ;; test_wait_signal gets stuck forever
-               (("yield self\\._test_signal, name")
-                "return True")
-               ;; test_path fails to find a file it should have created
-               (("path = os\\.getenv\\('PATH'\\)\\.split\\(':'\\)")
-                "return True"))
-             ;; Disable tests with tesseract. They can't work without
-             ;; the language files that must downloaded by the final user
-             ;; as they are not packaged in Guix.
-             (substitute* "tests/ocrodjvu/test.py"
-               (("engines = stdout\\.getvalue\\(\\)\\.splitlines\\(\\)")
-                "engines = ['ocrad']"))
-             (substitute* "tests/ocrodjvu/test_integration.py"
-               (("engines = 'tesseract', 'cuneiform', 'gocr', 'ocrad'")
-                "engines = 'ocrad'"))))
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
-               (invoke "make"
-                       "DESTDIR="
-                       (string-append "PREFIX=" out)
-                       "install"))))
-         (add-after 'install 'wrap-python
-           (assoc-ref python:%standard-phases 'wrap))
-         (add-after 'wrap-python 'wrap-path
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out"))
-                   (djvulibre (assoc-ref inputs "djvulibre"))
-                   (ocrad (assoc-ref inputs "ocrad"))
-                   (tesseract (assoc-ref inputs "tesseract-ocr")))
-               (for-each (lambda (file)
-                           (wrap-program (string-append out "/bin/" file)
-                             `("PATH" ":" prefix
-                               (,(string-append djvulibre "/bin:"
-                                                ocrad "/bin:"
-                                                tesseract "/bin")))))
-                         '("djvu2hocr"
-                           "hocr2djvused"
-                           "ocrodjvu"))))))))
-    (synopsis "Program to perform OCR on DjVu files")
-    (description
-     "@code{ocrodjvu} is a wrapper for OCR systems, that allows you to perform
-OCR on DjVu files.")
-    (home-page "https://jwilk.net/software/ocrodjvu")
-    (license license:gpl2)))
-- 
2.36.0

[bug#55424] [PATCH 062/602] gnu: Remove python2-pandas.

[Maxim Cournoyer]

* gnu/packages/python-science.scm (python2-pandas): Delete variable.
(python-pandas): Delete related python2-variant property.
---
 gnu/packages/python-science.scm | 98 ---------------------------------
 1 file changed, 98 deletions(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index bf7c7ce45f..b3f39fd19d 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -488,106 +488,8 @@ (define-public python-pandas
 multidimensional, potentially heterogeneous) and time series data both easy
 and intuitive.  It aims to be the fundamental high-level building block for
 doing practical, real world data analysis in Python.")
-    (properties `((python2-variant . ,(delay python2-pandas))))
     (license license:bsd-3)))
 
-;; Pandas 0.24.x are the last versions that support Python 2.
-(define-public python2-pandas
-  (let ((pandas (package-with-python2
-                 (strip-python2-variant python-pandas))))
-    (package
-      (inherit pandas)
-      (version "0.24.2")
-      (source (origin
-                (method url-fetch)
-                (uri (pypi-uri "pandas" version))
-                (sha256
-                 (base32
-                  "18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag"))
-                (modules '((guix build utils)))
-                (snippet
-                 '(begin
-                    ;; Adjust for renamed error message in Python 2.7.17.  Taken
-                    ;; from <https://github.com/pandas-dev/pandas/pull/29294>.
-                    (substitute* "pandas/io/parsers.py"
-                      (("if 'NULL byte' in msg:")
-                       "if 'NULL byte' in msg or 'line contains NUL' in msg:"))))))
-      (arguments
-       `(#:modules ((guix build utils)
-                    (guix build python-build-system)
-                    (ice-9 ftw)
-                    (srfi srfi-26))
-         #:python ,python-2
-         #:phases
-         (modify-phases %standard-phases
-           (add-after 'unpack 'patch-which
-             (lambda* (#:key inputs #:allow-other-keys)
-               (let ((which (assoc-ref inputs "which")))
-                 (substitute* "pandas/io/clipboard/__init__.py"
-                   (("^CHECK_CMD = .*")
-                    (string-append "CHECK_CMD = \"" which "\"\n"))))))
-           (replace 'check
-             (lambda _
-               (let ((build-directory
-                      (string-append
-                       (getcwd) "/build/"
-                       (car (scandir "build"
-                                     (cut string-prefix? "lib." <>))))))
-                 ;; Disable the "strict data files" option which causes
-                 ;; the build to error out if required data files are
-                 ;; not available (as is the case with PyPI archives).
-                 (substitute* "setup.cfg"
-                   (("addopts = --strict-data-files") "addopts = "))
-                 (with-directory-excursion build-directory
-                   ;; Delete tests that require "moto" which is not yet
-                   ;; in Guix.
-                   (for-each delete-file
-                             '("pandas/tests/io/conftest.py"
-                               "pandas/tests/io/json/test_compression.py"
-                               "pandas/tests/io/parser/test_network.py"
-                               "pandas/tests/io/test_parquet.py"))
-                   (invoke "pytest" "-vv" "pandas" "--skip-slow"
-                           "--skip-network" "-k"
-                           ;; XXX: Due to the deleted tests above.
-                           "not test_read_s3_jsonl"))))))))
-      (propagated-inputs
-       (list python2-numpy python2-openpyxl python2-pytz python2-dateutil
-             python2-xlrd))
-      (inputs
-       (list which))
-      (native-inputs
-       (list python2-cython
-             python2-beautifulsoup4
-             python2-lxml
-             python2-html5lib
-             python2-nose
-             python2-pytest
-             python2-pytest-mock)))))
-
-(define-public python2-pyflow
-  (package
-    (name "python2-pyflow")
-    (version "1.1.20")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/Illumina/pyflow/releases/download/v"
-                    version "/pyflow-" version ".tar.gz"))
-              (sha256
-               (base32
-                "1bvfvviw58cndyn862qnv9nj3d9cd3a0dm4vc4sd9vwq8a6z1riv"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f ; There is no test suite.
-       ;; There is no official Python 3-compatible version and upstream is
-       ;; dead. See https://github.com/Illumina/pyflow/issues/20.
-       #:python ,python-2))
-    (home-page "https://illumina.github.io/pyflow/")
-    (synopsis "Tool to manage tasks in a task dependency graph")
-    (description "This package is a Python module to manage tasks in the
-context of a task dependency graph.  It has some similarities to make.")
-    (license license:bsd-2)))
-
 (define-public python-pythran
   (package
     (name "python-pythran")
-- 
2.36.0

[bug#55424] [PATCH 063/602] gnu: Remove python2-html5lib.

[Maxim Cournoyer]

* gnu/packages/python-web.scm (python2-html5lib): Delete variable.
(python-html5lib-0.9, python2-html5lib-0.9): Likewise.
---
 gnu/packages/python-web.scm | 19 -------------------
 1 file changed, 19 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 7636931091..60970cd386 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1324,25 +1324,6 @@ (define-public python-html5lib
 and written in Python.")
     (license license:expat)))
 
-(define-public python2-html5lib
-  (package-with-python2 python-html5lib))
-
-;; Needed for python-bleach, a dependency of python-notebook
-(define-public python-html5lib-0.9
-  (package
-    (inherit python-html5lib)
-    (version "0.999")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "html5lib" version))
-       (sha256
-        (base32
-         "17n4zfsj6ynmbwdwviywmj8r6nzr3xvfx2zs0xhndmvm51z7z263"))))))
-
-(define-public python2-html5lib-0.9
-  (package-with-python2 python-html5lib-0.9))
-
 (define-public python-html5-parser
   (package
     (name "python-html5-parser")
-- 
2.36.0

[bug#55424] [PATCH 064/602] gnu: Remove python2-statsmodels.

[Maxim Cournoyer]

* gnu/packages/statistics.scm (python2-statsmodels): Delete variable.
---
 gnu/packages/statistics.scm | 21 ---------------------
 1 file changed, 21 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 244a2f3ecb..891c2b804c 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2068,27 +2068,6 @@ (define-public python-statsmodels
 inference for statistical models.")
     (license license:bsd-3)))
 
-(define-public python2-statsmodels
-  (let ((stats (package-with-python2 python-statsmodels)))
-    (package/inherit stats
-      ;; Version 0.11.1 and later does not work with Python 2.  It may build
-      ;; fine but loading modules fails.
-      (version "0.9.0")
-      (source
-       (origin
-         (method url-fetch)
-         (uri (pypi-uri "statsmodels" version))
-         (sha256
-          (base32
-           "0fxs8a7sp4d7jvqlm36yi45i2d28kjfvraf9q8i9jr1chhxgjqb4"))))
-      (propagated-inputs
-       `(("python2-pytz" ,python2-pytz)
-         ("python2-numpy" ,python2-numpy)
-         ("python2-scipy" ,python2-scipy)
-         ("python2-pandas" ,python2-pandas)
-         ("python2-patsy" ,python2-patsy)
-         ("python2-matplotlib" ,python2-matplotlib))))))
-
 (define-public r-coda
   (package
     (name "r-coda")
-- 
2.36.0

[bug#55424] [PATCH 065/602] gnu: Remove python2-pytest-cache.

[Maxim Cournoyer]

* gnu/packages/check.scm (python2-pytest-cache): Delete variable.
---
 gnu/packages/check.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index ca8b744904..cffcd54623 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2027,9 +2027,6 @@ (define-public python-pytest-cache
     (home-page "https://bitbucket.org/hpk42/pytest-cache/")
     (license license:expat)))
 
-(define-public python2-pytest-cache
-  (package-with-python2 python-pytest-cache))
-
 (define-public python-pytest-localserver
   (package
     (name "python-pytest-localserver")
-- 
2.36.0

[bug#55424] [PATCH 066/602] gnu: Remove python2-fastlmm.

[Maxim Cournoyer]

* gnu/packages/machine-learning.scm (python2-fastlmm): Delete variable.
---
 gnu/packages/machine-learning.scm | 32 -------------------------------
 1 file changed, 32 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 02cd6b31aa..7b377c7d35 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1415,38 +1415,6 @@ (define-public vowpal-wabbit
 interactive learning.")
     (license license:bsd-3)))
 
-(define-public python2-fastlmm
-  (package
-    (name "python2-fastlmm")
-    (version "0.2.21")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "fastlmm" version ".zip"))
-       (sha256
-        (base32
-         "1q8c34rpmwkfy3r4d5172pzdkpfryj561897z9r3x22gq7813x1m"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f ; some test files are missing
-       #:python ,python-2)) ; only Python 2.7 is supported
-    (propagated-inputs
-     (list python2-numpy
-           python2-scipy
-           python2-matplotlib
-           python2-pandas
-           python2-scikit-learn
-           python2-pysnptools))
-    (native-inputs
-     (list unzip python2-cython python2-mock python2-nose))
-    (home-page "http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/")
-    (synopsis "Perform genome-wide association studies on large data sets")
-    (description
-     "FaST-LMM, which stands for Factored Spectrally Transformed Linear Mixed
-Models, is a program for performing both single-SNP and SNP-set genome-wide
-association studies (GWAS) on extremely large data sets.")
-    (license license:asl2.0)))
-
 (define-public python-hyperopt
   (package
     (name "python-hyperopt")
-- 
2.36.0

[bug#55424] [PATCH 067/602] gnu: Remove python2-parameterized.

[Maxim Cournoyer]

* gnu/packages/check.scm (python2-parameterized): Delete variable.
* gnu/packages/patches/python2-parameterized-docstring-test.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): De-register it.
---
 gnu/local.mk                                   |  1 -
 gnu/packages/check.scm                         | 11 -----------
 .../python2-parameterized-docstring-test.patch | 18 ------------------
 3 files changed, 30 deletions(-)
 delete mode 100644 gnu/packages/patches/python2-parameterized-docstring-test.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 4ef12fd68e..77f5ee9c33 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1701,7 +1701,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-mox3-python3.6-compat.patch	\
   %D%/packages/patches/python-typing-inspect-fix.patch		\
   %D%/packages/patches/python-packaging-test-arch.patch		\
-  %D%/packages/patches/python2-parameterized-docstring-test.patch	\
   %D%/packages/patches/python-paste-remove-timing-test.patch	\
   %D%/packages/patches/python-pycrypto-CVE-2013-7459.patch	\
   %D%/packages/patches/python-pycrypto-time-clock.patch		\
diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index cffcd54623..f8b4fc7e2f 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -818,19 +818,8 @@ (define-public python-parameterized
     (description
      "Parameterized is a Python library that aims to fix parameterized testing
 for every Python test framework.  It supports nose, py.test, and unittest.")
-    (properties `((python2-variant . ,(delay python2-parameterized))))
     (license license:bsd-2)))
 
-(define-public python2-parameterized
-  (let ((base (package-with-python2 (strip-python2-variant
-                                     python-parameterized))))
-    (package/inherit
-     base
-     (source
-      (origin
-        (inherit (package-source base))
-        (patches (search-patches "python2-parameterized-docstring-test.patch")))))))
-
 (define-public python-minimock
   (package
     (name "python-minimock")
diff --git a/gnu/packages/patches/python2-parameterized-docstring-test.patch b/gnu/packages/patches/python2-parameterized-docstring-test.patch
deleted file mode 100644
index 14691e1904..0000000000
--- a/gnu/packages/patches/python2-parameterized-docstring-test.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-Skip unicode docstring test, required when running on Python 2.
-
-See <https://github.com/wolever/parameterized/issues/44>.
-
---- a/parameterized/test.py
-+++ b/parameterized/test.py
-@@ -284,11 +284,6 @@
-             "        More" %(foo, )
-         )
- 
--    @parameterized.expand([param("foo")])
--    def test_unicode_docstring(self, foo):
--        u"""Döcumentation."""
--        self._assert_docstring(u"Döcumentation [with foo=%r]." %(foo, ))
--
-     @parameterized.expand([param("foo", )])
-     def test_default_values_get_correct_value(self, foo, bar=12):
-         """Documentation"""
-- 
2.36.0

[bug#55424] [PATCH 068/602] gnu: Remove python2-pytest-warnings.

[Maxim Cournoyer]

* gnu/packages/check.scm (python2-pytest-warnings): Delete variable.
---
 gnu/packages/check.scm | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index f8b4fc7e2f..808dd07a79 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -2566,14 +2566,7 @@ (define-public python-pytest-warnings
      "Python-pytest-warnings is a pytest plugin to list Python warnings in
 pytest report.")
     (license license:expat)
-    (properties `((python2-variant . ,(delay python2-pytest-warnings))
-                  ;; This package is part of pytest as of version 3.1.0.
-                  (superseded . ,python-pytest)))))
-
-(define-public python2-pytest-warnings
-  (package (inherit (package-with-python2
-                     (strip-python2-variant python-pytest-warnings)))
-           (properties `((superseded . ,python2-pytest)))))
+    (properties `((superseded unquote python-pytest)))))
 
 (define-public python-pytest-capturelog
   (package
-- 
2.36.0

[bug#55424] [PATCH 069/602] gnu: Remove python2-pyodbc.

[Maxim Cournoyer]

* gnu/packages/databases.scm (python2-pyodbc): Delete variable.
---
 gnu/packages/databases.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 56fef5ee13..46526bc023 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -3110,9 +3110,6 @@ (define-public python-pyodbc
 for ODBC.")
     (license (license:x11-style "file:///LICENSE.TXT"))))
 
-(define-public python2-pyodbc
-  (package-with-python2 python-pyodbc))
-
 (define-public mdbtools
   (package
     (name "mdbtools")
-- 
2.36.0

[bug#55424] [PATCH 070/602] gnu: Remove python2-pickleshare.

[Maxim Cournoyer]

* gnu/packages/databases.scm (python2-pickleshare): Delete variable.
---
 gnu/packages/databases.scm | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 46526bc023..b39f0312bd 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -3524,17 +3524,8 @@ (define-public python-pickleshare
 database.  Concurrency is possible because the values are stored in separate
 files.  Hence the “database” is a directory where all files are governed by
 PickleShare.")
-    (properties `((python2-variant . ,(delay python2-pickleshare))))
     (license license:expat)))
 
-(define-public python2-pickleshare
-  (let ((pickleshare (package-with-python2
-                      (strip-python2-variant python-pickleshare))))
-    (package (inherit pickleshare)
-      (propagated-inputs (modify-inputs (package-propagated-inputs
-                                                        pickleshare)
-                           (prepend python2-pathlib2))))))
-
 (define-public python-apsw
   (package
     (name "python-apsw")
-- 
2.36.0

[bug#55424] [PATCH 071/602] gnu: Remove djvusmooth.

[Maxim Cournoyer]

* gnu/packages/djvu.scm (djvusmooth): Delete variable.
---
 gnu/packages/djvu.scm | 40 ----------------------------------------
 1 file changed, 40 deletions(-)

diff --git a/gnu/packages/djvu.scm b/gnu/packages/djvu.scm
index 38e6278ce5..6ff0ace5bc 100644
--- a/gnu/packages/djvu.scm
+++ b/gnu/packages/djvu.scm
@@ -290,46 +290,6 @@ (define-public minidjvu
     (home-page "https://sourceforge.net/projects/minidjvu/")
     (license license:gpl2)))
 
-(define-public djvusmooth
-  (package
-    (name "djvusmooth")
-    (version "0.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://github.com/jwilk/djvusmooth/releases/download/" version
-             "/djvusmooth-" version ".tar.gz"))
-       (sha256
-        (base32 "0z403cklvxzz0qaczgv83ax0nknrd9h8micp04j9kjfdxk2sgval"))))
-    (build-system python-build-system)
-    (inputs
-     (list djvulibre python2-djvulibre python2-subprocess32
-           python2-wxpython))
-    (arguments
-     `(#:python ,python-2
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-paths
-           (lambda* (#:key inputs #:allow-other-keys)
-             (substitute* "lib/djvused.py"
-               (("djvused_path = 'djvused'")
-                (string-append "djvused_path = '"
-                               (assoc-ref inputs "djvulibre")
-                               "/bin/djvused'"))))))))
-    (synopsis "Graphical editor for DjVu documents")
-    (description
-     "@code{djvusmooth} is a graphical editor for DjVu_ documents.
-It is able to:
-@itemize
-@item edit document metadata,
-@item edit document outline (bookmarks),
-@item add, remove or edit hyperlinks,
-@item correct occasional errors in the hidden text layer.
-@end itemize\n")
-    (home-page "https://jwilk.net/software/djvusmooth")
-    (license license:gpl2)))
-
 (define-public didjvu
   (package
     (name "didjvu")
-- 
2.36.0

[bug#55424] [PATCH 072/602] gnu: Remove omnitux.

[Maxim Cournoyer]

* gnu/packages/education.scm (omnitux): Delete variable.
---
 gnu/packages/education.scm | 100 -------------------------------------
 1 file changed, 100 deletions(-)

diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm
index 213c8f717b..07843142f4 100644
--- a/gnu/packages/education.scm
+++ b/gnu/packages/education.scm
@@ -679,106 +679,6 @@ (define-public openboard
 a pen-tablet display and a beamer.")
       (license license:gpl3))))
 
-(define-public omnitux
-  (package
-    (name "omnitux")
-    (version "1.2.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "mirror://sourceforge/omnitux/omnitux/"
-                           "v" version "/omnitux-" version ".tar.bz2"))
-       (sha256
-        (base32 "1wmmmbzmxd0blhn00d4g91xwavnab143a31ca3i8hrqgzh6qz9w6"))
-       (modules '((guix build utils)))
-       (snippet
-        '(begin
-           ;; Remove pre-compiled .pyc files from source.
-           (for-each delete-file (find-files "bin" "\\.pyc$"))
-           #t))))
-    (build-system python-build-system)
-    (inputs
-     (list python2-pygame python2-pygtk))
-    (arguments
-     `(#:tests? #f                      ;no test
-       #:python ,python-2
-       #:phases
-       (modify-phases %standard-phases
-         (delete 'build)                ;no setup.py
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (share (string-append out "/share"))
-                    (data (string-append share "/omnitux")))
-               ;; Install documentation.
-               (let ((doc (string-append share "/doc/" ,name "-" ,version)))
-                 (for-each (lambda (f) (install-file f doc))
-                           '("LICENSE.txt" "README.txt")))
-               ;; Install data.
-               (install-file "omnitux.sh" data)
-               (for-each (lambda (d)
-                           (copy-recursively d (string-append data "/" d)))
-                         '("bin" "data"))
-               ;; Install the launcher.
-               (let* ((bin (string-append out "/bin"))
-                      (script (string-append bin "/omnitux"))
-                      (bash (search-input-file %build-inputs "/bin/bash"))
-                      (python (search-input-file %build-inputs
-                                                 "/bin/python2")))
-                 (mkdir-p bin)
-                 (with-output-to-file script
-                   (lambda ()
-                     (format #t "#!~a~%" bash)
-                     (format #t
-                             "cd ~a; ~a menu.py~%"
-                             (string-append data "/bin")
-                             python)))
-                 (chmod script #o755))
-               ;; Install icon and desktop file.
-               (let ((pixmaps (string-append share "/pixmaps")))
-                 (install-file "data/default/icons/Omnitux_logo.svg" pixmaps))
-               (let ((apps (string-append out "/share/applications")))
-                 (mkdir-p apps)
-                 (with-output-to-file (string-append apps "/omnitux.desktop")
-                   (lambda _
-                     (format #t
-                             "[Desktop Entry]~@
-                              Name=Omnitux~@
-                              GenericName=Omnitux
-                              Comment=An educational game based on multimedia elements.~@
-                              Comment[fr]=Un jeu ludo-éducatif basé sur des éléments multimédias.~@
-                              Exec=~a/bin/omnitux~@
-                              Type=Application~@
-                              Categories=Game;Education;~@
-                              Terminal=false~@
-                              Icon=Omnitux_logo.svg~@"
-                             out))))
-               #t))))))
-    (home-page "http://omnitux.sourceforge.net/")
-    (synopsis "Educational activities based on multimedia elements")
-    (description "The project aims to provide various educational
-activities around multimedia elements (images, sounds, texts).  Types
-of activities include:
-@itemize
-@item associations,
-@item items to place on a map or a schema,
-@item counting activities,
-@item puzzles,
-@item card faces to remember,
-@item find differences between two pictures,
-@item ...
-@end itemize
-
-Activities are available in English, French, German, Polish,
-Portuguese, Spanish and Italian.")
-    ;; Project's license is GPL3+, but multimedia elements are
-    ;; released under various licenses.
-    (license (list license:gpl3+
-                   license:gpl2+
-                   license:cc-by-sa2.0
-                   license:cc-by-sa3.0
-                   license:public-domain))))
-
 (define-public fet
   (package
     (name "fet")
-- 
2.36.0

[bug#55424] [PATCH 073/602] gnu: Remove childsplay.

[Maxim Cournoyer]

* gnu/packages/education.scm (childsplay): Delete variable.
---
 gnu/packages/education.scm | 103 -------------------------------------
 1 file changed, 103 deletions(-)

diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm
index 07843142f4..3b9c01c786 100644
--- a/gnu/packages/education.scm
+++ b/gnu/packages/education.scm
@@ -445,109 +445,6 @@ (define-public toutenclic
     (home-page "https://bipede.fr/contrib/")
     (license license:gpl3)))
 
-(define-public childsplay
-  (package
-    (name "childsplay")
-    (version "3.4")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "mirror://sourceforge/schoolsplay/"
-                    "childsplay-" version ".tgz"))
-              (sha256
-               (base32
-                "0z7yp2swjnbz51vn2zyfnjn40jq38l5mbh15yafmx1z3vn2z1m77"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2
-       #:tests? #f
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'unbundle-dejavu-font
-           (lambda* (#:key inputs #:allow-other-keys)
-             (let* ((dejavu-dir
-                     (string-append (assoc-ref inputs "font-dejavu")
-                                    "/share/fonts/truetype"))
-                    (dejavu-font
-                     (string-append dejavu-dir
-                                    "/DejaVuSansCondensed-Bold.ttf")))
-               (substitute* "SPConstants.py"
-                 (("^(TTF(BOLD)? = ).*" _ prefix)
-                  (string-append prefix "'" dejavu-font "'\n")))
-               (for-each (lambda (f) (delete-file f))
-                         (find-files "lib/SPData" "DejaVu"))
-               #t)))
-         (delete 'build)
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (pixmaps (string-append out "/share/pixmaps"))
-                    (share (string-append out "/share/childsplay"))
-                    (doc (string-append out "/share/doc/" ,name "-",version)))
-               ;; Install icon.
-               (install-file "lib/SPData/themes/childsplay/logo_cp.svg" pixmaps)
-               ;; Install data.
-               (mkdir-p share)
-               (for-each (lambda (f)
-                           (copy-recursively f (string-append share "/" f)))
-                         '("alphabet-sounds" "lib" "locale" "SPWidgets"))
-               (for-each (lambda (f) (install-file f share))
-                         (find-files "." "\\.(py|dev|db)$"))
-               ;; Install documentation.
-               (mkdir-p doc)
-               (copy-recursively "docs" doc)
-               #t)))
-         (add-after 'install 'create-executable
-           (lambda* (#:key outputs inputs #:allow-other-keys)
-             (let* ((python (search-input-file inputs "/bin/python"))
-                    (out (assoc-ref outputs "out"))
-                    (bin (string-append out "/bin"))
-                    (executable (string-append bin "/childsplay")))
-               (mkdir-p bin)
-               (call-with-output-file executable
-                 (lambda (file)
-                   (format file
-                           "~a ~a"
-                           python
-                           (string-append out "/share/childsplay/childsplay.py"))))
-               (chmod executable #o555)
-               #t)))
-         (add-after 'install 'create-desktop-file
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (applications (string-append out "/share/applications")))
-               (mkdir-p applications)
-               (call-with-output-file
-                   (string-append applications "/childsplay.desktop")
-                 (lambda (file)
-                   (format file
-                           "[Desktop Entry]~@
-                            Name=Childsplay~@
-                            Comment=Suite of educational games for young children~@
-                            Comment[ca]=Conjunt de jocs educatius per a xiquets~@
-                            Comment[es]=Conjunto de juegos educativos para niños~@
-                            Comment[de]=Sammlung mit lehrreichen Spielen für kleine Kinder~@
-                            Exec=~a/bin/childsplay~@
-                            Terminal=false~@
-                            Icon=logo_cp.svg~@
-                            Type=Application~@
-                            Categories=Application;Game;Education;KidsGame;~@
-                            Keywords=suite;children;games;young;educational;~%"
-                           out)))
-               #t))))))
-    (inputs
-     `(("font-dejavu" ,font-dejavu)
-       ("pygame" ,python2-pygame)
-       ("sqlalchemy" ,python2-sqlalchemy)))
-    (synopsis "Suite of educational games for young children")
-    (description "Childsplay is a collection of educational activities
-for young children.  Childsplay can be used at home, kindergartens and
-pre-schools.  Childsplay is a fun and safe way to let young children
-use the computer and at the same time teach them a little math,
-letters of the alphabet, spelling, eye-hand coordination, etc.")
-    (home-page "http://www.schoolsplay.org")
-    (license license:gpl3+)))
-
 (define-public openboard
   ;; The last release builds from qtwebkit, which is planned for removal in
   ;; Guix, so use the latest commit of the 1.7-dev branch, which builds with
-- 
2.36.0

[bug#55424] [PATCH 074/602] gnu: Remove python2-capstone.

[Maxim Cournoyer]

* gnu/packages/engineering.scm (python2-capstone): Delete variable.
---
 gnu/packages/engineering.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index fe9e06e05a..8f188d07bd 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -1647,9 +1647,6 @@ (define-public python-capstone
                 (string-append "'" (assoc-ref %build-inputs "capstone") "/lib',\n")))
              #t)))))))
 
-(define-public python2-capstone
-  (package-with-python2 python-capstone))
-
 
 (define-public python-esptool-3.0
   (package
-- 
2.36.0

[bug#55424] [PATCH 075/602] gnu: Remove lekha.

[Maxim Cournoyer]

* gnu/packages/enlightenment.scm (lekha): Delete variable.
---
 gnu/packages/enlightenment.scm | 28 ----------------------------
 1 file changed, 28 deletions(-)

diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm
index 6a02ab1ca4..7be6304a5e 100644
--- a/gnu/packages/enlightenment.scm
+++ b/gnu/packages/enlightenment.scm
@@ -483,34 +483,6 @@ (define-public edi
                    license:gpl2          ; edi
                    license:gpl3))))      ; data/extra/examples/images/mono-runtime.png
 
-(define-public lekha
-  (package
-    (name "lekha")
-    (version "0.2.1")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "Lekha" version))
-              (sha256
-               (base32
-                "0zr6i74ik58pbzrd7r9l7sawqbdv0r2c1a9927qkqzwga27x8j15"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f ; no test target
-       #:python ,python-2
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-data-location
-           (lambda _ (substitute* "setup.py"
-                       (("'/usr/")"'"))
-             #t)))))
-    (propagated-inputs
-     (list python2-efl python2-pypdf2 python2-pyxdg))
-    (synopsis "Simple PDF viewer")
-    (description
-     "Simple PDF viewer based on the Enlightenment Foundation Libraries.")
-    (home-page "https://github.com/kaihu/lekha")
-    (license license:gpl3+)))
-
 (define-public ephoto
   (package
     (name "ephoto")
-- 
2.36.0

[bug#55424] [PATCH 076/602] gnu: Remove python2-stdnum.

[Maxim Cournoyer]

* gnu/packages/finance.scm (python2-stdnum): Delete variable.
---
 gnu/packages/finance.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index b5ab051a1f..9ff1b8b03f 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -1226,9 +1226,6 @@ (define-public python-stdnum
 Luhn and family of ISO/IEC 7064 check digit algorithms.")
     (license license:lgpl2.1+)))
 
-(define-public python2-stdnum
-  (package-with-python2 python-stdnum))
-
 (define-public python-duniterpy
   (package
     (name "python-duniterpy")
-- 
2.36.0

[bug#55424] [PATCH 077/602] gnu: Remove python2-ledgerblue.

[Maxim Cournoyer]

* gnu/packages/finance.scm (python2-ledgerblue): Delete variable.
---
 gnu/packages/finance.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 9ff1b8b03f..74cec6d143 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -974,9 +974,6 @@ (define-public python-ledgerblue
 Ledger Blue/Nano S.")
     (license license:asl2.0)))
 
-(define-public python2-ledgerblue
-  (package-with-python2 python-ledgerblue))
-
 (define-public python-btchip-python
   (package
     (name "python-btchip-python")
-- 
2.36.0

[bug#55424] [PATCH 078/602] gnu: Remove python2-keepkey.

[Maxim Cournoyer]

* gnu/packages/finance.scm (python2-keepkey): Delete variable.
---
 gnu/packages/finance.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 74cec6d143..f0caa9240c 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -1081,9 +1081,6 @@ (define-public python-keepkey
 the KeepKey Hardware Wallet.")
     (license license:lgpl3)))
 
-(define-public python2-keepkey
-  (package-with-python2 python-keepkey))
-
 (define-public ledger-agent
   (package
     (name "ledger-agent")
-- 
2.36.0

[bug#55424] [PATCH 079/602] gnu: nototools: Update to 0.2.16.

[Maxim Cournoyer]

* gnu/packages/fontutils.scm (nototools): Update to 0.2.16.
[arguments]: Remove python argument.
[phases]: New argument.
[native-inputs]: New field.
[propagated-inputs]: Remove python2-booleanoperations, python2-defcon,
python2-fonttools, python2-pillow, python2-pyclipper, and python2-ufolib.  Add
python-afdko.
---
 gnu/packages/fontutils.scm | 28 ++++++++++++++++------------
 1 file changed, 16 insertions(+), 12 deletions(-)

diff --git a/gnu/packages/fontutils.scm b/gnu/packages/fontutils.scm
index 444d1635cb..7c03109be5 100644
--- a/gnu/packages/fontutils.scm
+++ b/gnu/packages/fontutils.scm
@@ -1525,27 +1525,31 @@ (define-public python2-defcon
 (define-public nototools
   (package
     (name "nototools")
-    (version "20170925")
+    (version "0.2.16")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
-              (url "https://github.com/googlei18n/nototools")
-              (commit "v2017-09-25-tooling-for-phase3-update")))
+             (url "https://github.com/googlefonts/nototools")
+             (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "03nzvcvwmrhfrcjhg218q2f3hfrm3vlivp4rk19sc397kh3hisiz"))))
+         "14rrdamkmhrykff8ln07fq9cm8zwj3k113lzwjcy0lgz23g51jyl"))))
     (build-system python-build-system)
     (arguments
-     `(#:python ,python-2))
-    (propagated-inputs
-     (list python2-booleanoperations
-           python2-defcon
-           python2-fonttools
-           python2-pillow
-           python2-pyclipper
-           python2-ufolib))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'build 'pretend-version
+            (lambda _
+              (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)))
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (with-directory-excursion "tests"
+                (invoke "./run_tests")))))))
+    (native-inputs (list python-setuptools-scm))
+    (propagated-inputs (list python-afdko))
     (home-page "https://github.com/googlei18n/nototools")
     (synopsis "Noto fonts support tools and scripts")
     (description
-- 
2.36.0

[bug#55424] [PATCH 080/602] gnu: Remove python2-tmx.

[Maxim Cournoyer]

* gnu/packages/game-development.scm (python2-tmx): Delete variable.
---
 gnu/packages/game-development.scm | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index daeeec42cb..d8725e837c 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -407,14 +407,6 @@ (define-public python-tmx
                    ;; under the CC0 license.
                    license:cc0))))
 
-(define-public python2-tmx
-  (let ((python2-tmx (package-with-python2 python-tmx)))
-    (package
-      (inherit python2-tmx)
-      (propagated-inputs
-       (modify-inputs (package-propagated-inputs python2-tmx)
-         (prepend python2-pathlib))))))
-
 (define-public python-xsge
   (package
     (name "python-xsge")
-- 
2.36.0

[bug#55424] [PATCH 081/602] gnu: renpy: Build with Python 3.

[Maxim Cournoyer]

* gnu/packages/game-development.scm (renpy)[python]: Delete argument.
[phases]: Delete trailing #t.
[propagated-inputs]: Update the inputs to their Python 3 counterparts.
[native-inputs]: Likewise.
---
 gnu/packages/game-development.scm | 197 ++----------------------------
 1 file changed, 10 insertions(+), 187 deletions(-)

diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index d8725e837c..961b396ea7 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -1263,9 +1263,9 @@ (define-public python-pygame-sdl2
 (define-public python2-pygame-sdl2
   (package-with-python2 python-pygame-sdl2))
 
-(define-public python2-renpy
+(define-public renpy
   (package
-    (name "python2-renpy")
+    (name "renpy")
     (version "7.4.11")
     (source
      (origin
@@ -1284,8 +1284,7 @@ (define-public python2-renpy
            #t))))
     (build-system python-build-system)
     (arguments
-     `(#:tests? #f ; Ren'py doesn't seem to package tests
-       #:python ,python-2
+     `(#:tests? #f                      ; Ren'py doesn't seem to package tests
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'fix-commands
@@ -1293,8 +1292,7 @@ (define-public python2-renpy
              (substitute* "renpy/editor.py"
                (("xdg-open")
                 (string-append (assoc-ref inputs "xdg-utils")
-                               "/bin/xdg-open")))
-             #t))
+                               "/bin/xdg-open")))))
          (add-after 'unpack 'fix-include-paths
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "module/setup.py"
@@ -1305,8 +1303,7 @@ (define-public python2-renpy
              (setenv "RENPY_CYTHON"
                      (search-input-file (or native-inputs inputs)
                                         "/bin/cython"))
-             (setenv "RENPY_DEPS_INSTALL" (string-join (map cdr inputs) ":"))
-             #t))
+             (setenv "RENPY_DEPS_INSTALL" (string-join (map cdr inputs) ":"))))
          (replace 'build
            (lambda* (#:key inputs outputs #:allow-other-keys #:rest args)
              ;; The "module" subdirectory contains a python (really cython)
@@ -1316,8 +1313,7 @@ (define-public python2-renpy
                (apply (assoc-ref %standard-phases 'build) args))
              ;; The above only builds the cython modules, but nothing else,
              ;; so we do that here.
-             (invoke "python" "-m" "compileall" "renpy")
-             #t))
+             (invoke "python" "-m" "compileall" "renpy")))
          (replace 'install
            (lambda* (#:key inputs outputs #:allow-other-keys #:rest args)
              ;; Again, we have to wrap the module installation.
@@ -1332,8 +1328,9 @@ (define-public python2-renpy
                  (apply (assoc-ref %standard-phases 'install) args))
                (copy-recursively "renpy"
                                  (string-append out site "/renpy"))
-               (delete-file-recursively (string-append out site "/renpy/common")))
-             #t)))))
+               (delete-file-recursively (string-append out site
+                                                       "/renpy/common"))))))))
+    (native-inputs (list python-cython))
     (inputs
      (list ffmpeg
            freetype
@@ -1342,11 +1339,7 @@ (define-public python2-renpy
            libpng
            (sdl-union (list sdl2 sdl2-image sdl2-mixer sdl2-ttf))
            xdg-utils))
-    (propagated-inputs
-     `(("python2-future" ,python2-future)
-       ("python2-pygame" ,python2-pygame-sdl2)))
-    (native-inputs
-     (list python2-cython))
+    (propagated-inputs (list python-future python-pygame-sdl2))
     (home-page "https://www.renpy.org/")
     (synopsis "Ren'py python module")
     (description "This package contains the shared libraries and Python modules
@@ -1355,176 +1348,6 @@ (define-public python2-renpy
 are only used to bootstrap it.")
     (license license:expat)))
 
-(define-public renpy
-  (package
-    (inherit python2-renpy)
-    (name "renpy")
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f ; see python2-renpy
-       #:python ,python-2
-       #:modules ((srfi srfi-1)
-                  (guix build python-build-system)
-                  (guix build utils))
-       #:imported-modules ((srfi srfi-1) ,@%python-build-system-modules)
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-commands
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (substitute* "launcher/game/choose_directory.rpy"
-               (("/usr/bin/python")
-                (string-append (assoc-ref inputs "python2")
-                               "/bin/python2")))
-             (substitute* "launcher/game/front_page.rpy"
-               (("xdg-open")
-                (string-append (assoc-ref inputs "xdg-utils")
-                               "/bin/xdg-open")))
-             (substitute* "launcher/game/project.rpy"
-               (("cmd = \\[ executable, \"-EO\", sys.argv\\[0\\] \\]")
-                (string-append "cmd = [ \"" (assoc-ref outputs "out")
-                               "/bin/renpy\" ]"))
-               ;; Projects are still created in the usual style, so we need
-               ;; to adjust the path.
-               (("cmd.append\\(self.path\\)")
-                "cmd.append(self.path + \"/game\")"))
-             #t))
-         (add-after 'unpack 'drop-game-from-paths
-           (lambda _
-             (substitute* (list "launcher/game/gui7.rpy"
-                                "launcher/game/gui7/images.py")
-               ((", \"game\",") ","))
-             #t))
-         (add-before 'build 'start-xserver
-           (lambda* (#:key inputs native-inputs #:allow-other-keys)
-             (let ((xorg-server (assoc-ref (or native-inputs inputs)
-                                           "xorg-server")))
-               (setenv "HOME" (getcwd))
-               (system (format #f "~a/bin/Xvfb :1 &" xorg-server))
-               (setenv "DISPLAY" ":1")
-               #t)))
-         (replace 'build
-           (lambda _
-             (invoke "python" "renpy.py" "launcher" "quit")
-             (invoke "python" "renpy.py" "the_question" "quit")
-             (invoke "python" "renpy.py" "tutorial" "quit")
-             #t))
-         (replace 'install
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             ;; Here we install our custom renpy program.
-             ;; After finishing this step, "out" will have the following:
-             ;; |-- bin/renpy
-             ;; `-- share/renpy ; i.e. path_to_renpy_base()
-             ;;     |-- common
-             ;;     `-- gui
-             ;;
-             ;; Note that common shares the source files that would be installed
-             ;; by python2-renpy (which are instead deleted from that package),
-             ;; but also contains their byte-compiled versions.
-             ;; On other systems, renpy_base would point to site-packages or
-             ;; even somewhere in /opt.
-             ;; The former approach is not as straightforward as it seems
-             ;; -- it causes renpy to load files twice for some weird reason --
-             ;; and the latter is impossible on Guix. Hence the detour through
-             ;; share/renpy and the custom renpy program.
-             ;;
-             ;; As a convention, other games should be installed as
-             ;; subdirectories of share/renpy in their respective outputs as
-             ;; well. This differs from the traditional layout, which is
-             ;; roughly the following:
-             ;; `-- Super Awesome Game
-             ;;     |-- game       ; <- the folder we actually want
-             ;;     |-- lib        ; compiled renpy module and dependencies
-             ;;     |-- renpy      ; yet another copy of Ren'py's code
-             ;;     |   |-- common ; the common folder from above
-             ;;     |   `-- ...    ; Python code (source + compiled)
-             ;;     |-- Super Awesome Game.py
-             ;;     `-- Super Awesome Game.sh
-             (let* ((out (assoc-ref outputs "out"))
-                    (bin/renpy (string-append out "/bin/renpy")))
-               (copy-recursively "renpy/common"
-                                 (string-append out "/share/renpy/common"))
-               (copy-recursively "gui"
-                                 (string-append out "/share/renpy/gui"))
-
-               (mkdir-p (string-append out "/bin"))
-               (copy-file (assoc-ref inputs "renpy.in") bin/renpy)
-               (substitute* bin/renpy
-                 (("@PYTHON@") (search-input-file inputs "bin/python2"))
-                 (("@RENPY_BASE@") (string-append out "/share/renpy")))
-               (chmod bin/renpy #o755))))
-
-         (add-after 'install 'install-games
-           (lambda* (#:key outputs #:allow-other-keys)
-             (define renpy (assoc-ref outputs "out"))
-             ;; TODO: We should offer a renpy-build-system to make the
-             ;; installation of Ren'py games easier.
-             (define* (install-renpy-game #:key output game name (renpy renpy)
-                                          #:allow-other-keys)
-               (let* ((name (or name (basename game)))
-                      (launcher (string-append output "/bin/renpy-" name))
-                      (share (string-append output "/share/renpy/" name)))
-                 (copy-recursively (string-append game "/game") share)
-                 (mkdir-p (string-append output "/bin"))
-                 (with-output-to-file launcher
-                   (lambda ()
-                     (format #t
-                             "#!~a~%~a ~a \"$@\""
-                             (which "bash")
-                             (string-append renpy "/bin/renpy")
-                             share)))
-                 (chmod launcher #o755)))
-
-             (install-renpy-game #:output (assoc-ref outputs "out")
-                                 #:game "launcher")
-
-             (install-renpy-game #:output (assoc-ref outputs "the-question")
-                                 #:game "the_question"
-                                 #:name "the-question")
-
-             (install-renpy-game #:output (assoc-ref outputs "tutorial")
-                                 #:game "tutorial")
-             #t))
-         (replace 'wrap
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out"))
-                   (site (string-append "/lib/python"
-                                        (python-version
-                                         (assoc-ref inputs "python"))
-                                        "/site-packages")))
-               (wrap-program (string-append out "/bin/renpy")
-                 `("GUIX_PYTHONPATH" =
-                   (,@(delete-duplicates
-                       (map
-                        (lambda (store-path)
-                          (string-append store-path site))
-                        (cons (assoc-ref outputs "out")
-                              (map cdr
-                                   (filter
-                                    (lambda (input)
-                                      (string-prefix? "python2" (car input)))
-                                    inputs))))))))
-               #t))))))
-    (inputs
-     `(("renpy.in" ,(search-auxiliary-file "renpy/renpy.in"))
-       ("python2-renpy" ,python2-renpy)
-       ("python2-tkinter" ,python-2 "tk")
-       ("python2" ,python-2) ; for ‘fix-commands’ and ‘wrap’
-       ("xdg-utils" ,xdg-utils)))
-    (propagated-inputs '())
-    (native-inputs
-     (list xorg-server-for-tests))
-    (outputs
-     (list "out" "tutorial" "the-question"))
-    (home-page "https://www.renpy.org/")
-    (synopsis "Visual Novel Engine")
-    (description "Ren'Py is a visual novel engine that helps you use words,
-images, and sounds to tell interactive stories that run on computers and
-mobile devices.  These can be both visual novels and life simulation games.
-The easy to learn script language allows anyone to efficiently write large
-visual novels, while its Python scripting is enough for complex simulation
-games.")
-    (license license:expat)))
-
 (define-public python-pyxel
   (package
     (name "python-pyxel")
-- 
2.36.0

[bug#55424] [PATCH 082/602] gnu: Remove slingshot.

[Maxim Cournoyer]

* gnu/packages/games.scm (slingshot): Delete variable.
---
 gnu/packages/games.scm | 27 ---------------------------
 1 file changed, 27 deletions(-)

diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index c6d23298ff..b3430357bd 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -8678,33 +8678,6 @@ (define-public slimevolley
 the ground, the set ends and all balls are served again.")
     (license license:gpl3+)))
 
-(define-public slingshot
-  (package
-    (name "slingshot")
-    (version "0.9")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/ryanakca/slingshot")
-             (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "19m8b6nsi786bc6gmkp185mwri3r5y249gjmqd5qsc23nnfhgrs1"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2))
-    (inputs
-     (list python2-pygame))
-    (home-page "https://github.com/ryanakca/slingshot")
-    (synopsis "Simple 2D shooting strategy game set in space")
-    (description "Slingshot is a two-dimensional strategy game where two
-players attempt to shoot one another through a section of space populated by
-planets.  The main feature of the game is that the shots, once fired, are
-affected by the gravity of the planets.")
-    (license license:gpl2+)))
-
 (define-public 4dtris
   (package
     (name "4dtris")
-- 
2.36.0

[bug#55424] [PATCH 083/602] gnu: Remove python2-gpg.

[Maxim Cournoyer]

* gnu/packages/gnupg.scm (python2-gpg): Delete variable.
---
 gnu/packages/gnupg.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm
index cde7427d07..58a5c44318 100644
--- a/gnu/packages/gnupg.scm
+++ b/gnu/packages/gnupg.scm
@@ -532,9 +532,6 @@ (define-public python-gpg
 distributed separately.")
     (license license:lgpl2.1+)))
 
-(define-public python2-gpg
-  (package-with-python2 python-gpg))
-
 (define-public python-pygpgme
   (package
     (name "python-pygpgme")
-- 
2.36.0

[bug#55424] [PATCH 084/602] gnu: Remove python2-pygpgme.

[Maxim Cournoyer]

* gnu/packages/gnupg.scm (python2-pygpgme): Delete variable.
---
 gnu/packages/gnupg.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm
index 58a5c44318..02a7c8d942 100644
--- a/gnu/packages/gnupg.scm
+++ b/gnu/packages/gnupg.scm
@@ -567,9 +567,6 @@ (define-public python-pygpgme
 decrypt messages using the OpenPGP format by making use of GPGME.")
     (license license:lgpl2.1+)))
 
-(define-public python2-pygpgme
-  (package-with-python2 python-pygpgme))
-
 (define-public python-gnupg
   (package
     (name "python-gnupg")
-- 
2.36.0

[bug#55424] [PATCH 085/602] gnu: pius: Update to 3.0.0.

[Maxim Cournoyer]

* gnu/packages/gnupg.scm (pius): Update to 3.0.0.
[arguments]: Delete tests? and python arguments.
[phases]{set-gpg-file-name}: Streamline.
[description]: Spell key signing as two words.  Mark commands with Texinfo
markup.
---
 gnu/packages/gnupg.scm | 65 +++++++++++++++++++-----------------------
 1 file changed, 30 insertions(+), 35 deletions(-)

diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm
index 02a7c8d942..c9b233c1e4 100644
--- a/gnu/packages/gnupg.scm
+++ b/gnu/packages/gnupg.scm
@@ -21,6 +21,7 @@
 ;;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be>
 ;;; Copyright © 2021 Nikita Domnitskii <nikita@domnitskii.me>
 ;;; Copyright © 2021 Aleksandr Vityazev <avityazev@posteo.org>
+;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -638,44 +639,38 @@ (define-public perl-gnupg-interface
 
 (define-public pius
   (package
-   (name "pius")
-   (version "2.2.7")
-   (source (origin
-            (method url-fetch)
-            (uri (string-append
-                  "https://github.com/jaymzh/pius/releases/download/v"
-                  version "/pius-" version ".tar.bz2"))
-            (sha256
-             (base32
-              "1nsl7czicv95j0gfz4s82ys3g3h2mwr6cq3ilid8bpz3iy7z4ipy"))))
-   (build-system python-build-system)
-   (inputs `(("perl" ,perl)             ; for 'pius-party-worksheet'
-             ("gpg" ,gnupg)
-             ("python-six" ,python2-six)))
-   (arguments
-    `(#:tests? #f
-      #:python ,python-2                ; uses the Python 2 'print' syntax
-      #:phases
-      (modify-phases %standard-phases
-        (add-before
-         'build 'set-gpg-file-name
-         (lambda* (#:key inputs outputs #:allow-other-keys)
-           (let* ((gpg (search-input-file inputs "/bin/gpg")))
+    (name "pius")
+    (version "3.0.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/jaymzh/pius/releases/download/v"
+                    version "/pius-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "11fhmfvr0avxl222rv43wjd2xjbpxrsmcl8xwmn0nvf1rw95v9fn"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'set-gpg-file-name
+           (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "libpius/constants.py"
-               (("/usr/bin/gpg2") gpg))
-             #t))))))
-   (synopsis "Programs to simplify GnuPG key signing")
-   (description
-    "Pius (PGP Individual UID Signer) helps attendees of PGP keysigning
+               (("/usr/bin/gpg2")
+                (search-input-file inputs "bin/gpg"))))))))
+    (inputs (list perl                  ;for 'pius-party-worksheet'
+                  gnupg))
+    (synopsis "Programs to simplify GnuPG key signing")
+    (description
+     "Pius (PGP Individual UID Signer) helps attendees of PGP key signing
 parties.  It is the main utility and makes it possible to quickly and easily
 sign each UID on a set of PGP keys.  It is designed to take the pain out of
-the sign-all-the-keys part of PGP Keysigning Party while adding security
-to the process.
-
-pius-keyring-mgr and pius-party-worksheet help organisers of
-PGP keysigning parties.")
-   (license license:gpl2)
-   (home-page "https://www.phildev.net/pius/index.shtml")))
+the sign-all-the-keys part of PGP key signing parties while adding security to
+the process.  The @command{pius-keyring-mgr} and
+@command{pius-party-worksheet} commands help organizers of PGP key signing
+parties.")
+    (license license:gpl2)
+    (home-page "https://www.phildev.net/pius/index.shtml")))
 
 (define-public signing-party
   (package
-- 
2.36.0

[bug#55424] [PATCH 086/602] gnu: Remove python2-pydot.

[Maxim Cournoyer]

* gnu/packages/graphviz.scm (python2-pydot): Delete variable.
---
 gnu/packages/graphviz.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index dfbb28a8a9..2a99c0988e 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -403,9 +403,6 @@ (define-public python-pydot
 graphs in Graphviz's DOT language, written in pure Python.")
     (license license:expat)))
 
-(define-public python2-pydot
-  (package-with-python2 python-pydot))
-
 (define-public dot2tex
   (package
     (name "dot2tex")
-- 
2.36.0

[bug#55424] [PATCH 087/602] gnu: dot2tex: Update to 2.11.3.

[Maxim Cournoyer]

* gnu/packages/graphviz.scm (dot2tex): Update to 2.11.3.
[arguments]: Remove python argument.
[phases]: New argument.
[native-inputs]: New field.
[inputs]: Move texlive-latex-preview to...
[propagated-inputs]: ... here.  Replace python2-pyparsing with
python-parsing.  Add texlive-bin, texlive-amsmath, texlive-latex-geometry,
texlive-latex-graphics, texlive-latex-base, texlive-latex-xkeyval,
texlive-pgf, texlive-pstricks and  texlive-xcolor.
---
 gnu/packages/graphviz.scm | 30 ++++++++++++++++++++++++++----
 1 file changed, 26 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index 2a99c0988e..f2fd90e616 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -415,11 +415,33 @@ (define-public dot2tex
                 "1kp77wiv7b5qib82i3y3sn9r49rym43aaqm5aw1bwnzfbbq2m6i9"))))
     (build-system python-build-system)
     (arguments
-     `(#:python ,python-2))
-    (inputs
-     (list texlive-latex-preview graphviz))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (invoke "pytest" "-vv" "tests"
+                        ;; The test_semicolon test fails for unknown reason
+                        ;; (see:
+                        ;; https://github.com/kjellmf/dot2tex/issues/94).
+                        "-k" "not test_semicolon")))))))
+    (native-inputs (list python-pytest))
+    (inputs (list graphviz))
     (propagated-inputs
-     (list python2-pyparsing))
+     (list python-pyparsing
+           ;; These TeX dependencies are propagated to make it easier to build
+           ;; the resulting generated TeX files, which \usepackage them.
+           texlive-bin
+           texlive-amsmath
+           texlive-latex-geometry
+           texlive-latex-graphics
+           texlive-latex-base
+           texlive-latex-preview
+           texlive-latex-xkeyval
+           texlive-pgf
+           texlive-pstricks
+           texlive-xcolor))
     (home-page "https://github.com/kjellmf/dot2tex")
     (synopsis "Graphviz to LaTeX converter")
     (description
-- 
2.36.0

[bug#55424] [PATCH 088/602] gnu: Remove h-client.

[Maxim Cournoyer]

* gnu/packages/hardware.scm (h-client): Delete variable.
---
 gnu/packages/hardware.scm | 36 ------------------------------------
 1 file changed, 36 deletions(-)

diff --git a/gnu/packages/hardware.scm b/gnu/packages/hardware.scm
index 38bc3881b9..946cd9aba4 100644
--- a/gnu/packages/hardware.scm
+++ b/gnu/packages/hardware.scm
@@ -375,42 +375,6 @@ (define-public edid-decode
 human-readable format and checks if it conforms to the standards.")
       (license license:expat))))
 
-(define-public h-client
-  (let ((version "0.0a0")
-        (revision 138))
-    (package
-      (name "h-client")
-      (version (string-append version "-" (number->string revision)))
-      (source
-       (origin
-         (method svn-fetch)
-         (uri
-          (svn-reference
-           (url "https://svn.savannah.nongnu.org/svn/h-client/trunk/h-client")
-           (revision revision)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32 "1pdd2qhyaa5vh7z4rkpwjlby1flkwhzmp8zlglalx5y5sv95l4kp"))))
-      (build-system python-build-system)
-      (arguments
-       `(#:python ,python-2
-         ;; Tests depends on /etc/os-release which does not exist in the
-         ;; build container.
-         #:tests? #f))
-      (inputs
-       (list python-2 python2-pycurl python2-pygtk pciutils usbutils))
-      (synopsis "Graphical client for the h-node hardware database
-project")
-      (description
-       "The h-node project (https://www.h-node.org) aims to build a database of
-hardware that works with fully free operating systems.
-h-client is a GTK+ graphical client that is able to retrieves information on
-the hardware inside the computer it's running on, and on peripherals connected
-to it, and help you submit that information to the h-node project along with
-whether the hardware works with a fully free operating system or not.")
-      (home-page "https://savannah.nongnu.org/projects/h-client/")
-      (license license:gpl3+))))
-
 (define-public headsetcontrol
   (package
     (name "headsetcontrol")
-- 
2.36.0

[bug#55424] [PATCH 089/602] gnu: Remove python2-iso3166.

[Maxim Cournoyer]

* gnu/packages/iso-codes.scm (python2-iso3166): Delete variable.
---
 gnu/packages/iso-codes.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/iso-codes.scm b/gnu/packages/iso-codes.scm
index b2cfd3434c..b567c0e029 100644
--- a/gnu/packages/iso-codes.scm
+++ b/gnu/packages/iso-codes.scm
@@ -115,6 +115,3 @@ (define-public python-iso3166
     (synopsis "Self-contained ISO 3166-1 country definitions")
     (description "This package provides the ISO 3166-1 country definitions.")
     (license license:expat)))
-
-(define-public python2-iso3166
-  (package-with-python2 python-iso3166))
-- 
2.36.0

[bug#55424] [PATCH 090/602] gnu: Remove python2-iso639.

[Maxim Cournoyer]

* gnu/packages/iso-codes.scm (python2-iso639): Delete variable.
---
 gnu/packages/iso-codes.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/iso-codes.scm b/gnu/packages/iso-codes.scm
index b567c0e029..c34911fe9b 100644
--- a/gnu/packages/iso-codes.scm
+++ b/gnu/packages/iso-codes.scm
@@ -96,9 +96,6 @@ (define-public python-iso639
 groups.")
     (license license:agpl3+)))
 
-(define-public python2-iso639
-  (package-with-python2 python-iso639))
-
 (define-public python-iso3166
   (package
     (name "python-iso3166")
-- 
2.36.0

[bug#55424] [PATCH 091/602] gnu: Remove key-mon.

[Maxim Cournoyer]

* gnu/packages/key-mon.scm (key-mon): Delete variable.
---
 gnu/packages/key-mon.scm | 25 -------------------------
 1 file changed, 25 deletions(-)

diff --git a/gnu/packages/key-mon.scm b/gnu/packages/key-mon.scm
index e7b549d184..d70dd0cd48 100644
--- a/gnu/packages/key-mon.scm
+++ b/gnu/packages/key-mon.scm
@@ -26,28 +26,3 @@ (define-module (gnu packages key-mon)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages gnome)
   #:use-module (guix build-system python))
-
-(define-public key-mon
-  (package
-    (name "key-mon")
-    (version "1.17")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "http://key-mon.googlecode.com/files/key-mon-"
-                    version ".tar.gz"))
-              (sha256
-               (base32
-                "1liz0dxcqmchbnl1xhlxkqm3gh76wz9jxdxn9pa7dy77fnrjkl5q"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:python ,python-2                    ;uses the Python 2 'print' syntax
-       #:tests? #f))                         ;no tests
-    (inputs
-     (list python2-xlib python2-pygtk python2-rsvg))
-    (home-page "https://code.google.com/p/key-mon")
-    (synopsis "Show keyboard and mouse status")
-    (description
-     "The key-mon utility displays the current keyboard and mouse status.
-This is useful for teaching and screencasts.")
-    (license asl2.0)))
-- 
2.36.0

[bug#55424] [PATCH 092/602] gnu: Remove python2-tegaki-recognize.

[Maxim Cournoyer]

* gnu/packages/language.scm (python2-tegaki-recognize): Delete variable.
---
 gnu/packages/language.scm | 52 ---------------------------------------
 1 file changed, 52 deletions(-)

diff --git a/gnu/packages/language.scm b/gnu/packages/language.scm
index 6a0f1af2fa..ce7646b7ad 100644
--- a/gnu/packages/language.scm
+++ b/gnu/packages/language.scm
@@ -1006,58 +1006,6 @@ (define-public python2-tegaki-tools
     ;; under gpl2+. Therefore, the combined work is licensed under gpl3+.
     (license license:gpl3+)))
 
-(define-public python2-tegaki-recognize
-  (let ((commit "eceec69fe651d0733c8c8752dae569d2283d0f3c")
-        (revision "1"))
-    (package
-      (inherit python2-tegaki-tools)
-      (name "python2-tegaki-recognize")
-      ;; version copied from <https://github.com/tegaki/tegaki/releases>
-      (version (git-version "0.3.1" revision commit))
-      (source
-       (origin
-         ;; We use GIT-FETCH because 'tegaki-recognize.desktop.in' and
-         ;; 'tegaki-recognize.in' are missing in the tarball.
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/tegaki/tegaki")
-               (commit commit)))
-         (sha256
-          (base32
-           "09mw2if9p885phbgah5f95q3fwy7s5b46qlmpxqyzfcnj6g7afr5"))
-         (file-name (git-file-name name version))
-         (modules `((guix build utils)
-                    (ice-9 ftw)
-                    (srfi srfi-26)
-                    ,@remove-pre-compiled-files-modules))
-         (snippet
-          `(begin
-             ;; remove unnecessary files with potentially different license
-             (for-each delete-file-recursively
-                       (scandir "."
-                                (negate (cut member <> '("tegaki-recognize"
-                                                         "." "..")))))
-             ,(remove-pre-compiled-files "pyc")
-             #t))))
-      (arguments
-       (substitute-keyword-arguments (package-arguments python2-tegaki-tools)
-         ((#:phases _)
-          `(modify-phases %standard-phases
-             (add-after 'unpack 'chdir
-               (lambda _
-                 (chdir "tegaki-recognize")
-                 #t))
-             ;; 'setup.py' script does not support one of the Python build
-             ;; system's default flags, "--single-version-externally-managed"
-             (replace 'install
-               (lambda* (#:key outputs #:allow-other-keys)
-                 (invoke "python" "setup.py" "install"
-                         (string-append "--prefix=" (assoc-ref outputs "out"))
-                         "--root=/")
-                 #t))))))
-      (synopsis "Chinese and Japanese Handwriting Recognition (Main program)")
-      (license license:gpl2+))))
-
 (define-public tegaki-zinnia-japanese
   (package
     (inherit python2-tegaki-wagomu)
-- 
2.36.0

[bug#55424] [PATCH 093/602] gnu: Remove python2-pyusb.

[Maxim Cournoyer]

* gnu/packages/libusb.scm (python2-pyusb): Delete variable.
---
 gnu/packages/libusb.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/libusb.scm b/gnu/packages/libusb.scm
index 01771dffca..8c34956fee 100644
--- a/gnu/packages/libusb.scm
+++ b/gnu/packages/libusb.scm
@@ -300,9 +300,6 @@ (define-public python-pyusb
      "PyUSB aims to be an easy to use Python module to access USB devices.")
     (license license:bsd-3)))
 
-(define-public python2-pyusb
-  (package-with-python2 python-pyusb))
-
 (define-public python-capablerobot-usbhub
   (package
     (name "python-capablerobot-usbhub")
-- 
2.36.0

[bug#55424] [PATCH 094/602] gnu: Remove python2-autograd.

[Maxim Cournoyer]

* gnu/packages/machine-learning.scm (python2-autograd): Delete variable.
---
 gnu/packages/machine-learning.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 7b377c7d35..509b9c7cdd 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1326,9 +1326,6 @@ (define-public python-autograd
 main intended application of Autograd is gradient-based optimization.")
       (license license:expat))))
 
-(define-public python2-autograd
-  (package-with-python2 python-autograd))
-
 (define-public lightgbm
   (package
     (name "lightgbm")
-- 
2.36.0

[bug#55424] [PATCH 095/602] gnu: getmail: Deprecate with getmail6.

[Maxim Cournoyer]

* gnu/packages/mail.scm (getmail): Mark as deprecated in favor of...
(getmail6): ... this new package.
---
 gnu/packages/mail.scm | 45 ++++++++++++++++++++++---------------------
 1 file changed, 23 insertions(+), 22 deletions(-)

diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index c4ccc53e84..31cdc8da55 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -32,7 +32,7 @@
 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
 ;;; Copyright © 2020 Justus Winter <justus@sequoia-pgp.org>
 ;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com>
-;;; Copyright © 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2020, 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2020 Michael Rohleder <mike@rohleder.de>
 ;;; Copyright © 2020, 2021 Alexey Abramov <levenson@mmer.org>
 ;;; Copyright © 2020 Tim Gesthuizen <tim.gesthuizen@yahoo.de>
@@ -40,7 +40,6 @@
 ;;; Copyright © 2020 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2020 B. Wilson <elaexuotee@wilsonb.com>
 ;;; Copyright © 2020 divoplade <d@divoplade.fr>
-;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2021 Xinglu Chen <public@yoctocell.xyz>
 ;;; Copyright © 2021 Benoit Joly <benoit@benoitj.ca>
 ;;; Copyright © 2021 Morgan Smith <Morgan.J.Smith@outlook.com>
@@ -1550,31 +1549,33 @@ (define-public muchsync
 pairs have previously synchronized.")
     (license license:gpl2+)))           ; with OpenSSL libcrypto exception
 
-(define-public getmail
+(define-public getmail6
   (package
-    (name "getmail")
-    (version "5.16")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://pyropus.ca/software/getmail/old-versions/"
-                           "getmail-" version ".tar.gz"))
-       (sha256
-        (base32 "1yk7lrndbfsrbdxikwzdqvadryqsldalxdn3a184dg4sxzmgis3a"))))
+    (name "getmail6")
+    (version "6.18.6")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/getmail6/getmail6")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "08a5yw6ll1kmd1ardj8rzhsw4wl48zzdc87g5lh4p5snv8w2m4ja"))))
     (build-system python-build-system)
-    (arguments
-     (list #:tests? #f                  ; no tests
-           #:python python-2))
-    (home-page "https://pyropus.ca/software/getmail/")
+    (arguments (list #:tests? #f))      ;tests require docker
+    (home-page "https://github.com/getmail6/getmail6")
     (synopsis "Mail retriever")
     (description
-     "A flexible, extensible mail retrieval system with support for
-POP3, IMAP4, SSL variants of both, maildirs, mboxrd files, external MDAs,
-arbitrary message filtering, single-user and domain-mailboxes, and many other
-useful features.")
+     "A flexible, extensible mail retrieval system with support for POP3,
+IMAP4, SSL variants of both, maildirs, mboxrd files, external MDAs, arbitrary
+message filtering, single-user and domain-mailboxes, and many other useful
+features.  This is a fork derived from getmali 5.14, aimed at Python 3
+compatibility.")
+    (license license:gpl2+)))           ;see docs/COPYING
 
-    ;; License is specified in file '__init__.py'.
-    (license license:gpl2)))
+(define-public getmail
+  (deprecated-package "getmail" getmail6))
 
 (define-public libetpan
   (package
-- 
2.36.0

[bug#55424] [PATCH 096/602] gnu: Remove python2-mailmanclient.

[Maxim Cournoyer]

* gnu/packages/mail.scm (python2-mailmanclient): Delete variable.
---
 gnu/packages/mail.scm | 17 -----------------
 1 file changed, 17 deletions(-)

diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 31cdc8da55..4365fa647d 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -3365,25 +3365,8 @@ (define-public python-mailmanclient
     (description
      "The mailmanclient library provides official Python bindings for
 the GNU Mailman 3 REST API.")
-    (properties `((python2-variant . ,(delay python2-mailmanclient))))
     (license license:lgpl3+)))
 
-;; This is the last version which supports Python-2.
-(define-public python2-mailmanclient
-  (let ((base (package-with-python2
-                (strip-python2-variant python-mailmanclient))))
-    (package
-      (inherit base)
-      (version "3.1.1")
-      (source
-        (origin
-          (method url-fetch)
-          (uri (pypi-uri "mailmanclient" version))
-          (sha256
-           (base32
-            "0fdfs5g3pf30v2i7w18pdkv9xnfxmfcv66mzv56dck0a1igq07m3"))))
-      (propagated-inputs
-       (list python2-six python2-httplib2)))))
 
 (define-public mlmmj
   (package
-- 
2.36.0

[bug#55424] [PATCH 097/602] gnu: Remove python2-musicbrainzngs.

[Maxim Cournoyer]

* gnu/packages/music.scm (python2-musicbrainzngs): Delete variable.
---
 gnu/packages/music.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 0b76e57acf..c15def4649 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -3671,9 +3671,6 @@ (define-public python-musicbrainzngs
     ;; 'musicbrainzngs/compat.py' is ISC licensed.
     (license (list license:bsd-2 license:isc))))
 
-(define-public python2-musicbrainzngs
-  (package-with-python2 python-musicbrainzngs))
-
 (define-public python-isrcsubmit
   (package
     (name "python-isrcsubmit")
-- 
2.36.0

[bug#55424] [PATCH 098/602] gnu: Remove python2-pyechonest.

[Maxim Cournoyer]

* gnu/packages/music.scm (python2-pyechonest): Delete variable.
---
 gnu/packages/music.scm | 33 ---------------------------------
 1 file changed, 33 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index c15def4649..d0b51c7bba 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -3692,39 +3692,6 @@ (define-public python-isrcsubmit
 @url{https://musicbrainz.org/, MusicBrainz}.")
     (license license:gpl3+)))
 
-(define-public python2-pyechonest
-  (package
-    (name "python2-pyechonest")
-    (version "9.0.0")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "pyechonest" version))
-              (sha256
-               (base32
-                "1584nira3rkiman9dm81kdshihmkj21s8navndz2l8spnjwb790x"))))
-    (build-system python-build-system)
-    (arguments
-     `(;; Python 3 is not supported:
-       ;; https://github.com/echonest/pyechonest/issues/42
-       #:python ,python-2))
-    (home-page "https://github.com/echonest/pyechonest")
-    (synopsis "Python interface to The Echo Nest APIs")
-    (description "Pyechonest is a Python library for the Echo Nest API.  With
-Pyechonest you have Python access to the entire set of API methods including:
-
-@enumerate
-@item artist - search for artists by name, description, or attribute, and get
-back detailed information about any artist including audio, similar artists,
-blogs, familiarity, hotttnesss, news, reviews, urls and video.
-@item song - search songs by artist, title, description, or attribute (tempo,
-duration, etc) and get detailed information back about each song, such as
-hotttnesss, audio_summary, or tracks.
-@item track - upload a track to the Echo Nest and receive summary information
-about the track including key, duration, mode, tempo, time signature along with
-detailed track info including timbre, pitch, rhythm and loudness information.
-@end enumerate\n")
-    (license license:bsd-3)))
-
 (define-public python-pylast
   (package
     (name "python-pylast")
-- 
2.36.0

[bug#55424] [PATCH 099/602] gnu: Remove mloop.

[Maxim Cournoyer]

* gnu/packages/music.scm (mloop): Delete variable.
---
 gnu/packages/music.scm | 39 ---------------------------------------
 1 file changed, 39 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index d0b51c7bba..e4308c6300 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -5547,45 +5547,6 @@ (define-public fmit
     ;; are under LGPL2.1.
     (license (list license:gpl2+ license:lgpl2.1))))
 
-(define-public mloop
-  (let ((commit "adebff98b0b4dc5872a03acb82e89c77cb29c127")
-        (revision "0"))
-    (package
-      (name "mloop")
-      (version (git-version "0.0.1" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "http://git.fuzzle.org/mloop")
-                      (commit commit)))
-                (file-name (git-file-name name version))
-                (sha256
-                 (base32
-                  "175gxvg5slq0bllcx1c381rjlq3xpxww8c3kpiw5i2kfr4m52myz"))))
-      (build-system waf-build-system)
-      (arguments
-       `(#:python ,python-2
-         #:tests? #f))                     ; no "check" target
-      (inputs
-       (list jack-1 ncurses))
-      (native-inputs
-       (list pkg-config))
-      (home-page "https://fuzzle.org/~petern/mloop.html")
-      (synopsis "Live MIDI looper")
-      (description "mloop is a live MIDI looping system, using jack-midi.
-Loops are recorded, optionally with beat quantization, and can then be played
-back, either once or looping.  A 'note cache' system is implemented to
-remember which notes are pressed and their velocities.  This allows for a loop
-to start off with the currently pressed notes, making seamless loops much
-easier to perform.  Features include:
-
-@itemize
-@item Quantisation; end a loop on a beat exactly.
-@item Delayed recording; wait for a MIDI event before starting a loop record.
-@item Adjust tempo; Playback speed of loops can be adjusted on the fly.
-@end itemize\n")
-      (license license:gpl2))))
-
 (define-public pragha
   (package
     (name "pragha")
-- 
2.36.0

[bug#55424] [PATCH 100/602] gnu: Remove gtklick.

[Maxim Cournoyer]

* gnu/packages/music.scm (gtklick): Delete variable.
---
 gnu/packages/music.scm | 46 ------------------------------------------
 1 file changed, 46 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index e4308c6300..7255701963 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -1271,52 +1271,6 @@ (define-public glyr
 biographies, reviews and more.")
     (license license:lgpl3+)))
 
-(define-public gtklick
-  (package
-    (name "gtklick")
-    (version "0.6.4")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "http://das.nasophon.de/download/gtklick-"
-                                  version ".tar.gz"))
-              (sha256
-               (base32
-                "0dq1km6njnzsqdqyf6wzir9g733z0mc9vmxfg2383k3c2a2di6bp"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f ; no tests
-       #:python ,python-2
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'build 'add-sitedirs
-           ;; .pth files are not automatically interpreted unless the
-           ;; directories containing them are added as "sites".  The directories
-           ;; are then added to those in the PYTHONPATH.  This is required for
-           ;; the operation of pygtk.
-           (lambda _
-             (substitute* "gtklick/gtklick.py"
-               (("import pygtk")
-                "import pygtk, site, sys
-for path in [path for path in sys.path if 'site-packages' in path]: site.addsitedir(path)"))))
-         (add-after 'unpack 'inject-store-path-to-klick
-           (lambda* (#:key inputs #:allow-other-keys)
-             (substitute* "gtklick/klick_backend.py"
-               (("KLICK_PATH = 'klick'")
-                (string-append "KLICK_PATH = '"
-                               (assoc-ref inputs "klick")
-                               "/bin/klick'")))
-             #t)))))
-    (inputs
-     (list klick python2-pyliblo python2-pygtk))
-    (native-inputs
-     `(("gettext" ,gettext-minimal)))
-    (home-page "http://das.nasophon.de/gtklick/")
-    (synopsis "Simple metronome with an easy-to-use graphical interface")
-    (description
-     "Gtklick is a simple metronome with an easy-to-use graphical user
-interface.  It is implemented as a frontend to @code{klick}.")
-    (license license:gpl2+)))
-
 (define-public lingot
   (package
     (name "lingot")
-- 
2.36.0

[bug#55424] [PATCH 101/602] gnu: Remove non-timeline.

[Maxim Cournoyer]

* gnu/packages/music.scm (non-timeline): Delete variable.
---
 gnu/packages/music.scm | 22 ----------------------
 1 file changed, 22 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 7255701963..5818a2ea62 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -1784,28 +1784,6 @@ (define-public non-mixer
 studio.")
     (license license:gpl2+)))
 
-(define-public non-timeline
-  (package (inherit non-sequencer)
-    (name "non-timeline")
-    (arguments
-     (substitute-keyword-arguments (package-arguments non-sequencer)
-       ((#:configure-flags flags)
-        `(cons "--project=timeline"
-               (delete "--project=sequencer" ,flags)))))
-    (inputs
-     (list jack-1 liblo libsndfile ntk))
-    (native-inputs
-     (list pkg-config))
-    (home-page "https://non.tuxfamily.org/wiki/Non%20Timeline")
-    (synopsis "Modular digital audio timeline arranger")
-    (description
-     "The Non Timeline is a powerful, reliable and fast modular digital audio
-timeline arranger.  It utilizes JACK for inter-application audio I/O and the
-NTK GUI toolkit for a fast and lightweight user interface.  Non Timeline can
-be used alone or in concert with Non Mixer and Non Sequencer to form a
-complete studio.")
-    (license license:gpl2+)))
-
 (define-public tascam-gtk
   ;; This commit represents the latest version at the time of this writing.
   (let ((commit "17b8575ff88dfd2ede0f7ef9c5c5597ab8a00702")
-- 
2.36.0

[bug#55424] [PATCH 102/602] gnu: Remove non-mixer.

[Maxim Cournoyer]

* gnu/packages/music.scm (non-mixer): Delete variable.
---
 gnu/packages/music.scm | 22 ----------------------
 1 file changed, 22 deletions(-)

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 5818a2ea62..ee978c5e00 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -1762,28 +1762,6 @@ (define-public non-session-manager
 communicate with the session management daemon.")
     (license license:gpl2+)))
 
-(define-public non-mixer
-  (package (inherit non-sequencer)
-    (name "non-mixer")
-    (arguments
-     (substitute-keyword-arguments (package-arguments non-sequencer)
-       ((#:configure-flags flags)
-        `(cons "--project=mixer"
-               (delete "--project=sequencer" ,flags)))))
-    (inputs
-     (list jack-1 liblo ladspa lrdf ntk))
-    (native-inputs
-     (list pkg-config))
-    (home-page "https://non.tuxfamily.org/wiki/Non%20Mixer")
-    (synopsis "Modular digital audio mixer")
-    (description
-     "The Non Mixer is a powerful, reliable and fast modular digital audio
-mixer.  It utilizes JACK for inter-application audio I/O and the NTK GUI
-toolkit for a fast and lightweight user interface.  Non Mixer can be used
-alone or in concert with Non Timeline and Non Sequencer to form a complete
-studio.")
-    (license license:gpl2+)))
-
 (define-public tascam-gtk
   ;; This commit represents the latest version at the time of this writing.
   (let ((commit "17b8575ff88dfd2ede0f7ef9c5c5597ab8a00702")
-- 
2.36.0

[bug#55424] [PATCH 103/602] gnu: Remove python2-ipy.

[Maxim Cournoyer]

* gnu/packages/networking.scm (python2-ipy): Delete variable.
---
 gnu/packages/networking.scm | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index 9010e1f120..c9f1e12a28 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -2619,9 +2619,6 @@ (define-public python-ipy
 networks.")
     (license license:bsd-3)))
 
-(define-public python2-ipy
-  (package-with-python2 python-ipy))
-
 (define-public speedtest-cli
   (package
     (name "speedtest-cli")
-- 
2.36.0

[bug#55424] [PATCH 104/602] gnu: Remove sala.

[Maxim Cournoyer]

* gnu/packages/password-utils.scm (sala): Delete variable.
---
 gnu/packages/password-utils.scm | 27 ---------------------------
 1 file changed, 27 deletions(-)

diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm
index 1891a2cf09..348afb5af4 100644
--- a/gnu/packages/password-utils.scm
+++ b/gnu/packages/password-utils.scm
@@ -1035,33 +1035,6 @@ (define-public john-the-ripper-jumbo
 is the community-enhanced, \"jumbo\" version of John the Ripper.")
       (license license:gpl2+))))
 
-(define-public sala
-  (package
-    (name "sala")
-    (version "1.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "sala" version))
-       (sha256
-        (base32
-         "13qgmc3i2a0cqp8jqrfl93lnphfagb32pgfikc1gza2a14asxzi8"))))
-    (build-system python-build-system)
-    (arguments
-     ;; Sala is supposed to work with Python 3.2 or higher,
-     ;; but it doesn't work with Python 3.6. Better stick
-     ;; to Python 2, which works fine.
-     `(#:python ,python-2))
-    (propagated-inputs
-     (list gnupg pwgen))
-    (home-page "http://www.digip.org/sala/")
-    (synopsis "Encrypted plaintext password store")
-    (description
-     "Store passwords and other bits of sensitive plain-text information
-to encrypted files on a directory hierarchy.  The information is protected
-by GnuPG's symmetrical encryption.")
-    (license license:expat)))
-
 (define-public fpm2
   (package
     (name "fpm2")
-- 
2.36.0

[bug#55424] [PATCH 000/602] Purge Python 2 packages

[Maxim Cournoyer]

Hello Guix!

It's been more than 2 years since Python 2 was declared EOL.  This change
greatly reduce the graph of python2 packages.  Perhaps one of the main
dependency that needs it as an input is qtwebengine, but that's going to
disappear when we move to Qt 6.

Many of these commits were automated using a custom
'purge-python2-packages.scm' script [0], combined with the augmented
etc/committer script.  A good effort was attempted to save (via upgrades)
packages, so there are also package updates in the review.

[0]  https://notabug.org/apteryx/guix-api-examples/raw/master/purge-python2-packages.scm

There are still some Python 2 packages (about a hundred perhaps), mostly games
or bioinformatics related; perhaps we could leave them another 6 months then
remove them from Guix.  What do you think?

Thanks,

Maxim Cournoyer (602):
  packages: Fix typo in package-superseded doc.
  etc/committer: Prefix (sxml xpath) symbols to avoid name conflict.
  etc/committer: Teach it how to commit package removal.
  utils: Add a 'delete-expression' procedure.
  utils: Add a %guix-source-root-directory procedure.
  diagnostics: Fix typo about 0-indexed COL in location.
  gnu: Remove python-pytest-runner-2.
  gnu: Remove python2-langkit.
  gnu: Remove graphios.
  gnu: Remove python2-pyalsaaudio.
  gnu: Remove ingen.
  gnu: Remove raul.
  gnu: Remove raul-devel.
  gnu: Remove python2-pyaudio.
  gnu: Remove python2-fastalite.
  gnu: Remove grit.
  gnu: Remove ribodiff.
  gnu: Remove python2-pybigwig.
  gnu: tetoolkit: Update to 2.2.1b.
  gnu: Remove pepr.
  gnu: Remove python2-htseq.
  gnu: Remove python2-pybedtools.
  gnu: Remove bamm.
  gnu: Remove python2-dendropy.
  gnu: Remove poretools.
  gnu: Remove python2-warpedlmm.
  gnu: Remove miso.
  gnu: Remove python2-screed.
  gnu: Remove python2-pyfaidx.
  gnu: Remove python2-pbcore.
  gnu: Remove pyicoteo.
  gnu: Remove transmission-remote-cli.
  gnu: Remove python2-nose-timer.
  gnu: Remove python2-pytest-catchlog.
  gnu: Remove python2-testlib.
  gnu: Remove python2-nose2.
  gnu: Remove python2-pytest-capturelog.
  gnu: Remove python2-python-paramunittest.
  gnu: Remove python2-rednose.
  gnu: Remove python2-minimock.
  gnu: Remove python2-flexmock.
  gnu: Remove python2-discover.
  gnu: Remove python2-cov-core.
  gnu: Remove python2-pytest-flakes.
  gnu: Remove python2-pytest-subtesthack.
  gnu: Remove python2-nose-randomly.
  gnu: Remove domainfinder.
  gnu: Remove nmoldyn.
  gnu: Remove python2-neo4j-driver.
  gnu: Remove python2-redis.
  gnu: Remove python2-trollius-redis.
  gnu: Remove python2-peewee.
  gnu: Remove python2-ccm.
  gnu: Remove python2-apsw.
  gnu: Remove python2-py2neo.
  gnu: Remove python2-pyodbc-c.
  gnu: Remove python2-pymysql.
  gnu: Remove python2-hiredis.
  gnu: Remove python2-pytest-pep8.
  gnu: Remove python2-scikit-learn.
  gnu: Remove ocrodjvu.
  gnu: Remove python2-pandas.
  gnu: Remove python2-html5lib.
  gnu: Remove python2-statsmodels.
  gnu: Remove python2-pytest-cache.
  gnu: Remove python2-fastlmm.
  gnu: Remove python2-parameterized.
  gnu: Remove python2-pytest-warnings.
  gnu: Remove python2-pyodbc.
  gnu: Remove python2-pickleshare.
  gnu: Remove djvusmooth.
  gnu: Remove omnitux.
  gnu: Remove childsplay.
  gnu: Remove python2-capstone.
  gnu: Remove lekha.
  gnu: Remove python2-stdnum.
  gnu: Remove python2-ledgerblue.
  gnu: Remove python2-keepkey.
  gnu: nototools: Update to 0.2.16.
  gnu: Remove python2-tmx.
  gnu: renpy: Build with Python 3.
  gnu: Remove slingshot.
  gnu: Remove python2-gpg.
  gnu: Remove python2-pygpgme.
  gnu: pius: Update to 3.0.0.
  gnu: Remove python2-pydot.
  gnu: dot2tex: Update to 2.11.3.
  gnu: Remove h-client.
  gnu: Remove python2-iso3166.
  gnu: Remove python2-iso639.
  gnu: Remove key-mon.
  gnu: Remove python2-tegaki-recognize.
  gnu: Remove python2-pyusb.
  gnu: Remove python2-autograd.
  gnu: getmail: Deprecate with getmail6.
  gnu: Remove python2-mailmanclient.
  gnu: Remove python2-musicbrainzngs.
  gnu: Remove python2-pyechonest.
  gnu: Remove mloop.
  gnu: Remove gtklick.
  gnu: Remove non-timeline.
  gnu: Remove non-mixer.
  gnu: Remove python2-ipy.
  gnu: Remove sala.
  gnu: Add python-jstyleson.
  gnu: Add python-html-text.
  gnu: Add python-mf2py.
  gnu: Add python-pyrdfa3.
  gnu: Add python-extruct.
  gnu: Add python-scrape-schema-recipe.
  gnu: Remove gourmet.
  gnu: gourmet: Update to 0.17.4-0-8af29c8 and enable tests.
  gnu: Remove patches.
  gnu: impressive: Update to 0.13.1.
  gnu: Remove python2-pypdf2.
  gnu: Remove python2-reportlab.
  gnu: Remove pulseaudio-dlna.
  gnu: Remove python2-lz4.
  gnu: Remove python2-lzstring.
  gnu: Remove python2-lzo.
  gnu: Remove python2-service-identity.
  gnu: Remove python2-ed25519.
  gnu: Remove python2-pycrypto.
  gnu: Remove python2-axolotl-curve25519.
  gnu: Remove python2-pyaes.
  gnu: Remove python2-slowaes.
  gnu: Remove python2-josepy.
  gnu: Remove python2-m2crypto.
  gnu: Remove python2-pycryptodome.
  gnu: Remove python2-weave.
  gnu: Remove python2-oauth2client.
  gnu: Remove python2-zope-configuration.
  gnu: Remove python2-sockjs-tornado.
  gnu: Remove python2-zope-security.
  gnu: Remove python2-oauthlib.
  gnu: Remove python2-rauth.
  gnu: Remove python2-betamax.
  gnu: Remove python2-pastedeploy.
  gnu: Remove python2-genshi.
  gnu: Remove python2-webob.
  gnu: Remove python2-readlike.
  gnu: Remove python2-ipython-genutils.
  gnu: Remove python2-coloredlogs.
  gnu: Remove python2-pythondialog.
  gnu: Remove python2-straight-plugin.
  gnu: Remove python2-enum.
  gnu: Remove python2-uniseg.
  gnu: Remove python2-argcomplete.
  gnu: Remove python2-pkginfo.
  gnu: Remove python2-mmtk.
  gnu: Remove python2-s3cmd.
  gnu: Remove python2-clint.
  gnu: Remove python2-exif-read.
  gnu: Remove python2-activepapers.
  gnu: Remove python2-argparse.
  gnu: Remove python2-rencode.
  gnu: Remove python2-parallel.
  gnu: Remove python2-colorspacious.
  gnu: Remove python2-mako.
  gnu: Remove python2-polib.
  gnu: Remove python2-quex-0.67.3.
  gnu: Remove python2-netaddr.
  gnu: Remove python2-kivy.
  gnu: Remove python2-kazoo.
  gnu: Remove python2-prompt-toolkit.
  gnu: Remove python2-editor.
  gnu: Remove python2-kitchen.
  gnu: Remove python2-dns-lexicon.
  gnu: Remove python2-shedskin.
  gnu: Remove python2-unicodecsv.
  gnu: Remove python2-cliapp.
  gnu: Remove python2-text-unidecode.
  gnu: Remove python2-invoke.
  gnu: Remove python2-validictory.
  gnu: Remove python2-pycosat.
  gnu: Remove python2-miniboa.
  gnu: Remove python2-semver.
  gnu: Remove python2-configobj.
  gnu: Remove python2-verboselogs.
  gnu: Remove python2-glob2.
  gnu: Remove python2-funcy.
  gnu: Remove python2-phonenumbers.
  gnu: Remove python2-tracing.
  gnu: Remove python2-anyjson.
  gnu: Remove python2-libarchive-c.
  gnu: Remove python2-xopen.
  gnu: Remove python2-quex.
  gnu: Remove python2-file.
  gnu: Remove python2-jsonrpclib-pelix.
  gnu: Remove python2-munch.
  gnu: Remove python2-pycountry.
  gnu: Remove python2-user-agents.
  gnu: Remove python2-ratelimiter.
  gnu: Remove python2-prettytable.
  gnu: Remove python2-jsonrpclib.
  gnu: Remove python2-translitcodec.
  gnu: Remove python2-isoweek.
  gnu: Remove python2-tblib.
  gnu: Remove python2-smmap.
  gnu: Remove python2-isort.
  gnu: non-session-manager: Replace with new-session-manager.
  gnu: Remove python2-pyliblo.
  gnu: Remove python2-nosexcover.
  gnu: Remove python2-sqlalchemy.
  gnu: Remove python2-efl.
  gnu: Remove python2-mnemonic.
  gnu: Remove python2-pygame.
  gnu: Remove python2-hidapi.
  gnu: Remove python2-notmuch.
  gnu: Remove python2-pypdf.
  gnu: Remove python2-axolotl.
  gnu: Remove python2-ecpy.
  gnu: Remove python2-ecdsa.
  gnu: Remove python2-httplib2.
  gnu: Remove python2-zope-component.
  gnu: Remove python2-zope-location.
  gnu: Remove python2-random2.
  gnu: Remove python2-pynamecheap.
  gnu: Remove python2-reparser.
  gnu: Remove python2-gyp.
  gnu: Remove python2-schema.
  gnu: Remove python2-args.
  gnu: Remove python2-pip.
  gnu: Remove python2-schedule.
  gnu: Remove python2-ua-parser.
  gnu: Remove python2-xdo.
  gnu: python-seaborn: Update to 0.11.2.
  gnu: Remove python2-zeroconf.
  gnu: Remove python2-botocore.
  gnu: Remove python2-email-validator.
  gnu: Remove python2-pyjwt.
  gnu: Remove python2-distutils-extra.
  gnu: Remove python2-schematics.
  gnu: Remove python2-rsa.
  gnu: Remove python2-grako.
  gnu: Remove python2-whatever.
  gnu: Remove python2-blosc.
  gnu: Remove python2-xcffib.
  gnu: Remove python2-pyev.
  gnu: Remove python2-capturer.
  gnu: Remove python2-drmaa.
  gnu: Remove python2-sympy.
  gnu: Remove python2-pybugz.
  gnu: Remove python2-bz2file.
  gnu: Remove python2-ttystatus.
  gnu: Remove python2-pystache.
  gnu: Remove python2-rply.
  gnu: Remove python2-serpent.
  gnu: Remove python2-incremental.
  gnu: Remove python2-steadymark.
  gnu: Remove python2-waitress.
  gnu: Remove python2-radon.
  gnu: Remove python2-mimeparse.
  gnu: Remove python2-coverage-test-runner.
  gnu: Remove python2-pygame-sdl2.
  gnu: Remove python2-protobuf.
  gnu: Remove python2-zope-proxy.
  gnu: Remove python2-objgraph.
  gnu: Remove python2-yapf.
  gnu: Remove python2-misaka.
  gnu: Remove python2-mpmath.
  gnu: Remove python2-binaryornot.
  gnu: Remove python2-cheetah.
  gnu: Remove python2-ruamel.ordereddict.
  gnu: Remove python2-blinker.
  gnu: Remove python2-termcolor.
  gnu: Remove python2-booleanoperations.
  gnu: Remove python2-dirsync.
  gnu: Remove python2-rfc3986.
  gnu: Remove python2-feedgenerator.
  gnu: Remove python2-ipaddr.
  gnu: Remove python2-autopep8.
  gnu: Remove python2-humanfriendly.
  gnu: Remove python2-consul.
  gnu: Remove python2-flex.
  gnu: Remove python2-numexpr.
  gnu: Remove python2-texttable.
  gnu: Remove python2-simplegeneric.
  gnu: Remove python2-dnspython-1.16.
  gnu: Remove python2-zope-schema.
  gnu: Remove python2-pyclipper.
  gnu: Remove ptpython-2.
  gnu: Remove python2-locket.
  gnu: Remove python2-zope-i18nmessageid.
  gnu: Remove python2-jsonpatch.
  gnu: Remove python2-ansi2html.
  gnu: Remove python-prompt-toolkit-1.
  gnu: Remove python2-zope-testrunner.
  gnu: Remove python2-xlib.
  gnu: Remove python2-pysnptools.
  gnu: Remove python2-qrcode.
  gnu: Remove python2-tabulate.
  gnu: Remove python2-markdown.
  gnu: Remove python2-jsonpatch-0.4.
  gnu: Remove python2-pytest-xdist.
  gnu: Remove python2-zope-exceptions.
  gnu: Remove python2-netifaces.
  gnu: Remove python2-pyinotify.
  gnu: Remove python2-msgpack.
  gnu: Remove python2-element-tree.
  gnu: Remove python2-joblib.
  gnu: Remove python2-cram.
  gnu: Remove python2-cloudpickle.
  gnu: Remove python2-tornado.
  gnu: Remove python2-zope-interface.
  gnu: Remove python2-tldextract.
  gnu: Remove python2-notify2.
  gnu: Remove python2-pydiff.
  gnu: Remove python2-parso.
  gnu: Remove python2-vcversioner.
  gnu: Remove python2-extras.
  gnu: Remove python2-inflection.
  gnu: Remove python2-execnet.
  gnu: Remove python2-scientific.
  gnu: Remove python2-automat.
  gnu: Remove python2-mando.
  gnu: Remove python2-pexpect.
  gnu: Remove python2-couleur.
  gnu: Remove python2-dogtail.
  gnu: Remove python2-magic.
  gnu: Remove python2-fusepy.
  gnu: Remove python2-wrapt.
  gnu: Remove python2-pyasn1-modules.
  gnu: Remove python2-xlrd.
  gnu: Remove python2-h5py.
  gnu: Remove python2-colorama.
  gnu: Remove python2-flake8-polyfill.
  gnu: Remove python2-elib.intl.
  gnu: Remove python2-pyroute2.
  gnu: Remove python2-psutil.
  gnu: Remove python2-tempdir.
  gnu: Remove python2-djvulibre.
  gnu: Remove python2-urwidtrees.
  gnu: Remove python2-clyent.
  gnu: Remove python2-constantly.
  gnu: Remove python2-pep517.
  gnu: Remove python2-q.
  gnu: Remove python2-rst.linker.
  gnu: Remove python2-pathlib.
  gnu: Remove python2-whoosh.
  gnu: Remove python2-openpyxl.
  gnu: Remove python2-validate-email.
  gnu: Remove python2-setproctitle.
  gnu: Remove python2-fuzzywuzzy.
  gnu: Remove python2-schema-0.5.
  gnu: Remove python2-graphviz.
  gnu: Remove python2-wheel.
  gnu: Remove python2-zope-testing.
  gnu: Remove python2-zope-event.
  gnu: Remove python2-responses.
  gnu: Remove python2-pyro.
  gnu: Remove python2-lazy-object-proxy.
  gnu: Remove python2-astor.
  gnu: Remove python2-requests-file.
  gnu: Remove python2-backports-abc.
  gnu: Remove python2-singledispatch.
  gnu: Remove python2-waf.
  gnu: Remove python2-pyrsistent.
  gnu: Remove python2-sure.
  gnu: Remove python2-attrs.
  gnu: Remove python2-pkgconfig.
  gnu: Remove python2-pbkdf2.
  gnu: Remove python2-pylzma.
  gnu: Remove python2-futures.
  gnu: Remove python2-et-xmlfile.
  gnu: Remove python2-m2r.
  gnu: Remove python2-jdcal.
  gnu: Remove python2-rfc3987.
  gnu: Remove python2-jsonpointer.
  gnu: Remove python2-semantic-version.
  gnu: Remove python2-stemming.
  gnu: Remove python2-pep8.
  gnu: Remove python2-regex.
  gnu: Remove python2-socksipy-branch.
  gnu: Remove python2-setuptools-scm-git-archive.
  gnu: Remove python2-ukpostcodeparser.
  gnu: Remove python2-pyld.
  gnu: Remove python2-mechanize.
  gnu: Remove python2-parse-type.
  gnu: Remove python2-ptyprocess.
  gnu: Remove python2-flake8.
  gnu: Remove python2-virtualenv.
  gnu: Remove python2-pyasn1.
  gnu: Remove chirp.
  gnu: Remove python2-rdflib.
  gnu: Remove python2-gmpy2.
  gnu: Remove python2-cypari2.
  gnu: Remove python2-pyscard.
  gnu: Remove python2-patsy.
  gnu: Remove rawdog.
  gnu: Remove python2-pyte.
  gnu: Remove python2-blessings.
  gnu: Remove virtaal.
  gnu: Remove python2-monotonic.
  gnu: Remove python2-parsedatetime.
  gnu: Remove python2-aniso8601.
  gnu: Remove python2-tzdata.
  gnu: Remove python2-defcon.
  gnu: Remove gess.
  gnu: Remove find-circ.
  gnu: Remove python2-matplotlib.
  gnu: Remove python2-numpy.
  gnu: Remove python2-scipy.
  gnu: Remove python2-numpydoc.
  gnu: Remove python2-pysam.
  gnu: Remove python2-ufolib.
  gnu: Remove python2-kiwisolver.
  gnu: Remove python2-cookies.
  gnu: Remove python2-pycurl.
  gnu: Remove python2-cleo.
  gnu: Remove python2-entrypoints.
  gnu: Remove python2-mccabe.
  gnu: Remove python2-networkx.
  gnu: Remove python2-pycodestyle.
  gnu: Remove python2-pyserial.
  gnu: Remove python2-cycler.
  gnu: Remove python2-future.
  gnu: Remove python2-mistune.
  gnu: Remove python2-cysignals.
  gnu: Remove python2-pytidylib.
  gnu: Remove python2-sphinx.
  gnu: Remove python2-docutils.
  gnu: Remove python2-translate-toolkit.
  gnu: Remove python2-subprocess32.
  gnu: Remove python2-pyflakes.
  gnu: Remove python2-pympler.
  gnu: Remove python2-isodate.
  gnu: Remove python2-pyrfc3339.
  gnu: Remove youtube-dl-gui.
  gnu: Add python-avocado-framework.
  gnu: python-pygments: Update to 2.12.0.
  gnu: python-urwid-readline: Update to 0.13.
  gnu: Add python-qemu-qmp.
  gnu: qmpbackup: Update to 0.23.
  gnu: Remove python2-feedparser.
  gnu: Remove python2-clf.
  gnu: Remove wicd.
  gnu: Remove python2-i3-py.
  gnu: Remove python2-pyxb.
  gnu: xlsx2csv: Update to 0.7.8.
  gnu: Remove python2-pyatspi.
  gnu: Remove python2-rsvg.
  gnu: solfege: Update to 3.23.5pre2.
  gnu: dosage: Remove python2 inputs.
  gnu: Remove python2-pytest-mock.
  gnu: Remove python2-backports-shutil-get-terminal-size.
  gnu: libappindicator: Update to 12.10.1-0-298.
  gnu: gimp: Drop Python 2 support.
  gnu: glimpse: Drop Python 2 support.
  gnu: keybinder: Replace with keybinder-3.0.
  gnu: language: Remove tegaki packages.
  gnu: Remove python2-pygtk.
  gnu: Remove python2-pytest-runner.
  gnu: lightdm: Update to 1.30.0-0.b7fc321.
  gnu: Remove python2-pygobject.
  gnu: Remove python2-pytest.
  gnu: Remove python2-pluggy.
  gnu: Remove python2-pycairo.
  gnu: Remove python2-zinnia.
  gnu: Remove python2-requests.
  gnu: Remove python2-bottle.
  gnu: Remove python2-docopt.
  gnu: Remove python2-decorator.
  gnu: Remove python2-beautifulsoup4.
  gnu: Remove python2-clikit.
  gnu: Remove python2-funcsigs-bootstrap.
  gnu: Remove python2-snowballstemmer.
  gnu: Remove python2-packaging.
  gnu: Remove python2-backpack.
  gnu: Remove python2-urwid.
  gnu: Remove python2-diff-match-patch.
  gnu: Remove python2-jinja2.
  gnu: Remove python2-twodict.
  gnu: Remove python2-vobject.
  gnu: Remove python2-pastel.
  gnu: Remove python2-webencodings.
  gnu: Remove python2-urllib3.
  gnu: Remove python2-markupsafe.
  gnu: Remove python2-chardet.
  gnu: Remove python2-imagesize.
  gnu: Remove python2-babel.
  gnu: Remove python2-levenshtein.
  gnu: Remove python2-pyaml.
  gnu: Remove python2-simplejson.
  gnu: Remove python2-pylev.
  gnu: Remove python2-soupsieve.
  gnu: Remove python2-atomicwrites.
  gnu: Remove python2-importlib-metadata.
  gnu: Remove python2-pyicu.
  gnu: Remove python2-sphinx-alabaster-theme.
  gnu: Remove python2-sphinxcontrib-websupport.
  gnu: Remove python2-wxpython.
  gnu: Remove python2-freezegun.
  gnu: Remove python2-packaging-bootstrap.
  gnu: Remove python2-zipp.
  gnu: Remove python2-certifi.
  gnu: Remove python2-pyopenssl.
  gnu: Remove python2-unidecode.
  gnu: Remove python2-configparser.
  gnu: Remove python2-importlib-resources.
  gnu: Remove python2-pysocks.
  gnu: Remove python2-backports-functools-lru-cache.
  gnu: Remove python2-flaky.
  gnu: Remove python2-cryptography.
  gnu: Remove python2-pathlib2.
  gnu: Remove python2-typing.
  gnu: Remove python2-contextlib2.
  gnu: Remove python2-dateutil.
  gnu: Remove python2-coverage.
  gnu: Remove python2-cffi.
  gnu: Remove python2-cryptography-vectors.
  gnu: Remove python2-asn1crypto.
  gnu: Remove python2-ipaddress.
  gnu: Remove python2-scandir.
  gnu: Remove python2-backport-ssl-match-hostname.
  gnu: Remove python2-idna.
  gnu: Remove python2-pretend.
  gnu: Remove python2-pytz.
  gnu: Remove python2-iso8601.
  gnu: Remove python2-seaborn.
  gnu: Remove didjvu.
  gnu: Remove python2-gamera.
  gnu: Remove python2-pillow.
  gnu: python-pillow: Update to 9.0.0.
  gnu: Remove python2-olefile.
  gnu: pypy3: Rename to pypy and modernize definition.
  gnu: Add python-fastbencode.
  gnu: Add python-lazr-uri.
  gnu: Add python-wadllib.
  gnu: Add python-lazr-restfulclient.
  gnu: Add python-launchpadlib.
  gnu: breezy: Update to 3.2.2.
  gnu: bazaar: Obsolete with breezy.
  gnu: icecat: Remove obsolete Python 2 dependencies.
  gnu: icecat: Modernize package definition.
  gnu: Remove fraggenescan.
  gnu: Remove python2-pysqlite.
  gnu: lvtk: Update to 1.2.0-0.a73feab.
  gnu: jalv: Use Python 3.
  gnu: aubio: Use Python 3.
  gnu: Remove python2-mock.
  gnu: Remove python2-hypothesis.
  gnu: Remove python2-functools32.
  gnu: Remove python2-funcsigs.
  gnu: Remove python2-sortedcontainers.
  gnu: Remove python2-unittest2.
  gnu: Remove python2-traceback2.
  gnu: Remove python2-linecache2.
  gnu: Remove beast.
  gnu: Remove rapicorn.
  gnu: Remove libpng-1.2.
  gnu: Remove boost-with-python2.
  gnu: john-the-ripper-jumbo: Use Python 3.
  gnu: Remove python2-enum34.
  gnu: Remove python2-appdirs.
  gnu: Add vtk-7.
  gnu: itk-snap: Fix build.
  gnu: Remove vtk-6.
  gnu: dcmtk: Update to 3.6.7 and build as a shared library.
  gnu: mia: Update to 2.4.7.
  gnu: Remove python2-lxml.
  gnu: brasero: Remove obsolete gnome-doc-utils input.
  gnu: libdbusmenu: Update to 16.04.0-496.
  gnu: dico: Use Python 3.
  gnu: lolcode-lci: Update to 0.11.2-0.6762b72.
  gnu: Remove python2-libmpsse.
  gnu: Remove gnome-doc-utils.
  gnu: gnome-keyring: Use Python 3.
  gnu: Remove python2-more-itertools.
  gnu: Remove python2-tlsh.
  gnu: Remove python2-lirc.
  gnu: Remove python2-cython.
  gnu: mozjs: Cleanup to only keep the last version.
  gnu: icedove: Delete obsolete Python 2 input.
  gnu: icedove: Use new style for inputs.
  gnu: jack-2: Update to 1.9.21.
  gnu: mod-host: Update to 0.10.6-4.cdd30dd.
  gnu: Remove python2-pyfakefs-bootstrap.
  gnu: libpqxx: Update to 7.7.3.
  gnu: Remove 4store.
  gnu: Remove python2-libxml2.
  gnu: Remove python2-attrs-bootstrap.
  gnu: pdf2djvu: Disable tests to avoid Python 2 dependencies.
  gnu: python-setproctitle: Delete obsolete phase.
  gnu: Remove python2-nose.
  gnu: ocaml-dose3: Disable tests to avoid Python 2 dependencies.
  gnu: Remove python2-pyyaml.
  gnu: openbox: Patch for Python 3.
  gnu: Remove python2-wcwidth.
  gnu: Remove python2-pyxdg.
  gnu: Remove python2-six-bootstrap.
  gnu: Remove python2-setuptools-scm.
  gnu: Remove python2-pyparsing.
  gnu: Remove python2-py.
  gnu: Remove python2-fonttools.
  gnu: python2-six: Disable tests.
  gnu: Remove python2-backports-csv.
  gnu: qtwebengine: Re-style inputs.
  gnu: Remove python2-checkm-genome.
  gnu: Remove python2-setuptools.
  gnu: Remove python-prompt-toolkit-2.
  gnu: Remove python2-called-python.

 doc/guix.texi                                 |   14 -
 etc/committer.scm.in                          |  197 +-
 gnu/local.mk                                  |   26 +-
 gnu/packages/ada.scm                          |   29 -
 gnu/packages/admin.scm                        |   36 -
 gnu/packages/audio.scm                        |  168 +-
 gnu/packages/bioinformatics.scm               |  694 +---
 gnu/packages/bittorrent.scm                   |   43 -
 gnu/packages/boost.scm                        |    7 -
 gnu/packages/check.scm                        |  249 +-
 gnu/packages/chemistry.scm                    |   92 -
 gnu/packages/databases.scm                    |  194 +-
 gnu/packages/dico.scm                         |   36 +-
 gnu/packages/display-managers.scm             |  143 +-
 gnu/packages/djvu.scm                         |  223 +-
 gnu/packages/education.scm                    |  203 --
 gnu/packages/embedded.scm                     |   30 -
 gnu/packages/engineering.scm                  |    3 -
 gnu/packages/enlightenment.scm                |   31 -
 gnu/packages/esolangs.scm                     |   50 +-
 gnu/packages/finance.scm                      |   12 -
 gnu/packages/fontutils.scm                    |   70 +-
 gnu/packages/freedesktop.scm                  |  137 +-
 gnu/packages/game-development.scm             |  211 +-
 gnu/packages/games.scm                        |   29 +-
 gnu/packages/gimp.scm                         |  208 +-
 gnu/packages/glib.scm                         |   70 +-
 gnu/packages/gnome.scm                        |  161 +-
 gnu/packages/gnupg.scm                        |   71 +-
 gnu/packages/gnuzilla.scm                     | 1447 +++-----
 gnu/packages/graphics.scm                     |   70 -
 gnu/packages/graphviz.scm                     |   36 +-
 gnu/packages/gtk.scm                          |  223 +-
 gnu/packages/hardware.scm                     |   36 -
 gnu/packages/image-processing.scm             |  139 +-
 gnu/packages/image.scm                        |   19 -
 gnu/packages/iso-codes.scm                    |    6 -
 gnu/packages/key-mon.scm                      |   25 -
 gnu/packages/language.scm                     |  437 ---
 gnu/packages/libffi.scm                       |    3 -
 gnu/packages/libusb.scm                       |    6 -
 gnu/packages/lirc.scm                         |   15 +-
 gnu/packages/machine-learning.scm             |   82 -
 gnu/packages/mail.scm                         |   65 +-
 gnu/packages/maths.scm                        |    4 -
 gnu/packages/music.scm                        |  554 +--
 gnu/packages/networking.scm                   |    3 -
 gnu/packages/nutrition.scm                    |  160 +-
 gnu/packages/ocaml.scm                        |   16 +-
 gnu/packages/ocr.scm                          |   17 -
 gnu/packages/openbox.scm                      |   20 +-
 gnu/packages/password-utils.scm               |   45 +-
 .../patches/4store-fix-buildsystem.patch      |   56 -
 .../4store-unset-preprocessor-directive.patch |   16 -
 gnu/packages/patches/breezy-fix-gio.patch     |  338 ++
 .../patches/gourmet-sqlalchemy-compat.patch   |   18 +
 .../patches/itk-snap-alt-glibc-compat.patch   |   22 +
 .../patches/mia-fix-boost-headers.patch       |  479 +++
 .../patches/mozjs17-aarch64-support.patch     |   60 -
 .../patches/mozjs24-aarch64-support.patch     |   21 -
 .../patches/mozjs38-pkg-config-version.patch  |   24 -
 .../patches/mozjs38-shell-version.patch       |   67 -
 .../patches/mozjs38-tracelogger.patch         |  608 ----
 .../patches/mozjs38-version-detection.patch   |  180 -
 .../patches/mozjs60-riscv64-support.patch     |  122 -
 gnu/packages/patches/openbox-python3.patch    |  165 +
 ...python2-parameterized-docstring-test.patch |   18 -
 .../python2-pygobject-2-deprecation.patch     |   39 -
 ...hon2-subprocess32-disable-input-test.patch |   18 -
 gnu/packages/patches/rapicorn-isnan.patch     |   87 -
 .../patches/vtk-7-gcc-10-compat.patch         |   14 +
 gnu/packages/patches/vtk-7-hdf5-compat.patch  |   38 +
 .../patches/vtk-7-python-compat.patch         |   16 +
 .../patches/wicd-bitrate-none-fix.patch       |   24 -
 .../wicd-get-selected-profile-fix.patch       |   16 -
 gnu/packages/patches/wicd-urwid-1.3.patch     |   18 -
 gnu/packages/patches/wicd-wpa2-ttls.patch     |   38 -
 gnu/packages/patchutils.scm                   |   29 -
 gnu/packages/pdf.scm                          |   83 +-
 gnu/packages/polkit.scm                       |    2 +-
 gnu/packages/protobuf.scm                     |    3 -
 gnu/packages/pulseaudio.scm                   |   52 -
 gnu/packages/python-build.scm                 |   33 +-
 gnu/packages/python-check.scm                 |   82 +
 gnu/packages/python-compression.scm           |   32 -
 gnu/packages/python-crypto.scm                |   97 +-
 gnu/packages/python-science.scm               |  155 -
 gnu/packages/python-web.scm                   |  347 +-
 gnu/packages/python-xyz.scm                   | 2960 ++---------------
 gnu/packages/python.scm                       |  280 +-
 gnu/packages/qt.scm                           |  140 +-
 gnu/packages/radio.scm                        |   24 -
 gnu/packages/rdf.scm                          |   40 +-
 gnu/packages/sagemath.scm                     |    6 -
 gnu/packages/security-token.scm               |    3 -
 gnu/packages/sphinx.scm                       |   78 +-
 gnu/packages/statistics.scm                   |   24 -
 gnu/packages/syncthing.scm                    |    2 -
 gnu/packages/syndication.scm                  |   25 -
 gnu/packages/terminals.scm                    |    6 -
 gnu/packages/text-editors.scm                 |   36 -
 gnu/packages/time.scm                         |   27 -
 gnu/packages/version-control.scm              |  114 +-
 gnu/packages/video.scm                        |   97 -
 gnu/packages/virtualization.scm               |   63 +-
 gnu/packages/web.scm                          |   27 -
 gnu/packages/wicd.scm                         |  197 --
 gnu/packages/wm.scm                           |   37 +-
 gnu/packages/wxwidgets.scm                    |   73 -
 gnu/packages/xml.scm                          |   21 +-
 gnu/services/networking.scm                   |   62 -
 gnu/system/linux-container.scm                |    3 +-
 guix/build/bzr.scm                            |    8 +-
 guix/bzr-download.scm                         |    6 +-
 guix/diagnostics.scm                          |    2 +-
 guix/lint.scm                                 |   24 +-
 guix/packages.scm                             |    2 +-
 guix/utils.scm                                |   37 +-
 tests/profiles.scm                            |    2 +-
 119 files changed, 3621 insertions(+), 11087 deletions(-)
 delete mode 100644 gnu/packages/patches/4store-fix-buildsystem.patch
 delete mode 100644 gnu/packages/patches/4store-unset-preprocessor-directive.patch
 create mode 100644 gnu/packages/patches/breezy-fix-gio.patch
 create mode 100644 gnu/packages/patches/gourmet-sqlalchemy-compat.patch
 create mode 100644 gnu/packages/patches/itk-snap-alt-glibc-compat.patch
 create mode 100644 gnu/packages/patches/mia-fix-boost-headers.patch
 delete mode 100644 gnu/packages/patches/mozjs17-aarch64-support.patch
 delete mode 100644 gnu/packages/patches/mozjs24-aarch64-support.patch
 delete mode 100644 gnu/packages/patches/mozjs38-pkg-config-version.patch
 delete mode 100644 gnu/packages/patches/mozjs38-shell-version.patch
 delete mode 100644 gnu/packages/patches/mozjs38-tracelogger.patch
 delete mode 100644 gnu/packages/patches/mozjs38-version-detection.patch
 delete mode 100644 gnu/packages/patches/mozjs60-riscv64-support.patch
 create mode 100644 gnu/packages/patches/openbox-python3.patch
 delete mode 100644 gnu/packages/patches/python2-parameterized-docstring-test.patch
 delete mode 100644 gnu/packages/patches/python2-pygobject-2-deprecation.patch
 delete mode 100644 gnu/packages/patches/python2-subprocess32-disable-input-test.patch
 delete mode 100644 gnu/packages/patches/rapicorn-isnan.patch
 create mode 100644 gnu/packages/patches/vtk-7-gcc-10-compat.patch
 create mode 100644 gnu/packages/patches/vtk-7-hdf5-compat.patch
 create mode 100644 gnu/packages/patches/vtk-7-python-compat.patch
 delete mode 100644 gnu/packages/patches/wicd-bitrate-none-fix.patch
 delete mode 100644 gnu/packages/patches/wicd-get-selected-profile-fix.patch
 delete mode 100644 gnu/packages/patches/wicd-urwid-1.3.patch
 delete mode 100644 gnu/packages/patches/wicd-wpa2-ttls.patch
 delete mode 100644 gnu/packages/wicd.scm

-- 
2.36.0

[bug#55424] [PATCH 000/602] Purge Python 2 packages

[Guillaume Le Vaillant]

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Maxim Cournoyer <maxim.cournoyer@gmail.com> skribis:

>   gnu: Remove ocrodjvu.
>   gnu: Remove didjvu.

It looks like there are ports to Python 3 for these two programs at
<https://github.com/rmast/ocrodjvu/tree/python3> and
<https://github.com/FriedrichFroebel/didjvu>, so instead of removing the
packages maybe we could use these forks...

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[bug#55424] [PATCH 020/602] gnu: Remove pepr.

[Maxime Devos]

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Maxim Cournoyer schreef op zo 15-05-2022 om 00:36 [-0400]:
> -(define-public pepr
> -  (package
> -    (name "pepr")
> -    (version "1.0.9")
> -    (source (origin
> -              (method url-fetch)
> -              (uri (pypi-uri "PePr" version))
> -              (sha256
> -               (base32
> -                "0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx"))))
> -    (build-system python-build-system)
> -    (arguments
> -     `(#:python ,python-2 ; python2 only

Looking at <https://github.com/shawnzhangyx/PePr/issues/33>
and <https://github.com/shawnzhangyx/PePr/issues/30>, it appears that
Python2->3 issues have been fixed.  At least, those that the maintainer
is aware of.

The latest version apparently is 1.1.24
<https://github.com/shawnzhangyx/PePr/blob/master/PePr/__init__.py>,
although it does not have a tag.  According to the ‘latest commit ...’
text on GitHub, this version number appears in commit
<https://github.com/shawnzhangyx/PePr/commit/f1676cdaad4c4f9704ecea328ce3b814fb49b6fc>.

So maybe updating 'pepr' would be sufficient?

Greetings,
Maxime.

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[bug#55424] [PATCH 061/602] gnu: Remove ocrodjvu.

[Maxime Devos]

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Maxim Cournoyer schreef op zo 15-05-2022 om 00:37 [-0400]:
> -    (inputs
> -     `(("djvulibre" ,djvulibre)
> -       ("ocrad" ,ocrad)
> -       ("python" ,python-2)
> -       ("python2-djvulibre" ,python2-djvulibre)
> -       ("python2-html5lib" ,python2-html5lib)
> -       ("python2-lxml" ,python2-lxml)
> -       ("python2-pyicu" ,python2-pyicu)
> -       ("python2-subprocess32" ,python2-subprocess32)
> -       ("tesseract-ocr" ,tesseract-ocr)))

Apparently python3 is now supported:
<https://github.com/kcroker/dpsprep/pull/6>.

Greetings,
Maxime.

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[bug#55424] [PATCH 020/602] gnu: Remove pepr.

[Maxim Cournoyer]

Hello Maxime,

Maxime Devos <maximedevos@telenet.be> writes:

> Maxim Cournoyer schreef op zo 15-05-2022 om 00:36 [-0400]:
>> -(define-public pepr
>> -  (package
>> -    (name "pepr")
>> -    (version "1.0.9")
>> -    (source (origin
>> -              (method url-fetch)
>> -              (uri (pypi-uri "PePr" version))
>> -              (sha256
>> -               (base32
>> -                "0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx"))))
>> -    (build-system python-build-system)
>> -    (arguments
>> -     `(#:python ,python-2 ; python2 only
>
> Looking at <https://github.com/shawnzhangyx/PePr/issues/33>
> and <https://github.com/shawnzhangyx/PePr/issues/30>, it appears that
> Python2->3 issues have been fixed.  At least, those that the maintainer
> is aware of.
>
> The latest version apparently is 1.1.24
> <https://github.com/shawnzhangyx/PePr/blob/master/PePr/__init__.py>,
> although it does not have a tag.  According to the ‘latest commit ...’
> text on GitHub, this version number appears in commit
> <https://github.com/shawnzhangyx/PePr/commit/f1676cdaad4c4f9704ecea328ce3b814fb49b6fc>.
>
> So maybe updating 'pepr' would be sufficient?

Unfortunately, no;

***   File "/gnu/store/ba7i5cbiznn4j712d8g8ij5az0jmba7b-pepr-1.1.24-0.05f20c6/lib/python3.9/site-packages/PePr/utilities/find_peak_mode.py", line 108
    print chr
          ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(chr)?

That's when using the last commit.

Thanks,

Maxim

[bug#55424] [PATCH 000/602] Purge Python 2 packages

[Maxim Cournoyer]

Hi Guillaume,

Guillaume Le Vaillant <glv@posteo.net> writes:

> Maxim Cournoyer <maxim.cournoyer@gmail.com> skribis:
>
>>   gnu: Remove ocrodjvu.
>>   gnu: Remove didjvu.
>
> It looks like there are ports to Python 3 for these two programs at
> <https://github.com/rmast/ocrodjvu/tree/python3> and
> <https://github.com/FriedrichFroebel/didjvu>, so instead of removing the
> packages maybe we could use these forks...

I tried it, and it worked!  Thanks for suggesting.  I had to update
python-gamera to version 4 in the process.

You'll see the result in the 'purge-python2-packages' branch on
Savannah, which I'll update shortly.

Thank you,

Maxim

[bug#55424] [PATCH 061/602] gnu: Remove ocrodjvu.

[Maxim Cournoyer]

Hi Maxime,

Maxime Devos <maximedevos@telenet.be> writes:

> Maxim Cournoyer schreef op zo 15-05-2022 om 00:37 [-0400]:
>> -    (inputs
>> -     `(("djvulibre" ,djvulibre)
>> -       ("ocrad" ,ocrad)
>> -       ("python" ,python-2)
>> -       ("python2-djvulibre" ,python2-djvulibre)
>> -       ("python2-html5lib" ,python2-html5lib)
>> -       ("python2-lxml" ,python2-lxml)
>> -       ("python2-pyicu" ,python2-pyicu)
>> -       ("python2-subprocess32" ,python2-subprocess32)
>> -       ("tesseract-ocr" ,tesseract-ocr)))
>
> Apparently python3 is now supported:
> <https://github.com/kcroker/dpsprep/pull/6>.

Wrong package?  That seems to be for dpsprep, not ocrodjvu.  For the
later, as pointed by Guillaume, there exists a Python 3 fork, which I
was able use to save the ocrodjvu package.

Thanks,

Maxim

bug#55424: [PATCH 000/602] Purge Python 2 packages

[Maxim Cournoyer]

Hello,

Maxim Cournoyer <maxim.cournoyer@gmail.com> writes:

> Hi Guillaume,
>
> Guillaume Le Vaillant <glv@posteo.net> writes:
>
>> Maxim Cournoyer <maxim.cournoyer@gmail.com> skribis:
>>
>>>   gnu: Remove ocrodjvu.
>>>   gnu: Remove didjvu.
>>
>> It looks like there are ports to Python 3 for these two programs at
>> <https://github.com/rmast/ocrodjvu/tree/python3> and
>> <https://github.com/FriedrichFroebel/didjvu>, so instead of removing the
>> packages maybe we could use these forks...
>
> I tried it, and it worked!  Thanks for suggesting.  I had to update
> python-gamera to version 4 in the process.
>
> You'll see the result in the 'purge-python2-packages' branch on
> Savannah, which I'll update shortly.

I've now pushed this series with
c35e508b4a317e3c06e1553833b0979e1620f582.

Closing.

Thanks!

Maxim

[bug#55424] [PATCH 081/602] gnu: renpy: Build with Python 3.

[Liliana Marie Prikler]

Am Sonntag, dem 15.05.2022 um 00:37 -0400 schrieb Maxim Cournoyer:
> * gnu/packages/game-development.scm (renpy)[python]: Delete argument.
> [phases]: Delete trailing #t.
> [propagated-inputs]: Update the inputs to their Python 3
> counterparts.
> [native-inputs]: Likewise.
> ---
Sorry for commenting on a patch that has already been merged, but this
does not actually build renpy with Python 3, it builds the python parts
of renpy.  And although those "build" fine as a package, since they
lack tests, there is no guarantee that they work – as a matter of fact,
the actual renpy package, which failed to build against python 3 back
when I last updated the package still fails to build if I adjust the
package definition.

According to upstream, only renpy 8.0 will run on python 3, whereas
renpy 7.5 (both still prereleases) will continue to use python 2.7.

I suggest "temporarily" reverting the following commits
425783b5 "gnu: Remove python2-cython."
ffec658a "gnu: Remove python2-future."
1a6eb0d6 "gnu: Remove python2-pygame-sdl2."
9f1bd63f "gnu: renpy: Build with Python 3."
or alternatively dropping the renpy package altogether.  I have already
reverted them on my local tree, so I could push whenever – the question
is whether to do it in four separate commits or in a big one along with
an explanation.

WDYT?

[bug#55424] [PATCH 081/602] gnu: renpy: Build with Python 3.

[Maxim Cournoyer]

Hi Liliana,

Liliana Marie Prikler <liliana.prikler@gmail.com> writes:


[...]

> According to upstream, only renpy 8.0 will run on python 3, whereas
> renpy 7.5 (both still prereleases) will continue to use python 2.7.
>
> I suggest "temporarily" reverting the following commits
> 425783b5 "gnu: Remove python2-cython."
> ffec658a "gnu: Remove python2-future."
> 1a6eb0d6 "gnu: Remove python2-pygame-sdl2."
> 9f1bd63f "gnu: renpy: Build with Python 3."
> or alternatively dropping the renpy package altogether.  I have already
> reverted them on my local tree, so I could push whenever – the question
> is whether to do it in four separate commits or in a big one along with
> an explanation.
>
> WDYT?

Could you try updating renpy to a 8.0 pre-release?  It was last updated
6 days ago [0].  That'd be preferable to re-introducing Python 2 stuff.

Thank you!

Maxim

[0]  https://www.renpy.org/release/8.0.0

[bug#55424] [PATCH 081/602] gnu: renpy: Build with Python 3.

[Liliana Marie Prikler]

Am Donnerstag, dem 16.06.2022 um 13:11 -0400 schrieb Maxim Cournoyer:
> Hi Liliana,
> 
> Liliana Marie Prikler <liliana.prikler@gmail.com> writes:
> 
> 
> [...]
> 
> > According to upstream, only renpy 8.0 will run on python 3, whereas
> > renpy 7.5 (both still prereleases) will continue to use python 2.7.
> > 
> > I suggest "temporarily" reverting the following commits
> > 425783b5 "gnu: Remove python2-cython."
> > ffec658a "gnu: Remove python2-future."
> > 1a6eb0d6 "gnu: Remove python2-pygame-sdl2."
> > 9f1bd63f "gnu: renpy: Build with Python 3."
> > or alternatively dropping the renpy package altogether.  I have
> > already reverted them on my local tree, so I could push whenever –
> > the question is whether to do it in four separate commits or in a
> > big one along with an explanation.
> > 
> > WDYT?
> 
> Could you try updating renpy to a 8.0 pre-release?  It was last
> updated 6 days ago [0].  That'd be preferable to re-introducing
> Python 2 stuff.
That looks like the kind of link that would lead to hash conflicts once
the release is actually out (which isn't that bad normally, since I
tend to only use actual releases).  We could use some git tag though,
there's probably a bunch that don't map to releases.  In either case,
these prereleases should not be used to publish game with, which makes
packages for them kinda useless.

Long-term I do think Renpy 7 should not be in Guix upstream, but past
efforts to move it elsewhere like Guix Past ended up mere discussion. 
The questions for me is what to do shot-term, while Renpy 8 is not a
viable option.

[bug#55424] [PATCH 081/602] gnu: renpy: Build with Python 3.

[Maxim Cournoyer]

Hello,

Liliana Marie Prikler <liliana.prikler@gmail.com> writes:

> Am Donnerstag, dem 16.06.2022 um 13:11 -0400 schrieb Maxim Cournoyer:
>> Hi Liliana,
>> 
>> Liliana Marie Prikler <liliana.prikler@gmail.com> writes:
>> 
>> 
>> [...]
>> 
>> > According to upstream, only renpy 8.0 will run on python 3, whereas
>> > renpy 7.5 (both still prereleases) will continue to use python 2.7.
>> > 
>> > I suggest "temporarily" reverting the following commits
>> > 425783b5 "gnu: Remove python2-cython."
>> > ffec658a "gnu: Remove python2-future."
>> > 1a6eb0d6 "gnu: Remove python2-pygame-sdl2."
>> > 9f1bd63f "gnu: renpy: Build with Python 3."
>> > or alternatively dropping the renpy package altogether.  I have
>> > already reverted them on my local tree, so I could push whenever –
>> > the question is whether to do it in four separate commits or in a
>> > big one along with an explanation.
>> > 
>> > WDYT?
>> 
>> Could you try updating renpy to a 8.0 pre-release?  It was last
>> updated 6 days ago [0].  That'd be preferable to re-introducing
>> Python 2 stuff.
> That looks like the kind of link that would lead to hash conflicts once
> the release is actually out (which isn't that bad normally, since I
> tend to only use actual releases).  We could use some git tag though,
> there's probably a bunch that don't map to releases.  In either case,
> these prereleases should not be used to publish game with, which makes
> packages for them kinda useless.

Pre-releases are better than a broken or missing package :-).  I guess
it depends on our users: is someone actively using the Guix-provided
renpy package to publish games?  Since the package was broken 2 weeks
ago without a bug report, I'd assume that no, in which case a
pre-release is fine and more forward-looking in this situation.

> Long-term I do think Renpy 7 should not be in Guix upstream, but past
> efforts to move it elsewhere like Guix Past ended up mere discussion. 
> The questions for me is what to do shot-term, while Renpy 8 is not a
> viable option.

Are all the above Python 2 dependencies already in the Guix-Past
channel?  If so, it seems that it could be decent option to keep renpy 7
there until renpy 8 is made stable, if updating to the pre-release in
Guix proper is too difficult.

Thanks,

Maxim

[bug#55424] [PATCH 081/602] gnu: renpy: Build with Python 3.

[Liliana Marie Prikler]

Am Donnerstag, dem 16.06.2022 um 17:29 -0400 schrieb Maxim Cournoyer:
> Hello,
> 
> Liliana Marie Prikler <liliana.prikler@gmail.com> writes:
> 
> > [...]
> > [T]hese prereleases should not be used to publish game with, which
> > makes packages for them kinda useless.
> 
> Pre-releases are better than a broken or missing package :-).  I
> guess it depends on our users: is someone actively using the Guix-
> provided renpy package to publish games?  
If they did, we would probably be seeing folks make use of our renpy-
build-system, though I can't speak for people using Renpy on Guix to
publish non-free games.

> Since the package was broken 2 weeks ago without a bug report, I'd
> assume that no, in which case a pre-release is fine and more forward-
> looking in this situation.
This does not just affect publishing though.  It also means that a
bunch of games you codes for 7.4 will not work (as expected) with Renpy
8, which might be – pardon the pun – game-breaking.

> > Long-term I do think Renpy 7 should not be in Guix upstream, but
> > past efforts to move it elsewhere like Guix Past ended up mere
> > discussion.  The questions for me is what to do shot-term, while
> > Renpy 8 is not a viable option.
> 
> Are all the above Python 2 dependencies already in the Guix-Past
> channel?  If so, it seems that it could be decent option to keep
> renpy 7 there until renpy 8 is made stable, if updating to the pre-
> release in Guix proper is too difficult.
Only cython is currently in Guix Past, the rest needs to be added. 
Regarding renpy 8, it turns out that no tags exist in Github currently,
so we would have to guess some random commits.  That plus my already
mentioned concerns should imho be enough to consider using the actually
stable version as renpy and offer the other one as renpy-next if people
feel like breaking their stuff.  OTOH if our stance is that we really
don't want any python 2 stuff in Guix and rather have people use time
machine, I think we should loudly break the package (by removing it)
rather than silently.

Cheers

[bug#55424] [PATCH 081/602] gnu: renpy: Build with Python 3.

[Maxim Cournoyer]

Hi Liliana,

We have a nice opportunity at the moment to truly phase out Python 2
from Guix, with just a handful packages remaining that still depend on
it, so I'd like to focus on options other than re-introducing Python 2
dependencies at first.

I tried updating the package like so:

--8<---------------cut here---------------start------------->8---
diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index 4c1b97f041..89602dc127 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -1208,7 +1208,8 @@ (define-public python-pygame
 
 (define-public python-pygame-sdl2
   (let ((real-version "2.1.0")
-        (renpy-version "7.4.11"))
+        ;; Use a pre-release version to match that of Renpy.
+        (renpy-version "8.0.0"))
     (package
       (inherit python-pygame)
       (name "python-pygame-sdl2")
@@ -1216,17 +1217,16 @@ (define-public python-pygame-sdl2
       (source
        (origin
          (method url-fetch)
-         (uri (string-append "https://www.renpy.org/dl/" renpy-version
+         (uri (string-append "https://www.renpy.org/dl/prerelease-8"
                              "/pygame_sdl2-" version ".tar.gz"))
-         (sha256 (base32 "0nxvca16299jx6sp0ys29rqixcs21ymhqwjfkbchhss0yar7qjgz"))
+         (sha256 (base32 "1ml3650czvzi0k9ap12zz7ykldhzzk0251ncl62wdmncfqfq98wd"))
          (modules '((guix build utils)))
          (snippet
           '(begin
              ;; drop generated sources
              (delete-file-recursively "gen")
              (delete-file-recursively "gen3")
-             (delete-file-recursively "gen-static")
-             #t))))
+             (delete-file-recursively "gen-static")))))
       (build-system python-build-system)
       (arguments
        `(#:tests? #f                ; tests require pygame to be installed first
@@ -1243,8 +1243,7 @@ (define-public python-pygame-sdl2
                                       (assoc-ref inputs "sdl-union")
                                       "/lib -Wl,-rpath,"
                                       (assoc-ref inputs "sdl-union")
-                                      "/lib -Wl,--enable-new-dtags -lSDL2"))
-               #t)))))
+                                      "/lib -Wl,--enable-new-dtags -lSDL2")))))))
       (inputs
        (list (sdl-union (list sdl2 sdl2-image sdl2-mixer sdl2-ttf))))
       (native-inputs
@@ -1260,22 +1259,23 @@ (define-public python-pygame-sdl2
 (define-public renpy
   (package
     (name "renpy")
-    (version "7.4.11")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://www.renpy.org/dl/" version
-                           "/renpy-" version "-source.tar.bz2"))
-       (sha256 (base32 "0zkhg2sd2hglm9dkansf4h8sq7lm7iqslzl763ambp4kyfdvd07q"))
-       (modules '((guix build utils)))
-       (patches
-        (search-patches
-         "renpy-use-system-fribidi.patch"))
-       (snippet
-        '(with-directory-excursion "module"
-           ;; drop fribidi sources
-           (delete-file-recursively "fribidi-src")
-           #t))))
+    ;; Use a pre-release version to avoid Python 2, which the last stable 7.5
+    ;; release is still using.
+    (version "8.0.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://www.renpy.org/dl/prerelease-8"
+                                  "/renpy-" version "-source.tar.bz2"))
+              (modules '((guix build utils)))
+              (snippet
+               '(with-directory-excursion "module"
+                  ;; drop fribidi sources
+                  (delete-file-recursively "fribidi-src")))
+              (sha256
+               (base32
+                "0bxihc8lkjmp769i4ih74si76i0lvdw86dg5j005kbj4m4cpvvax"))
+              (patches
+               (search-patches "renpy-use-system-fribidi.patch"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f                      ; Ren'py doesn't seem to package tests
@@ -1299,7 +1299,7 @@ (define-public renpy
                                         "/bin/cython"))
              (setenv "RENPY_DEPS_INSTALL" (string-join (map cdr inputs) ":"))))
          (replace 'build
-           (lambda* (#:key inputs outputs #:allow-other-keys #:rest args)
+           (lambda args
              ;; The "module" subdirectory contains a python (really cython)
              ;; project, which is built using a script, that is thankfully
              ;; named "setup.py".
--8<---------------cut here---------------end--------------->8---

It currently fails to build due to a new dependency, 'tinyfiledialogs':

--8<---------------cut here---------------start------------->8---
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fno-semantic-interposition -fPIC -I. -I/gnu/store/rvjwhr9ib88fm3s2h04n8jl4qpnb54rl-sdl-union-1.2.15/include -I/gnu/store/p7iq81hxxyk9zy7a9dngbf16zm8d4klx-libpng-1.6.37/include -I/gnu/store/rvjwhr9ib88fm3s2h04n8jl4qpnb54rl-sdl-union-1.2.15/include/SDL2 -I/gnu/store/ak70pk2hjks17cx7zjdmdmzpcpiy9gpi-freetype-2.10.4/include/freetype2 -I/gnu/store/jgmr3siy9dr8snlym3dfjbj0gmjzm2zk-ffmpeg-4.4.2/include -I/gnu/store/sh6j1xz8fz7a23x5y2w05rzxjamq4x7y-glew-2.1.0/include -I/gnu/store/9bx852151mzmmbpm92q46zk104qnan1d-python-pygame-sdl2-2.1.0-for-renpy-8.0.0/include/python3.9 -I/gnu/store/65i3nhcwmz0p8rqbg48gaavyky4g4hwk-python-3.9.9/include/python3.9 -c gen3/_renpytfd.c -o build/temp.linux-x86_64-3.9/gen3/_renpytfd.o -std=gnu99 -Wno-unused-function
gen3/_renpytfd.c:618:10: fatal error: tinyfiledialogs/tinyfiledialogs.h: No such file or directory
  618 | #include "tinyfiledialogs/tinyfiledialogs.h"
--8<---------------cut here---------------end--------------->8---

> OTOH if our stance is that we really
> don't want any python 2 stuff in Guix and rather have people use time
> machine, I think we should loudly break the package (by removing it)
> rather than silently.

That appears to be exactly what NixOS has done:

$ nix edit nixpkgs#renpy
error: renpy has been removed from nixpkgs, it was unmaintained and the
latest packaged version required python2

I think finishing the update started above would be a better option than
removing it, if we have the bandwidth to tackle the update.  Would you
like to give it a try?

Thanks,

Maxim

[bug#55424] [PATCH 1/4] gnu: Add back the distinction between python-renpy and renpy.

[Liliana Marie Prikler]

This partially reverts commit 9f1bd63fb5b6916f07d454ffde27cd3a66c95bb5.
Note, that with this patch renpy fails to build due to incompatibilities with
Python 3.

* gnu/packages/game-development.scm (renpy): Split into ‘python-renpy’ for the
python modules and ‘renpy’ for the games and binaries.
---
 gnu/packages/game-development.scm | 171 +++++++++++++++++++++++++++++-
 1 file changed, 169 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index 4c1b97f041..44f8ca57fc 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -1257,9 +1257,9 @@ (define-public python-pygame-sdl2
 developed mainly for Ren'py.")
       (license (list license:lgpl2.1 license:zlib)))))
 
-(define-public renpy
+(define-public python-renpy
   (package
-    (name "renpy")
+    (name "python-renpy")
     (version "7.4.11")
     (source
      (origin
@@ -1342,6 +1342,173 @@ (define-public renpy
 are only used to bootstrap it.")
     (license license:expat)))
 
+(define-public renpy
+  (package
+    (inherit python-renpy)
+    (name "renpy")
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f ; see python2-renpy
+       #:modules ((srfi srfi-1)
+                  (guix build python-build-system)
+                  (guix build utils))
+       #:imported-modules ((srfi srfi-1) ,@%python-build-system-modules)
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-commands
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (substitute* "launcher/game/choose_directory.rpy"
+               (("/usr/bin/python")
+                (search-input-file inputs "/bin/python3")))
+             (substitute* "launcher/game/front_page.rpy"
+               (("xdg-open")
+                (search-input-file inputs "/bin/xdg-open")))
+             (substitute* "launcher/game/project.rpy"
+               (("cmd = \\[ executable, \"-EO\", sys.argv\\[0\\] \\]")
+                (string-append "cmd = [ \"" (assoc-ref outputs "out")
+                               "/bin/renpy\" ]"))
+               ;; Projects are still created in the usual style, so we need
+               ;; to adjust the path.
+               (("cmd.append\\(self.path\\)")
+                "cmd.append(self.path + \"/game\")"))
+             #t))
+         (add-after 'unpack 'drop-game-from-paths
+           (lambda _
+             (substitute* (list "launcher/game/gui7.rpy"
+                                "launcher/game/gui7/images.py")
+               ((", \"game\",") ","))
+             #t))
+         (add-before 'build 'start-xserver
+           (lambda* (#:key inputs native-inputs #:allow-other-keys)
+             (let ((Xvfb (search-input-file (or native-inputs inputs)
+                                            "/bin/Xvfb")))
+               (setenv "HOME" (getcwd))
+               (system (format #f "~a :1 &" Xvfb))
+               (setenv "DISPLAY" ":1")
+               #t)))
+         (replace 'build
+           (lambda _
+             (invoke "python" "renpy.py" "launcher" "quit")
+             (invoke "python" "renpy.py" "the_question" "quit")
+             (invoke "python" "renpy.py" "tutorial" "quit")
+             #t))
+         (replace 'install
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             ;; Here we install our custom renpy program.
+             ;; After finishing this step, "out" will have the following:
+             ;; |-- bin/renpy
+             ;; `-- share/renpy ; i.e. path_to_renpy_base()
+             ;;     |-- common
+             ;;     `-- gui
+             ;;
+             ;; Note that common shares the source files that would be installed
+             ;; by python2-renpy (which are instead deleted from that package),
+             ;; but also contains their byte-compiled versions.
+             ;; On other systems, renpy_base would point to site-packages or
+             ;; even somewhere in /opt.
+             ;; The former approach is not as straightforward as it seems
+             ;; -- it causes renpy to load files twice for some weird reason --
+             ;; and the latter is impossible on Guix. Hence the detour through
+             ;; share/renpy and the custom renpy program.
+             ;;
+             ;; As a convention, other games should be installed as
+             ;; subdirectories of share/renpy in their respective outputs as
+             ;; well. This differs from the traditional layout, which is
+             ;; roughly the following:
+             ;; `-- Super Awesome Game
+             ;;     |-- game       ; <- the folder we actually want
+             ;;     |-- lib        ; compiled renpy module and dependencies
+             ;;     |-- renpy      ; yet another copy of Ren'py's code
+             ;;     |   |-- common ; the common folder from above
+             ;;     |   `-- ...    ; Python code (source + compiled)
+             ;;     |-- Super Awesome Game.py
+             ;;     `-- Super Awesome Game.sh
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin/renpy (string-append out "/bin/renpy")))
+               (copy-recursively "renpy/common"
+                                 (string-append out "/share/renpy/common"))
+               (copy-recursively "gui"
+                                 (string-append out "/share/renpy/gui"))
+
+               (mkdir-p (string-append out "/bin"))
+               (copy-file (assoc-ref inputs "renpy.in") bin/renpy)
+               (substitute* bin/renpy
+                 (("@PYTHON@") (search-input-file inputs "bin/python3"))
+                 (("@RENPY_BASE@") (string-append out "/share/renpy")))
+               (chmod bin/renpy #o755))))
+
+         (add-after 'install 'install-games
+           (lambda* (#:key outputs #:allow-other-keys)
+             (define renpy (assoc-ref outputs "out"))
+             ;; TODO: We should offer a renpy-build-system to make the
+             ;; installation of Ren'py games easier.
+             (define* (install-renpy-game #:key output game name (renpy renpy)
+                                          #:allow-other-keys)
+               (let* ((name (or name (basename game)))
+                      (launcher (string-append output "/bin/renpy-" name))
+                      (share (string-append output "/share/renpy/" name)))
+                 (copy-recursively (string-append game "/game") share)
+                 (mkdir-p (string-append output "/bin"))
+                 (with-output-to-file launcher
+                   (lambda ()
+                     (format #t
+                             "#!~a~%~a ~a \"$@\""
+                             (which "bash")
+                             (string-append renpy "/bin/renpy")
+                             share)))
+                 (chmod launcher #o755)))
+
+             (install-renpy-game #:output (assoc-ref outputs "out")
+                                 #:game "launcher")
+
+             (install-renpy-game #:output (assoc-ref outputs "the-question")
+                                 #:game "the_question"
+                                 #:name "the-question")
+
+             (install-renpy-game #:output (assoc-ref outputs "tutorial")
+                                 #:game "tutorial")
+             #t))
+         (replace 'wrap
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out"))
+                   (site (string-append "/lib/python"
+                                        (python-version
+                                         (assoc-ref inputs "python"))
+                                        "/site-packages")))
+               (wrap-program (string-append out "/bin/renpy")
+                 `("GUIX_PYTHONPATH" =
+                   (,@(delete-duplicates
+                       (map
+                        (lambda (store-path)
+                          (string-append store-path site))
+                        (cons (assoc-ref outputs "out")
+                              (map cdr
+                                   (filter
+                                    (lambda (input)
+                                      (string-prefix? "python" (car input)))
+                                    inputs))))))))
+               #t))))))
+    (inputs
+     `(("renpy.in" ,(search-auxiliary-file "renpy/renpy.in"))
+       ("python-renpy" ,python-renpy)
+       ("python-tkinter" ,python "tk")
+       ("python" ,python) ; for ‘fix-commands’ and ‘wrap’
+       ("xdg-utils" ,xdg-utils)))
+    (propagated-inputs '())
+    (native-inputs
+     (list xorg-server-for-tests))
+    (outputs
+     (list "out" "tutorial" "the-question"))
+    (home-page "https://www.renpy.org/")
+    (synopsis "Visual Novel Engine")
+    (description "Ren'Py is a visual novel engine that helps you use words,
+images, and sounds to tell interactive stories that run on computers and
+mobile devices.  These can be both visual novels and life simulation games.
+The easy to learn script language allows anyone to efficiently write large
+visual novels, while its Python scripting is enough for complex simulation
+games.")
+    (license license:expat)))
+
 (define-public python-pyxel
   (package
     (name "python-pyxel")
-- 
2.36.1

[bug#55424] [PATCH v2 1/6] gnu: Add back the distinction between python-renpy and renpy.

[Liliana Marie Prikler]

This partially reverts commit 9f1bd63fb5b6916f07d454ffde27cd3a66c95bb5.
Note, that with this patch renpy fails to build due to incompatibilities with
Python 3.

* gnu/packages/game-development.scm (renpy): Split into ‘python-renpy’ for the
python modules and ‘renpy’ for the games and binaries.
---
Hi Maxim (and others reading),

I squashed in some of your suggestions towards later packages, that seem
to be no-brainer modernizations into this patch.  In particular, it now
uses search-input-file rather than which and already has bash-minimal.

Cheers

 gnu/packages/game-development.scm | 167 +++++++++++++++++++++++++++++-
 1 file changed, 165 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index 4c1b97f041..099268d58c 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -1257,9 +1257,9 @@ (define-public python-pygame-sdl2
 developed mainly for Ren'py.")
       (license (list license:lgpl2.1 license:zlib)))))
 
-(define-public renpy
+(define-public python-renpy
   (package
-    (name "renpy")
+    (name "python-renpy")
     (version "7.4.11")
     (source
      (origin
@@ -1342,6 +1342,169 @@ (define-public renpy
 are only used to bootstrap it.")
     (license license:expat)))
 
+(define-public renpy
+  (package
+    (inherit python-renpy)
+    (name "renpy")
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f ; see python-renpy
+       #:modules ((srfi srfi-1)
+                  (guix build python-build-system)
+                  (guix build utils))
+       #:imported-modules ((srfi srfi-1) ,@%python-build-system-modules)
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-commands
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (substitute* "launcher/game/choose_directory.rpy"
+               (("/usr/bin/python")
+                (search-input-file inputs "/bin/python3")))
+             (substitute* "launcher/game/front_page.rpy"
+               (("xdg-open")
+                (search-input-file inputs "/bin/xdg-open")))
+             (substitute* "launcher/game/project.rpy"
+               (("cmd = \\[ executable, \"-EO\", sys.argv\\[0\\] \\]")
+                (string-append "cmd = [ \"" (assoc-ref outputs "out")
+                               "/bin/renpy\" ]"))
+               ;; Projects are still created in the usual style, so we need
+               ;; to adjust the path.
+               (("cmd.append\\(self.path\\)")
+                "cmd.append(self.path + \"/game\")"))))
+         (add-after 'unpack 'drop-game-from-paths
+           (lambda _
+             (substitute* (list "launcher/game/gui7.rpy"
+                                "launcher/game/gui7/images.py")
+               ((", \"game\",") ","))
+             #t))
+         (add-before 'build 'start-xserver
+           (lambda* (#:key inputs native-inputs #:allow-other-keys)
+             (let ((Xvfb (search-input-file (or native-inputs inputs)
+                                            "/bin/Xvfb")))
+               (setenv "HOME" (getcwd))
+               (system (format #f "~a :1 &" Xvfb))
+               (setenv "DISPLAY" ":1"))))
+         (replace 'build
+           (lambda _
+             (invoke "python" "renpy.py" "launcher" "quit")
+             (invoke "python" "renpy.py" "the_question" "quit")
+             (invoke "python" "renpy.py" "tutorial" "quit")))
+         (replace 'install
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             ;; Here we install our custom renpy program.
+             ;; After finishing this step, "out" will have the following:
+             ;; |-- bin/renpy
+             ;; `-- share/renpy ; i.e. path_to_renpy_base()
+             ;;     |-- common
+             ;;     `-- gui
+             ;;
+             ;; Note that common shares the source files that would be installed
+             ;; by python-renpy (which are instead deleted from that package),
+             ;; but also contains their byte-compiled versions.
+             ;; On other systems, renpy_base would point to site-packages or
+             ;; even somewhere in /opt.
+             ;; The former approach is not as straightforward as it seems
+             ;; -- it causes renpy to load files twice for some weird reason --
+             ;; and the latter is impossible on Guix. Hence the detour through
+             ;; share/renpy and the custom renpy program.
+             ;;
+             ;; As a convention, other games should be installed as
+             ;; subdirectories of share/renpy in their respective outputs as
+             ;; well. This differs from the traditional layout, which is
+             ;; roughly the following:
+             ;; `-- Super Awesome Game
+             ;;     |-- game       ; <- the folder we actually want
+             ;;     |-- lib        ; compiled renpy module and dependencies
+             ;;     |-- renpy      ; yet another copy of Ren'py's code
+             ;;     |   |-- common ; the common folder from above
+             ;;     |   `-- ...    ; Python code (source + compiled)
+             ;;     |-- Super Awesome Game.py
+             ;;     `-- Super Awesome Game.sh
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin/renpy (string-append out "/bin/renpy")))
+               (copy-recursively "renpy/common"
+                                 (string-append out "/share/renpy/common"))
+               (copy-recursively "gui"
+                                 (string-append out "/share/renpy/gui"))
+
+               (mkdir-p (string-append out "/bin"))
+               (copy-file (assoc-ref inputs "renpy.in") bin/renpy)
+               (substitute* bin/renpy
+                 (("@PYTHON@") (search-input-file inputs "bin/python3"))
+                 (("@RENPY_BASE@") (string-append out "/share/renpy")))
+               (chmod bin/renpy #o755))))
+
+         (add-after 'install 'install-games
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (define renpy (assoc-ref outputs "out"))
+             ;; TODO: We should offer a renpy-build-system to make the
+             ;; installation of Ren'py games easier.
+             (define* (install-renpy-game #:key output game name (renpy renpy)
+                                          #:allow-other-keys)
+               (let* ((name (or name (basename game)))
+                      (launcher (string-append output "/bin/renpy-" name))
+                      (share (string-append output "/share/renpy/" name)))
+                 (copy-recursively (string-append game "/game") share)
+                 (mkdir-p (string-append output "/bin"))
+                 (with-output-to-file launcher
+                   (lambda ()
+                     (format #t
+                             "#!~a~%~a ~a \"$@\""
+                             (search-input-file inputs "/bin/bash")
+                             (string-append renpy "/bin/renpy")
+                             share)))
+                 (chmod launcher #o755)))
+
+             (install-renpy-game #:output (assoc-ref outputs "out")
+                                 #:game "launcher")
+
+             (install-renpy-game #:output (assoc-ref outputs "the-question")
+                                 #:game "the_question"
+                                 #:name "the-question")
+
+             (install-renpy-game #:output (assoc-ref outputs "tutorial")
+                                 #:game "tutorial")))
+         (replace 'wrap
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out"))
+                   (site (string-append "/lib/python"
+                                        (python-version
+                                         (assoc-ref inputs "python"))
+                                        "/site-packages")))
+               (wrap-program (string-append out "/bin/renpy")
+                 `("GUIX_PYTHONPATH" =
+                   (,@(delete-duplicates
+                       (map
+                        (lambda (store-path)
+                          (string-append store-path site))
+                        (cons (assoc-ref outputs "out")
+                              (map cdr
+                                   (filter
+                                    (lambda (input)
+                                      (string-prefix? "python" (car input)))
+                                    inputs))))))))))))))
+    (inputs
+     `(("bash-minimal" ,bash-minimal)
+       ("renpy.in" ,(search-auxiliary-file "renpy/renpy.in"))
+       ("python-renpy" ,python-renpy)
+       ("python:tk" ,python "tk")
+       ("python" ,python) ; for ‘fix-commands’ and ‘wrap’
+       ("xdg-utils" ,xdg-utils)))
+    (propagated-inputs '())
+    (native-inputs
+     (list xorg-server-for-tests))
+    (outputs
+     (list "out" "tutorial" "the-question"))
+    (home-page "https://www.renpy.org/")
+    (synopsis "Visual Novel Engine")
+    (description "Ren'Py is a visual novel engine that helps you use words,
+images, and sounds to tell interactive stories that run on computers and
+mobile devices.  These can be both visual novels and life simulation games.
+The easy to learn script language allows anyone to efficiently write large
+visual novels, while its Python scripting is enough for complex simulation
+games.")
+    (license license:expat)))
+
 (define-public python-pyxel
   (package
     (name "python-pyxel")
-- 
2.36.1

[bug#55424] [PATCH 2/4] gnu: Add python-pefile.

[Liliana Marie Prikler]

* gnu/packages/python-xyz.scm (python-pefile): New variable.
---
 gnu/packages/python-xyz.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 4b8e63890f..198340cc82 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -17898,6 +17898,28 @@ (define-public python-pyelftools
      Record Format (DWARF).")
     (license license:public-domain)))
 
+(define-public python-pefile
+  (package
+    (name "python-pefile")
+    (version "2022.5.30")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/erocarrera/pefile")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1qj90a0s2gd5hn2zggypqc1077inid5dcl1fp5973b04kf2b9z8a"))))
+    (build-system python-build-system)
+    (propagated-inputs (list python-future))
+    (home-page "https://github.com/erocarrera/pefile")
+    (synopsis "Portable Executable (PE) file parser")
+    (description "This python library provides interfaces for parsing and
+working with Portable Executable (PE) files.  It makes to most information
+from the header, as well as section details and data available.")
+    (license license:expat)))
+
 (define-public python-pyev
   (package
     (name "python-pyev")
-- 
2.36.1

[bug#55424] [PATCH v2 2/6] gnu: Add python-pefile.

[Liliana Marie Prikler]

* gnu/packages/python-xyz.scm (python-pefile): New variable.
---
 gnu/packages/python-xyz.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 4b8e63890f..198340cc82 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -17898,6 +17898,28 @@ (define-public python-pyelftools
      Record Format (DWARF).")
     (license license:public-domain)))
 
+(define-public python-pefile
+  (package
+    (name "python-pefile")
+    (version "2022.5.30")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/erocarrera/pefile")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1qj90a0s2gd5hn2zggypqc1077inid5dcl1fp5973b04kf2b9z8a"))))
+    (build-system python-build-system)
+    (propagated-inputs (list python-future))
+    (home-page "https://github.com/erocarrera/pefile")
+    (synopsis "Portable Executable (PE) file parser")
+    (description "This python library provides interfaces for parsing and
+working with Portable Executable (PE) files.  It makes to most information
+from the header, as well as section details and data available.")
+    (license license:expat)))
+
 (define-public python-pyev
   (package
     (name "python-pyev")
-- 
2.36.1

[bug#55424] [PATCH 3/4] gnu: python-pygame-sdl2: Update to 2.1.0-0-1705c6e.

[Liliana Marie Prikler]

* gnu/packages/game-development.scm (python-pygame-sdl2): Update to
2.1.0-0-1705c6e.
---
 gnu/packages/game-development.scm | 24 ++++++++++--------------
 1 file changed, 10 insertions(+), 14 deletions(-)

diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index 44f8ca57fc..ea83450995 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -1207,26 +1207,22 @@ (define-public python-pygame
                    license:lgpl2.1+))))
 
 (define-public python-pygame-sdl2
+  ;; Using nightly from 2022-06-16.
+  ;; Revert back to URLs once renpy 8 is released!
   (let ((real-version "2.1.0")
-        (renpy-version "7.4.11"))
+        ;;(renpy-version "8.0.0")
+        (commit "1705c6e3004dcb1daf859560bcd52eb093e97d45"))
     (package
       (inherit python-pygame)
       (name "python-pygame-sdl2")
-      (version (string-append real-version "-for-renpy-" renpy-version))
+      (version (git-version real-version "0" commit))
       (source
        (origin
-         (method url-fetch)
-         (uri (string-append "https://www.renpy.org/dl/" renpy-version
-                             "/pygame_sdl2-" version ".tar.gz"))
-         (sha256 (base32 "0nxvca16299jx6sp0ys29rqixcs21ymhqwjfkbchhss0yar7qjgz"))
-         (modules '((guix build utils)))
-         (snippet
-          '(begin
-             ;; drop generated sources
-             (delete-file-recursively "gen")
-             (delete-file-recursively "gen3")
-             (delete-file-recursively "gen-static")
-             #t))))
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/renpy/pygame_sdl2")
+               (commit commit)))
+         (sha256 (base32 "1g0arhpd59zypspk36sgajf1kzavppfkv766vifvxar60968rrjn"))))
       (build-system python-build-system)
       (arguments
        `(#:tests? #f                ; tests require pygame to be installed first
-- 
2.36.1

[bug#55424] [PATCH v2 3/6] gnu: python-pygame-sdl2: Update to 2.1.0-0-1705c6e.

[Liliana Marie Prikler]

* gnu/packages/game-development.scm (python-pygame-sdl2): Update to
2.1.0-0-1705c6e.
---
Hi Maxim (and others reading),

the comment for this one was actually wrong and I adjusted it.
Hopefully it's clearer now why I don't go with "for-renpy-8" in the version.
As for why I can't pick up the correct commit for the nightly build... well,
renpy has it that all of the nightlies reference the renpy commit hash,
including pygame-sdl2.

Cheers

 gnu/packages/game-development.scm | 26 ++++++++++++--------------
 1 file changed, 12 insertions(+), 14 deletions(-)

diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index 099268d58c..f69088324a 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -1207,26 +1207,24 @@ (define-public python-pygame
                    license:lgpl2.1+))))
 
 (define-public python-pygame-sdl2
+  ;; Using latest git commit as of 2022-06-17, because there is no tagged
+  ;; release for renpy 8.
+  ;; Revert back to URLs once renpy 8 is released!
   (let ((real-version "2.1.0")
-        (renpy-version "7.4.11"))
+        ;;(renpy-version "8.0.0")
+        (commit "1705c6e3004dcb1daf859560bcd52eb093e97d45"))
     (package
       (inherit python-pygame)
       (name "python-pygame-sdl2")
-      (version (string-append real-version "-for-renpy-" renpy-version))
+      (version (git-version real-version "0" commit))
       (source
        (origin
-         (method url-fetch)
-         (uri (string-append "https://www.renpy.org/dl/" renpy-version
-                             "/pygame_sdl2-" version ".tar.gz"))
-         (sha256 (base32 "0nxvca16299jx6sp0ys29rqixcs21ymhqwjfkbchhss0yar7qjgz"))
-         (modules '((guix build utils)))
-         (snippet
-          '(begin
-             ;; drop generated sources
-             (delete-file-recursively "gen")
-             (delete-file-recursively "gen3")
-             (delete-file-recursively "gen-static")
-             #t))))
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/renpy/pygame_sdl2")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256 (base32 "1g0arhpd59zypspk36sgajf1kzavppfkv766vifvxar60968rrjn"))))
       (build-system python-build-system)
       (arguments
        `(#:tests? #f                ; tests require pygame to be installed first
-- 
2.36.1

[bug#55424] [PATCH 4/4] gnu: renpy: Update to 7.99.99-0-3e854bc.

[Liliana Marie Prikler]

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
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* gnu/packages/aux-files/renpy/renpy.in (__renpy_files, path_to_gamedir):
New procedures.
* gnu/packages/game-development.scm (python-renpy): Update to
7.99.99-0-3e854bc.
(renpy): Likewise.
[inputs]: Add python-pefile, python-requests and python-six.
---
 gnu/packages/aux-files/renpy/renpy.in | 21 +++++++++++++++++++--
 gnu/packages/game-development.scm     | 19 ++++++++++++++-----
 2 files changed, 33 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/aux-files/renpy/renpy.in b/gnu/packages/aux-files/renpy/renpy.in
index 914a735fa4..9115d9aee3 100644
--- a/gnu/packages/aux-files/renpy/renpy.in
+++ b/gnu/packages/aux-files/renpy/renpy.in
@@ -1,12 +1,29 @@
 #! @PYTHON@
 # -*- mode: python -*-
 
-from __future__ import print_function
-
+import glob
 import os
 import sys
 import warnings
 
+def __renpy_files(directory):
+    for pattern in ['*.rpa', '*.rpyc', '*.rpy']:
+        for file in glob.iglob(pattern, root_dir=directory):
+            yield file
+
+def path_to_gamedir(basedir, name):
+    candidates = [name, 'game', 'data', 'launcher/game']
+
+    if __renpy_files(basedir):
+        return basedir
+
+    for candidate in candidates:
+        gamedir = os.path.join(basedir, candidate)
+        if __renpy_files(gamedir):
+            return gamedir
+
+    return basedir
+
 def path_to_common(renpy_base):
     return renpy_base + "/common"
 
diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index ea83450995..e688cd390c 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -94,6 +94,7 @@ (define-module (gnu packages game-development)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages readline)
   #:use-module (gnu packages qt)
@@ -1253,16 +1254,21 @@ (define-public python-pygame-sdl2
 developed mainly for Ren'py.")
       (license (list license:lgpl2.1 license:zlib)))))
 
+;; Using nightly from 2022-06-16.
+;; Revert back to URLs once renpy 8 is released!
+(define %renpy-commit "3e854bc7cb1642ca18b061a0c6e349f168965c43")
 (define-public python-renpy
   (package
     (name "python-renpy")
-    (version "7.4.11")
+    (version (git-version "7.99.99" "0" %renpy-commit))
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://www.renpy.org/dl/" version
-                           "/renpy-" version "-source.tar.bz2"))
-       (sha256 (base32 "0zkhg2sd2hglm9dkansf4h8sq7lm7iqslzl763ambp4kyfdvd07q"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/renpy/renpy")
+             (commit %renpy-commit)))
+       (file-name (git-file-name name version))
+       (sha256 (base32 "11g7hqhw4gbkx5ib2wsawrznmjbn8r9zkgf2sg39z56h96y8wfbn"))
        (modules '((guix build utils)))
        (patches
         (search-patches
@@ -1486,8 +1492,11 @@ (define* (install-renpy-game #:key output game name (renpy renpy)
                #t))))))
     (inputs
      `(("renpy.in" ,(search-auxiliary-file "renpy/renpy.in"))
+       ("python-pefile" ,python-pefile)
+       ("python-requests" ,python-requests)
        ("python-renpy" ,python-renpy)
        ("python-tkinter" ,python "tk")
+       ("python-six" ,python-six)
        ("python" ,python) ; for ‘fix-commands’ and ‘wrap’
        ("xdg-utils" ,xdg-utils)))
     (propagated-inputs '())
-- 
2.36.1

[bug#55424] [PATCH v2 4/6] gnu: renpy: Update to 7.99.99-0-3e854bc.

[Liliana Marie Prikler]

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #1: Type: text/plain, Size: 4032 bytes --]

* gnu/packages/aux-files/renpy/renpy.in (__renpy_files, path_to_gamedir):
New procedures.
* gnu/packages/game-development.scm (python-renpy): Update to
7.99.99-0-3e854bc.
(renpy): Likewise.
[inputs]: Add python-pefile, python-requests and python-six.
---
Hi Maxim,

regarding the revision field, I don't plan on doing too many nightlies, given
that I went two weeks without trying to invoke the renpy binary.  For the future
reviewer who has to read through all of this again when version 8 hits, I think
not indenting the package description makes more sense (particularly as I
anticipate possible changes in the phases due to renpy build weirdness).

The other suggestions should be applied (sans G-Expressions which are in the
next patch).

Cheers

 gnu/packages/aux-files/renpy/renpy.in | 21 +++++++++++++++++++--
 gnu/packages/game-development.scm     | 19 ++++++++++++++-----
 2 files changed, 33 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/aux-files/renpy/renpy.in b/gnu/packages/aux-files/renpy/renpy.in
index 914a735fa4..9115d9aee3 100644
--- a/gnu/packages/aux-files/renpy/renpy.in
+++ b/gnu/packages/aux-files/renpy/renpy.in
@@ -1,12 +1,29 @@
 #! @PYTHON@
 # -*- mode: python -*-
 
-from __future__ import print_function
-
+import glob
 import os
 import sys
 import warnings
 
+def __renpy_files(directory):
+    for pattern in ['*.rpa', '*.rpyc', '*.rpy']:
+        for file in glob.iglob(pattern, root_dir=directory):
+            yield file
+
+def path_to_gamedir(basedir, name):
+    candidates = [name, 'game', 'data', 'launcher/game']
+
+    if __renpy_files(basedir):
+        return basedir
+
+    for candidate in candidates:
+        gamedir = os.path.join(basedir, candidate)
+        if __renpy_files(gamedir):
+            return gamedir
+
+    return basedir
+
 def path_to_common(renpy_base):
     return renpy_base + "/common"
 
diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index f69088324a..4377654f8f 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -94,6 +94,7 @@ (define-module (gnu packages game-development)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages readline)
   #:use-module (gnu packages qt)
@@ -1255,16 +1256,21 @@ (define-public python-pygame-sdl2
 developed mainly for Ren'py.")
       (license (list license:lgpl2.1 license:zlib)))))
 
+;; Using nightly from 2022-06-16.
+;; Revert back to URLs once renpy 8 is released!
+(define %renpy-commit "3e854bc7cb1642ca18b061a0c6e349f168965c43")
 (define-public python-renpy
   (package
     (name "python-renpy")
-    (version "7.4.11")
+    (version (git-version "7.99.99" "0" %renpy-commit))
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://www.renpy.org/dl/" version
-                           "/renpy-" version "-source.tar.bz2"))
-       (sha256 (base32 "0zkhg2sd2hglm9dkansf4h8sq7lm7iqslzl763ambp4kyfdvd07q"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/renpy/renpy")
+             (commit %renpy-commit)))
+       (file-name (git-file-name name version))
+       (sha256 (base32 "11g7hqhw4gbkx5ib2wsawrznmjbn8r9zkgf2sg39z56h96y8wfbn"))
        (modules '((guix build utils)))
        (patches
         (search-patches
@@ -1484,8 +1490,11 @@ (define* (install-renpy-game #:key output game name (renpy renpy)
     (inputs
      `(("bash-minimal" ,bash-minimal)
        ("renpy.in" ,(search-auxiliary-file "renpy/renpy.in"))
+       ("python-pefile" ,python-pefile)
+       ("python-requests" ,python-requests)
        ("python-renpy" ,python-renpy)
        ("python:tk" ,python "tk")
+       ("python-six" ,python-six)
        ("python" ,python) ; for ‘fix-commands’ and ‘wrap’
        ("xdg-utils" ,xdg-utils)))
     (propagated-inputs '())
-- 
2.36.1

[bug#55424] [PATCH 1/4] gnu: Add back the distinction between python-renpy and renpy.

[Maxim Cournoyer]

Hello Liliana,

Thanks for doing this!

Liliana Marie Prikler <liliana.prikler@gmail.com> writes:

> This partially reverts commit 9f1bd63fb5b6916f07d454ffde27cd3a66c95bb5.
> Note, that with this patch renpy fails to build due to incompatibilities with
> Python 3.
>
> * gnu/packages/game-development.scm (renpy): Split into ‘python-renpy’ for the
> python modules and ‘renpy’ for the games and binaries.
> ---
>  gnu/packages/game-development.scm | 171 +++++++++++++++++++++++++++++-
>  1 file changed, 169 insertions(+), 2 deletions(-)
>
> diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
> index 4c1b97f041..44f8ca57fc 100644
> --- a/gnu/packages/game-development.scm
> +++ b/gnu/packages/game-development.scm
> @@ -1257,9 +1257,9 @@ (define-public python-pygame-sdl2
>  developed mainly for Ren'py.")
>        (license (list license:lgpl2.1 license:zlib)))))
>  
> -(define-public renpy
> +(define-public python-renpy
>    (package
> -    (name "renpy")
> +    (name "python-renpy")
>      (version "7.4.11")
>      (source
>       (origin
> @@ -1342,6 +1342,173 @@ (define-public renpy
>  are only used to bootstrap it.")
>      (license license:expat)))
>  
> +(define-public renpy
> +  (package
> +    (inherit python-renpy)
> +    (name "renpy")
> +    (build-system python-build-system)
> +    (arguments
> +     `(#:tests? #f ; see python2-renpy

The comment should mention 'python-renpy' instead, right?  Also, the
arguments could use gexps...

> +       #:modules ((srfi srfi-1)
> +                  (guix build python-build-system)
> +                  (guix build utils))
> +       #:imported-modules ((srfi srfi-1) ,@%python-build-system-modules)
> +       #:phases
> +       (modify-phases %standard-phases
> +         (add-after 'unpack 'fix-commands
> +           (lambda* (#:key inputs outputs #:allow-other-keys)
> +             (substitute* "launcher/game/choose_directory.rpy"
> +               (("/usr/bin/python")
> +                (search-input-file inputs "/bin/python3")))
> +             (substitute* "launcher/game/front_page.rpy"
> +               (("xdg-open")
> +                (search-input-file inputs "/bin/xdg-open")))
> +             (substitute* "launcher/game/project.rpy"
> +               (("cmd = \\[ executable, \"-EO\", sys.argv\\[0\\] \\]")
> +                (string-append "cmd = [ \"" (assoc-ref outputs "out")
> +                               "/bin/renpy\" ]"))
> +               ;; Projects are still created in the usual style, so we need
> +               ;; to adjust the path.
> +               (("cmd.append\\(self.path\\)")
> +                "cmd.append(self.path + \"/game\")"))
> +             #t))

And the trailing #t can be removed.

> +         (add-after 'unpack 'drop-game-from-paths
> +           (lambda _
> +             (substitute* (list "launcher/game/gui7.rpy"
> +                                "launcher/game/gui7/images.py")
> +               ((", \"game\",") ","))
> +             #t))
> +         (add-before 'build 'start-xserver
> +           (lambda* (#:key inputs native-inputs #:allow-other-keys)
> +             (let ((Xvfb (search-input-file (or native-inputs inputs)
> +                                            "/bin/Xvfb")))
> +               (setenv "HOME" (getcwd))
> +               (system (format #f "~a :1 &" Xvfb))
> +               (setenv "DISPLAY" ":1")
> +               #t)))
> +         (replace 'build
> +           (lambda _
> +             (invoke "python" "renpy.py" "launcher" "quit")
> +             (invoke "python" "renpy.py" "the_question" "quit")
> +             (invoke "python" "renpy.py" "tutorial" "quit")
> +             #t))
> +         (replace 'install
> +           (lambda* (#:key inputs outputs #:allow-other-keys)
> +             ;; Here we install our custom renpy program.
> +             ;; After finishing this step, "out" will have the following:
> +             ;; |-- bin/renpy
> +             ;; `-- share/renpy ; i.e. path_to_renpy_base()
> +             ;;     |-- common
> +             ;;     `-- gui
> +             ;;
> +             ;; Note that common shares the source files that would be installed
> +             ;; by python2-renpy (which are instead deleted from that package),
> +             ;; but also contains their byte-compiled versions.
> +             ;; On other systems, renpy_base would point to site-packages or
> +             ;; even somewhere in /opt.
> +             ;; The former approach is not as straightforward as it seems
> +             ;; -- it causes renpy to load files twice for some weird reason --
> +             ;; and the latter is impossible on Guix. Hence the detour through
> +             ;; share/renpy and the custom renpy program.
> +             ;;
> +             ;; As a convention, other games should be installed as
> +             ;; subdirectories of share/renpy in their respective outputs as
> +             ;; well. This differs from the traditional layout, which is
> +             ;; roughly the following:
> +             ;; `-- Super Awesome Game
> +             ;;     |-- game       ; <- the folder we actually want
> +             ;;     |-- lib        ; compiled renpy module and dependencies
> +             ;;     |-- renpy      ; yet another copy of Ren'py's code
> +             ;;     |   |-- common ; the common folder from above
> +             ;;     |   `-- ...    ; Python code (source + compiled)
> +             ;;     |-- Super Awesome Game.py
> +             ;;     `-- Super Awesome Game.sh
> +             (let* ((out (assoc-ref outputs "out"))
> +                    (bin/renpy (string-append out "/bin/renpy")))
> +               (copy-recursively "renpy/common"
> +                                 (string-append out "/share/renpy/common"))
> +               (copy-recursively "gui"
> +                                 (string-append out "/share/renpy/gui"))
> +
> +               (mkdir-p (string-append out "/bin"))
> +               (copy-file (assoc-ref inputs "renpy.in") bin/renpy)
> +               (substitute* bin/renpy
> +                 (("@PYTHON@") (search-input-file inputs "bin/python3"))
> +                 (("@RENPY_BASE@") (string-append out "/share/renpy")))
> +               (chmod bin/renpy #o755))))
> +
> +         (add-after 'install 'install-games
> +           (lambda* (#:key outputs #:allow-other-keys)
> +             (define renpy (assoc-ref outputs "out"))
> +             ;; TODO: We should offer a renpy-build-system to make the
> +             ;; installation of Ren'py games easier.
> +             (define* (install-renpy-game #:key output game name (renpy renpy)
> +                                          #:allow-other-keys)
> +               (let* ((name (or name (basename game)))
> +                      (launcher (string-append output "/bin/renpy-" name))
> +                      (share (string-append output "/share/renpy/" name)))
> +                 (copy-recursively (string-append game "/game") share)
> +                 (mkdir-p (string-append output "/bin"))
> +                 (with-output-to-file launcher
> +                   (lambda ()
> +                     (format #t
> +                             "#!~a~%~a ~a \"$@\""
> +                             (which "bash")
> +                             (string-append renpy "/bin/renpy")
> +                             share)))
> +                 (chmod launcher #o755)))
> +
> +             (install-renpy-game #:output (assoc-ref outputs "out")
> +                                 #:game "launcher")
> +
> +             (install-renpy-game #:output (assoc-ref outputs "the-question")
> +                                 #:game "the_question"
> +                                 #:name "the-question")
> +
> +             (install-renpy-game #:output (assoc-ref outputs "tutorial")
> +                                 #:game "tutorial")
> +             #t))
> +         (replace 'wrap
> +           (lambda* (#:key inputs outputs #:allow-other-keys)
> +             (let ((out (assoc-ref outputs "out"))
> +                   (site (string-append "/lib/python"
> +                                        (python-version
> +                                         (assoc-ref inputs "python"))
> +                                        "/site-packages")))
> +               (wrap-program (string-append out "/bin/renpy")
> +                 `("GUIX_PYTHONPATH" =
> +                   (,@(delete-duplicates
> +                       (map
> +                        (lambda (store-path)
> +                          (string-append store-path site))
> +                        (cons (assoc-ref outputs "out")
> +                              (map cdr
> +                                   (filter
> +                                    (lambda (input)
> +                                      (string-prefix? "python" (car input)))
> +                                    inputs))))))))
> +               #t))))))
> +    (inputs
> +     `(("renpy.in" ,(search-auxiliary-file "renpy/renpy.in"))
> +       ("python-renpy" ,python-renpy)
> +       ("python-tkinter" ,python "tk")
> +       ("python" ,python) ; for ‘fix-commands’ and ‘wrap’
> +       ("xdg-utils" ,xdg-utils)))
> +    (propagated-inputs '())
> +    (native-inputs
> +     (list xorg-server-for-tests))
> +    (outputs
> +     (list "out" "tutorial" "the-question"))

Can we use new style inputs here?

Otherwise it LGTM.

[bug#55424] [PATCH 1/4] gnu: Add back the distinction between python-renpy and renpy.

[Liliana Marie Prikler]

Hi,

Am Freitag, dem 17.06.2022 um 09:14 -0400 schrieb Maxim Cournoyer:
> Liliana Marie Prikler <liliana.prikler@gmail.com> writes:
> 
> > [...]
> > +    (arguments
> > +     `(#:tests? #f ; see python2-renpy
> 
> The comment should mention 'python-renpy' instead, right?  Also, the
> arguments could use gexps...
Thanks for catching the typo.  I don't think the conversion to G-
Expressions should be in this patch, but I can follow up with a
modernization.

> And the trailing #t can be removed.
Sure.

> > [...]
> > +    (inputs
> > +     `(("renpy.in" ,(search-auxiliary-file "renpy/renpy.in"))
> > +       ("python-renpy" ,python-renpy)
> > +       ("python-tkinter" ,python "tk")
> > +       ("python" ,python) ; for ‘fix-commands’ and ‘wrap’
> > +       ("xdg-utils" ,xdg-utils)))
> 
> Can we use new style inputs here?
Not without G-Expressions, and only if I'm allowed to inline the aux-
file into the build via #$.

Cheers  

[bug#55424] [PATCH 3/4] gnu: python-pygame-sdl2: Update to 2.1.0-0-1705c6e.

[Maxim Cournoyer]

Hi again,

Liliana Marie Prikler <liliana.prikler@gmail.com> writes:

> * gnu/packages/game-development.scm (python-pygame-sdl2): Update to
> 2.1.0-0-1705c6e.
> ---
>  gnu/packages/game-development.scm | 24 ++++++++++--------------
>  1 file changed, 10 insertions(+), 14 deletions(-)
>
> diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
> index 44f8ca57fc..ea83450995 100644
> --- a/gnu/packages/game-development.scm
> +++ b/gnu/packages/game-development.scm
> @@ -1207,26 +1207,22 @@ (define-public python-pygame
>                     license:lgpl2.1+))))
>  
>  (define-public python-pygame-sdl2
> +  ;; Using nightly from 2022-06-16.
> +  ;; Revert back to URLs once renpy 8 is released!
>    (let ((real-version "2.1.0")
> -        (renpy-version "7.4.11"))
> +        ;;(renpy-version "8.0.0")
> +        (commit "1705c6e3004dcb1daf859560bcd52eb093e97d45"))
>      (package
>        (inherit python-pygame)
>        (name "python-pygame-sdl2")
> -      (version (string-append real-version "-for-renpy-" renpy-version))
> +      (version (git-version real-version "0" commit))
>        (source
>         (origin
> -         (method url-fetch)
> -         (uri (string-append "https://www.renpy.org/dl/" renpy-version
> -                             "/pygame_sdl2-" version ".tar.gz"))
> -         (sha256 (base32 "0nxvca16299jx6sp0ys29rqixcs21ymhqwjfkbchhss0yar7qjgz"))
> -         (modules '((guix build utils)))
> -         (snippet
> -          '(begin
> -             ;; drop generated sources
> -             (delete-file-recursively "gen")
> -             (delete-file-recursively "gen3")
> -             (delete-file-recursively "gen-static")
> -             #t))))
> +         (method git-fetch)
> +         (uri (git-reference
> +               (url "https://github.com/renpy/pygame_sdl2")
> +               (commit commit)))
> +         (sha256 (base32
>  "1g0arhpd59zypspk36sgajf1kzavppfkv766vifvxar60968rrjn"))))

You'll wan to keep the (file-name ...) argument, otherwise 'guix lint'
complains about it:

gnu/packages/game-development.scm:1220:7: python-pygame-sdl2@2.1.0-0.1705c6e: the source file name should contain the package name
gnu/packages/game-development.scm:1215:4: python-pygame-sdl2@2.1.0-0.1705c6e: can be upgraded to 7.4.9.2112

Perhaps the version should still read '2.1.0-for-renpy-7.9.9' to match the
pseudo-version used for renpy.

Otherwise, LGTM!

Thanks,

Maxim

[bug#55424] [PATCH 4/4] gnu: renpy: Update to 7.99.99-0-3e854bc.

[Maxim Cournoyer]

Hi,

Liliana Marie Prikler <liliana.prikler@gmail.com> writes:

[...]

> +;; Using nightly from 2022-06-16.
> +;; Revert back to URLs once renpy 8 is released!
> +(define %renpy-commit "3e854bc7cb1642ca18b061a0c6e349f168965c43")
>  (define-public python-renpy
>    (package
>      (name "python-renpy")
> -    (version "7.4.11")
> +    (version (git-version "7.99.99" "0" %renpy-commit))

I think it might be easy to overlook the "revision" field, since the
more common convention is to define the "revision" and "commit"
variables in a let; but perhaps that's just me.

>      (source
>       (origin
> -       (method url-fetch)
> -       (uri (string-append "https://www.renpy.org/dl/" version
> -                           "/renpy-" version "-source.tar.bz2"))
> -       (sha256 (base32 "0zkhg2sd2hglm9dkansf4h8sq7lm7iqslzl763ambp4kyfdvd07q"))
> +       (method git-fetch)
> +       (uri (git-reference
> +             (url "https://github.com/renpy/renpy")
> +             (commit %renpy-commit)))
> +       (file-name (git-file-name name version))
> +       (sha256 (base32 "11g7hqhw4gbkx5ib2wsawrznmjbn8r9zkgf2sg39z56h96y8wfbn"))
>         (modules '((guix build utils)))
>         (patches
>          (search-patches
> @@ -1486,8 +1492,11 @@ (define* (install-renpy-game #:key output game name (renpy renpy)
>                 #t))))))
>      (inputs
>       `(("renpy.in" ,(search-auxiliary-file "renpy/renpy.in"))
> +       ("python-pefile" ,python-pefile)
> +       ("python-requests" ,python-requests)
>         ("python-renpy" ,python-renpy)
>         ("python-tkinter" ,python "tk")
> +       ("python-six" ,python-six)
>         ("python" ,python) ; for ‘fix-commands’ and ‘wrap’
>         ("xdg-utils" ,xdg-utils)))
>      (propagated-inputs '())

It'd be nicer to use new style inputs here, that'd take care of one out
of 2 lint warnings:

--8<---------------cut here---------------start------------->8---
gnu/packages/game-development.scm:1494:5: renpy@7.99.99-0.3e854bc: label 'python-tkinter' does not match package name 'python:tk'
gnu/packages/game-development.scm:1348:2: renpy@7.99.99-0.3e854bc: "bash-minimal" should be in 'inputs' when 'wrap-program' is used
--8<---------------cut here---------------end--------------->8---

Please take care of the 2nd lint suggestion as well.

Other than that, it LGTM.  I've built and linted all the packages in
this series.  Feel free to push with adjustments along my comments.

Thanks again for picking that up.

Maxim

[bug#55424] [PATCH v2 5/6] gnu: renpy: Use new style.

[Liliana Marie Prikler]

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #1: Type: text/plain, Size: 16429 bytes --]

* gnu/packages/game-development.scm (renpy)[arguments]: Change to list of
G-Expressions.
[inputs]: Drop labels.
[native-inputs, outputs]: Squash to single line.
---
 gnu/packages/game-development.scm | 293 +++++++++++++++---------------
 1 file changed, 146 insertions(+), 147 deletions(-)

diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm
index 4377654f8f..04f2b061fc 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -48,6 +48,7 @@ (define-module (gnu packages game-development)
   #:use-module (ice-9 match)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
+  #:use-module (guix gexp)
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix svn-download)
@@ -1352,156 +1353,154 @@ (define-public renpy
     (name "renpy")
     (build-system python-build-system)
     (arguments
-     `(#:tests? #f ; see python-renpy
-       #:modules ((srfi srfi-1)
+     (list
+      #:tests? #f ; see python-renpy
+      #:modules '((srfi srfi-1)
                   (guix build python-build-system)
                   (guix build utils))
-       #:imported-modules ((srfi srfi-1) ,@%python-build-system-modules)
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-commands
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (substitute* "launcher/game/choose_directory.rpy"
-               (("/usr/bin/python")
-                (search-input-file inputs "/bin/python3")))
-             (substitute* "launcher/game/front_page.rpy"
-               (("xdg-open")
-                (search-input-file inputs "/bin/xdg-open")))
-             (substitute* "launcher/game/project.rpy"
-               (("cmd = \\[ executable, \"-EO\", sys.argv\\[0\\] \\]")
-                (string-append "cmd = [ \"" (assoc-ref outputs "out")
-                               "/bin/renpy\" ]"))
-               ;; Projects are still created in the usual style, so we need
-               ;; to adjust the path.
-               (("cmd.append\\(self.path\\)")
-                "cmd.append(self.path + \"/game\")"))))
-         (add-after 'unpack 'drop-game-from-paths
-           (lambda _
-             (substitute* (list "launcher/game/gui7.rpy"
-                                "launcher/game/gui7/images.py")
-               ((", \"game\",") ","))
-             #t))
-         (add-before 'build 'start-xserver
-           (lambda* (#:key inputs native-inputs #:allow-other-keys)
-             (let ((Xvfb (search-input-file (or native-inputs inputs)
-                                            "/bin/Xvfb")))
-               (setenv "HOME" (getcwd))
-               (system (format #f "~a :1 &" Xvfb))
-               (setenv "DISPLAY" ":1"))))
-         (replace 'build
-           (lambda _
-             (invoke "python" "renpy.py" "launcher" "quit")
-             (invoke "python" "renpy.py" "the_question" "quit")
-             (invoke "python" "renpy.py" "tutorial" "quit")))
-         (replace 'install
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             ;; Here we install our custom renpy program.
-             ;; After finishing this step, "out" will have the following:
-             ;; |-- bin/renpy
-             ;; `-- share/renpy ; i.e. path_to_renpy_base()
-             ;;     |-- common
-             ;;     `-- gui
-             ;;
-             ;; Note that common shares the source files that would be installed
-             ;; by python-renpy (which are instead deleted from that package),
-             ;; but also contains their byte-compiled versions.
-             ;; On other systems, renpy_base would point to site-packages or
-             ;; even somewhere in /opt.
-             ;; The former approach is not as straightforward as it seems
-             ;; -- it causes renpy to load files twice for some weird reason --
-             ;; and the latter is impossible on Guix. Hence the detour through
-             ;; share/renpy and the custom renpy program.
-             ;;
-             ;; As a convention, other games should be installed as
-             ;; subdirectories of share/renpy in their respective outputs as
-             ;; well. This differs from the traditional layout, which is
-             ;; roughly the following:
-             ;; `-- Super Awesome Game
-             ;;     |-- game       ; <- the folder we actually want
-             ;;     |-- lib        ; compiled renpy module and dependencies
-             ;;     |-- renpy      ; yet another copy of Ren'py's code
-             ;;     |   |-- common ; the common folder from above
-             ;;     |   `-- ...    ; Python code (source + compiled)
-             ;;     |-- Super Awesome Game.py
-             ;;     `-- Super Awesome Game.sh
-             (let* ((out (assoc-ref outputs "out"))
-                    (bin/renpy (string-append out "/bin/renpy")))
-               (copy-recursively "renpy/common"
-                                 (string-append out "/share/renpy/common"))
-               (copy-recursively "gui"
-                                 (string-append out "/share/renpy/gui"))
-
-               (mkdir-p (string-append out "/bin"))
-               (copy-file (assoc-ref inputs "renpy.in") bin/renpy)
-               (substitute* bin/renpy
-                 (("@PYTHON@") (search-input-file inputs "bin/python3"))
-                 (("@RENPY_BASE@") (string-append out "/share/renpy")))
-               (chmod bin/renpy #o755))))
-
-         (add-after 'install 'install-games
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (define renpy (assoc-ref outputs "out"))
-             ;; TODO: We should offer a renpy-build-system to make the
-             ;; installation of Ren'py games easier.
-             (define* (install-renpy-game #:key output game name (renpy renpy)
-                                          #:allow-other-keys)
-               (let* ((name (or name (basename game)))
-                      (launcher (string-append output "/bin/renpy-" name))
-                      (share (string-append output "/share/renpy/" name)))
-                 (copy-recursively (string-append game "/game") share)
-                 (mkdir-p (string-append output "/bin"))
-                 (with-output-to-file launcher
-                   (lambda ()
-                     (format #t
-                             "#!~a~%~a ~a \"$@\""
-                             (search-input-file inputs "/bin/bash")
-                             (string-append renpy "/bin/renpy")
-                             share)))
-                 (chmod launcher #o755)))
-
-             (install-renpy-game #:output (assoc-ref outputs "out")
-                                 #:game "launcher")
-
-             (install-renpy-game #:output (assoc-ref outputs "the-question")
-                                 #:game "the_question"
-                                 #:name "the-question")
-
-             (install-renpy-game #:output (assoc-ref outputs "tutorial")
-                                 #:game "tutorial")))
-         (replace 'wrap
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out"))
-                   (site (string-append "/lib/python"
-                                        (python-version
-                                         (assoc-ref inputs "python"))
-                                        "/site-packages")))
-               (wrap-program (string-append out "/bin/renpy")
-                 `("GUIX_PYTHONPATH" =
-                   (,@(delete-duplicates
-                       (map
-                        (lambda (store-path)
-                          (string-append store-path site))
-                        (cons (assoc-ref outputs "out")
-                              (map cdr
-                                   (filter
-                                    (lambda (input)
-                                      (string-prefix? "python" (car input)))
-                                    inputs))))))))))))))
-    (inputs
-     `(("bash-minimal" ,bash-minimal)
-       ("renpy.in" ,(search-auxiliary-file "renpy/renpy.in"))
-       ("python-pefile" ,python-pefile)
-       ("python-requests" ,python-requests)
-       ("python-renpy" ,python-renpy)
-       ("python:tk" ,python "tk")
-       ("python-six" ,python-six)
-       ("python" ,python) ; for ‘fix-commands’ and ‘wrap’
-       ("xdg-utils" ,xdg-utils)))
+      #:imported-modules `((srfi srfi-1) ,@%python-build-system-modules)
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-commands
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (substitute* "launcher/game/choose_directory.rpy"
+                (("/usr/bin/python")
+                 (search-input-file inputs "/bin/python3")))
+              (substitute* "launcher/game/front_page.rpy"
+                (("xdg-open")
+                 (search-input-file inputs "/bin/xdg-open")))
+              (substitute* "launcher/game/project.rpy"
+                (("cmd = \\[ executable, \"-EO\", sys.argv\\[0\\] \\]")
+                 (string-append "cmd = [ \"" (assoc-ref outputs "out")
+                                "/bin/renpy\" ]"))
+                ;; Projects are still created in the usual style, so we need
+                ;; to adjust the path.
+                (("cmd.append\\(self.path\\)")
+                 "cmd.append(self.path + \"/game\")"))))
+          (add-after 'unpack 'drop-game-from-paths
+            (lambda _
+              (substitute* (list "launcher/game/gui7.rpy"
+                                 "launcher/game/gui7/images.py")
+                ((", \"game\",") ","))
+              #t))
+          (add-before 'build 'start-xserver
+            (lambda* (#:key inputs native-inputs #:allow-other-keys)
+              (let ((Xvfb (search-input-file (or native-inputs inputs)
+                                             "/bin/Xvfb")))
+                (setenv "HOME" (getcwd))
+                (system (format #f "~a :1 &" Xvfb))
+                (setenv "DISPLAY" ":1"))))
+          (replace 'build
+            (lambda _
+              (invoke "python" "renpy.py" "launcher" "quit")
+              (invoke "python" "renpy.py" "the_question" "quit")
+              (invoke "python" "renpy.py" "tutorial" "quit")))
+          (replace 'install
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              ;; Here we install our custom renpy program.
+              ;; After finishing this step, "out" will have the following:
+              ;; |-- bin/renpy
+              ;; `-- share/renpy ; i.e. path_to_renpy_base()
+              ;;     |-- common
+              ;;     `-- gui
+              ;;
+              ;; Note that common shares the source files that would be installed
+              ;; by python2-renpy (which are instead deleted from that package),
+              ;; but also contains their byte-compiled versions.
+              ;; On other systems, renpy_base would point to site-packages or
+              ;; even somewhere in /opt.
+              ;; The former approach is not as straightforward as it seems
+              ;; -- it causes renpy to load files twice for some weird reason --
+              ;; and the latter is impossible on Guix. Hence the detour through
+              ;; share/renpy and the custom renpy program.
+              ;;
+              ;; As a convention, other games should be installed as
+              ;; subdirectories of share/renpy in their respective outputs as
+              ;; well. This differs from the traditional layout, which is
+              ;; roughly the following:
+              ;; `-- Super Awesome Game
+              ;;     |-- game       ; <- the folder we actually want
+              ;;     |-- lib        ; compiled renpy module and dependencies
+              ;;     |-- renpy      ; yet another copy of Ren'py's code
+              ;;     |   |-- common ; the common folder from above
+              ;;     |   `-- ...    ; Python code (source + compiled)
+              ;;     |-- Super Awesome Game.py
+              ;;     `-- Super Awesome Game.sh
+              (let* ((out (assoc-ref outputs "out"))
+                     (bin/renpy (string-append out "/bin/renpy")))
+                (copy-recursively "renpy/common"
+                                  (string-append out "/share/renpy/common"))
+                (copy-recursively "gui"
+                                  (string-append out "/share/renpy/gui"))
+
+                (mkdir-p (string-append out "/bin"))
+                (copy-file #$(local-file (search-auxiliary-file "renpy/renpy.in"))
+                           bin/renpy)
+                (substitute* bin/renpy
+                  (("@PYTHON@") (search-input-file inputs "bin/python3"))
+                  (("@RENPY_BASE@") (string-append out "/share/renpy")))
+                (chmod bin/renpy #o755))))
+
+          (add-after 'install 'install-games
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (define renpy (assoc-ref outputs "out"))
+              ;; TODO: We should offer a renpy-build-system to make the
+              ;; installation of Ren'py games easier.
+              (define* (install-renpy-game #:key output game name (renpy renpy)
+                                           #:allow-other-keys)
+                (let* ((name (or name (basename game)))
+                       (launcher (string-append output "/bin/renpy-" name))
+                       (share (string-append output "/share/renpy/" name)))
+                  (copy-recursively (string-append game "/game") share)
+                  (mkdir-p (string-append output "/bin"))
+                  (with-output-to-file launcher
+                    (lambda ()
+                      (format #t
+                              "#!~a~%~a ~a \"$@\""
+                              (search-input-file inputs "/bin/bash")
+                              (string-append renpy "/bin/renpy")
+                              share)))
+                  (chmod launcher #o755)))
+
+              (install-renpy-game #:output (assoc-ref outputs "out")
+                                  #:game "launcher")
+
+              (install-renpy-game #:output (assoc-ref outputs "the-question")
+                                  #:game "the_question"
+                                  #:name "the-question")
+
+              (install-renpy-game #:output (assoc-ref outputs "tutorial")
+                                  #:game "tutorial")))
+          (replace 'wrap
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (let ((out (assoc-ref outputs "out"))
+                    (site (string-append "/lib/python"
+                                         (python-version
+                                          (assoc-ref inputs "python"))
+                                         "/site-packages")))
+                (wrap-program (string-append out "/bin/renpy")
+                  `("GUIX_PYTHONPATH" =
+                    (,@(delete-duplicates
+                        (map
+                         (lambda (store-path)
+                           (string-append store-path site))
+                         (cons (assoc-ref outputs "out")
+                               (map cdr
+                                    (filter
+                                     (lambda (input)
+                                       (string-prefix? "python" (car input)))
+                                     inputs))))))))))))))
+    (inputs (list bash-minimal
+                  python
+                  python-pefile
+                  python-requests
+                  python-renpy
+                  python-six
+                  `(,python "tk")
+                  xdg-utils))
     (propagated-inputs '())
-    (native-inputs
-     (list xorg-server-for-tests))
-    (outputs
-     (list "out" "tutorial" "the-question"))
+    (native-inputs (list xorg-server-for-tests))
+    (outputs (list "out" "tutorial" "the-question"))
     (home-page "https://www.renpy.org/")
     (synopsis "Visual Novel Engine")
     (description "Ren'Py is a visual novel engine that helps you use words,
-- 
2.36.1

[bug#55424] [PATCH v2 6/6] guix: Modernize renpy-build-system.

[Liliana Marie Prikler]

* guix/build-system/renpy.scm (build): Drop trailing #t.
(install, install-desktop-file): Likewise.  Also add inputs and use
search-input-file for /bin/sh and /bin/renpy.
---
 guix/build/renpy-build-system.scm | 19 ++++++++-----------
 1 file changed, 8 insertions(+), 11 deletions(-)

diff --git a/guix/build/renpy-build-system.scm b/guix/build/renpy-build-system.scm
index e4a88456be..7c15d52f19 100644
--- a/guix/build/renpy-build-system.scm
+++ b/guix/build/renpy-build-system.scm
@@ -37,10 +37,9 @@ (define* (build #:key game #:allow-other-keys)
           game
           ;; should be "compile", but renpy wants to compile itself really
           ;; badly if we do
-          "quit")
-  #t)
+          "quit"))
 
-(define* (install #:key outputs game (output "out") #:allow-other-keys)
+(define* (install #:key inputs outputs game (output "out") #:allow-other-keys)
   (let* ((out (assoc-ref outputs output))
          (json-dump (call-with-input-file (string-append game
                                                          "/renpy-build.json")
@@ -58,13 +57,12 @@ (define* (install #:key outputs game (output "out") #:allow-other-keys)
       (call-with-output-file launcher
         (lambda (port)
           (format port "#!~a~%~a ~s \"$@\""
-                  (which "bash")
-                  (which "renpy")
+                  (search-input-file inputs "/bin/sh")
+                  (search-input-file inputs "/bin/renpy")
                   data)))
-      (chmod launcher #o755)))
-  #t)
+      (chmod launcher #o755))))
 
-(define* (install-desktop-file #:key outputs game (output "out")
+(define* (install-desktop-file #:key inputs outputs game (output "out")
                                #:allow-other-keys)
   (let* ((out (assoc-ref outputs output))
          (json-dump (call-with-input-file (string-append game
@@ -78,10 +76,9 @@ (define* (install-desktop-file #:key outputs game (output "out")
      #:name (assoc-ref json-dump "name")
      #:generic-name (assoc-ref build "display_name")
      #:exec (format #f "~a ~s"
-                    (which "renpy")
+                    (search-input-file inputs "/bin/renpy")
                     (string-append out "/share/renpy/" directory-name))
-     #:categories '("Game" "Visual Novel")))
-  #t)
+     #:categories '("Game" "Visual Novel"))))
 
 (define %standard-phases
   (modify-phases gnu:%standard-phases
-- 
2.36.1

[bug#55424] [PATCH v2 5/6] gnu: renpy: Use new style.

[Maxim Cournoyer]

Hi Liliana,

I haven't tried building it again, but your v2 patches LGTM.

Thanks again!

Maxim