[bug#50481] [PATCH 0/3] Update python-rdflib.

[bug#50481] [PATCH 0/3] Update python-rdflib.

[Arun Isaac]

Hi,

This patchset adds python-berkeleydb and updates python-rdflib to the latest
version. python-rdflib no longer supports python2. So, I have also removed the
python2-rdflib package.

Regards,
Arun

Arun Isaac (3):
  gnu: Add python-berkeleydb.
  gnu: python-rdflib: Update to 6.0.0.
  gnu: python2-rdflib: Remove package.

 gnu/packages/python-xyz.scm | 41 +++++++++++++++++++++++++++
 gnu/packages/rdf.scm        | 56 ++++++++++++++++++++++---------------
 2 files changed, 74 insertions(+), 23 deletions(-)

-- 
2.33.0

[bug#50481] [PATCH 1/3] gnu: Add python-berkeleydb.

[Arun Isaac]

* gnu/packages/python-xyz.scm (python-berkeleydb): New variable.
---
 gnu/packages/python-xyz.scm | 41 +++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 7c70829de9..a7020b7615 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -26556,3 +26556,44 @@ files and directories and adds a datestamp in standard ISO 8601+ format
 YYYY-MM-DD at the beginning of the file or directory name.")
       (home-page "https://github.com/novoid/date2name")
       (license license:gpl3+))))
+
+(define-public python-berkeleydb
+  (package
+    (name "python-berkeleydb")
+    (version "18.1.4")
+    (source
+     (origin
+       ;; We use the upstream repository, as the tests are not included in the
+       ;; PyPI releases.
+       (method hg-fetch)
+       (uri (hg-reference
+             (url "https://hg.jcea.es/pybsddb/")
+             (changeset version)))
+       (file-name (string-append name "-" version "-checkout"))
+       (sha256
+        (base32
+         "0xj0l73ns6xph5pmysna7g4rdla1alvh2s2k2crhwv8yghjmnjqi"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'unpack 'suppress-license-warning
+           (lambda* (#:key inputs #:allow-other-keys)
+             (setenv "BERKELEYDB_DIR" (assoc-ref inputs "bdb"))
+             (setenv "YES_I_HAVE_THE_RIGHT_TO_USE_THIS_BERKELEY_DB_VERSION" "1")))
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (invoke "./test.py" "-v")))))))
+    (inputs
+     `(("bdb" ,bdb)))
+    (home-page "https://www.jcea.es/programacion/pybsddb.htm")
+    (synopsis "Python bindings for Oracle Berkeley DB")
+    (description "This package provides a nearly complete wrapping of the
+Oracle/Sleepycat C API for the Database Environment, Database, Cursor, Log
+Cursor, Sequence and Transaction objects, and each of these is exposed as a
+Python type in the berkeleydb.db module.  The database objects can use various
+access methods: btree, hash, recno, queue and heap.  Oracle Berkeley DB
+distributed transactions, Oracle Berkeley DB Replication Manager and Oracle
+Berkeley DB Base Replication are supported.")
+    (license license:bsd-3)))
-- 
2.33.0

[bug#50481] [PATCH 2/3] gnu: python-rdflib: Update to 6.0.0.

[Arun Isaac]

* gnu/packages/rdf.scm (python-rdflib): Update to 6.0.0.
[arguments]: Replace check phase. Enable tests.
[native-inputs]: Add python-black, python-coverage,
python-doctest-ignore-unicode, python-flake8, python-networkx and
python-nose-timer.
[propagated-inputs]: Add python-berkeleydb.
---
 gnu/packages/rdf.scm | 53 +++++++++++++++++++++++++++-----------------
 1 file changed, 33 insertions(+), 20 deletions(-)

diff --git a/gnu/packages/rdf.scm b/gnu/packages/rdf.scm
index fb84d8053d..d09c28402a 100644
--- a/gnu/packages/rdf.scm
+++ b/gnu/packages/rdf.scm
@@ -7,6 +7,7 @@
 ;;; Copyright © 2020 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2020 pukkamustard <pukkamustard@posteo.net>
+;;; Copyright © 2021 Arun Isaac <arunisaac@systemreboot.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -337,31 +338,43 @@ ideal (e.g. in LV2 implementations or embedded applications).")
 (define-public python-rdflib
   (package
     (name "python-rdflib")
-    (version "4.2.2")
+    (version "6.0.0")
     (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "rdflib" version))
-        (sha256
-         (base32
-          "0398c714znnhaa2x7v51b269hk20iz073knq2mvmqp2ma92z27fs"))))
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "rdflib" version))
+       (sha256
+        (base32
+         "0ycqczf33irq0ai6wpg4vxd9xwlpq3c41hsy411xvx16xdbxgr3w"))))
     (build-system python-build-system)
     (arguments
-     '(;; FIXME: Three test failures. Should be fixed next release.
-       #:tests? #f))
-       ;; #:phases
-       ;; (modify-phases %standard-phases
-       ;;   (replace 'check
-       ;;     (lambda _
-       ;;       ;; Run tests from the build directory so python3 only
-       ;;       ;; sees the installed 2to3 version.
-       ;;       (invoke "nosetests" "--where=./build/src"))))))
+     '(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key outputs tests? #:allow-other-keys)
+             (when tests?
+               ;; Make installed package available for running the tests.
+               (setenv "PATH" (string-append (assoc-ref outputs "out")
+                                             "/bin:" (getenv "PATH")))
+               (invoke "nosetests"
+                       ;; Exclude tests that require network access.
+                       "--exclude" "^test_sparql_service$"
+                       "--exclude" "^testGuessFormatForParse$"
+                       "--exclude" "^test_onedotone$"
+                       "--exclude" "^rdflib$")))))))
     (native-inputs
-     `(("python-nose" ,python-nose)))
+     `(("python-black" ,python-black)
+       ("python-coverage" ,python-coverage)
+       ("python-doctest-ignore-unicode" ,python-doctest-ignore-unicode)
+       ("python-flake8" ,python-flake8)
+       ("python-networkx" ,python-networkx)
+       ("python-nose" ,python-nose)
+       ("python-nose-timer" ,python-nose-timer)))
     (propagated-inputs
-      `(("python-html5lib" ,python-html5lib)
-        ("python-isodate" ,python-isodate)
-        ("python-pyparsing" ,python-pyparsing)))
+     `(("python-berkeleydb" ,python-berkeleydb)
+       ("python-html5lib" ,python-html5lib)
+       ("python-isodate" ,python-isodate)
+       ("python-pyparsing" ,python-pyparsing)))
     (home-page "https://github.com/RDFLib/rdflib")
     (synopsis "Python RDF library")
     (description
-- 
2.33.0

[bug#50481] [PATCH 3/3] gnu: python2-rdflib: Remove package.

[Arun Isaac]

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

diff --git a/gnu/packages/rdf.scm b/gnu/packages/rdf.scm
index d09c28402a..95b4ec72be 100644
--- a/gnu/packages/rdf.scm
+++ b/gnu/packages/rdf.scm
@@ -383,9 +383,6 @@ powerful language for representing information.")
     (license (license:non-copyleft "file://LICENSE"
                                    "See LICENSE in the distribution."))))
 
-(define-public python2-rdflib
-  (package-with-python2 python-rdflib))
-
 (define-public python-rdflib-jsonld
   (package
     (name "python-rdflib-jsonld")
-- 
2.33.0

[bug#50481] [PATCH 0/3] Update python-rdflib.

[Ludovic Courtès]

Hi,

Arun Isaac <arunisaac@systemreboot.net> skribis:

>   gnu: Add python-berkeleydb.
>   gnu: python-rdflib: Update to 6.0.0.
>   gnu: python2-rdflib: Remove package.

As long as dependents still build (which I haven’t tested), LGTM!

Thanks,
Ludo’.

[bug#50481] [PATCH 0/3] Update python-rdflib.

[Arun Isaac]

[-- Attachment #1: Type: text/plain, Size: 303 bytes --]


Hi Ludo,

>>   gnu: python-rdflib: Update to 6.0.0.
>
> As long as dependents still build (which I haven’t tested), LGTM!

Thanks for the reminder! It looks like this upgrade breaks cwltool,
python-prov, python-rdflib-jsonld and python-schema-salad. I am fixing
them now.

Regards,
Arun

[-- Attachment #2: signature.asc --]
[-- Type: application/pgp-signature, Size: 524 bytes --]

bug#50481: [PATCH 0/3] Update python-rdflib.

[Arun Isaac]

[-- Attachment #1: Type: text/plain, Size: 142 bytes --]


Hi Ludo,

It looks like Marius updated python-rdflib in
2a4c271e614d069423519af4be5511a0c25156f1. So, I'm closing this issue.

Regards,
Arun

[-- Attachment #2: signature.asc --]
[-- Type: application/pgp-signature, Size: 524 bytes --]