[bug#69736] [PATCH 0/7] Add toil

[bug#69736] [PATCH 0/7] Add toil

[Arun Isaac]

This patchset adds toil.

The linter warns that there is a collision between different versions of
python-pyparsing. However, it is not possible to avoid that collision without
upgrading python-pyparsing. And, the python-pyparsing upgrade is very
complex. It requires rebuilding the world. It also introduces a dependency
cycle since the latest version of python-pyparsing switches to the
pyproject-build-system.

Arun Isaac (7):
  gnu: Add python-typing-extensions-4.10.
  gnu: Add python-pypubsub.
  gnu: Add python-addict.
  gnu: Add python-prefixed.
  gnu: Add python-enlighten.
  gnu: Add python-cwltool.
  gnu: Add python-toil.

 gnu/packages/bioinformatics.scm | 74 +++++++++++++++++++++++++++++
 gnu/packages/python-build.scm   | 13 ++++++
 gnu/packages/python-xyz.scm     | 83 +++++++++++++++++++++++++++++++++
 3 files changed, 170 insertions(+)


base-commit: 001dfb89579856b8695b33b59f484f36e313347f
-- 
2.41.0

[bug#69736] [PATCH 1/7] gnu: Add python-typing-extensions-4.10.

[Arun Isaac]

* gnu/packages/python-build.scm (python-typing-extensions-4.10): New variable.

Change-Id: I82d9538e76353b39cce082020a939e1a8fb7badc
---
 gnu/packages/python-build.scm | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/gnu/packages/python-build.scm b/gnu/packages/python-build.scm
index 2ea457cdba..adf26f7f8b 100644
--- a/gnu/packages/python-build.scm
+++ b/gnu/packages/python-build.scm
@@ -10,6 +10,7 @@
 ;;; Copyright © 2020, 2021, 2022, 2023 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2022 Garek Dyszel <garekdyszel@disroot.org>
 ;;; Copyright © 2022 Greg Hogan <code@greghogan.com>
+;;; Copyright © 2024 Arun Isaac <arunisaac@systemreboot.net>
 
 ;;;
 ;;; This file is part of GNU Guix.
@@ -252,6 +253,18 @@ (define-public python-typing-extensions
 @end enumerate\n")
     (license license:psfl)))
 
+;; TODO: Remove this package once python-typing-extensions is updated.
+(define-public python-typing-extensions-4.10
+  (package
+    (inherit python-typing-extensions)
+    (version "4.10.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "typing_extensions" version))
+              (sha256
+               (base32
+                "1jxkj4pni8pdyrn79sq441lsp40xzw363n0qvfc6zfcgkv4dgaxh"))))))
+
 \f
 ;;;
 ;;; Python builder packages.
-- 
2.41.0

[bug#69736] [PATCH 2/7] gnu: Add python-pypubsub.

[Arun Isaac]

* gnu/packages/python-xyz.scm (python-pypubsub): New variable.

Change-Id: Id8f06bd592b6273cff282aa628f05503a67519b0
---
 gnu/packages/python-xyz.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 0c72caeca0..ed9b1c9140 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7768,6 +7768,32 @@ (define-public python-blinker
 interested parties to subscribe to events, or \"signals\".")
     (license license:expat)))
 
+(define-public python-pypubsub
+  (package
+    (name "python-pypubsub")
+    (version "4.0.3")
+    ;; There is no source tarball on PyPI.
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/schollii/pypubsub")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "02j74w28wzmdvxkk8i561ywjgizjifq3hgcl080yj0rvkd3wivlb"))))
+    (build-system python-build-system)
+    (home-page "https://github.com/schollii/pypubsub")
+    (synopsis "Python publish-subscribe library")
+    (description "@code{python-pypubsub} provides a pure Python
+publish-subscribe API to facilitate event-based or message-based architecture
+in a single-process application.  It is centered on the notion of a topic;
+senders publish messages of a given topic, and listeners subscribe to messages
+of a given topic, all inside the same process.  The package also supports a
+variety of advanced features that facilitate debugging and maintaining topics
+and messages in larger desktop or server-based applications.")
+    (license license:bsd-2)))
+
 (define-public pelican
   (package
     (name "pelican")
-- 
2.41.0

[bug#69736] [PATCH 3/7] gnu: Add python-addict.

[Arun Isaac]

* gnu/packages/python-xyz.scm (python-addict): New variable.

Change-Id: I1554d17495bf9337067422f2118f8b46e51abead
---
 gnu/packages/python-xyz.scm | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index ed9b1c9140..34b894a351 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -23058,6 +23058,23 @@ (define-public python-attrdict3
 both as keys and as attributes.")
     (license license:expat)))
 
+(define-public python-addict
+  (package
+    (name "python-addict")
+    (version "2.4.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "addict" version))
+              (sha256
+               (base32
+                "1574sicy5ydx9pvva3lbx8qp56z9jbdwbj26aqgjhyh61q723cmk"))))
+    (build-system pyproject-build-system)
+    (home-page "https://github.com/mewwts/addict")
+    (synopsis "Python dictionary with attribute accessible values")
+    (description "@code{python-addict} provides dictionaries whose items can
+be get and set using both attribute and item syntax.")
+    (license license:expat)))
+
 (define-public python-attrs
   (package
     (name "python-attrs")
-- 
2.41.0

[bug#69736] [PATCH 4/7] gnu: Add python-prefixed.

[Arun Isaac]

* gnu/packages/python-xyz.scm (python-prefixed): New variable.

Change-Id: I1398953059feb740dfdd9abe12bd0aa7abe3714e
---
 gnu/packages/python-xyz.scm | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 34b894a351..87204b392f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -32516,6 +32516,24 @@ (define-public python-quicktions
 is the cythonized version of @code{fractions.Fraction}.")
     (license license:psfl)))
 
+(define-public python-prefixed
+  (package
+    (name "python-prefixed")
+    (version "0.7.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "prefixed" version))
+              (sha256
+               (base32
+                "1sdvxwy4kvcxvnq1nx70j1ccx5ga6wdb478vqd5azf1fc1gd2m0b"))))
+    (build-system pyproject-build-system)
+    (home-page "https://github.com/Rockhopper-Technologies/prefixed")
+    (synopsis "Prefixed alternative numeric library")
+    (description "@code{python-prefixed} provides an alternative
+implementation of the built-in float which supports formatted output with
+SI (decimal) and IEC (binary) prefixes.")
+    (license license:mpl2.0)))
+
 (define-public python-pathvalidate
   (package
     (name "python-pathvalidate")
-- 
2.41.0

[bug#69736] [PATCH 5/7] gnu: Add python-enlighten.

[Arun Isaac]

* gnu/packages/python-xyz.scm (python-enlighten): New variable.

Change-Id: Ifcc1e71cf012eb3b7e2c0ceef7d288cea9fa6a91
---
 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 87204b392f..755f64e361 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -17869,6 +17869,28 @@ (define-public python-progressbar33
     ;; Either or both of these licenses may be selected.
     (license (list license:lgpl2.1+ license:bsd-3))))
 
+(define-public python-enlighten
+  (package
+    (name "python-enlighten")
+    (version "1.12.4")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "enlighten" version))
+              (sha256
+               (base32
+                "0psvglhi0c7d7pdk9rfb8scnv3xbq2fz78619x2mxvz094mxkwvm"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs
+     (list python-blessed python-prefixed))
+    (home-page "https://github.com/Rockhopper-Technologies/enlighten")
+    (synopsis "Console progress bar library")
+    (description "@code{python-enlighten} is a console progress bar library
+for Python.  The main advantage of Enlighten is that it allows writing to
+stdout and stderr without any redirection or additional code---just print or
+log as you normally would.  Enlighten also includes experimental support for
+Jupyter Notebooks.")
+    (license license:mpl2.0)))
+
 (define-public python-colorama
   (package
    (name "python-colorama")
-- 
2.41.0

[bug#69736] [PATCH 6/7] gnu: Add python-cwltool.

[Arun Isaac]

* gnu/packages/bioinformatics.scm (python-cwltool): New variable.

Change-Id: Ic374d4c02b69c4e6c923d1cc17e629d4a3a6221c
---
 gnu/packages/bioinformatics.scm | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b8ecea013c..68577ded17 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5326,6 +5326,18 @@ (define-public cwltool
 CWL descriptions.")
     (license license:asl2.0)))
 
+;; python-toil tightly integrates with cwltool using it as a library. So,
+;; create a library version of cwltool where inputs become propagated inputs.
+(define-public python-cwltool
+  (package
+    (inherit cwltool)
+    (name "python-cwltool")
+    (inputs
+     (list node))
+    (propagated-inputs
+     (modify-inputs (package-inputs cwltool)
+       (delete "node")))))
+
 (define-public python-dendropy
   (package
     (name "python-dendropy")
-- 
2.41.0

[bug#69736] [PATCH 7/7] gnu: Add python-toil.

[Arun Isaac]

* gnu/packages/bioinformatics.scm (python-toil): New variable.

Change-Id: I1a6c071eaa9169c1e0cd7c74d1117490ee7bf267
---
 gnu/packages/bioinformatics.scm | 62 +++++++++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 68577ded17..aed57796cd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -87,6 +87,7 @@ (define-module (gnu packages bioinformatics)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages datastructures)
   #:use-module (gnu packages dlang)
+  #:use-module (gnu packages docker)
   #:use-module (gnu packages file)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages gawk)
@@ -5338,6 +5339,67 @@ (define-public python-cwltool
      (modify-inputs (package-inputs cwltool)
        (delete "node")))))
 
+(define-public python-toil
+  (package
+    (name "python-toil")
+    (version "6.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "toil" version))
+              (sha256
+               (base32
+                "0hwaihnncsfxw0sf3iigvgw6nylrb56lpk8qjadkgazr98dsp4ha"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'disable-optional-features
+            (lambda _
+              (substitute* "requirements-cwl.txt"
+                ;; Loosen version restrictions on ruamel.yaml.
+                (("ruamel.yaml[<>=.,[:digit:]]*\n") "ruamel.yaml\n")
+                ;; Remove optional dependency on galaxy-util and
+                ;; galaxy-tool-util. TODO: Package these and restore these
+                ;; dependencies.
+                (("galaxy-util[^\n]*") "")
+                (("galaxy-tool-util[^\n]*") ""))
+              ;; Disable optional wdl, wes and mesos features. We don't yet
+              ;; have dependencies packaged for them. TODO: Package these
+              ;; dependencies and enable these features.
+              (substitute* "setup.py"
+                (("\"wdl\",") "")
+                (("toil-cwl-runner = toil.cwl.cwltoil:main \\[cwl\\]")
+                 "toil-cwl-runner = toil.cwl.cwltoil:main")
+                (("'toil-wdl-runner = toil.wdl.wdltoil:main \\[wdl\\]',") "")
+                (("'toil-wes-cwl-runner = toil.server.cli.wes_cwl_runner:main \\[server\\]',") "")
+                (("'_toil_mesos_executor = toil.batchSystems.mesos.executor:main \\[mesos\\]',") "")))))))
+    (propagated-inputs
+     (list python-addict
+           python-cachecontrol
+           python-configargparse
+           python-cwltool
+           python-dateutil
+           python-dill
+           python-docker
+           python-enlighten
+           python-psutil
+           python-pypubsub
+           python-pytz
+           python-pyyaml
+           python-requests
+           python-ruamel.yaml
+           python-typing-extensions-4.10
+           python-urllib3))
+    (home-page "https://github.com/DataBiosphere/toil")
+    (synopsis "Scalable, efficient and cross-platform workflow engine")
+    (description "Toil is a scalable, efficient, cross-platform pipeline
+management system, written entirely in Python, and designed around the
+principles of functional programming.")
+    (license (list license:asl2.0    ;; main license
+                   license:expat)))) ;; src/toil/batchSystems/lsf.py and
+                                     ;; src/toil/batchSystems/lsfHelper.py
+
 (define-public python-dendropy
   (package
     (name "python-dendropy")
-- 
2.41.0