[bug#58490] gnu: Add python-mdurl, python-markdown-it-py, python-mdit-py-plugins, python-sphinx-gallery-0.7.0 and python-jupytext.

[bug#58490] gnu: Add python-mdurl, python-markdown-it-py, python-mdit-py-plugins, python-sphinx-gallery-0.7.0 and python-jupytext.

[MadalinIonel.Patrascu]

[-- Attachment #1: Type: text/plain, Size: 2 bytes --]



[-- Attachment #2: Type: text/html, Size: 377 bytes --]

[bug#58490] [PATCH 1/5] gnu: Add python-mdurl. X-Debbugs-Cc: rekado@elephly.net

[Mădălin Ionel Patrașcu]

* gnu/packages/python-xyz.scm (python-mdurl): New variable.
---
 gnu/packages/python-xyz.scm | 38 ++++++++++++++++++++++++++++++++++++-
 1 file changed, 37 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 8575d4a67e..b95d598c07 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -66,7 +66,7 @@
 ;;; Copyright © 2019, 2020, 2021 Giacomo Leidi <goodoldpaul@autistici.org>
 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
 ;;; Copyright © 2019, 2020, 2021, 2022 Tanguy Le Carrour <tanguy@bioneland.org>
-;;; Copyright © 2019, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2019, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2020 Riku Viitanen <riku.viitanen@protonmail.com>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;; Copyright © 2020 sirgazil <sirgazil@zoho.com>
@@ -625,6 +625,42 @@ (define-public python-lunr
 that best match text queries.")
     (license license:expat)))
 
+(define-public python-mdurl
+  (package
+    (name "python-mdurl")
+    (version "0.1.2")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "mdurl" version))
+              (sha256
+               (base32
+                "1fn1hy35h9grggwqax90zcb52inlfxrxsm27vlqqz8zfyllkshdv"))))
+    (build-system python-build-system)
+    (arguments
+     (list
+      #:tests? #f ;pypi source does not contains tests
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'build
+            (lambda _
+              (invoke "flit" "build")))
+           (replace 'install
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (add-installed-pythonpath inputs outputs)
+               (for-each
+                 (lambda (wheel)
+                   (format #t wheel)
+                   (invoke "python" "-m" "pip" "install"
+                            wheel (string-append "--prefix=" #$output)))
+                 (find-files "dist" "\\.whl$")))))))
+    (native-inputs (list python-flit))
+    (home-page "https://github.com/executablebooks/mdurl")
+    (synopsis "Markdown URL utilities")
+    (description
+      "This package implements a @code{Python} port of the @code{JavaScript}
+@code{mdurl}.")
+    (license license:expat)))
+
 (define-public python-mrkd
   (package
     (name "python-mrkd")

base-commit: 9ed65e6af77893b658a7159b091b5002892c2f95
-- 
2.37.3

[bug#58490] [PATCH 2/5] gnu: Add python-markdown-it-py. X-Debbugs-Cc: rekado@elephly.net

[Mădălin Ionel Patrașcu]

* gnu/packages/python-xyz.scm (python-markdown-it-py): 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 b95d598c07..33b6c62346 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4017,6 +4017,47 @@ (define-public python-virtualenv
      "Virtualenv is a tool to create isolated Python environments.")
     (license license:expat)))
 
+(define-public python-markdown-it-py
+  (package
+    (name "python-markdown-it-py")
+    (version "2.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "markdown-it-py" version))
+              (sha256
+               (base32
+                "1nh75i72584r70alhqc479gys04s5m5g3vq601yf2njbs7z5jzng"))))
+    (build-system python-build-system)
+    (arguments
+     (list
+      #:tests? #f ;;pypi source does not contains tests
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'build
+           (lambda _
+             (invoke "flit" "build")))
+          (replace 'install
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (add-installed-pythonpath inputs outputs)
+              (for-each
+                (lambda (wheel)
+                  (format #t wheel)
+                   (invoke "python" "-m" "pip" "install"
+                           wheel (string-append "--prefix=" #$output)))
+                (find-files "dist" "\\.whl$")))))))
+    (native-inputs (list python-flit))
+    (propagated-inputs
+      (list python-mdurl
+            python-typing-extensions))
+    (home-page "https://github.com/executablebooks/markdown-it-py")
+    (synopsis "Python port of markdown-it")
+    (description
+     "This is a @code{Python} port of the well used @code{markdown-it}, and some
+of its associated plugins.  The driving design philosophy of the port has been
+to change as little of the fundamental code structure (file names, function name,
+etc) as possible.")
+    (license license:expat)))
+
 (define-public python-markupsafe
   (package
     (name "python-markupsafe")
-- 
2.37.3

[bug#58490] [PATCH 3/5] gnu: Add python-mdit-py-plugins. X-Debbugs-Cc: rekado@elephly.net

[Mădălin Ionel Patrașcu]

* gnu/packages/python-xyz.scm (python-mdit-py-plugins): New variable.
---
 gnu/packages/python-xyz.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 33b6c62346..6c111bcb82 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -625,6 +625,33 @@ (define-public python-lunr
 that best match text queries.")
     (license license:expat)))
 
+(define-public python-mdit-py-plugins
+  (package
+    (name "python-mdit-py-plugins")
+    (version "0.3.0")
+    (source
+      (origin
+       (method url-fetch)
+       (uri (pypi-uri "mdit-py-plugins" version))
+       (sha256
+         (base32
+           "0l4pwsn2q30j160zjg79qa8v2brc4zl295rgrkpbfspcxr8lzhpc"))))
+    (build-system python-build-system)
+    (propagated-inputs (list python-markdown-it-py))
+    (native-inputs
+      (list python-coverage
+            python-pytest
+            python-pytest-cov
+            python-pytest-regressions))
+    (home-page "https://github.com/executablebooks/mdit-py-plugins")
+    (synopsis "Collection of plugins for markdown-it-py")
+    (description
+     "This package contains a collection of plugins for @code{markdown-it-py}
+like: @code{amsmath}, @code{attrs}, @code{container}, @code{definition list},
+@code{dollarmath}, @code{field list}, @code{footnote}, @code{textmath},
+@code{wordcount}.")
+    (license license:expat)))
+
 (define-public python-mdurl
   (package
     (name "python-mdurl")
-- 
2.37.3

[bug#58490] [PATCH 4/5] gnu: Add python-sphinx-gallery-0.7.0. X-Debbugs-Cc: rekado@elephly.net

[Mădălin Ionel Patrașcu]

* gnu/packages/sphinx.scm (python-sphinx-gallery-0.7.0): New variable.
---
 gnu/packages/sphinx.scm | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index 2d53b7f3ac..fddeeb96c6 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -18,6 +18,7 @@
 ;;; Copyright © 2021, 2022 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2021 Hugo Lecomte <hugo.lecomte@inria.fr>
 ;;; Copyright © 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -549,6 +550,23 @@ (define-public python-sphinx-gallery
 from any set of Python scripts and puts it into an examples gallery.")
     (license license:bsd-3)))
 
+(define-public python-sphinx-gallery-0.7.0
+  (package (inherit python-sphinx-gallery)
+    (version "0.7.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "sphinx-gallery" version))
+              (sha256
+               (base32
+                "10255yyj7104ad6cibkmrwfpfgkl5675jfn3hd0sn63pjhndgsh5"))))
+  (build-system python-build-system)
+  (arguments `())
+  (native-inputs
+    (list python-pytest
+          python-numpy))
+  (propagated-inputs (list python-sphinx))))
+
+
 (define-public python-sphinx-me
   (package
     (name "python-sphinx-me")
-- 
2.37.3

[bug#58490] [PATCH 5/5] gnu: Add python-jupytext. X-Debbugs-Cc: rekado@elephly.net

[Mădălin Ionel Patrașcu]

* gnu/packages/python-xyz.scm (python-jupytext): New variable.
---
 gnu/packages/python-xyz.scm | 77 +++++++++++++++++++++++++++++++++++++
 1 file changed, 77 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 6c111bcb82..51753e279a 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -319,6 +319,83 @@ (define-public python-janus
 design}.")
     (license license:asl2.0)))
 
+(define-public python-jupytext
+  (package
+    (name "python-jupytext")
+    (version "1.14.1")
+    (source
+      (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/mwouts/jupytext")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0gqpvphrp2ja9ggadx0rrk0sqbpz6kqqg62qqmw4k17469lphc8c"))))
+    (build-system python-build-system)
+    (arguments
+     (list
+       #:phases
+       #~(modify-phases %standard-phases
+           (add-after 'unpack 'relax-requirements
+             (lambda _
+               (substitute* "tests/utils.py"
+                 ;; is required isort > 5.3.0 but the authors made a confusion
+                 ;; between string comparations and version parsing comparasion
+                 (("or isort_version\\(\\) <= \"5\\.3\\.0\"")
+                   "")
+                 (("\"python_kernel\"")
+                   "\"python3\""))))
+           (replace 'check
+             (lambda* (#:key tests? inputs outputs #:allow-other-keys)
+               ;; some tests fails when HOME=/homeless-shelter.
+               (setenv "HOME" "/tmp")
+               ;; OSError: [Errno 18] Invalid cross-device link
+               (setenv "TMPDIR" "/tmp")
+               (add-installed-pythonpath inputs outputs)
+               (when tests?
+                 (let ((disabled-tests
+                         (list "test_create_header_with_set_formats"
+                               "test_pre_commit_hook"
+                               "test_sync_with_pre_commit_hook")))
+                      (invoke "pytest" "-vv" "-k"
+                              (string-append "not "
+                                             (string-join disabled-tests
+                                                " and not "))))))))))
+    (native-inputs
+      (list git
+            python-autopep8
+            python-black
+            python-flake8
+            python-gitpython
+            python-isort
+            python-ipython-genutils
+            python-jupyter-server
+            python-pre-commit
+            python-pytest
+            python-pyaml
+            python-sphinx-gallery-0.7.0))
+    (propagated-inputs
+      (list python-markdown-it-py
+            python-mdit-py-plugins
+            python-nbformat))
+    (home-page "https://github.com/mwouts/jupytext")
+    (synopsis
+     "Jupyter notebooks as Markdown documents, Julia, Python or R scripts")
+    (description
+     "@code{Jupytext} is a plugin for @code{Jupyter} that can save @code{Jupyter
+notebooks} as either @code{Markdown} files or scripts in many languages.  Common
+use cases for @code{Jupytext} are:
+@itemize
+@item
+version control on Jupyter Notebooks
+@item
+editing, merging or refactoring notebooks in your favorite text editor
+@item
+applying Q&A checks on notebooks.
+@end itemize")
+    (license license:expat)))
+
 (define-public python-logzero
   (package
     (name "python-logzero")
-- 
2.37.3

bug#58490: Add python-jupytext.

[Ricardo Wurmus]

Hi,

I applied these patches with a number of changes.

- removed @code{} syntax around proper names
- removed unnecessary build phase
- fixed indentation
- used single semicolon for line comments
- did not apply patch for python-sphinx-gallery-0.7.0 because it’s not
  needed
- use git-minimal

Thanks for the patches!

-- 
Ricardo