[bug#68456] [PATCH v4 1/6] gnu: Add python-pygments-2.16.

[bug#68456] [PATCH v4 1/6] gnu: Add python-pygments-2.16.

[Giacomo Leidi via Guix-patches via]

This patch has also been sent to the python-team branch with bug #66884.

* gnu/packages/python-xyz.scm (python-pygments-2.16): New variable.

Change-Id: I863fc1aaea9930991b6f92643befbde7ba1a335c
---
 gnu/packages/python-xyz.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 37d7dd0dd5..5f159c39d1 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -6202,6 +6202,27 @@ (define-public python-pygments
      "Pygments is a syntax highlighting package written in Python.")
     (license license:bsd-2)))
 
+(define-public python-pygments-2.16
+  (package
+    (inherit python-pygments)
+    (version "2.16.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "Pygments" version))
+       (sha256
+        (base32
+         "0abfx7n0mgpxk05f2kini3p78wsp1yi7lh0yjk49pii0914z1bqx"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      ;; Some tests require sphinx, which depends on this, so we only run
+      ;; basic tests.
+      '(list "--ignore-glob=tests/*/*")))
+    (native-inputs
+     (list python-pytest))))
+
 (define-public python-pygments-github-lexers
   (package
     (name "python-pygments-github-lexers")

base-commit: bcc9cd1aaeb53c323b199623de4fafe8594d1a95
-- 
2.41.0

[bug#68460] [PATCH v4 2/6] gnu: python-markdown-it-py: Update to 3.0.0.

[Giacomo Leidi via Guix-patches via]

* gnu/packages/python-xyz.scm (python-markdown-it-py): Update to 3.0.0;
(python-markdown-it-py-2.1): new variable.

* gnu/packages/sphinx.scm (python-myst-parser)[propagated-inputs]:
Use python-markdown-it-py-2.1.

Change-Id: I009ad2fd7cd314e2073621f2cbe00ff97cb7e63c
---
 gnu/packages/python-xyz.scm | 15 +++++++++++++--
 gnu/packages/sphinx.scm     |  2 +-
 2 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 5f159c39d1..a0ad12a29f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -5502,13 +5502,13 @@ (define-public python-makefun
 (define-public python-markdown-it-py
   (package
     (name "python-markdown-it-py")
-    (version "2.1.0")
+    (version "3.0.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "markdown-it-py" version))
               (sha256
                (base32
-                "1nh75i72584r70alhqc479gys04s5m5g3vq601yf2njbs7z5jzng"))))
+                "1swgvyiavak0nmfb31lq5zck5chwhmyf6qb6qwpcav86zaa0mxp3"))))
     (build-system pyproject-build-system)
     (arguments (list #:tests? #f))      ;pypi source does not contains tests
     (native-inputs (list python-flit))
@@ -5524,6 +5524,17 @@ (define-public python-markdown-it-py
 possible.")
     (license license:expat)))
 
+(define-public python-markdown-it-py-2.1
+  (package
+    (inherit python-markdown-it-py)
+    (version "2.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "markdown-it-py" version))
+              (sha256
+               (base32
+                "1nh75i72584r70alhqc479gys04s5m5g3vq601yf2njbs7z5jzng"))))))
+
 (define-public python-markupsafe
   (package
     (name "python-markupsafe")
diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index 7e5a929241..89196086f2 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -792,7 +792,7 @@ (define-public python-myst-parser
      (list python-docutils
            python-jinja2
            python-linkify-it-py
-           python-markdown-it-py
+           python-markdown-it-py-2.1
            python-linkify-it-py
            python-mdit-py-plugins
            python-pyyaml
-- 
2.41.0

[bug#68459] [PATCH v4 3/6] gnu: python-rich: Update to 13.7.0.

[Giacomo Leidi via Guix-patches via]

* gnu/packages/bioinformatics.scm (multiqc)[propagated-inputs]: Use
python-rich-12.4.

* gnu/packages/python-xyz.scm (python-rich): Update to 13.7.0;
[source]: switch to git-origin to have tests;
[build-system]: switch to pyproject-build-system;
[arguments]: remove it since this boilerplate is now handled by the
pyproject-build-system;
[propagated-inputs]: remove python-colorama as it's not listed on
pyproject.toml;
replace python-commonmark with python-markdown-it-py;
use python-pygments-2.16;
move python-attrs from here...;
[native-inputs]: ...to here;
drop "tests" input;
add python-pytest-cov;
[home-page]: https://github.com/willmcgugan/rich now redirects to
https://github.com/Textualize/rich ;
(python-rich-12.4): new variable;
(pelican)[propagated-inputs]: use python-pygments-2.16.

* gnu/packages/python-web.scm (httpie)[propagated-inputs]: Use
python-pygments-2.16.

Change-Id: I16ea6f27d24f84d86db659c224705c81fac3b42e
---
 gnu/packages/bioinformatics.scm |  2 +-
 gnu/packages/python-web.scm     |  2 +-
 gnu/packages/python-xyz.scm     | 64 ++++++++++++++++-----------------
 3 files changed, 33 insertions(+), 35 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f75254ed9f..60d0dc6f8f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12512,7 +12512,7 @@ (define-public multiqc
            python-numpy
            python-pyyaml
            python-requests
-           python-rich
+           python-rich-12.4
            python-rich-click
            python-simplejson
            python-spectra))
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 567b01f396..74ec405a94 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1208,7 +1208,7 @@ (define-public httpie
      '(#:tests? #f))
     (propagated-inputs
      (list python-colorama
-           python-pygments
+           python-pygments-2.16
            python-requests
            python-requests-toolbelt
            python-pysocks
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index a0ad12a29f..cef458e0fc 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7205,7 +7205,7 @@ (define-public pelican
            python-feedgenerator
            python-jinja2
            python-markdown
-           python-pygments
+           python-pygments-2.16
            python-pytz
            python-rich
            python-unidecode))
@@ -18585,49 +18585,47 @@ (define-public python-slugid
 (define-public python-rich
   (package
     (name "python-rich")
-    (version "12.4.1")
+    (version "13.7.0")
     (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "rich" version))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/Textualize/rich")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "149vjb4cpf9mz14iig0b6d8065dm8aslp6pc45g9ipmp1wf00ffj"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs tests? #:allow-other-keys)
-             (when tests?
-               (copy-recursively (string-append
-                                  (assoc-ref inputs "tests") "/tests")
-                                 "tests")
-               (invoke "python" "-m" "pytest" "-vv")))))))
+                "0qyhw2vvk17qdmfrmi45z4dd0fkwx3l2qrf3iy0yc2y7pfgrmg9g"))))
+    (build-system pyproject-build-system)
     (propagated-inputs
-     (list python-attrs python-colorama python-commonmark python-pygments
-           python-typing-extensions))
+     (list python-markdown-it-py python-pygments-2.16 python-typing-extensions))
     (native-inputs
-     `(("python-pytest" ,python-pytest)
-       ("tests"
-        ;; The release on pypi comes without tests.  We can't build from this
-        ;; checkout, though, because installation requires an invocation of
-        ;; poetry.
-        ,(origin
-           (method git-fetch)
-           (uri (git-reference
-                 (url "https://github.com/willmcgugan/rich")
-                 (commit (string-append "v" version))))
-           (file-name (git-file-name name version))
-           (sha256
-            (base32
-             "17c3gljn8zv32xnpsgd3fqgqn4r7cdfqri41hridcpbhssdgkyp9"))))))
-    (home-page "https://github.com/willmcgugan/rich")
+     (list poetry python-attr python-pytest python-pytest-cov))
+    (home-page "https://github.com/Textualize/rich")
     (synopsis "Render rich text and more to the terminal")
     (description
      "This is a Python package for rendering rich text, tables, progress bars,
 syntax highlighting, markdown and more to the terminal.")
     (license license:expat)))
 
+(define-public python-rich-12.4
+  (package
+    (inherit python-rich)
+    (version "12.4.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/Textualize/rich")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name "python-rich" version))
+              (sha256
+               (base32
+                "17c3gljn8zv32xnpsgd3fqgqn4r7cdfqri41hridcpbhssdgkyp9"))))
+    (propagated-inputs
+     (list python-colorama
+           python-commonmark
+           python-pygments
+           python-typing-extensions))))
+
 (define-public python-rich-click
   (package
     (name "python-rich-click")
-- 
2.41.0

[bug#68457] [PATCH v4 4/6] gnu: python-jupytext: Update to 1.15.2.

[Giacomo Leidi via Guix-patches via]

* gnu/packages/python-xyz.scm (python-jupytext): Update to 1.15.2;
[build-system]: switch to pyproject-build-system;
[arguments]<phases>: add setup-test-environment phase, use check phase
from build system and move test flags from here...
<test-flags>: ... to here.

Change-Id: Iaec4090823715230e26865d4639871fb7c565802
---
 gnu/packages/python-xyz.scm | 26 +++++++++++---------------
 1 file changed, 11 insertions(+), 15 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index cef458e0fc..b4b95637c7 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -336,7 +336,7 @@ (define-public python-janus
 (define-public python-jupytext
   (package
     (name "python-jupytext")
-    (version "1.14.4")
+    (version "1.15.2")
     (source
      (origin
        (method git-fetch)
@@ -345,27 +345,23 @@ (define-public python-jupytext
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "19d443vx597zzxna09qpync9iic3mris80bwm3kd8xaxaq0zq9w4"))))
-    (build-system python-build-system)
+        (base32 "0zi2b2g9b2dkzl69li5rwc17pdcxj8cxzlysd8s6jqbcc37jiwqs"))))
+    (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags
+      #~'("-k" #$(string-join (list "not test_create_header_with_set_formats"
+                                    "test_pre_commit_hook"
+                                    "test_sync_with_pre_commit_hook")
+                              " and not "))
       #:phases
       #~(modify-phases %standard-phases
-          (replace 'check
-            (lambda* (#:key tests? #:allow-other-keys)
+          (add-before 'check 'setup-test-environment
+            (lambda _
               ;; some tests fail when HOME=/homeless-shelter.
               (setenv "HOME" "/tmp")
               ;; OSError: [Errno 18] Invalid cross-device link
-              (setenv "TMPDIR" "/tmp")
-              (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 "))))))))))
+              (setenv "TMPDIR" "/tmp"))))))
     (native-inputs
      (list git-minimal
            pre-commit
-- 
2.41.0

[bug#68458] [PATCH v4 5/6] gnu: python-mdit-py-plugins: Update to 0.4.0.

[Giacomo Leidi via Guix-patches via]

* gnu/packages/python-xyz.scm (python-mdit-py-plugins): Update to 0.4.0;
(python-mdit-py-plugins-0.3): new variable.

* gnu/packages/python-xyz.scm (python-myst-parser)[propagated-inputs]:
Use python-mdit-py-plugins-0.3.

Change-Id: I06ddbee6055b570ee2d40f3e4f0a478a4413b4fe
---
 gnu/packages/python-xyz.scm | 21 +++++++++++++++++++--
 gnu/packages/sphinx.scm     |  2 +-
 2 files changed, 20 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b4b95637c7..e2013a3995 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -906,7 +906,7 @@ (define-public python-lunr
 (define-public python-mdit-py-plugins
   (package
     (name "python-mdit-py-plugins")
-    (version "0.3.1")
+    (version "0.4.0")
     (source (origin
               (method git-fetch)        ;for tests
               (uri (git-reference
@@ -915,7 +915,7 @@ (define-public python-mdit-py-plugins
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "00ybbfb6dzn9q5qnvnm8bmhd84s215ik7pcdb4r35zhwiv2ikizz"))))
+                "1790fcf3nd9c5j37fx87x3ivfyihk6l74jxj1qxvw3qfyb96w4k0"))))
     (build-system pyproject-build-system)
     (propagated-inputs
      (list python-markdown-it-py
@@ -943,6 +943,23 @@ (define-public python-mdit-py-plugins
 @end enumerate")
     (license license:expat)))
 
+(define-public python-mdit-py-plugins-0.3
+  (package
+    (inherit python-mdit-py-plugins)
+    (version "0.3.1")
+    (source (origin
+              (method git-fetch)        ;for tests
+              (uri (git-reference
+                    (url "https://github.com/executablebooks/mdit-py-plugins")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name "python-mdit-py-plugins" version))
+              (sha256
+               (base32
+                "00ybbfb6dzn9q5qnvnm8bmhd84s215ik7pcdb4r35zhwiv2ikizz"))))
+        (propagated-inputs
+         (modify-inputs (package-propagated-inputs python-mdit-py-plugins)
+           (replace "python-markdown-it-py" python-markdown-it-py-2.1)))))
+
 (define-public python-mdurl
   (package
     (name "python-mdurl")
diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index 89196086f2..40a65e45b5 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -794,7 +794,7 @@ (define-public python-myst-parser
            python-linkify-it-py
            python-markdown-it-py-2.1
            python-linkify-it-py
-           python-mdit-py-plugins
+           python-mdit-py-plugins-0.3
            python-pyyaml
            python-sphinx
            python-typing-extensions))
-- 
2.41.0

[bug#68461] [PATCH v4 6/6] gnu: python-textual: Update to 0.47.1.

[Giacomo Leidi via Guix-patches via]

* gnu/packages/python-xyz.scm (python-textual): Update to 0.47.1;
[source]: switch to git-origin;
[build-system]: switch to pyproject-build-system;
[arguments]<test-flags>: disable failing tests;
<phases>: use check phase from pyproject-build-system and adapt build
machinery to our old version of poetry;
[propagated-inputs]: adapt to pyproject.toml;
[native-inputs] add poetry and python-pytest-asyncio.

Change-Id: I1060b25cb2ec439f26a4348305bc05fd0b09cf07
---
 gnu/packages/python-xyz.scm | 58 ++++++++++++++++++++++---------------
 1 file changed, 34 insertions(+), 24 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e2013a3995..997b40172e 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -18665,20 +18665,8 @@ (define-public python-rich-click
 (define-public python-textual
   (package
     (name "python-textual")
-    (version "0.1.18")
+    (version "0.47.1")
     (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "textual" version))
-              (sha256
-               (base32
-                "08yg5a51hz1axfj5hx28hx31gq5apcj6vpkkmawmiplisa73z25j"))))
-    (build-system python-build-system)
-    (arguments
-     (let ((tests
-            ;; The release on pypi comes without tests.  We can't build
-            ;; from this checkout, though, because installation requires
-            ;; an invocation of poetry.
-            (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/Textualize/textual")
@@ -18686,19 +18674,41 @@ (define-public python-textual
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0b3ycwqhp21mg9fvmadgxhgbvkwq6fd784l2xcmvy77rravrnnax")))))
-       (list #:phases
-             #~(modify-phases %standard-phases
-                 (replace 'check
-                   (lambda* (#:key tests? #:allow-other-keys)
-                     (when tests?
-                       (copy-recursively #$(file-append tests "/tests")
-                                         "tests")
-                       (invoke "python" "-m" "pytest" "-vv"))))))))
+                "1984v02n2wa7rqgq0f0mkma8fd0nnnbgfwcwgmpsd8xl1wlrjmj4"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; 3 failed, 1932 passed, 1 skipped, 4 xfailed, 10 warnings in 115.19s (0:01:55)
+      #:test-flags
+      #~'("-k"
+          ;; this test fails because of an AssertionError:
+          ;; assert app.devtools is not None
+          #$(string-append "not test_textual_env_var"
+                           ;; these tests require python-tresitter-languages
+                           " and not test_register_language"
+                           " and not test_register_language_existing_language"))
+      #:phases #~(modify-phases %standard-phases
+                   ;; TODO: This is because of our old version of poetry.
+                   ;; It can be removed once it's been updated to a current one.
+                   (add-after 'unpack 'adapt-pyproject.toml
+                     (lambda _
+                       (substitute* "pyproject.toml"
+                         (("group\\.dev\\.") "dev-"))))
+                   ;; snapshot tests require syrupy
+                   (add-after 'adapt-pyproject.toml 'remove-snapshot-tests
+                     (lambda _
+                       (delete-file "tests/snapshot_tests/test_snapshots.py"))))))
     (propagated-inputs
-     (list python-rich python-typing-extensions))
+     (list python-importlib-metadata
+           python-linkify-it-py
+           python-markdown-it-py
+           python-mdit-py-plugins
+           python-rich
+           python-typing-extensions))
     (native-inputs
-     (list python-pytest))
+     (list poetry
+           python-pytest
+           python-pytest-asyncio))
     (home-page "https://github.com/Textualize/textual")
     (synopsis "Build text user interfaces in Python")
     (description "Textual is a @acronym{TUI, Text User Interface} framework
-- 
2.41.0

bug#68456: Close issue

[paul via Guix-patches via]

This issue was opened by mistake, apologies for the noise.

bug#68461: Close issue

[paul via Guix-patches via]

This issue was opened by mistake, apologies for the noise.

bug#68458: Close issue

[paul via Guix-patches via]

This issue was opened by mistake, apologies for the noise.

bug#68457: Close issue

[paul via Guix-patches via]

This issue was opened by mistake, apologies for the noise.

bug#68459: Close issue

[paul via Guix-patches via]

This issue was opened by mistake, apologies for the noise.

bug#68460: Close issue

[paul via Guix-patches via]

This issue was opened by mistake, apologies for the noise.