[bug#69980] [PATCH 00/13] Update and cleanup pre-commit & friends.

[bug#69980] [PATCH 00/13] Update and cleanup pre-commit & friends.

[Vinicius Monego]

Vinicius Monego (13):
  gnu: python-loguru: Remove pre-commit from native-inputs.
  gnu: python-jsonargparse: Remove pre-commit from native-inputs.
  gnu: python-traitlets: Remove pre-commit from native-inputs.
  gnu: python-seaborn: Remove pre-commit from native-inputs.
  gnu: python-rich-click: Remove pre-commit from native-inputs.
  gnu: python-lazy-loader: Remove pre-commit from native-inputs.
  gnu: python-jupytext: Remove pre-commit from native-inputs.
  gnu: python-omnipath: Remove pre-commit from native-inputs.
  gnu: python-cfgv: Update to 3.4.0.
  gnu: Add python-ukkonen.
  gnu: python-identify: Update to 2.5.35.
  gnu: python-nodeenv: Update to 1.8.0.
  gnu: pre-commit: Update to 3.6.2.

 gnu/packages/python-web.scm      |   1 -
 gnu/packages/python-xyz.scm      |  81 +++++++++++------------
 gnu/packages/version-control.scm | 106 +++++++++++++------------------
 3 files changed, 85 insertions(+), 103 deletions(-)


base-commit: bf530017f0e847ae895919b32ef37d79fa636a1e
-- 
2.39.2

[bug#69980] [PATCH 01/13] gnu: python-loguru: Remove pre-commit from native-inputs.

[Vinicius Monego]

* gnu/packages/python-xyz.scm (python-loguru)[native-inputs]: Remove
python-pre-commit.

Change-Id: Id14b518c310c47c19d5911f694248cab22f50d8d
---
 gnu/packages/python-xyz.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index aad89d251e..7b7e56a538 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -31941,7 +31941,6 @@ (define-public python-loguru
     (native-inputs (list python-colorama
                          python-freezegun
                          python-mypy
-                         python-pre-commit
                          python-pytest
                          python-pytest-cov
                          python-pytest-mypy-plugins
-- 
2.39.2

[bug#69980] [PATCH 02/13] gnu: python-jsonargparse: Remove pre-commit from native-inputs.

[Vinicius Monego]

* gnu/packages/python-xyz.scm (python-jsonargparse)[native-inputs]: Remove
python-pre-commit.

Change-Id: Iac844f4521f985cb07ef407b999dfc7f61605bca
---
 gnu/packages/python-xyz.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 7b7e56a538..2aec657662 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4241,7 +4241,6 @@ (define-public python-jsonargparse
     (native-inputs
      (list python-attrs
            python-coverage
-           python-pre-commit
            python-pycodestyle
            python-pydantic
            python-pytest
-- 
2.39.2

[bug#69980] [PATCH 03/13] gnu: python-traitlets: Remove pre-commit from native-inputs.

[Vinicius Monego]

* gnu/packages/python-xyz.scm (python-traitlets)[native-inputs]: Remove
python-pre-commit.

Change-Id: I3d36f47e8955c648282bc707fafa57ba00cda933
---
 gnu/packages/python-xyz.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 2aec657662..261dde03a2 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -11708,7 +11708,6 @@ (define-public python-traitlets
     (build-system pyproject-build-system)
     (native-inputs
      (list python-hatchling
-           python-pre-commit
            python-pytest
            python-pytest-mock))
     (home-page "https://ipython.org")
-- 
2.39.2

[bug#69980] [PATCH 04/13] gnu: python-seaborn: Remove pre-commit from native-inputs.

[Vinicius Monego]

* gnu/packages/python-xyz.scm (python-seaborn)[native-inputs]: Remove
python-pre-commit.

Change-Id: I8b7016f1d8103dd9297626b7ec74a120fa1c848b
---
 gnu/packages/python-xyz.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 261dde03a2..898c884fa5 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -13133,7 +13133,6 @@ (define-public python-seaborn
     (native-inputs
      (list python-flake8
            python-flit-core
-           python-pre-commit
            python-pytest
            python-pytest-cov
            python-pytest-xdist))
-- 
2.39.2

[bug#69980] [PATCH 05/13] gnu: python-rich-click: Remove pre-commit from native-inputs.

[Vinicius Monego]

* gnu/packages/python-xyz.scm (python-rich-click)[native-inputs]: Remove
python-pre-commit.

Change-Id: I7a1de6166e4fe9f255cff8819b4779e76d7a4537
---
 gnu/packages/python-xyz.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 898c884fa5..d8056bc127 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -19588,7 +19588,6 @@ (define-public python-rich-click
     (build-system python-build-system)
     (propagated-inputs
      (list python-click python-importlib-metadata python-rich))
-    (native-inputs (list python-pre-commit))
     (home-page "https://github.com/ewels/rich-click")
     (synopsis "Format click help output nicely with rich")
     (description "Click is a \"Python package for creating beautiful command
-- 
2.39.2

[bug#69980] [PATCH 06/13] gnu: python-lazy-loader: Remove pre-commit from native-inputs.

[Vinicius Monego]

* gnu/packages/python-xyz.scm (python-lazy-loader)[native-inputs]: Remove
python-pre-commit.

Change-Id: Id360c7c6a34457d95084227805fcd0bad1b30e12
---
 gnu/packages/python-xyz.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index d8056bc127..77c29edb45 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -20981,8 +20981,7 @@ (define-public python-lazy-loader
                 "0dwghffnsjjf4pi4gwbl43rx04jmap375hdamafs5cpm6j78js1v"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-pre-commit
-           python-pytest
+     (list python-pytest
            python-pytest-cov))
     (propagated-inputs
      (list python-flit-core))
-- 
2.39.2

[bug#69980] [PATCH 07/13] gnu: python-jupytext: Remove pre-commit from native-inputs.

[Vinicius Monego]

* gnu/packages/python-xyz.scm (python-jupytext)[native-inputs]: Remove
pre-commit.

Change-Id: I9e43aa760ef11ffabd0d374593e2e1ea77e9b086
---
 gnu/packages/python-xyz.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 77c29edb45..23a6490154 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -375,7 +375,6 @@ (define-public python-jupytext
                                                       " and not "))))))))))
     (native-inputs
      (list git-minimal
-           pre-commit
            python-autopep8
            python-black
            python-flake8
-- 
2.39.2

[bug#69980] [PATCH 08/13] gnu: python-omnipath: Remove pre-commit from native-inputs.

[Vinicius Monego]

* gnu/packages/python-xyz.scm (python-omnipath)[native-inputs]: Remove
python-pre-commit.

Change-Id: Idfdf978df55e2c3cb3c8447aa18456cc9de4c4c2
---
 gnu/packages/python-web.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index fc01fc4b83..bbe4ddd788 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2101,7 +2101,6 @@ (define-public python-omnipath
            python-wrapt))
     (native-inputs
      (list python-bump2version
-           python-pre-commit
            python-pytest
            python-pytest-mock
            python-requests-mock
-- 
2.39.2

[bug#69980] [PATCH 09/13] gnu: python-cfgv: Update to 3.4.0.

[Vinicius Monego]

* gnu/packages/python-xyz.scm (python-cfgv): Update to 3.4.0.
[build-system]: Use pyproject-build-system.
[arguments]: Do not override the check phase.

Change-Id: Id666a57e4d619697ffa272893930f1c94d5c283e
---
 gnu/packages/python-xyz.scm | 13 +++----------
 1 file changed, 3 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 23a6490154..cead8ece1d 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -26902,7 +26902,7 @@ (define-public python-dns-lexicon
 (define-public python-cfgv
   (package
     (name "python-cfgv")
-    (version "3.3.1")
+    (version "3.4.0")
     (source
      (origin
        ;; There are no tests in the PyPI tarball.
@@ -26912,15 +26912,8 @@ (define-public python-cfgv
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1pci97cmn3v45sfch9s3lshidrl0309ls9byidic0l8drkwnkwcj"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (invoke "pytest" "-vv")))))))
+        (base32 "0g7jg6dssyax6k85lk8afs8qdzgq138g6ij0jmmhgdv5fzks6k9z"))))
+    (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest))
     (home-page "https://github.com/asottile/cfgv")
-- 
2.39.2

[bug#69980] [PATCH 10/13] gnu: Add python-ukkonen.

[Vinicius Monego]

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

Change-Id: I826b003f1c22e5bf28829d9f2adc5f467d17ed45
---
 gnu/packages/python-xyz.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index cead8ece1d..03fdccba78 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -26691,6 +26691,29 @@ (define-public python-requests-file
 library to allow local file system access via @code{file://} URLs.")
     (license license:asl2.0)))
 
+(define-public python-ukkonen
+  (package
+    (name "python-ukkonen")
+    (version "1.0.1")
+    (source
+     (origin
+       ;; There are no tests in the PyPI tarball.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/asottile/ukkonen")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "17gspl2dsykg000275svvyam4k7wz9ypi9xrfrmsgcgryczravlc"))))
+    (build-system pyproject-build-system)
+    (native-inputs (list python-pytest))
+    (propagated-inputs (list python-cffi))
+    (home-page "https://github.com/asottile/ukkonen")
+    (synopsis "Implementation of bounded Levenshtein distance (Ukkonen)")
+    (description "This package is an implementation of of bounded Levenshtein
+distance (Ukkonen).")
+    (license license:expat)))
+
 (define-public python-identify
   (package
     (name "python-identify")
-- 
2.39.2

[bug#69980] [PATCH 11/13] gnu: python-identify: Update to 2.5.35.

[Vinicius Monego]

* gnu/packages/python-xyz.scm (python-identify): Update to 2.5.35.
[build-system]: Use pyproject-build-system.
[arguments]: Use G-Expressions. Do not override the check phase.
[native-inputs]: Add python-ukkonen.

Change-Id: I970507dc358029b4e2cc0a295d19db4b28202544
---
 gnu/packages/python-xyz.scm | 20 ++++++++------------
 1 file changed, 8 insertions(+), 12 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 03fdccba78..d7af0646fc 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -26717,7 +26717,7 @@ (define-public python-ukkonen
 (define-public python-identify
   (package
     (name "python-identify")
-    (version "1.4.25")
+    (version "2.5.35")
     (source
      (origin
        ;; There are no tests in the PyPI tarball.
@@ -26727,19 +26727,15 @@ (define-public python-identify
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1fqgci6skckcq0x5pnxh6k2qjzn1ndsrgha1j6wwv1ld4g9bd3hz"))))
-    (build-system python-build-system)
+        (base32 "0w1wnh4y6xll3980m555k5g4iwwk31pwjx4j0b5x88bdvfml0h4i"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         ;; system-error "utime" "~A" ("No such file or directory")
-         (delete 'ensure-no-mtimes-pre-1980)
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (invoke "pytest" "-vv")))))))
+     (list
+      #:phases #~(modify-phases %standard-phases
+                   ;; system-error "utime" "~A" ("No such file or directory")
+                   (delete 'ensure-no-mtimes-pre-1980))))
     (native-inputs
-     (list python-coverage python-pytest))
+     (list python-coverage python-pytest python-ukkonen))
     (propagated-inputs
      (list python-editdistance))
     (home-page "https://github.com/chriskuehl/identify")
-- 
2.39.2

[bug#69980] [PATCH 11/13] gnu: python-identify: Update to 2.5.35.

[Nicolas Graves via Guix-patches via]

lint complains about permanent redirect from
https://github.com/chriskuehl/identify to
https://github.com/pre-commit/identify


On 2024-03-24 13:40, Vinicius Monego wrote:

> * gnu/packages/python-xyz.scm (python-identify): Update to 2.5.35.
> [build-system]: Use pyproject-build-system.
> [arguments]: Use G-Expressions. Do not override the check phase.
> [native-inputs]: Add python-ukkonen.
>
> Change-Id: I970507dc358029b4e2cc0a295d19db4b28202544
> ---
>  gnu/packages/python-xyz.scm | 20 ++++++++------------
>  1 file changed, 8 insertions(+), 12 deletions(-)
>
> diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
> index 03fdccba78..d7af0646fc 100644
> --- a/gnu/packages/python-xyz.scm
> +++ b/gnu/packages/python-xyz.scm
> @@ -26717,7 +26717,7 @@ (define-public python-ukkonen
>  (define-public python-identify
>    (package
>      (name "python-identify")
> -    (version "1.4.25")
> +    (version "2.5.35")
>      (source
>       (origin
>         ;; There are no tests in the PyPI tarball.
> @@ -26727,19 +26727,15 @@ (define-public python-identify
>               (commit (string-append "v" version))))
>         (file-name (git-file-name name version))
>         (sha256
> -        (base32 "1fqgci6skckcq0x5pnxh6k2qjzn1ndsrgha1j6wwv1ld4g9bd3hz"))))
> -    (build-system python-build-system)
> +        (base32 "0w1wnh4y6xll3980m555k5g4iwwk31pwjx4j0b5x88bdvfml0h4i"))))
> +    (build-system pyproject-build-system)
>      (arguments
> -     `(#:phases
> -       (modify-phases %standard-phases
> -         ;; system-error "utime" "~A" ("No such file or directory")
> -         (delete 'ensure-no-mtimes-pre-1980)
> -         (replace 'check
> -           (lambda* (#:key tests? #:allow-other-keys)
> -             (when tests?
> -               (invoke "pytest" "-vv")))))))
> +     (list
> +      #:phases #~(modify-phases %standard-phases
> +                   ;; system-error "utime" "~A" ("No such file or directory")
> +                   (delete 'ensure-no-mtimes-pre-1980))))
>      (native-inputs
> -     (list python-coverage python-pytest))
> +     (list python-coverage python-pytest python-ukkonen))
>      (propagated-inputs
>       (list python-editdistance))
>      (home-page "https://github.com/chriskuehl/identify")

-- 
Best regards,
Nicolas Graves

[bug#69980] [PATCH 12/13] gnu: python-nodeenv: Update to 1.8.0.

[Vinicius Monego]

* gnu/packages/python-xyz.scm (python-nodeenv): Update to 1.8.0.
[build-system]: Use pyproject-build-system.
[arguments]: Do not override the check phase, skip tests in #:test-flags
instead.

Change-Id: I01ca1948c30327827d6f76697b471a4d90cd6530
---
 gnu/packages/python-xyz.scm | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index d7af0646fc..b8abe5fd75 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -26813,7 +26813,7 @@ (define-public python-tldr
 (define-public python-nodeenv
   (package
     (name "python-nodeenv")
-    (version "1.4.0")
+    (version "1.8.0")
     (source
      (origin
        ;; There's no tarball in PyPI.
@@ -26823,15 +26823,13 @@ (define-public python-nodeenv
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0y443icx0w7jlzmxmmcm4q8dqfiwgafbb9cp8jpm68mbqxbz40a7"))))
-    (build-system python-build-system)
+        (base32 "0g8zp8zw5nnfc14ml0sil9yh7lnpz3xrdkazdkwg6pf5jqsxlvv9"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda _
-             ;; This test fails. It tries to open a network socket.
-             (invoke "pytest" "-vv" "-k" "not test_smoke"))))))
+     (list #:test-flags
+           #~(list "-k" (string-append
+                         "not test_smoke"
+                         " and not test_smoke_n_system_special_chars"))))
     (native-inputs
      (list python-coverage python-mock python-pytest))
     (home-page "https://ekalinin.github.io/nodeenv/")
-- 
2.39.2

[bug#69980] [PATCH 13/13] gnu: pre-commit: Update to 3.6.2.

[Vinicius Monego]

* gnu/packages/version-control.scm (pre-commit): Update to 3.6.2.
[build-system]: Use pyproject-build-system.
[arguments]: Use G-Expressions. Do not override the check phase, skip the
tests in #:test-flags instead. Don't make source tree writable in the
prepare-check-env phase.
[native-inputs]: Use the new style.

Change-Id: I4a1c56ce0903d6aa185d65d39c03c9566a6cf0d9
---
 gnu/packages/version-control.scm | 106 +++++++++++++------------------
 1 file changed, 43 insertions(+), 63 deletions(-)

diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 946b1f5aac..1fc3c7274e 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -29,7 +29,7 @@
 ;;; Copyright © 2020, 2021 Brice Waegeneire <brice@waegenei.re>
 ;;; Copyright © 2020 John D. Boy <jboy@bius.moe>
 ;;; Copyright © 2020, 2023 Janneke Nieuwenhuizen <janneke@gnu.org>
-;;; Copyright © 2020, 2021, 2022, 2023 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2020, 2021, 2022, 2023, 2024 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2020 Tanguy Le Carrour <tanguy@bioneland.org>
 ;;; Copyright © 2020, 2021, 2022 Michael Rohleder <mike@rohleder.de>
 ;;; Copyright © 2021 Greg Hogan <code@greghogan.com>
@@ -1987,7 +1987,7 @@ (define-public gitile
 (define-public pre-commit
   (package
     (name "pre-commit") ;formerly known as python-pre-commit
-    (version "3.3.3")
+    (version "3.6.2")
     (source
      (origin
        (method git-fetch)               ; no tests in PyPI release
@@ -1996,73 +1996,53 @@ (define-public pre-commit
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1spkg3ld3s6l7wz24lcywlf1z2ywp751bcdlxjfdsln76bi9ylp8"))
+        (base32 "01b8mphyvm961n8hsk4ajqqgm5vwkr2kbi837s231bablnhs8ldf"))
        (modules '((guix build utils)))
        (snippet '(substitute* "setup.cfg"
                    (("virtualenv>=20.10.0") ;our virtualenv (20.3.1) is fine
                     "virtualenv>=20.0.8")))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-before 'check 'prepare-check-env
-           (lambda _
-             ;; Change from /homeless-shelter to /tmp for write permission.
-             (setenv "HOME" "/tmp")
-             ;; Environment variables used in the tests.
-             (setenv "GIT_AUTHOR_NAME" "Your Name")
-             (setenv "GIT_COMMITTER_NAME" "Your Name")
-             (setenv "GIT_AUTHOR_EMAIL" "you@example.com")
-             (setenv "GIT_COMMITTER_EMAIL" "you@example.com")
-             ;; Some tests still fail with PermissionError.  Make the source
-             ;; tree writable.
-             (for-each make-file-writable (find-files "."))
-             ;; Some tests will need a working git repository.
-             (invoke "git" "init")
-             (invoke "git" "config" "--global" "user.name" "Your Name")
-             (invoke "git" "config" "--global" "user.email" "you@example.com")))
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (add-installed-pythonpath inputs outputs)
-             (when tests?
-               ;; The file below contains 30+ tests that fail because they
-               ;; depend on tools from multiple languages (cargo, npm, cpan,
-               ;; Rscript, etc).  Other tests are passing, but it's more
-               ;; convenient to skip the file than list 30 tests to skip.
-               (invoke "pytest" "--ignore=tests/repository_test.py"
-                       ;; Ruby and Node tests require node and gem.
-                       "--ignore=tests/languages/node_test.py"
-                       "--ignore=tests/languages/ruby_test.py"
-                       ;; Skip lang-specific (network) tests added in 3.1.1
-                       "--ignore=tests/languages/conda_test.py"
-                       "--ignore=tests/languages/coursier_test.py"
-                       "--ignore=tests/languages/dart_test.py"
-                       "--ignore=tests/languages/docker_test.py"
-                       "--ignore=tests/languages/docker_image_test.py"
-                       "--ignore=tests/languages/dotnet_test.py"
-                       "--ignore=tests/languages/golang_test.py"
-                       "--ignore=tests/languages/lua_test.py"
-                       "--ignore=tests/languages/perl_test.py"
-                       "--ignore=tests/languages/rust_test.py"
-                       "--ignore=tests/languages/swift_test.py"
-                       "-k"
-                       (string-append
-                        ;; TODO: these tests fail with AssertionError.  It may
-                        ;; be possible to fix them.
-                        "not test_install_existing_hooks_no_overwrite"
-                        " and not test_uninstall_restores_legacy_hooks"
-                        " and not test_installed_from_venv"
-                        " and not test_healthy_venv_creator"
-                        " and not test_r_hook and not test_r_inline"))))))))
+     (list
+      ;; Skip language-specific tests because they depennd on language tools.
+      #:test-flags
+      #~(list "--ignore" "tests/languages"
+              ;; These fail with AssertionError.
+              "-k" (string-append
+                    "not test_additional_dependencies_roll_forward"
+                    " and not test_control_c_control_c_on_install"
+                    " and not test_invalidated_virtualenv"
+                    " and not test_local_python_repo"
+                    " and not test_install_existing_hooks_no_overwrite"
+                    " and not test_uninstall_restores_legacy_hooks"
+                    " and not test_installed_from_venv"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'prepare-check-env
+            (lambda _
+              ;; Change from /homeless-shelter to /tmp for write permission.
+              (setenv "HOME" "/tmp")
+              ;; Environment variables used in the tests.
+              (setenv "GIT_AUTHOR_NAME" "Your Name")
+              (setenv "GIT_COMMITTER_NAME" "Your Name")
+              (setenv "GIT_AUTHOR_EMAIL" "you@example.com")
+              (setenv "GIT_COMMITTER_EMAIL" "you@example.com")
+              ;; Some tests still fail with PermissionError.  Make the source
+              ;; tree writable.
+              ;; (for-each make-file-writable (find-files "."))
+              ;; Some tests will need a working git repository.
+              (invoke "git" "init")
+              (invoke "git" "config" "--global" "user.name" "Your Name")
+              (invoke "git" "config" "--global" "user.email" "you@example.com"))))))
     (native-inputs
-     `(("git" ,git-minimal)
-       ("python-covdefaults" ,python-covdefaults)
-       ("python-coverage" ,python-coverage)
-       ("python-distlib" ,python-distlib)
-       ("python-pytest" ,python-pytest)
-       ("python-pytest-env" ,python-pytest-env)
-       ("python-re-assert" ,python-re-assert)
-       ("which" ,which)))
+     (list git-minimal
+           python-covdefaults
+           python-coverage
+           python-distlib
+           python-pytest
+           python-pytest-env
+           python-re-assert
+           which))
     ;; Propagate because pre-commit is also used as a module.
     (propagated-inputs
      (list python-cfgv
-- 
2.39.2

[bug#69980] [PATCH v2 00/14] Update and cleanup pre-commit & friends.

[Nicolas Graves via Guix-patches via]

This patch series is a rebased (thus updated) and fixed (jupytext
wasn't building) version of Vinicius' original patch series.

Nicolas Graves (2):
  gnu: python-jupytext: Move to pyproject-build-system.
  gnu: jupytext: Fix pre-commit native-input removal.

Vinicius Monego (12):
  gnu: python-jsonargparse: Remove pre-commit from native-inputs.
  gnu: python-traitlets: Remove pre-commit from native-inputs.
  gnu: python-seaborn: Remove pre-commit from native-inputs.
  gnu: python-rich-click: Remove pre-commit from native-inputs.
  gnu: python-lazy-loader: Remove pre-commit from native-inputs.
  gnu: python-jupytext: Remove pre-commit from native-inputs.
  gnu: python-omnipath: Remove pre-commit from native-inputs.
  gnu: python-cfgv: Update to 3.4.0.
  gnu: Add python-ukkonen.
  gnu: python-identify: Update to 2.5.35.
  gnu: python-nodeenv: Update to 1.8.0.
  gnu: pre-commit: Update to 3.6.2.

 gnu/packages/python-web.scm      |   1 -
 gnu/packages/python-xyz.scm      | 106 ++++++++++++++++---------------
 gnu/packages/version-control.scm | 106 +++++++++++++------------------
 3 files changed, 98 insertions(+), 115 deletions(-)

-- 
2.41.0

[bug#69980] [PATCH v2 01/14] gnu: python-jsonargparse: Remove pre-commit from native-inputs.

[Nicolas Graves via Guix-patches via]

From: Vinicius Monego <monego@posteo.net>

* gnu/packages/python-xyz.scm (python-jsonargparse)[native-inputs]: Remove
python-pre-commit.

Change-Id: Iac844f4521f985cb07ef407b999dfc7f61605bca
---
 gnu/packages/python-xyz.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index bf989646f6b..f376e396da6 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4534,7 +4534,6 @@ (define-public python-jsonargparse
     (native-inputs
      (list python-attrs
            python-coverage
-           python-pre-commit
            python-pycodestyle
            python-pydantic
            python-pytest
-- 
2.41.0

[bug#69980] [PATCH v2 02/14] gnu: python-traitlets: Remove pre-commit from native-inputs.

[Nicolas Graves via Guix-patches via]

From: Vinicius Monego <monego@posteo.net>

* gnu/packages/python-xyz.scm (python-traitlets)[native-inputs]: Remove
python-pre-commit.

Change-Id: I3d36f47e8955c648282bc707fafa57ba00cda933
---
 gnu/packages/python-xyz.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f376e396da6..366bce92e5f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12327,7 +12327,6 @@ (define-public python-traitlets
      (list python-argcomplete
            python-hatchling
            python-mypy
-           python-pre-commit
            python-pytest
            python-pytest-mock
            python-pytest-mypy-testing))
-- 
2.41.0

[bug#69980] [PATCH v2 03/14] gnu: python-seaborn: Remove pre-commit from native-inputs.

[Nicolas Graves via Guix-patches via]

From: Vinicius Monego <monego@posteo.net>

* gnu/packages/python-xyz.scm (python-seaborn)[native-inputs]: Remove
python-pre-commit.

Change-Id: I8b7016f1d8103dd9297626b7ec74a120fa1c848b
---
 gnu/packages/python-xyz.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 366bce92e5f..1e4574f70a8 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -13848,7 +13848,6 @@ (define-public python-seaborn
     (native-inputs
      (list python-flake8
            python-flit-core
-           python-pre-commit
            python-pytest
            python-pytest-cov
            python-pytest-xdist))
-- 
2.41.0

[bug#69980] [PATCH v2 04/14] gnu: python-rich-click: Remove pre-commit from native-inputs.

[Nicolas Graves via Guix-patches via]

From: Vinicius Monego <monego@posteo.net>

* gnu/packages/python-xyz.scm (python-rich-click)[native-inputs]: Remove
python-pre-commit.

Change-Id: I7a1de6166e4fe9f255cff8819b4779e76d7a4537
---
 gnu/packages/python-xyz.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 1e4574f70a8..5c2b1bed608 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -20446,7 +20446,6 @@ (define-public python-rich-click
     (build-system python-build-system)
     (propagated-inputs
      (list python-click python-importlib-metadata python-rich))
-    (native-inputs (list python-pre-commit))
     (home-page "https://github.com/ewels/rich-click")
     (synopsis "Format click help output nicely with rich")
     (description "Click is a \"Python package for creating beautiful command
-- 
2.41.0

[bug#69980] [PATCH v2 05/14] gnu: python-lazy-loader: Remove pre-commit from native-inputs.

[Nicolas Graves via Guix-patches via]

From: Vinicius Monego <monego@posteo.net>

* gnu/packages/python-xyz.scm (python-lazy-loader)[native-inputs]: Remove
python-pre-commit.

Change-Id: Id360c7c6a34457d95084227805fcd0bad1b30e12
---
 gnu/packages/python-xyz.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 5c2b1bed608..a2e837dc790 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21865,8 +21865,7 @@ (define-public python-lazy-loader
                 "0dwghffnsjjf4pi4gwbl43rx04jmap375hdamafs5cpm6j78js1v"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-pre-commit
-           python-pytest
+     (list python-pytest
            python-pytest-cov))
     (propagated-inputs
      (list python-flit-core))
-- 
2.41.0

[bug#69980] [PATCH v2 06/14] gnu: python-jupytext: Remove pre-commit from native-inputs.

[Nicolas Graves via Guix-patches via]

From: Vinicius Monego <monego@posteo.net>

* gnu/packages/python-xyz.scm (python-jupytext)[native-inputs]: Remove
pre-commit.

Change-Id: I9e43aa760ef11ffabd0d374593e2e1ea77e9b086
---
 gnu/packages/python-xyz.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index a2e837dc790..1c93236c8b0 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -481,7 +481,6 @@ (define-public python-jupytext
                                                       " and not "))))))))))
     (native-inputs
      (list git-minimal
-           pre-commit
            python-autopep8
            python-black
            python-flake8
-- 
2.41.0

[bug#69980] [PATCH v2 07/14] gnu: python-omnipath: Remove pre-commit from native-inputs.

[Nicolas Graves via Guix-patches via]

From: Vinicius Monego <monego@posteo.net>

* gnu/packages/python-xyz.scm (python-omnipath)[native-inputs]: Remove
python-pre-commit.

Change-Id: Idfdf978df55e2c3cb3c8447aa18456cc9de4c4c2
---
 gnu/packages/python-web.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index dd1e005b721..3cebbbbe739 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2136,7 +2136,6 @@ (define-public python-omnipath
            python-wrapt))
     (native-inputs
      (list python-bump2version
-           python-pre-commit
            python-pytest
            python-pytest-mock
            python-pytest-socket
-- 
2.41.0

[bug#69980] [PATCH v2 08/14] gnu: python-cfgv: Update to 3.4.0.

[Nicolas Graves via Guix-patches via]

From: Vinicius Monego <monego@posteo.net>

* gnu/packages/python-xyz.scm (python-cfgv): Update to 3.4.0.
[build-system]: Use pyproject-build-system.
[arguments]: Do not override the check phase.

Change-Id: Id666a57e4d619697ffa272893930f1c94d5c283e
---
 gnu/packages/python-xyz.scm | 13 +++----------
 1 file changed, 3 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 1c93236c8b0..714e44b916d 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -27935,7 +27935,7 @@ (define-public python-dns-lexicon
 (define-public python-cfgv
   (package
     (name "python-cfgv")
-    (version "3.3.1")
+    (version "3.4.0")
     (source
      (origin
        ;; There are no tests in the PyPI tarball.
@@ -27945,15 +27945,8 @@ (define-public python-cfgv
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1pci97cmn3v45sfch9s3lshidrl0309ls9byidic0l8drkwnkwcj"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (invoke "pytest" "-vv")))))))
+        (base32 "0g7jg6dssyax6k85lk8afs8qdzgq138g6ij0jmmhgdv5fzks6k9z"))))
+    (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest))
     (home-page "https://github.com/asottile/cfgv")
-- 
2.41.0

[bug#69980] [PATCH v2 09/14] gnu: Add python-ukkonen.

[Nicolas Graves via Guix-patches via]

From: Vinicius Monego <monego@posteo.net>

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

Change-Id: I826b003f1c22e5bf28829d9f2adc5f467d17ed45
---
 gnu/packages/python-xyz.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 714e44b916d..67b167bfcc5 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -27724,6 +27724,29 @@ (define-public python-requests-file
 library to allow local file system access via @code{file://} URLs.")
     (license license:asl2.0)))
 
+(define-public python-ukkonen
+  (package
+    (name "python-ukkonen")
+    (version "1.0.1")
+    (source
+     (origin
+       ;; There are no tests in the PyPI tarball.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/asottile/ukkonen")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "17gspl2dsykg000275svvyam4k7wz9ypi9xrfrmsgcgryczravlc"))))
+    (build-system pyproject-build-system)
+    (native-inputs (list python-pytest))
+    (propagated-inputs (list python-cffi))
+    (home-page "https://github.com/asottile/ukkonen")
+    (synopsis "Implementation of bounded Levenshtein distance (Ukkonen)")
+    (description "This package is an implementation of of bounded Levenshtein
+distance (Ukkonen).")
+    (license license:expat)))
+
 (define-public python-identify
   (package
     (name "python-identify")
-- 
2.41.0

[bug#69980] [PATCH v2 10/14] gnu: python-identify: Update to 2.5.35.

[Nicolas Graves via Guix-patches via]

From: Vinicius Monego <monego@posteo.net>

* gnu/packages/python-xyz.scm (python-identify): Update to 2.5.35.
[build-system]: Use pyproject-build-system.
[arguments]: Use G-Expressions. Do not override the check phase.
[native-inputs]: Add python-ukkonen.

Change-Id: I970507dc358029b4e2cc0a295d19db4b28202544
---
 gnu/packages/python-xyz.scm | 20 ++++++++------------
 1 file changed, 8 insertions(+), 12 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 67b167bfcc5..443c484ce8e 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -27750,7 +27750,7 @@ (define-public python-ukkonen
 (define-public python-identify
   (package
     (name "python-identify")
-    (version "1.4.25")
+    (version "2.5.35")
     (source
      (origin
        ;; There are no tests in the PyPI tarball.
@@ -27760,19 +27760,15 @@ (define-public python-identify
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1fqgci6skckcq0x5pnxh6k2qjzn1ndsrgha1j6wwv1ld4g9bd3hz"))))
-    (build-system python-build-system)
+        (base32 "0w1wnh4y6xll3980m555k5g4iwwk31pwjx4j0b5x88bdvfml0h4i"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         ;; system-error "utime" "~A" ("No such file or directory")
-         (delete 'ensure-no-mtimes-pre-1980)
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (invoke "pytest" "-vv")))))))
+     (list
+      #:phases #~(modify-phases %standard-phases
+                   ;; system-error "utime" "~A" ("No such file or directory")
+                   (delete 'ensure-no-mtimes-pre-1980))))
     (native-inputs
-     (list python-coverage python-pytest))
+     (list python-coverage python-pytest python-ukkonen))
     (propagated-inputs
      (list python-editdistance))
     (home-page "https://github.com/chriskuehl/identify")
-- 
2.41.0

[bug#69980] [PATCH v2 11/14] gnu: python-nodeenv: Update to 1.8.0.

[Nicolas Graves via Guix-patches via]

From: Vinicius Monego <monego@posteo.net>

* gnu/packages/python-xyz.scm (python-nodeenv): Update to 1.8.0.
[build-system]: Use pyproject-build-system.
[arguments]: Do not override the check phase, skip tests in #:test-flags
instead.

Change-Id: I01ca1948c30327827d6f76697b471a4d90cd6530
---
 gnu/packages/python-xyz.scm | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 443c484ce8e..58405d1deaf 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -27846,7 +27846,7 @@ (define-public python-tldr
 (define-public python-nodeenv
   (package
     (name "python-nodeenv")
-    (version "1.4.0")
+    (version "1.8.0")
     (source
      (origin
        ;; There's no tarball in PyPI.
@@ -27856,15 +27856,13 @@ (define-public python-nodeenv
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0y443icx0w7jlzmxmmcm4q8dqfiwgafbb9cp8jpm68mbqxbz40a7"))))
-    (build-system python-build-system)
+        (base32 "0g8zp8zw5nnfc14ml0sil9yh7lnpz3xrdkazdkwg6pf5jqsxlvv9"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda _
-             ;; This test fails. It tries to open a network socket.
-             (invoke "pytest" "-vv" "-k" "not test_smoke"))))))
+     (list #:test-flags
+           #~(list "-k" (string-append
+                         "not test_smoke"
+                         " and not test_smoke_n_system_special_chars"))))
     (native-inputs
      (list python-coverage python-mock python-pytest))
     (home-page "https://ekalinin.github.io/nodeenv/")
-- 
2.41.0

[bug#69980] [PATCH v2 12/14] gnu: pre-commit: Update to 3.6.2.

[Nicolas Graves via Guix-patches via]

From: Vinicius Monego <monego@posteo.net>

* gnu/packages/version-control.scm (pre-commit): Update to 3.6.2.
[build-system]: Use pyproject-build-system.
[arguments]: Use G-Expressions. Do not override the check phase, skip the
tests in #:test-flags instead. Don't make source tree writable in the
prepare-check-env phase.
[native-inputs]: Use the new style.

Change-Id: I4a1c56ce0903d6aa185d65d39c03c9566a6cf0d9
---
 gnu/packages/version-control.scm | 106 +++++++++++++------------------
 1 file changed, 43 insertions(+), 63 deletions(-)

diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 2567acd2afc..226bcd4ad63 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -29,7 +29,7 @@
 ;;; Copyright © 2020, 2021 Brice Waegeneire <brice@waegenei.re>
 ;;; Copyright © 2020 John D. Boy <jboy@bius.moe>
 ;;; Copyright © 2020, 2023 Janneke Nieuwenhuizen <janneke@gnu.org>
-;;; Copyright © 2020, 2021, 2022, 2023 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2020, 2021, 2022, 2023, 2024 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2020 Tanguy Le Carrour <tanguy@bioneland.org>
 ;;; Copyright © 2020, 2021, 2022 Michael Rohleder <mike@rohleder.de>
 ;;; Copyright © 2021 Greg Hogan <code@greghogan.com>
@@ -2014,7 +2014,7 @@ (define-public gitile
 (define-public pre-commit
   (package
     (name "pre-commit") ;formerly known as python-pre-commit
-    (version "3.3.3")
+    (version "3.6.2")
     (source
      (origin
        (method git-fetch)               ; no tests in PyPI release
@@ -2023,73 +2023,53 @@ (define-public pre-commit
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1spkg3ld3s6l7wz24lcywlf1z2ywp751bcdlxjfdsln76bi9ylp8"))
+        (base32 "01b8mphyvm961n8hsk4ajqqgm5vwkr2kbi837s231bablnhs8ldf"))
        (modules '((guix build utils)))
        (snippet '(substitute* "setup.cfg"
                    (("virtualenv>=20.10.0") ;our virtualenv (20.3.1) is fine
                     "virtualenv>=20.0.8")))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-before 'check 'prepare-check-env
-           (lambda _
-             ;; Change from /homeless-shelter to /tmp for write permission.
-             (setenv "HOME" "/tmp")
-             ;; Environment variables used in the tests.
-             (setenv "GIT_AUTHOR_NAME" "Your Name")
-             (setenv "GIT_COMMITTER_NAME" "Your Name")
-             (setenv "GIT_AUTHOR_EMAIL" "you@example.com")
-             (setenv "GIT_COMMITTER_EMAIL" "you@example.com")
-             ;; Some tests still fail with PermissionError.  Make the source
-             ;; tree writable.
-             (for-each make-file-writable (find-files "."))
-             ;; Some tests will need a working git repository.
-             (invoke "git" "init")
-             (invoke "git" "config" "--global" "user.name" "Your Name")
-             (invoke "git" "config" "--global" "user.email" "you@example.com")))
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (add-installed-pythonpath inputs outputs)
-             (when tests?
-               ;; The file below contains 30+ tests that fail because they
-               ;; depend on tools from multiple languages (cargo, npm, cpan,
-               ;; Rscript, etc).  Other tests are passing, but it's more
-               ;; convenient to skip the file than list 30 tests to skip.
-               (invoke "pytest" "--ignore=tests/repository_test.py"
-                       ;; Ruby and Node tests require node and gem.
-                       "--ignore=tests/languages/node_test.py"
-                       "--ignore=tests/languages/ruby_test.py"
-                       ;; Skip lang-specific (network) tests added in 3.1.1
-                       "--ignore=tests/languages/conda_test.py"
-                       "--ignore=tests/languages/coursier_test.py"
-                       "--ignore=tests/languages/dart_test.py"
-                       "--ignore=tests/languages/docker_test.py"
-                       "--ignore=tests/languages/docker_image_test.py"
-                       "--ignore=tests/languages/dotnet_test.py"
-                       "--ignore=tests/languages/golang_test.py"
-                       "--ignore=tests/languages/lua_test.py"
-                       "--ignore=tests/languages/perl_test.py"
-                       "--ignore=tests/languages/rust_test.py"
-                       "--ignore=tests/languages/swift_test.py"
-                       "-k"
-                       (string-append
-                        ;; TODO: these tests fail with AssertionError.  It may
-                        ;; be possible to fix them.
-                        "not test_install_existing_hooks_no_overwrite"
-                        " and not test_uninstall_restores_legacy_hooks"
-                        " and not test_installed_from_venv"
-                        " and not test_healthy_venv_creator"
-                        " and not test_r_hook and not test_r_inline"))))))))
+     (list
+      ;; Skip language-specific tests because they depennd on language tools.
+      #:test-flags
+      #~(list "--ignore" "tests/languages"
+              ;; These fail with AssertionError.
+              "-k" (string-append
+                    "not test_additional_dependencies_roll_forward"
+                    " and not test_control_c_control_c_on_install"
+                    " and not test_invalidated_virtualenv"
+                    " and not test_local_python_repo"
+                    " and not test_install_existing_hooks_no_overwrite"
+                    " and not test_uninstall_restores_legacy_hooks"
+                    " and not test_installed_from_venv"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'prepare-check-env
+            (lambda _
+              ;; Change from /homeless-shelter to /tmp for write permission.
+              (setenv "HOME" "/tmp")
+              ;; Environment variables used in the tests.
+              (setenv "GIT_AUTHOR_NAME" "Your Name")
+              (setenv "GIT_COMMITTER_NAME" "Your Name")
+              (setenv "GIT_AUTHOR_EMAIL" "you@example.com")
+              (setenv "GIT_COMMITTER_EMAIL" "you@example.com")
+              ;; Some tests still fail with PermissionError.  Make the source
+              ;; tree writable.
+              ;; (for-each make-file-writable (find-files "."))
+              ;; Some tests will need a working git repository.
+              (invoke "git" "init")
+              (invoke "git" "config" "--global" "user.name" "Your Name")
+              (invoke "git" "config" "--global" "user.email" "you@example.com"))))))
     (native-inputs
-     `(("git" ,git-minimal)
-       ("python-covdefaults" ,python-covdefaults)
-       ("python-coverage" ,python-coverage)
-       ("python-distlib" ,python-distlib)
-       ("python-pytest" ,python-pytest)
-       ("python-pytest-env" ,python-pytest-env)
-       ("python-re-assert" ,python-re-assert)
-       ("which" ,which)))
+     (list git-minimal
+           python-covdefaults
+           python-coverage
+           python-distlib
+           python-pytest
+           python-pytest-env
+           python-re-assert
+           which))
     ;; Propagate because pre-commit is also used as a module.
     (propagated-inputs
      (list python-cfgv
-- 
2.41.0

[bug#69980] [PATCH v2 13/14] gnu: python-jupytext: Move to pyproject-build-system.

[Nicolas Graves via Guix-patches via]

* gnu/packages/python-xyz.scm (python-jupytext):
[build-system]: Move to pyproject-build-system.
[arguments]<#:test-flags>: Add flags.
<#:phases>: Remove 'check phase replacement.

Change-Id: I5d708c2fc76b609105c1551a6ed1755c56efcada
---
 gnu/packages/python-xyz.scm | 25 ++++++++++++-------------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 58405d1deaf..5dc1e512228 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -459,26 +459,25 @@ (define-public python-jupytext
        (file-name (git-file-name name version))
        (sha256
         (base32 "0bgf0c4py22ip7qfla8mrmypfh3bg151c8awsr1gvcbw7m4ni01k"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags
+      '(list "-k" (string-append
+                   "not "
+                   (string-join
+                    (list "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 'pre-check
+            (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
            python-autopep8
-- 
2.41.0

[bug#69980] [PATCH v2 14/14] gnu: jupytext: Fix pre-commit native-input removal.

[Nicolas Graves via Guix-patches via]

* gnu/packages/python-xyz.scm (jupytext):
  [arguments]<#:test-flags>: Add a flag to ignore pre_commit tests.

Change-Id: Ifa2097da721c4927ec304c51371eea96bc0cdf41
---
 gnu/packages/python-xyz.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 5dc1e512228..6fbc6f55591 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -469,7 +469,8 @@ (define-public python-jupytext
                     (list "test_create_header_with_set_formats"
                           "test_pre_commit_hook"
                           "test_sync_with_pre_commit_hook")
-                    " and not ")))
+                    " and not "))
+             "--ignore-glob=tests/test_pre_commit_*.py")
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'check 'pre-check
-- 
2.41.0