GNU bug report logs - #62100
[PATCH] gnu: Remove python-pre-commit.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: guix-patches <at> gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH] gnu: Remove python-pre-commit.
Date: Fri, 10 Mar 2023 17:17:27 +0000

* gnu/packages/python-xyz.scm (python-pre-commit): Delete variable.
* gnu/packages/version-control.scm (pre-commit): Add comment referencing
python-pre-commit.
---
Please apply this patch last, after the rest of the series.
Will cause ~70-80 rebuilds from what I can see.

pre-commit and python-pre-commit are duplicates, but pre-commit is better
packaged and newer. pre-commit should never be a native-input of python
packages: it's a package manager for commit linting, which is completely
irrelevant to builds.

Resolves 53502:
https://issues.guix.gnu.org/53502

 gnu/packages/python-xyz.scm      | 30 ------------------------------
 gnu/packages/version-control.scm |  2 +-
 2 files changed, 1 insertion(+), 31 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 8243bb9fd3..b2fb60f322 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -24284,36 +24284,6 @@ (define-public python-retrying
 @end itemize")
     (license license:asl2.0)))
 
-(define-public python-pre-commit
-  (package
-    (name "python-pre-commit")
-    (version "2.10.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "pre_commit" version))
-       (sha256
-        (base32 "1ycf6wpxrhxhdzz0vpryhbdxlwik5khgcvp3hxwvfr447a6k84zl"))))
-    (build-system python-build-system)
-    (arguments
-     ;; Tests fail with "AttributeError: module 'pre_commit.resources' has no
-     ;; attribute 'empty_template_setup'".
-     `(#:tests? #false))
-    (propagated-inputs
-     (list python-cfgv
-           python-identify
-           python-importlib-metadata
-           python-nodeenv
-           python-pyyaml
-           python-toml
-           python-virtualenv))
-    (home-page "https://github.com/pre-commit/pre-commit")
-    (synopsis "Framework for managing multi-language pre-commit hooks")
-    (description
-     "This package provides a framework for managing and maintaining
-multi-language pre-commit hooks.")
-    (license license:expat)))
-
 (define-public python-precis-i18n
   (package
     (name "python-precis-i18n")
diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 8b0997768d..96378a73d3 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -1667,7 +1667,7 @@ (define-public gitile
 
 (define-public pre-commit
   (package
-    (name "pre-commit")
+    (name "pre-commit") ;formerly known as python-pre-commit
     (version "2.20.0")
     (source
      (origin
-- 
2.38.1

Message #8 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH 01/13] gnu: python-jupytext: Remove python-pre-commit.
Date: Fri, 10 Mar 2023 17:21:56 +0000

* gnu/packages/python-xyz.scm (python-jupytext)[native-inputs]: Remove
python-pre-commit.
---
 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 83f3ec02ea..8ab6a44af7 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -358,7 +358,6 @@ (define-public python-jupytext
            python-isort
            python-ipython-genutils
            python-jupyter-server
-           python-pre-commit
            python-pytest
            python-pyaml))
     (propagated-inputs
-- 
2.38.1

Message #11 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH 02/13] gnu: python-bidict: Remove python-pre-commit.
Date: Fri, 10 Mar 2023 17:21:57 +0000

* gnu/packages/python-xyz.scm (python-bidict)[native-inputs]: Remove
python-pre-commit.
---
 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 8ab6a44af7..b491a33051 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1614,7 +1614,6 @@ (define-public python-bidict
     (native-inputs
      (list python-coverage
            python-hypothesis
-           python-pre-commit
            python-py
            python-pytest
            python-pytest-benchmark
-- 
2.38.1

Message #14 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH 03/13] gnu: python-pyjwt: Remove python-pre-commit.
Date: Fri, 10 Mar 2023 17:21:58 +0000

* gnu/packages/python-xyz.scm (python-pyjwt)[native-inputs]: Remove
python-pre-commit.
---
 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 b491a33051..de89059d32 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4085,7 +4085,6 @@ (define-public python-pyjwt
     (native-inputs
      (list python-coverage
            python-cryptography
-           python-pre-commit
            python-pytest
            python-sphinx
            python-sphinx-rtd-theme))
-- 
2.38.1

Message #17 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH 04/13] gnu: python-marshmallow: Remove python-pre-commit.
Date: Fri, 10 Mar 2023 17:21:59 +0000

* gnu/packages/python-xyz.scm (python-marshmallow)[native-inputs]: Remove
python-pre-commit.
---
 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 de89059d32..524133f69c 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21043,7 +21043,6 @@ (define-public python-marshmallow
      (list python-flake8
            python-flake8-bugbear
            python-mypy
-           python-pre-commit
            python-pytest
            python-pytz
            python-simplejson))
-- 
2.38.1

Message #20 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH 05/13] gnu: python-marshmallow-jsonapi: Remove
 python-pre-commit.
Date: Fri, 10 Mar 2023 17:22:00 +0000

* gnu/packages/python-xyz.scm (python-marshmallow-jsonapi)[native-inputs]:
Remove python-pre-commit.
---
 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 524133f69c..571ae16c31 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21071,7 +21071,6 @@ (define-public python-marshmallow-jsonapi
            python-flake8-bugbear
            python-flask
            python-mock
-           python-pre-commit
            python-pytest
            python-tox))
     (home-page "https://github.com/marshmallow-code/marshmallow-jsonapi")
-- 
2.38.1

Message #23 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH 06/13] gnu: python-apispec: Remove python-pre-commit.
Date: Fri, 10 Mar 2023 17:22:01 +0000

* gnu/packages/python-xyz.scm (python-apispec)[native-inputs]: Remove
python-pre-commit.
---
 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 571ae16c31..cb3c51ab59 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21106,7 +21106,6 @@ (define-public python-apispec
            python-flake8-bugbear
            python-marshmallow
            python-mypy
-           python-pre-commit
            python-pytest
            python-pyyaml))
     (home-page "https://github.com/marshmallow-code/apispec")
-- 
2.38.1

Message #26 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH 07/13] gnu: python-apispec-webframeworks: Remove
 python-pre-commit.
Date: Fri, 10 Mar 2023 17:22:02 +0000

* gnu/packages/python-xyz.scm (python-apispec-webframeworks)[native-inputs]:
Remove python-pre-commit.
---
 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 cb3c51ab59..908cfd12ed 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21133,7 +21133,6 @@ (define-public python-apispec-webframeworks
            python-flake8-bugbear
            python-flask
            python-mock
-           python-pre-commit
            python-pytest
            python-tornado
            python-tox))
-- 
2.38.1

Message #29 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH 08/13] gnu: python-minikanren: Remove python-pre-commit.
Date: Fri, 10 Mar 2023 17:22:03 +0000

* gnu/packages/python-xyz.scm (python-minikanren)[native-inputs]: Remove
python-pre-commit.
---
 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 908cfd12ed..8243bb9fd3 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -29312,8 +29312,7 @@ (define-public python-minikanren
            python-black
            python-sympy
            python-versioneer
-           python-coverage
-           python-pre-commit))
+           python-coverage))
     (propagated-inputs
      (list python-toolz python-cons python-multipledispatch
            python-etuples python-logical-unification))
-- 
2.38.1

Message #32 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH 09/13] gnu: python-doubletdetection: Remove python-pre-commit.
Date: Fri, 10 Mar 2023 17:22:04 +0000

* gnu/packages/bioinformatics.scm (python-doubletdetection)[native-inputs]:
Remove python-pre-commit.
---
 gnu/packages/bioinformatics.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0b1f36b347..bdd34fe67f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1347,8 +1347,7 @@ (define-public python-doubletdetection
      (list python-black
            python-flake8
            python-poetry-core
-           python-pytest
-           python-pre-commit))
+           python-pytest))
     (home-page "https://github.com/JonathanShor/DoubletDetection")
     (synopsis
      "This is a package to detect doublets in single-cell RNA-seq count matrices")
-- 
2.38.1

Message #35 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH 10/13] gnu: scvelo: Remove python-pre-commit.
Date: Fri, 10 Mar 2023 17:22:05 +0000

* gnu/packages/bioinformatics.scm (scvelo)[native-inputs]: Remove
python-pre-commit.
---
 gnu/packages/bioinformatics.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bdd34fe67f..06f9eb8ee3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -18152,7 +18152,6 @@ (define-public scvelo
      (list python-black
            python-flake8
            python-hypothesis
-           python-pre-commit
            python-pytest
            python-setuptools-scm
            python-wheel))
-- 
2.38.1

Message #38 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH 11/13] gnu: python-pytest-regressions: Remove
 python-pre-commit.
Date: Fri, 10 Mar 2023 17:22:06 +0000

* gnu/packages/check.scm (python-pytest-regressions)[native-inputs]: Remove
python-pre-commit.
---
 gnu/packages/check.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 44860e3018..0c8777a074 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -3519,7 +3519,6 @@ (define-public python-pytest-regressions
            python-numpy
            python-pandas
            python-pillow
-           python-pre-commit
            python-restructuredtext-lint
            python-tox
            python-setuptools-scm
-- 
2.38.1

Message #41 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH 12/13] gnu: mdpo: Remove python-pre-commit.
Date: Fri, 10 Mar 2023 17:22:07 +0000

* gnu/packages/gettext.scm (mdpo)[native-inputs]: Remove python-pre-commit.
---
 gnu/packages/gettext.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm
index c66e1f58d1..d1e51ab530 100644
--- a/gnu/packages/gettext.scm
+++ b/gnu/packages/gettext.scm
@@ -221,7 +221,6 @@ (define-public mdpo
            python-flake8-implicit-str-concat
            python-flake8-print
            python-isort
-           python-pre-commit
            python-pytest
            python-pytest-cov
            python-sphinx
-- 
2.38.1

Message #44 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH 13/13] gnu: python-sphinxcontrib-apidoc: Remove
 python-pre-commit.
Date: Fri, 10 Mar 2023 17:22:08 +0000

* gnu/packages/sphinx.scm (python-sphinxcontrib-apidoc)[native-inputs]: Remove
python-pre-commit.
---
 gnu/packages/sphinx.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index 5046fdaf85..addf4393b2 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -173,7 +173,6 @@ (define-public python-sphinxcontrib-apidoc
      `(#:tests? #f))                    ;requires python-pytest<4.0
     (native-inputs
      (list python-pbr
-           python-pre-commit
            python-pytest
            python-sphinx
            python-testrepository))
-- 
2.38.1

Message #47 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v2 01/15] gnu: pre-commit: Update to 3.1.1.
Date: Sat, 11 Mar 2023 01:31:11 +0000

* gnu/packages/version-control.scm (pre-commit): Update to 3.1.1.
[propagated-inputs]: Remove python-toml.
---
 gnu/packages/version-control.scm | 26 +++++++++++++++++++++-----
 1 file changed, 21 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 8b0997768d..85291b12b7 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -1667,8 +1667,8 @@ (define-public gitile
 
 (define-public pre-commit
   (package
-    (name "pre-commit")
-    (version "2.20.0")
+    (name "pre-commit") ;formerly known as python-pre-commit
+    (version "3.1.1")
     (source
      (origin
        (method git-fetch)               ; no tests in PyPI release
@@ -1677,7 +1677,11 @@ (define-public pre-commit
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "19jcg6nfnscp87h4wmbpw6r3lc8c75zkvb6wqgavq5dh7wkyg6pq"))))
+        (base32 "1rngcq1vd2phk45wp1cc5jz02wpi53fif0qwk633smfjcjj1kp41"))
+       (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)
     (arguments
      `(#:phases
@@ -1710,6 +1714,18 @@ (define-public pre-commit
                        ;; 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
@@ -1717,7 +1733,8 @@ (define-public pre-commit
                         "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_healthy_venv_creator"
+                        " and not test_r_hook and not test_r_inline"))))))))
     (native-inputs
      `(("git" ,git-minimal)
        ("python-covdefaults" ,python-covdefaults)
@@ -1733,7 +1750,6 @@ (define-public pre-commit
            python-identify
            python-nodeenv
            python-pyyaml
-           python-toml
            python-virtualenv))
     (home-page "https://pre-commit.com/")
     (synopsis "Framework for managing and maintaining pre-commit hooks")
-- 
2.38.1

Message #50 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v2 02/15] gnu: python-jupytext: Remove python-pre-commit.
Date: Sat, 11 Mar 2023 01:31:12 +0000

* gnu/packages/python-xyz.scm (python-jupytext)[native-inputs]: Remove
python-pre-commit.
[native-inputs]: Add pre-commit.
---
 gnu/packages/python-xyz.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 83f3ec02ea..4d76ab9bf6 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -351,6 +351,7 @@ (define-public python-jupytext
                                                       " and not "))))))))))
     (native-inputs
      (list git-minimal
+           pre-commit
            python-autopep8
            python-black
            python-flake8
@@ -358,7 +359,6 @@ (define-public python-jupytext
            python-isort
            python-ipython-genutils
            python-jupyter-server
-           python-pre-commit
            python-pytest
            python-pyaml))
     (propagated-inputs
-- 
2.38.1

Message #53 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v2 03/15] gnu: python-bidict: Remove python-pre-commit.
Date: Sat, 11 Mar 2023 01:31:13 +0000

* gnu/packages/python-xyz.scm (python-bidict)[native-inputs]: Remove
python-pre-commit.
---
 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 4d76ab9bf6..37953d9c7b 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1615,7 +1615,6 @@ (define-public python-bidict
     (native-inputs
      (list python-coverage
            python-hypothesis
-           python-pre-commit
            python-py
            python-pytest
            python-pytest-benchmark
-- 
2.38.1

Message #56 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v2 04/15] gnu: python-pyjwt: Remove python-pre-commit.
Date: Sat, 11 Mar 2023 01:31:14 +0000

* gnu/packages/python-xyz.scm (python-pyjwt)[native-inputs]: Remove
python-pre-commit.
---
 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 37953d9c7b..d16e2eceb2 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4086,7 +4086,6 @@ (define-public python-pyjwt
     (native-inputs
      (list python-coverage
            python-cryptography
-           python-pre-commit
            python-pytest
            python-sphinx
            python-sphinx-rtd-theme))
-- 
2.38.1

Message #59 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v2 05/15] gnu: python-marshmallow: Remove python-pre-commit.
Date: Sat, 11 Mar 2023 01:31:15 +0000

* gnu/packages/python-xyz.scm (python-marshmallow)[native-inputs]: Remove
python-pre-commit.
---
 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 d16e2eceb2..afc5ad845b 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21044,7 +21044,6 @@ (define-public python-marshmallow
      (list python-flake8
            python-flake8-bugbear
            python-mypy
-           python-pre-commit
            python-pytest
            python-pytz
            python-simplejson))
-- 
2.38.1

Message #62 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v2 06/15] gnu: python-marshmallow-jsonapi: Remove
 python-pre-commit.
Date: Sat, 11 Mar 2023 01:31:16 +0000

* gnu/packages/python-xyz.scm (python-marshmallow-jsonapi)[native-inputs]:
Remove python-pre-commit.
---
 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 afc5ad845b..d8c47421f6 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21072,7 +21072,6 @@ (define-public python-marshmallow-jsonapi
            python-flake8-bugbear
            python-flask
            python-mock
-           python-pre-commit
            python-pytest
            python-tox))
     (home-page "https://github.com/marshmallow-code/marshmallow-jsonapi")
-- 
2.38.1

Message #65 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v2 07/15] gnu: python-apispec: Remove python-pre-commit.
Date: Sat, 11 Mar 2023 01:31:17 +0000

* gnu/packages/python-xyz.scm (python-apispec)[native-inputs]: Remove
python-pre-commit.
---
 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 d8c47421f6..d43c91e8f7 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21107,7 +21107,6 @@ (define-public python-apispec
            python-flake8-bugbear
            python-marshmallow
            python-mypy
-           python-pre-commit
            python-pytest
            python-pyyaml))
     (home-page "https://github.com/marshmallow-code/apispec")
-- 
2.38.1

Message #68 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v2 08/15] gnu: python-apispec-webframeworks: Remove
 python-pre-commit.
Date: Sat, 11 Mar 2023 01:31:18 +0000

* gnu/packages/python-xyz.scm (python-apispec-webframeworks)[native-inputs]:
Remove python-pre-commit.
[native-inputs]: Add python-pyyaml.
---
 gnu/packages/python-xyz.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index d43c91e8f7..8e731c56c5 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21134,8 +21134,8 @@ (define-public python-apispec-webframeworks
            python-flake8-bugbear
            python-flask
            python-mock
-           python-pre-commit
            python-pytest
+           python-pyyaml
            python-tornado
            python-tox))
     (home-page "https://github.com/marshmallow-code/apispec-webframeworks")
-- 
2.38.1

Message #71 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v2 09/15] gnu: python-minikanren: Remove python-pre-commit.
Date: Sat, 11 Mar 2023 01:31:19 +0000

* gnu/packages/python-xyz.scm (python-minikanren)[native-inputs]: Remove
python-pre-commit.
---
 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 8e731c56c5..e910f33a29 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -29314,8 +29314,7 @@ (define-public python-minikanren
            python-black
            python-sympy
            python-versioneer
-           python-coverage
-           python-pre-commit))
+           python-coverage))
     (propagated-inputs
      (list python-toolz python-cons python-multipledispatch
            python-etuples python-logical-unification))
-- 
2.38.1

Message #74 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v2 10/15] gnu: python-doubletdetection: Remove
 python-pre-commit.
Date: Sat, 11 Mar 2023 01:31:20 +0000

* gnu/packages/bioinformatics.scm (python-doubletdetection)[native-inputs]:
Remove python-pre-commit.
---
 gnu/packages/bioinformatics.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0b1f36b347..bdd34fe67f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1347,8 +1347,7 @@ (define-public python-doubletdetection
      (list python-black
            python-flake8
            python-poetry-core
-           python-pytest
-           python-pre-commit))
+           python-pytest))
     (home-page "https://github.com/JonathanShor/DoubletDetection")
     (synopsis
      "This is a package to detect doublets in single-cell RNA-seq count matrices")
-- 
2.38.1

Message #77 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v2 11/15] gnu: scvelo: Remove python-pre-commit.
Date: Sat, 11 Mar 2023 01:31:21 +0000

* gnu/packages/bioinformatics.scm (scvelo)[native-inputs]: Remove
python-pre-commit.
---
 gnu/packages/bioinformatics.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bdd34fe67f..06f9eb8ee3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -18152,7 +18152,6 @@ (define-public scvelo
      (list python-black
            python-flake8
            python-hypothesis
-           python-pre-commit
            python-pytest
            python-setuptools-scm
            python-wheel))
-- 
2.38.1

Message #80 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v2 12/15] gnu: python-pytest-regressions: Remove
 python-pre-commit.
Date: Sat, 11 Mar 2023 01:31:22 +0000

* gnu/packages/check.scm (python-pytest-regressions)[native-inputs]: Remove
python-pre-commit.
---
 gnu/packages/check.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 44860e3018..0c8777a074 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -3519,7 +3519,6 @@ (define-public python-pytest-regressions
            python-numpy
            python-pandas
            python-pillow
-           python-pre-commit
            python-restructuredtext-lint
            python-tox
            python-setuptools-scm
-- 
2.38.1

Message #83 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v2 13/15] gnu: mdpo: Remove python-pre-commit.
Date: Sat, 11 Mar 2023 01:31:23 +0000

* gnu/packages/gettext.scm (mdpo)[native-inputs]: Remove python-pre-commit.
---
 gnu/packages/gettext.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm
index c66e1f58d1..d1e51ab530 100644
--- a/gnu/packages/gettext.scm
+++ b/gnu/packages/gettext.scm
@@ -221,7 +221,6 @@ (define-public mdpo
            python-flake8-implicit-str-concat
            python-flake8-print
            python-isort
-           python-pre-commit
            python-pytest
            python-pytest-cov
            python-sphinx
-- 
2.38.1

Message #86 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v2 14/15] gnu: python-sphinxcontrib-apidoc: Remove
 python-pre-commit.
Date: Sat, 11 Mar 2023 01:31:24 +0000

* gnu/packages/sphinx.scm (python-sphinxcontrib-apidoc)[native-inputs]: Remove
python-pre-commit.
---
 gnu/packages/sphinx.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index 5046fdaf85..addf4393b2 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -173,7 +173,6 @@ (define-public python-sphinxcontrib-apidoc
      `(#:tests? #f))                    ;requires python-pytest<4.0
     (native-inputs
      (list python-pbr
-           python-pre-commit
            python-pytest
            python-sphinx
            python-testrepository))
-- 
2.38.1

Message #89 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v2 15/15] gnu: Remove python-pre-commit.
Date: Sat, 11 Mar 2023 01:31:25 +0000

* gnu/packages/python-xyz.scm (python-pre-commit): Delete variable.
---
 gnu/packages/python-xyz.scm | 30 ------------------------------
 1 file changed, 30 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e910f33a29..58e558e627 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -24286,36 +24286,6 @@ (define-public python-retrying
 @end itemize")
     (license license:asl2.0)))
 
-(define-public python-pre-commit
-  (package
-    (name "python-pre-commit")
-    (version "2.10.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "pre_commit" version))
-       (sha256
-        (base32 "1ycf6wpxrhxhdzz0vpryhbdxlwik5khgcvp3hxwvfr447a6k84zl"))))
-    (build-system python-build-system)
-    (arguments
-     ;; Tests fail with "AttributeError: module 'pre_commit.resources' has no
-     ;; attribute 'empty_template_setup'".
-     `(#:tests? #false))
-    (propagated-inputs
-     (list python-cfgv
-           python-identify
-           python-importlib-metadata
-           python-nodeenv
-           python-pyyaml
-           python-toml
-           python-virtualenv))
-    (home-page "https://github.com/pre-commit/pre-commit")
-    (synopsis "Framework for managing multi-language pre-commit hooks")
-    (description
-     "This package provides a framework for managing and maintaining
-multi-language pre-commit hooks.")
-    (license license:expat)))
-
 (define-public python-precis-i18n
   (package
     (name "python-precis-i18n")
-- 
2.38.1

Message #92 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Liliana Marie Prikler <liliana.prikler <at> gmail.com>
To: Antero Mejr <antero <at> mailbox.org>, 62100 <at> debbugs.gnu.org
Subject: Re: [PATCH v2 02/15] gnu: python-jupytext: Remove python-pre-commit.
Date: Sat, 11 Mar 2023 08:52:31 +0100

Am Samstag, dem 11.03.2023 um 01:31 +0000 schrieb Antero Mejr:
> * gnu/packages/python-xyz.scm (python-jupytext)[native-inputs]:
> Remove python-pre-commit.
> [native-inputs]: Add pre-commit.
Should be "replace python-pre-commit with pre-commit".  Regarding the
first message in v1, shouldn't you be dropping this input altogether? 
(Though I suppose pre-commit being a developer tool doesn't stop people
from invoking it in their build files.)

Cheers

Message #95 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Lars-Dominik Braun <lars <at> 6xq.net>
To: Antero Mejr <antero <at> mailbox.org>
Cc: 62100 <at> debbugs.gnu.org
Subject: Re: [bug#62100] [PATCH] gnu: Remove python-pre-commit.
Date: Sat, 11 Mar 2023 08:56:51 +0100

Hi,

> * gnu/packages/python-xyz.scm (python-pre-commit): Delete variable.

usually we don’t delete variables just like that, because it breaks
existing manifests and channels depending on it. Please use
deprecated-package.

Perhaps we should also update the linter to flag this package or the
PyPi importer to not add it in the first place.

Cheers,
Lars

Message #98 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v3 01/16] gnu: pre-commit: Update to 3.1.1.
Date: Sat, 11 Mar 2023 13:39:30 +0000

* gnu/packages/version-control.scm (pre-commit): Update to 3.1.1.
[propagated-inputs]: Remove python-toml.
---
 gnu/packages/version-control.scm | 26 +++++++++++++++++++++-----
 1 file changed, 21 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 8b0997768d..85291b12b7 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -1667,8 +1667,8 @@ (define-public gitile
 
 (define-public pre-commit
   (package
-    (name "pre-commit")
-    (version "2.20.0")
+    (name "pre-commit") ;formerly known as python-pre-commit
+    (version "3.1.1")
     (source
      (origin
        (method git-fetch)               ; no tests in PyPI release
@@ -1677,7 +1677,11 @@ (define-public pre-commit
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "19jcg6nfnscp87h4wmbpw6r3lc8c75zkvb6wqgavq5dh7wkyg6pq"))))
+        (base32 "1rngcq1vd2phk45wp1cc5jz02wpi53fif0qwk633smfjcjj1kp41"))
+       (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)
     (arguments
      `(#:phases
@@ -1710,6 +1714,18 @@ (define-public pre-commit
                        ;; 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
@@ -1717,7 +1733,8 @@ (define-public pre-commit
                         "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_healthy_venv_creator"
+                        " and not test_r_hook and not test_r_inline"))))))))
     (native-inputs
      `(("git" ,git-minimal)
        ("python-covdefaults" ,python-covdefaults)
@@ -1733,7 +1750,6 @@ (define-public pre-commit
            python-identify
            python-nodeenv
            python-pyyaml
-           python-toml
            python-virtualenv))
     (home-page "https://pre-commit.com/")
     (synopsis "Framework for managing and maintaining pre-commit hooks")
-- 
2.38.1

Message #101 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v3 02/16] gnu: python-jupytext: Replace python-pre-commit with
 pre-commit.
Date: Sat, 11 Mar 2023 13:39:31 +0000

* gnu/packages/python-xyz.scm (python-jupytext)[native-inputs]: Remove
python-pre-commit.
[native-inputs]: Add pre-commit.
---
 gnu/packages/python-xyz.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 83f3ec02ea..4d76ab9bf6 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -351,6 +351,7 @@ (define-public python-jupytext
                                                       " and not "))))))))))
     (native-inputs
      (list git-minimal
+           pre-commit
            python-autopep8
            python-black
            python-flake8
@@ -358,7 +359,6 @@ (define-public python-jupytext
            python-isort
            python-ipython-genutils
            python-jupyter-server
-           python-pre-commit
            python-pytest
            python-pyaml))
     (propagated-inputs
-- 
2.38.1

Message #104 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v3 03/16] gnu: python-bidict: Remove python-pre-commit.
Date: Sat, 11 Mar 2023 13:39:32 +0000

* gnu/packages/python-xyz.scm (python-bidict)[native-inputs]: Remove
python-pre-commit.
---
 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 4d76ab9bf6..37953d9c7b 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -1615,7 +1615,6 @@ (define-public python-bidict
     (native-inputs
      (list python-coverage
            python-hypothesis
-           python-pre-commit
            python-py
            python-pytest
            python-pytest-benchmark
-- 
2.38.1

Message #107 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v3 04/16] gnu: python-pyjwt: Remove python-pre-commit.
Date: Sat, 11 Mar 2023 13:39:33 +0000

* gnu/packages/python-xyz.scm (python-pyjwt)[native-inputs]: Remove
python-pre-commit.
---
 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 37953d9c7b..d16e2eceb2 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4086,7 +4086,6 @@ (define-public python-pyjwt
     (native-inputs
      (list python-coverage
            python-cryptography
-           python-pre-commit
            python-pytest
            python-sphinx
            python-sphinx-rtd-theme))
-- 
2.38.1

Message #110 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v3 05/16] gnu: python-marshmallow: Remove python-pre-commit.
Date: Sat, 11 Mar 2023 13:39:34 +0000

* gnu/packages/python-xyz.scm (python-marshmallow)[native-inputs]: Remove
python-pre-commit.
---
 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 d16e2eceb2..afc5ad845b 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21044,7 +21044,6 @@ (define-public python-marshmallow
      (list python-flake8
            python-flake8-bugbear
            python-mypy
-           python-pre-commit
            python-pytest
            python-pytz
            python-simplejson))
-- 
2.38.1

Message #113 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v3 06/16] gnu: python-marshmallow-jsonapi: Remove
 python-pre-commit.
Date: Sat, 11 Mar 2023 13:39:35 +0000

* gnu/packages/python-xyz.scm (python-marshmallow-jsonapi)[native-inputs]:
Remove python-pre-commit.
---
 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 afc5ad845b..d8c47421f6 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21072,7 +21072,6 @@ (define-public python-marshmallow-jsonapi
            python-flake8-bugbear
            python-flask
            python-mock
-           python-pre-commit
            python-pytest
            python-tox))
     (home-page "https://github.com/marshmallow-code/marshmallow-jsonapi")
-- 
2.38.1

Message #116 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v3 07/16] gnu: python-apispec: Remove python-pre-commit.
Date: Sat, 11 Mar 2023 13:39:36 +0000

* gnu/packages/python-xyz.scm (python-apispec)[native-inputs]: Remove
python-pre-commit.
---
 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 d8c47421f6..d43c91e8f7 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21107,7 +21107,6 @@ (define-public python-apispec
            python-flake8-bugbear
            python-marshmallow
            python-mypy
-           python-pre-commit
            python-pytest
            python-pyyaml))
     (home-page "https://github.com/marshmallow-code/apispec")
-- 
2.38.1

Message #119 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v3 08/16] gnu: python-apispec-webframeworks: Remove
 python-pre-commit.
Date: Sat, 11 Mar 2023 13:39:37 +0000

* gnu/packages/python-xyz.scm (python-apispec-webframeworks)[native-inputs]:
Remove python-pre-commit.
[native-inputs]: Add python-pyyaml.
---
 gnu/packages/python-xyz.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index d43c91e8f7..8e731c56c5 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21134,8 +21134,8 @@ (define-public python-apispec-webframeworks
            python-flake8-bugbear
            python-flask
            python-mock
-           python-pre-commit
            python-pytest
+           python-pyyaml
            python-tornado
            python-tox))
     (home-page "https://github.com/marshmallow-code/apispec-webframeworks")
-- 
2.38.1

Message #122 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v3 09/16] gnu: python-minikanren: Remove python-pre-commit.
Date: Sat, 11 Mar 2023 13:39:38 +0000

* gnu/packages/python-xyz.scm (python-minikanren)[native-inputs]: Remove
python-pre-commit.
---
 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 8e731c56c5..e910f33a29 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -29314,8 +29314,7 @@ (define-public python-minikanren
            python-black
            python-sympy
            python-versioneer
-           python-coverage
-           python-pre-commit))
+           python-coverage))
     (propagated-inputs
      (list python-toolz python-cons python-multipledispatch
            python-etuples python-logical-unification))
-- 
2.38.1

Message #125 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v3 10/16] gnu: python-doubletdetection: Remove
 python-pre-commit.
Date: Sat, 11 Mar 2023 13:39:39 +0000

* gnu/packages/bioinformatics.scm (python-doubletdetection)[native-inputs]:
Remove python-pre-commit.
---
 gnu/packages/bioinformatics.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0b1f36b347..bdd34fe67f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1347,8 +1347,7 @@ (define-public python-doubletdetection
      (list python-black
            python-flake8
            python-poetry-core
-           python-pytest
-           python-pre-commit))
+           python-pytest))
     (home-page "https://github.com/JonathanShor/DoubletDetection")
     (synopsis
      "This is a package to detect doublets in single-cell RNA-seq count matrices")
-- 
2.38.1

Message #128 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v3 11/16] gnu: scvelo: Remove python-pre-commit.
Date: Sat, 11 Mar 2023 13:39:40 +0000

* gnu/packages/bioinformatics.scm (scvelo)[native-inputs]: Remove
python-pre-commit.
---
 gnu/packages/bioinformatics.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bdd34fe67f..06f9eb8ee3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -18152,7 +18152,6 @@ (define-public scvelo
      (list python-black
            python-flake8
            python-hypothesis
-           python-pre-commit
            python-pytest
            python-setuptools-scm
            python-wheel))
-- 
2.38.1

Message #131 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v3 12/16] gnu: python-pytest-regressions: Remove
 python-pre-commit.
Date: Sat, 11 Mar 2023 13:39:41 +0000

* gnu/packages/check.scm (python-pytest-regressions)[native-inputs]: Remove
python-pre-commit.
---
 gnu/packages/check.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 44860e3018..0c8777a074 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -3519,7 +3519,6 @@ (define-public python-pytest-regressions
            python-numpy
            python-pandas
            python-pillow
-           python-pre-commit
            python-restructuredtext-lint
            python-tox
            python-setuptools-scm
-- 
2.38.1

Message #134 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v3 13/16] gnu: mdpo: Remove python-pre-commit.
Date: Sat, 11 Mar 2023 13:39:42 +0000

* gnu/packages/gettext.scm (mdpo)[native-inputs]: Remove python-pre-commit.
---
 gnu/packages/gettext.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm
index c66e1f58d1..d1e51ab530 100644
--- a/gnu/packages/gettext.scm
+++ b/gnu/packages/gettext.scm
@@ -221,7 +221,6 @@ (define-public mdpo
            python-flake8-implicit-str-concat
            python-flake8-print
            python-isort
-           python-pre-commit
            python-pytest
            python-pytest-cov
            python-sphinx
-- 
2.38.1

Message #137 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v3 14/16] gnu: python-sphinxcontrib-apidoc: Remove
 python-pre-commit.
Date: Sat, 11 Mar 2023 13:39:43 +0000

* gnu/packages/sphinx.scm (python-sphinxcontrib-apidoc)[native-inputs]: Remove
python-pre-commit.
---
 gnu/packages/sphinx.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index 5046fdaf85..addf4393b2 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -173,7 +173,6 @@ (define-public python-sphinxcontrib-apidoc
      `(#:tests? #f))                    ;requires python-pytest<4.0
     (native-inputs
      (list python-pbr
-           python-pre-commit
            python-pytest
            python-sphinx
            python-testrepository))
-- 
2.38.1

Message #140 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v3 15/16] gnu: python-pre-commit: Replace with pre-commit.
Date: Sat, 11 Mar 2023 13:39:44 +0000

* gnu/packages/python-xyz.scm (python-pre-commit): Deprecate in favor of
pre-commit.
---
 gnu/packages/python-xyz.scm | 29 +----------------------------
 1 file changed, 1 insertion(+), 28 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e910f33a29..02ec564e8e 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -24287,34 +24287,7 @@ (define-public python-retrying
     (license license:asl2.0)))
 
 (define-public python-pre-commit
-  (package
-    (name "python-pre-commit")
-    (version "2.10.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "pre_commit" version))
-       (sha256
-        (base32 "1ycf6wpxrhxhdzz0vpryhbdxlwik5khgcvp3hxwvfr447a6k84zl"))))
-    (build-system python-build-system)
-    (arguments
-     ;; Tests fail with "AttributeError: module 'pre_commit.resources' has no
-     ;; attribute 'empty_template_setup'".
-     `(#:tests? #false))
-    (propagated-inputs
-     (list python-cfgv
-           python-identify
-           python-importlib-metadata
-           python-nodeenv
-           python-pyyaml
-           python-toml
-           python-virtualenv))
-    (home-page "https://github.com/pre-commit/pre-commit")
-    (synopsis "Framework for managing multi-language pre-commit hooks")
-    (description
-     "This package provides a framework for managing and maintaining
-multi-language pre-commit hooks.")
-    (license license:expat)))
+  (deprecated-package "python-pre-commit" pre-commit))
 
 (define-public python-precis-i18n
   (package
-- 
2.38.1

Message #143 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: 62100 <at> debbugs.gnu.org
Cc: Antero Mejr <antero <at> mailbox.org>
Subject: [PATCH v3 16/16] lint: Check that python-pre-commit is not an input.
Date: Sat, 11 Mar 2023 13:39:45 +0000

pre-commit should never be a native-input of python packages, it's a
package manager for commit linting that is irrelevant to builds.

* guix/lint.scm (check-inputs-should-not-be-an-input-at-all): Add entry
for python-pre-commit.
---
 guix/lint.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/guix/lint.scm b/guix/lint.scm
index 8e3976171f..17dcc23647 100644
--- a/guix/lint.scm
+++ b/guix/lint.scm
@@ -533,7 +533,8 @@ (define (check-inputs-should-not-be-an-input-at-all package)
   ;; Emit a warning if some inputs of PACKAGE are likely to should not be
   ;; an input at all.
   (let ((input-names '("python-setuptools"
-                       "python-pip")))
+                       "python-pip"
+                       "python-pre-commit")))
     (map (lambda (input)
            (make-warning
             package
-- 
2.38.1

Message #146 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: Lars-Dominik Braun <lars <at> 6xq.net>
Cc: 62100 <at> debbugs.gnu.org
Subject: Re: [bug#62100] [PATCH] gnu: Remove python-pre-commit.
Date: Sat, 11 Mar 2023 13:41:56 +0000

Lars-Dominik Braun <lars <at> 6xq.net> writes:

> usually we don’t delete variables just like that, because it breaks
> existing manifests and channels depending on it. Please use
> deprecated-package.

Fixed in v3.

> Perhaps we should also update the linter to flag this package or the
> PyPi importer to not add it in the first place.

Added python-pre-commit to the
check-inputs-should-not-be-an-input-at-all linter in v3.

Message #149 received at 62100 <at> debbugs.gnu.org (full text, mbox):

From: Antero Mejr <antero <at> mailbox.org>
To: Liliana Marie Prikler <liliana.prikler <at> gmail.com>
Cc: 62100 <at> debbugs.gnu.org
Subject: Re: [PATCH v2 02/15] gnu: python-jupytext: Remove python-pre-commit.
Date: Sat, 11 Mar 2023 13:44:30 +0000

Liliana Marie Prikler <liliana.prikler <at> gmail.com> writes:

> Am Samstag, dem 11.03.2023 um 01:31 +0000 schrieb Antero Mejr:
>> * gnu/packages/python-xyz.scm (python-jupytext)[native-inputs]:
>> Remove python-pre-commit.
>> [native-inputs]: Add pre-commit.
> Should be "replace python-pre-commit with pre-commit".  Regarding the
> first message in v1, shouldn't you be dropping this input altogether? 
> (Though I suppose pre-commit being a developer tool doesn't stop people
> from invoking it in their build files.)

Fixed that commit message in v3.

Yes, python-jupytext is an unusual case where they invoke pre-commit as
part of their tests.

Message #154 received at 62100-done <at> debbugs.gnu.org (full text, mbox):

From: Lars-Dominik Braun <lars <at> 6xq.net>
To: Antero Mejr <antero <at> mailbox.org>
Cc: 62100-done <at> debbugs.gnu.org
Subject: Re: [bug#62100] [PATCH] gnu: Remove python-pre-commit.
Date: Sun, 12 Mar 2023 12:14:43 +0100

Hi,

> Fixed in v3.

thanks. I pushed v3 as:

a70b9fb319 (lint: Check that python-pre-commit is not an input., 2023-03-11)
831baaf81e (gnu: python-pre-commit: Replace with pre-commit., 2023-03-11)
5c976c6b45 (gnu: python-sphinxcontrib-apidoc: Remove python-pre-commit., 2023-03-11)
dcc3bebfaf (gnu: mdpo: Remove python-pre-commit., 2023-03-11)
57a94b9eff (gnu: python-pytest-regressions: Remove python-pre-commit., 2023-03-11)
72b1fe77b2 (gnu: scvelo: Remove python-pre-commit., 2023-03-11)
ed59796de5 (gnu: python-doubletdetection: Remove python-pre-commit., 2023-03-11)
fb624c919f (gnu: python-minikanren: Remove python-pre-commit., 2023-03-11)
f19ab875ff (gnu: python-apispec-webframeworks: Remove python-pre-commit., 2023-03-11)
6181cce732 (gnu: python-apispec: Remove python-pre-commit., 2023-03-11)
2cfb7dbd2f (gnu: python-marshmallow-jsonapi: Remove python-pre-commit., 2023-03-11)
a83f3a13e6 (gnu: python-marshmallow: Remove python-pre-commit., 2023-03-11)
d456ced2d4 (gnu: python-pyjwt: Remove python-pre-commit., 2023-03-11)
622b92d935 (gnu: python-bidict: Remove python-pre-commit., 2023-03-11)
64d69c3f79 (gnu: python-jupytext: Replace python-pre-commit with pre-commit., 2023-03-11)
94c898cd9b (gnu: pre-commit: Update to 3.1.1., 2023-03-11)

Cheers,
Lars

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