Subject: [PATCH v5 07/48] build-system/pyproject: Remove python-flake8 inputs.

From: Nicolas Graves <[email-masked]>
Date: Thu, 27 Feb 2025 15:27:08 +0100

* gnu/packages/bioinformatics.scm (python-doubletdetection,
python-biom-format, python-metacells, python-ngesh)
* gnu/packages/ebook.scm (calibre)
* gnu/packages/engineering.scm (python-scikit-rf)
* gnu/packages/finance.scm (python-mt-940)
* gnu/packages/geo.scm (python-geopy)
* gnu/packages/gettext.scm (python-mdpo)
* gnu/packages/graph.scm (python-pygsp)
* gnu/packages/graphviz.scm (python-uqbar)
* gnu/packages/machine-learning.scm (python-funsor,
python-imbalanced-learn, python-captum, python-pymanopt,
python-pyro-api, python-pyro-ppl, python-linear-operator,
python-gpytorch)
* gnu/packages/python-web.scm (python-ovh, python-furl,
python-httplib2, python-http-ece, python-woob,
python-starsessions-for-pytorch-lightning)
* gnu/packages/python-xyz.scm (python-archspec, python-colorful,
python-pymd4c, python-flasgger, python-imageio,
python-importlib-ressources, python-seaborn, python-inflect,
python-yq, python-update-checker, python-eliot, python-dateparser,
python-jinja2-cli, python-verspec, python-mike,
python-simple-websocket)
* gnu/packages/simulation.scm (python-dolfin-adjoint)
* gnu/packages/statistics.scm (python-statsmodels)
* gnu/packages/vpn.scm (sshuttle)
* gnu/packages/wm.scm (qtile)
* gnu/packages/textutils.scm (python-panflute)
[native-inputs]: Remove python-flake8.

* gnu/packages/music.scm (python-mutagen):
  [arguments]<#:test-flags>: Ignore flake8 quality tests.
  [native-inputs]: Remove python-flake8.

* gnu/packages/protobuf.scm (python-pure-protobuf):
  [arguments]<#:phases>: Remove flake8 invocation from check phase.
  [native-inputs]: Remove python-flake8.
---
 gnu/packages/bioinformatics.scm   | 10 +++-------
 gnu/packages/ebook.scm            |  1 -
 gnu/packages/engineering.scm      |  1 -
 gnu/packages/finance.scm          |  4 +---
 gnu/packages/gettext.scm          |  1 -
 gnu/packages/graph.scm            |  3 +--
 gnu/packages/graphviz.scm         |  1 -
 gnu/packages/machine-learning.scm | 15 ++++-----------
 gnu/packages/music.scm            |  4 ++--
 gnu/packages/protobuf.scm         |  4 +---
 gnu/packages/python-web.scm       | 15 ++++-----------
 gnu/packages/python-xyz.scm       | 31 ++++++++++++-------------------
 gnu/packages/simulation.scm       |  1 -
 gnu/packages/statistics.scm       |  1 -
 gnu/packages/textutils.scm        |  1 -
 gnu/packages/vpn.scm              |  1 -
 gnu/packages/wm.scm               |  1 -
 17 files changed, 28 insertions(+), 67 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1a0ae8918e..bda5ab3a8f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2824,8 +2824,7 @@ (define-public python-doubletdetection
            python-scipy
            python-tqdm))
     (native-inputs
-     (list python-flake8
-           python-poetry-core
+     (list python-poetry-core
            python-pytest))
     (home-page "https://github.com/JonathanShor/DoubletDetection")
     (synopsis
@@ -3169,7 +3168,6 @@ (define-public python-metacells
                              python-threadpoolctl
                              python-umap-learn))
     (native-inputs (list python-bumpversion
-                         python-flake8
                          python-isort
                          python-mypy
                          python-mypy-extensions
@@ -3207,7 +3205,7 @@ (define-public python-ngesh
         (base32 "07sj4x95b5hvx57pw24f80sk4ag4hkg1z6wzym3pzi8n5gn85n1z"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-ete3 python-numpy python-six))
-    (native-inputs (list python-flake8 python-pytest python-twine
+    (native-inputs (list python-pytest python-twine
                          python-wheel))
     (home-page "https://github.com/tresoldi/ngesh")
     (synopsis "Library for phylogenetic tree simulation")
@@ -3923,7 +3921,6 @@ (define-public python-biom-format
     (propagated-inputs
      (list python-anndata
            python-click
-           python-flake8
            python-future
            python-h5py
            python-numpy
@@ -24051,8 +24048,7 @@ (define-public scvelo
            python-umap-learn
            pybind11))
     (native-inputs
-     (list python-flake8
-           python-hypothesis
+     (list python-hypothesis
            python-pytest
            python-setuptools-scm
            python-wheel))
diff --git a/gnu/packages/ebook.scm b/gnu/packages/ebook.scm
index 46ec951916..75e14801dd 100644
--- a/gnu/packages/ebook.scm
+++ b/gnu/packages/ebook.scm
@@ -156,7 +156,6 @@ (define-public calibre
     (native-inputs
      (list bash-minimal
            pkg-config
-           python-flake8
            python-pyqt-builder
            qtbase-5                     ; for qmake
            xdg-utils))
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index 8ca3b87ff2..3882a35d6b 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -2965,7 +2965,6 @@ (define-public python-scikit-rf
                              python-qtpy
                              python-scipy))
     (native-inputs (list python-coverage
-                         python-flake8
                          python-nbval
                          python-networkx
                          python-pytest
diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 9805679597..f3be674c01 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -2310,9 +2310,7 @@ (define-public python-mt-940
                         ;; Remove custom --cov flags.
                         (delete-file "pytest.ini")
                         (invoke "pytest" "-vv")))))))
-    (native-inputs (list python-flake8
-                         python-pytest
-                         python-pyyaml))
+    (native-inputs (list python-pytest python-pyyaml))
     (home-page "https://mt940.readthedocs.io/")
     (synopsis "Python parser for MT940-encoded SWIFT data")
     (description
diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm
index 7862c296bd..29cdbab915 100644
--- a/gnu/packages/gettext.scm
+++ b/gnu/packages/gettext.scm
@@ -226,7 +226,6 @@ (define-public mdpo
     (build-system python-build-system)
     (native-inputs
      (list python-bump2version
-           python-flake8
            python-flake8-implicit-str-concat
            python-flake8-print
            python-isort
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 75ebbff2db..57c4bd05ed 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -570,8 +570,7 @@ (define-public python-pygsp
                 "")))))))
     (propagated-inputs (list python-numpy python-scikit-image python-scipy))
     (native-inputs
-     (list python-coverage python-coveralls python-flake8
-           python-pytest))
+     (list python-coverage python-coveralls python-pytest))
     (home-page "https://github.com/epfl-lts2/pygsp")
     (synopsis "Graph Signal Processing in Python")
     (description "The PyGSP is a Python package to ease signal processing on
diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index defd53df73..0d3db31212 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -224,7 +224,6 @@ (define-public python-uqbar
 and not test_sphinx_book_text_broken_strict")))
     (native-inputs
      (list graphviz
-           python-flake8
            python-isort
            python-mypy
            python-pytest
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 480e534823..65cb08e2f3 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -229,8 +229,7 @@ (define-public python-funsor
     (propagated-inputs (list python-makefun python-multipledispatch
                              python-numpy python-opt-einsum
                              python-typing-extensions))
-    (native-inputs (list python-flake8
-                         python-isort
+    (native-inputs (list python-isort
                          python-nbsphinx
                          python-pandas
                          python-pillow
@@ -1143,7 +1142,6 @@ (define-public python-pymanopt
                ((",!=1.12\\.\\*") "")))))))
     (propagated-inputs (list python-numpy python-scipy))
     (native-inputs (list python-autograd
-                         python-flake8
                          python-flake8-bugbear
                          python-isort
                          python-matplotlib
@@ -2152,8 +2150,7 @@ (define-public python-imbalanced-learn
                               (getcwd)))))))
     (propagated-inputs (list python-joblib python-numpy python-scikit-learn
                              python-scipy python-threadpoolctl))
-    (native-inputs (list python-flake8
-                         python-keras
+    (native-inputs (list python-keras
                          python-mypy
                          python-pandas
                          python-pytest
@@ -5321,7 +5318,6 @@ (define-public python-captum
      (list python-matplotlib python-numpy python-pytorch python-tqdm))
     (native-inputs (list jupyter
                          python-annoy
-                         python-flake8
                          python-flask
                          python-flask-compress
                          python-ipython
@@ -5842,8 +5838,7 @@ (define-public python-pyro-api
     (build-system python-build-system)
     (arguments '(#:tests? #false)) ;requires pyro
     (native-inputs
-     (list python-flake8
-           python-ipython
+     (list python-ipython
            python-pytest
            python-sphinx
            python-sphinx-rtd-theme))
@@ -5900,8 +5895,7 @@ (define-public python-linear-operator
                              python-pytorch
                              python-scipy
                              python-typeguard))
-    (native-inputs (list python-flake8
-                         python-flake8-print
+    (native-inputs (list python-flake8-print
                          python-pytest
                          python-setuptools
                          python-setuptools-scm
@@ -5932,7 +5926,6 @@ (define-public python-gpytorch
                              python-scikit-learn
                              python-scipy))
     (native-inputs (list python-coverage
-                         python-flake8
                          python-flake8-print
                          python-nbval
                          python-pytest
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index bf47489d34..7d28ef4b58 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -4116,6 +4116,7 @@ (define-public python-mutagen
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags '(list "--ignore=tests/quality/test_flake8.py")
        #:phases
        #~(modify-phases %standard-phases
            (add-before 'check 'remove-hypothesis-deadlines
@@ -4126,8 +4127,7 @@ (define-public python-mutagen
                  (("( +)@given" all spaces)
                   (string-append spaces "@settings(deadline=None)\n" all))))))))
     (native-inputs
-     (list python-flake8
-           python-hypothesis
+     (list python-hypothesis
            python-pytest
            python-setuptools
            python-wheel))
diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm
index 9d81b1c508..203e4909d6 100644
--- a/gnu/packages/protobuf.scm
+++ b/gnu/packages/protobuf.scm
@@ -502,7 +502,7 @@ (define-public python-pure-protobuf
         (base32 "15dp5pvazd0jx4wzzh79080ah7hkpd3axh40al9vhzs2hf3v90hx"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-flake8 python-pytest python-pytest-cov python-isort))
+     (list python-pytest python-pytest-cov python-isort))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
@@ -510,8 +510,6 @@ (define-public python-pure-protobuf
            (lambda _
              (invoke "pytest" "--cov-report" "term-missing" "--cov"
                      "pure_protobuf")
-             (invoke "flake8" "pure_protobuf" "tests"
-                     "--ignore=F541")
              (invoke "isort" "-rc" "-c" "pure_protobuf" "tests"))))))
     (home-page "https://pypi.org/project/pure-protobuf/")
     (synopsis "Protobuf implementation using dataclasses")
diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 17c36189f7..c654f3f13d 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1605,7 +1605,6 @@ (define-public python-ovh
     (arguments (list #:tests? #f))      ; XXX: tests require networking
     (propagated-inputs (list python-requests))
     (native-inputs (list python-coverage
-                         python-flake8
                          python-isort
                          python-pytest
                          python-pytest-cov
@@ -1921,8 +1920,6 @@ (define-public python-furl
     (build-system python-build-system)
     (propagated-inputs
      (list python-six python-orderedmultidict))
-    (native-inputs
-     (list python-flake8))
     (home-page "https://github.com/gruns/furl")
     (synopsis "URL manipulation in Python")
     (description "Furl provides an easy-to-use alternative to the
@@ -1955,7 +1952,6 @@ (define-public python-httplib2
                  (("==") ">=")))))))
     (native-inputs
      (list python-cryptography
-           python-flake8
            python-future
            python-mock
            python-pytest
@@ -8583,7 +8579,7 @@ (define-public python-http-ece
     (propagated-inputs
      (list python-cryptography))
     (native-inputs
-     (list python-coverage python-flake8 python-mock python-nose))
+     (list python-coverage python-mock python-nose))
     (home-page "https://github.com/web-push-libs/encrypted-content-encoding")
     (synopsis "Encrypted Content Encoding for HTTP")
     (description
@@ -9048,8 +9044,7 @@ (define-public python-simple-websocket
      ;; Requires Internet access to resolve example.com
      (list #:test-flags '(list "--ignore=tests/test_client.py")))
     (propagated-inputs (list python-wsproto))
-    (native-inputs (list python-flake8
-                         python-pytest
+    (native-inputs (list python-pytest
                          python-pytest-cov
                          python-setuptools
                          python-tox
@@ -9660,8 +9655,7 @@ (define-public python-woob
            python-six
            python-unidecode))
     (native-inputs
-     (list python-coverage python-flake8 python-nose python-selenium
-           python-xunitparser))
+     (list python-coverage python-nose python-selenium python-xunitparser))
     (home-page "https://woob.tech/")
     (synopsis "Woob, Web Outside Of Browsers")
     (description "Woob is a collection of applications able to interact with
@@ -10321,8 +10315,7 @@ (define-public python-starsessions
            python-itsdangerous
            python-starlette))
     (native-inputs
-     (list python-flake8
-           python-httpx
+     (list python-httpx
            python-mypy
            python-poetry-core
            python-pytest
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f2c5f7fa63..52f7ebde3f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -396,8 +396,7 @@ (define-public python-archspec
                              python-scikit-learn
                              python-tables
                              python-typing-extensions))
-    (native-inputs (list python-flake8
-                         python-isort
+    (native-inputs (list python-isort
                          python-poetry-core
                          python-pytest
                          python-pytest-cov))
@@ -1555,8 +1554,7 @@ (define-public python-colorful
         (base32 "0kyy9qhvrb5m9h8xmri7c88i0k1g5qc7017anw39gx44an7mn33y"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-coverage python-flake8 python-pytest python-setuptools
-           python-wheel))
+     (list python-coverage python-pytest python-setuptools python-wheel))
     (propagated-inputs
      (list python-colorama))
     (home-page "http://github.com/timofurrer/colorful")
@@ -2926,7 +2924,7 @@ (define-public python-pymd4c
     (inputs
      (list md4c))
     (native-inputs
-     (list python-flake8 python-pkgconfig pkg-config))
+     (list python-pkgconfig pkg-config))
     (home-page "https://github.com/dominickpastore/pymd4c")
     (synopsis "Python bindings for MD4C")
     (description
@@ -12022,8 +12020,7 @@ (define-public python-imageio
     (propagated-inputs
      (list python-imageio-ffmpeg python-numpy python-pillow python-tifffile))
     (native-inputs
-     (list python-flake8
-           python-fsspec
+     (list python-fsspec
            python-pytest
            python-pytest-cov
            python-setuptools
@@ -12837,8 +12834,7 @@ (define-public python-importlib-resources
              (setenv "PYTHONPATH"
                      (string-append (getcwd) "/_custom_build")))))))
     (native-inputs
-     (list python-flake8
-           python-pytest
+     (list python-pytest
            python-pytest-black
            python-pytest-checkdocs
            python-pytest-cov
@@ -15110,8 +15106,7 @@ (define-public python-seaborn
            python-scipy
            python-statsmodels))
     (native-inputs
-     (list python-flake8
-           python-flit-core
+     (list python-flit-core
            python-ipykernel
            python-nbconvert
            python-numpydoc
@@ -28217,7 +28212,7 @@ (define-public python-yq
     (inputs
      (list python-argcomplete python-pyyaml python-xmltodict python-toml jq))
     (native-inputs
-     (list python-coverage python-flake8 python-setuptools-scm python-wheel))
+     (list python-coverage python-setuptools-scm python-wheel))
     (home-page "https://github.com/kislyuk/yq")
     (synopsis "Command-line YAML/XML processor")
     (description
@@ -29225,7 +29220,7 @@ (define-public python-update-checker
         (base32 "04yb5a9mi45ax50m2m0ih6gdvkk1j7gfmy83dd58i1f59axlabba"))))
     (build-system python-build-system)
     (propagated-inputs (list python-requests))
-    (native-inputs (list python-flake8 python-pytest))
+    (native-inputs (list python-pytest))
     (home-page "https://github.com/bboe/update_checker")
     (synopsis "Python module that will check for package updates")
     (description "This package provides a Python module that will check for
@@ -33558,7 +33553,6 @@ (define-public python-eliot
      (list python-boltons python-orjson python-pyrsistent python-zope-interface))
     (native-inputs
      (list python-coverage
-           python-flake8
            python-hypothesis
            python-pytest
            python-pytest-xdist
@@ -34346,7 +34340,7 @@ (define-public python-dateparser
      (list python-dateutil python-pytz python-regex python-ruamel.yaml
            python-tzlocal))
     (native-inputs
-     (list python-flake8 python-pytest python-parameterized tzdata-for-tests
+     (list python-pytest python-parameterized tzdata-for-tests
            python-setuptools python-wheel))
     (arguments
      `(#:phases
@@ -35772,8 +35766,7 @@ (define-public python-jinja2-cli
     (propagated-inputs
      (list python-jinja2))
     (native-inputs
-     (list python-flake8
-           python-jinja2
+     (list python-jinja2
            python-pytest
            python-setuptools
            python-wheel))
@@ -38326,7 +38319,7 @@ (define-public python-verspec
                (base32
                 "07n06wv85fm4vl1ird2mja0823js3x322wgs9gdnq1djjyk4ql64"))))
     (build-system python-build-system)
-    (native-inputs (list python-coverage python-flake8 python-mypy
+    (native-inputs (list python-coverage python-mypy
                          python-pretend python-pytest))
     (arguments
      `(#:phases (modify-phases %standard-phases
@@ -38763,7 +38756,7 @@ (define-public python-mike
                 "0yxp816x7s948xsd0fifvq9shg01xdxlifd9rzf5y2rd9iwz3hsn"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-coverage python-flake8 python-shtab))
+     (list python-coverage python-shtab))
     (propagated-inputs
      (list python-jinja2 python-mkdocs python-pyyaml python-verspec))
     (home-page "https://github.com/jimporter/mike")
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index 3af29aeeaa..1eed4fd180 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -1252,7 +1252,6 @@ (define-public python-dolfin-adjoint
      (list pkg-config
            python-coverage
            python-decorator
-           python-flake8
            python-pkgconfig
            python-pytest))
     (propagated-inputs
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index ceca13084e..58975e652f 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2670,7 +2670,6 @@ (define-public python-statsmodels
     (native-inputs
      (list python-colorama
            python-cython
-           python-flake8
            python-isort
            python-joblib
            python-matplotlib
diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index c886b009be..1bdd58269c 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -1758,7 +1758,6 @@ (define-public python-panflute
     (propagated-inputs (list python-click python-pyyaml))
     (native-inputs (list python-configparser
                          python-coverage
-                         python-flake8
                          python-pandocfilters
                          python-pytest
                          python-pytest-cov
diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm
index 0b62e8c7cf..53706a8de1 100644
--- a/gnu/packages/vpn.scm
+++ b/gnu/packages/vpn.scm
@@ -1034,7 +1034,6 @@ (define (install-man-page file)
     (native-inputs
      (list python-setuptools-scm
            ;; For tests only.
-           python-flake8
            python-mock
            python-poetry-core
            python-pytest-cov
diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm
index 0e6153d7bd..8d1bce1009 100644
--- a/gnu/packages/wm.scm
+++ b/gnu/packages/wm.scm
@@ -864,7 +864,6 @@ (define-public qtile
            python-xcffib))
     (native-inputs
       (list pkg-config
-            python-flake8
             python-pep8-naming
             python-pytest
             python-pytest-cov
-- 
2.48.1