gh-40166: Format toml files and add linter check
    
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### ⌛ Dependencies

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URL: #40166
Reported by: Tobias Diez
Reviewer(s):

Author: Release Manager

.github/workflows/lint.yml

@@ -44,3 +44,8 @@ jobs:
     - name: Validate docstring markup as RST
       if: (success() || failure()) && steps.deps.outcome == 'success'
       run: uv run --frozen --only-group lint -- flake8 --select=RST src/sage/ --config src/tox.ini
+    
+    - name: TOML format check with taplo
+      uses: docker://tamasfe/taplo:0.10.0
+      with:
+        args: format --check --diff pyproject.toml .taplo.toml 

.taplo.toml

@@ -0,0 +1,10 @@
+# TODO: Move to pyproject.toml once https://github.com/tamasfe/taplo/issues/603 is fixed
+
+[formatting]
+# https://taplo.tamasfe.dev/configuration/formatter-options.html
+align_comments = false
+align_entries = false
+array_auto_collapse = false
+reorder_arrays = true
+reorder_inline_tables = true
+reorder_keys = true

pyproject.toml

@@ -2,16 +2,16 @@
 build-backend = 'mesonpy'
 # Minimum requirements for the build system to execute.
 requires = [
-  'meson-python',
   'cypari2 >=2.2.1; sys_platform != "win32"',
+  'meson-python',
   # Exclude 1.12.0 because of https://github.com/sagemath/cysignals/issues/212
   'cysignals >=1.11.2, != 1.12.0',
   # Exclude 3.0.3 because of https://github.com/cython/cython/issues/5748
   'cython >=3.0, != 3.0.3',
   'gmpy2 ~=2.1.b999',
+  'jinja2',
   'memory_allocator',
   'numpy >=1.25',
-  'jinja2',
 ]
 [tool.meson-python.args]
 # Prevent meson from trying to install the autoconf subprojects
@@ -25,92 +25,92 @@ install = ['--skip-subprojects']
 setup = ['--default-library=static']
 
 [project]
-name = "sagemath"
-description = "Sage: Open Source Mathematics Software: Standard Python Library"
+authors = [
+  { email = "[email protected]", name = "The Sage Developers" },
+]
+classifiers = [
+  "Development Status :: 6 - Mature",
+  "Intended Audience :: Education",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
+  "Operating System :: MacOS :: MacOS X",
+  "Operating System :: POSIX",
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: Implementation :: CPython",
+  "Topic :: Scientific/Engineering :: Mathematics",
+]
 dependencies = [
-  'six >=1.15.0',
   'conway-polynomials >=0.8',
   'cypari2 >=2.2.1; sys_platform != "win32"',
+  'six >=1.15.0',
   # Exclude 1.12.0 because of https://github.com/sagemath/cysignals/issues/212
   'cysignals >=1.11.2, != 1.12.0',
   'cython >=3.0, != 3.0.3',
+  'fpylll >=0.5.9; sys_platform != "win32"',
   'gmpy2 ~=2.1.b999',
+  'ipykernel >=5.2.1',
+  'ipython >=8.9.0',
+  'ipywidgets >=7.5.1',
+  'jupyter-client',
+  'matplotlib >=3.7.0',
   'memory_allocator',
+  'mpmath >=1.1.0',
+  'networkx >=3.1',
   'numpy >=1.25',
+  'pexpect >=4.8.0',
+  'pillow >=7.2.0',
+  'platformdirs',
   # Issue #30922: pplpy 0.8.4 and earlier do not declare dependencies correctly
   'pplpy >=0.8.6; sys_platform != "win32"',
   'primecountpy; sys_platform != "win32"',
+  'ptyprocess > 0.5',
   'requests >=2.13.0',
+  'scipy >=1.11',
+  'sphinx >=5.2, <9',
+  'sympy >=1.6, <2.0',
   # According to https://github.com/python/typing_extensions/blob/main/CHANGELOG.md,
   # version 4.4.0 adds another Python 3.11 typing backport
   'typing_extensions >= 4.4.0; python_version<"3.11"',
-  'ipython >=8.9.0',
-  'pexpect >=4.8.0',
-  'platformdirs',
-  'sphinx >=5.2, <9',
-  'networkx >=3.1',
-  'scipy >=1.11',
-  'sympy >=1.6, <2.0',
-  'matplotlib >=3.7.0',
-  'pillow >=7.2.0',
-  'mpmath >=1.1.0',
-  'ipykernel >=5.2.1',
-  'jupyter-client',
-  'ipywidgets >=7.5.1',
-  'fpylll >=0.5.9; sys_platform != "win32"',
-  'ptyprocess > 0.5',
   # TODO: Remove this once the migration to meson is complete
   'pkgconfig',
   'traitlets',
 ]
+description = "Sage: Open Source Mathematics Software: Standard Python Library"
 dynamic = ["version"]
 license = { text = "GNU General Public License (GPL) v2 or later" }
-authors = [
-  { name = "The Sage Developers", email = "[email protected]" },
-]
-classifiers = [
-  "Development Status :: 6 - Mature",
-  "Intended Audience :: Education",
-  "Intended Audience :: Science/Research",
-  "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
-  "Operating System :: POSIX",
-  "Operating System :: MacOS :: MacOS X",
-  "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.11",
-  "Programming Language :: Python :: 3.12",
-  "Programming Language :: Python :: 3.13",
-  "Programming Language :: Python :: Implementation :: CPython",
-  "Topic :: Scientific/Engineering :: Mathematics",
-]
-urls = { Homepage = "https://www.sagemath.org" }
+name = "sagemath"
 requires-python = ">=3.11, <3.14"
+urls = { Homepage = "https://www.sagemath.org" }
 
 [project.optional-dependencies]
 R = ['rpy2 >=3.3']
 extra = [
-  'p_group_cohomology >=3.3',                                                         # Only used in tests
+  'igraph',
+  'lrcalc ~=2.1; sys_platform != "win32"',
+  'p_group_cohomology >=3.3', # Only used in tests
   'pycosat >=0.6.3',
   'pynormaliz >=2.18; platform_machine != "aarch64" and platform_machine != "arm64"', # Not yet available for Linux aarch64
-  'igraph',
   'sage_numerical_backends_coin',
-  'symengine >= 0.6.1',                                                               # Only used in tests
-  'lrcalc ~=2.1; sys_platform != "win32"',
+  'symengine >= 0.6.1', # Only used in tests
 ]
 giac = ['sagemath_giac']
 
 [project.readme]
-file = "README.md"
 content-type = "text/markdown"
+file = "README.md"
 
 [project.scripts]
 sage = "sage.cli:main"
 
 [tool.conda-lock]
-platforms = ['osx-64', 'linux-64', 'linux-aarch64', 'osx-arm64']
+platforms = ['linux-64', 'linux-aarch64', 'osx-64', 'osx-arm64']
 
 [tool.pytest.ini_options]
-python_files = "*_test.py"
 norecursedirs = "local prefix venv build builddir pkgs .git src/doc src/bin src/sage_setup/autogen/flint tools"
+python_files = "*_test.py"
 # The "no:warnings" is to stop pytest from capturing warnings so that they are printed to the output of the doctest
 addopts = "--import-mode importlib -p no:warnings"
 doctest_optionflags = "NORMALIZE_WHITESPACE ELLIPSIS"
@@ -120,22 +120,19 @@ consider_namespace_packages = true
 # External dependencies in the format proposed by https://peps.python.org/pep-0725
 [external]
 build-requires = [
+  "pkg:generic/pkg-config",
   "virtual:compiler/c",
   "virtual:compiler/cpp",
-  "pkg:generic/pkg-config",
 ]
 
 host-requires = [
-  "virtual:interface/blas",
-  "virtual:compiler/fortran",
   "pkg:generic/boost",
   "pkg:generic/cddlib",
   "pkg:generic/cliquer",
   "pkg:generic/ecl",
   "pkg:generic/ecm",
   "pkg:generic/fflas-ffpack",
   "pkg:generic/flint",
-  "pkg:generic/libgd",
   "pkg:generic/gap",
   "pkg:generic/gfan",
   "pkg:generic/givaro",
@@ -145,6 +142,7 @@ host-requires = [
   "pkg:generic/iml",
   "pkg:generic/lcalc",
   "pkg:generic/libbraiding",
+  "pkg:generic/libgd",
   "pkg:generic/libhomfly",
   "pkg:generic/linbox",
   "pkg:generic/lrcalc",
@@ -162,19 +160,21 @@ host-requires = [
   "pkg:generic/pari-galdata",
   "pkg:generic/pari-seadata",
   "pkg:generic/planarity",
-  "pkg:generic/primesieve",
   "pkg:generic/primecount",
+  "pkg:generic/primesieve",
   "pkg:generic/qhull",
   "pkg:generic/rw",
   "pkg:generic/singular",
   "pkg:generic/symmetrica",
   "pkg:generic/sympow",
+  "virtual:compiler/fortran",
+  "virtual:interface/blas",
 ]
 
 dependencies = [
-  "pkg:generic/sagemath-polytopes-db",
   "pkg:generic/sagemath-elliptic-curves",
   "pkg:generic/sagemath-graphs",
+  "pkg:generic/sagemath-polytopes-db",
   "pkg:generic/tachyon",
 ]
 
@@ -207,17 +207,17 @@ extra = [
 ]
 
 [dependency-groups]
-test = ["pytest", "pytest-xdist", "coverage"]
+dev = ["conda-lock", "grayskull", "meson", "pygithub", "toml", "tqdm", "uv"]
 docs = [
+  "furo",
+  "jupyter-sphinx",
+  "python-dateutil",
   "sphinx",
   "sphinx-copybutton",
   "sphinx-inline-tabs",
-  "jupyter-sphinx",
-  "furo",
-  "python-dateutil",
 ]
-lint = ["relint", "ruff", "pycodestyle", "flake8-rst-docstrings"]
-dev = ["tqdm", "pygithub", "meson", "conda-lock", "grayskull", "toml", "uv"]
+lint = ["flake8-rst-docstrings", "pycodestyle", "relint", "ruff"]
+test = ["coverage", "pytest", "pytest-xdist"]
 
 [tool.ruff]
 # https://docs.astral.sh/ruff/configuration
@@ -226,15 +226,15 @@ dev = ["tqdm", "pygithub", "meson", "conda-lock", "grayskull", "toml", "uv"]
 target-version = "py311"
 
 [tool.ruff.lint]
-select = [
-  "E",  # pycodestyle errors - https://docs.astral.sh/ruff/rules/#error-e
-  "F",  # pyflakes - https://docs.astral.sh/ruff/rules/#pyflakes-f
-  "I",  # isort - https://docs.astral.sh/ruff/rules/#isort-i
-  "PL", # pylint - https://docs.astral.sh/ruff/rules/#pylint-pl
-]
 ignore = [
   "E501", # Line too long - hard to avoid in doctests, and better handled by black.
 ]
+select = [
+  "E", # pycodestyle errors - https://docs.astral.sh/ruff/rules/#error-e
+  "F", # pyflakes - https://docs.astral.sh/ruff/rules/#pyflakes-f
+  "I", # isort - https://docs.astral.sh/ruff/rules/#isort-i
+  "PL", # pylint - https://docs.astral.sh/ruff/rules/#pylint-pl
+]
 
 [tool.ruff.lint.per-file-ignores]
 "all.py" = [