Format toml files and add linter check

Author: tobiasdiez

.github/workflows/lint.yml

@@ -42,3 +42,8 @@ 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 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"',
-    # 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',
-    'memory_allocator',
-    'numpy >=1.25',
-    'jinja2'
+  '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',
 ]
 [tool.meson-python.args]
 # Prevent meson from trying to install the autoconf subprojects
@@ -25,87 +25,92 @@ install = ['--skip-subprojects']
 setup = ['--default-library=static']
 
 [project]
-name = "sagemath"
-description = "Sage: Open Source Mathematics Software: Standard Python Library"
+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 :: 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"',
-    # 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',
-    'gmpy2 ~=2.1.b999',
-    'lrcalc ~=2.1; sys_platform != "win32"',
-    'memory_allocator',
-    'numpy >=1.25',
-    # Issue #30922: pplpy 0.8.4 and earlier do not declare dependencies correctly
-    'pplpy >=0.8.6; sys_platform != "win32"',
-    'primecountpy; sys_platform != "win32"',
-    'requests >=2.13.0',
-    # 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',
-    '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',
+  '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',
+  'gmpy2 ~=2.1.b999',
+  'lrcalc ~=2.1; sys_platform != "win32"',
+  'memory_allocator',
+  'numpy >=1.25',
+  # Issue #30922: pplpy 0.8.4 and earlier do not declare dependencies correctly
+  'pplpy >=0.8.6; sys_platform != "win32"',
+  'primecountpy; sys_platform != "win32"',
+  'requests >=2.13.0',
+  # According to https://github.com/python/typing_extensions/blob/main/CHANGELOG.md,
+  # version 4.4.0 adds another Python 3.11 typing backport
+  'fpylll >=0.5.9; sys_platform != "win32"',
+  'ipykernel >=5.2.1',
+  'ipython >=8.9.0',
+  'ipywidgets >=7.5.1',
+  'jupyter-client',
+  'matplotlib >=3.7.0',
+  'mpmath >=1.1.0',
+  'networkx >=3.1',
+  'pexpect >=4.8.0',
+  'pillow >=7.2.0',
+  'ptyprocess > 0.5',
+  'scipy >=1.11',
+  'sphinx >=5.2, <9',
+  'sympy >=1.6, <2.0',
+  'typing_extensions >= 4.4.0; python_version<"3.11"',
+  # 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"}
+license = { text = "GNU General Public License (GPL) v2 or later" }
+name = "sagemath"
 requires-python = ">=3.11, <3.14"
+urls = { Homepage = "https://www.sagemath.org" }
 
 [project.optional-dependencies]
 R = [
-    'rpy2 >=3.3',
+  'rpy2 >=3.3',
 ]
 giac = [
-    'sagemath_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'
+  '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"
@@ -115,14 +120,12 @@ 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/brial",
   "pkg:generic/cddlib",
@@ -132,7 +135,6 @@ host-requires = [
   "pkg:generic/ecm",
   "pkg:generic/fflas-ffpack",
   "pkg:generic/flint",
-  "pkg:generic/libgd",
   "pkg:generic/gap",
   "pkg:generic/gfan",
   "pkg:generic/givaro",
@@ -142,6 +144,7 @@ host-requires = [
   "pkg:generic/iml",
   "pkg:generic/lcalc",
   "pkg:generic/libbraiding",
+  "pkg:generic/libgd",
   "pkg:generic/libhomfly",
   "pkg:generic/linbox",
   "pkg:generic/lrcalc",
@@ -159,46 +162,48 @@ 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",
 ]
 
 [dependency-groups]
-test = [
-  "pytest",
-  "pytest-xdist",
-  "coverage",
+dev = [
+  "conda-lock",
+  "grayskull",
+  "meson",
+  "pygithub",
+  "toml",
+  "tqdm",
 ]
 docs = [
-  "sphinx", 
-  "sphinx-inline-tabs", 
   "furo",
+  "sphinx",
+  "sphinx-inline-tabs",
 ]
 lint = [
+  "flake8-rst-docstrings",
+  "pycodestyle",
   "relint",
   "ruff",
-  "pycodestyle",
-  "flake8-rst-docstrings",
 ]
-dev = [
-  "tqdm",
-  "pygithub",
-  "meson",
-  "conda-lock",
-  "grayskull",
-  "toml",
+test = [
+  "coverage",
+  "pytest",
+  "pytest-xdist",
 ]
 
 [tool.ruff]
@@ -208,15 +213,15 @@ dev = [
 target-version = "py311"
 
 [tool.ruff.lint]
+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
 ]
-ignore = [
-  "E501", # Line too long - hard to avoid in doctests, and better handled by black.
-]
 
 [tool.ruff.lint.per-file-ignores]
 "all.py" = [