Add requirements files for testing, linting, and documentation

.github/workflows/build.yml

@@ -242,7 +242,7 @@ jobs:
           # The following command checks that all modules can be imported.
           # The output also includes a long list of modules together with the number of tests in each module.
           # This can be ignored.
-          ./sage -python -m pip install pytest-xdist
+          ./sage -python -m pip install -r requirements/test-requirements.txt
           ./sage -python -m pytest -c tox.ini -qq --doctest --collect-only || true
         shell: sh .ci/docker-exec-script.sh BUILD /sage {0}
 
@@ -453,7 +453,7 @@ jobs:
           rm -rf /sage/.coverage
           ln -s $(pwd)/.coverage /sage/
           cd /sage
-          ./sage -python -m pip install coverage
+          ./sage -python -m pip install -r requirements/test-requirements.txt
           ./sage -python -m coverage run --rcfile=src/tox.ini src/bin/sage-runtests --force-lib --long -p4 --format github --random-seed=286735480429121101562228604801325644303 ${{ matrix.tests }}
         shell: sh .ci/docker-exec-script.sh BUILD . {0}
 
@@ -580,7 +580,7 @@ jobs:
           rm -rf /sage/.coverage
           ln -s $(pwd)/.coverage /sage/
           cd /sage
-          ./sage -python -m pip install coverage
+          ./sage -python -m pip install -r requirements/test-requirements.txt
           ./sage -python -m coverage combine --rcfile=src/tox.ini .coverage/coverage-*/.coverage
           ./sage -python -m coverage xml --rcfile=src/tox.ini --omit="/tmp/*"
           mkdir -p .coverage/coverage-report

pyproject.toml

@@ -90,8 +90,8 @@ platforms = [
     'osx-64', 'linux-64', 'linux-aarch64', 'osx-arm64'
 ]
 
-[external]
 # External dependencies in the format proposed by https://peps.python.org/pep-0725
+[external]
 build-requires = [
   "virtual:compiler/c",
   "virtual:compiler/cpp",
@@ -152,4 +152,22 @@ dependencies = [
   "pkg:generic/tachyon",
   "pkg:generic/sagemath-polytopes-db",
   "pkg:generic/sagemath-elliptic-curves",
+  "pkg:generic/sagemath-graphs",
+]
+
+[dependency-groups]
+test = [
+  "pytest",
+  "pytest-xdist",
+  "coverage",
+]
+docs = [
+  "sphinx", 
+  "sphinx-inline-tabs", 
+  "furo",
+]
+lint = [
+  "relint",
+  "pycodestyle",
+  "flake8-rst-docstrings",
 ]

requirements/ .gitignore

@@ -0,0 +1 @@
+*.in

requirements/docs-requirements.txt

@@ -0,0 +1,64 @@
+#
+# This file is autogenerated by pip-compile with Python 3.11
+# by the following command:
+#
+#    pip-compile --no-build-isolation --output-file=requirements/docs-requirements.txt requirements/docs.in
+#
+alabaster==0.7.16
+    # via sphinx
+babel==2.14.0
+    # via sphinx
+beautifulsoup4==4.12.3
+    # via furo
+certifi==2024.2.2
+    # via requests
+charset-normalizer==3.3.2
+    # via requests
+docutils==0.20.1
+    # via sphinx
+furo==2024.1.29
+    # via -r requirements/docs.in
+idna==3.6
+    # via requests
+imagesize==1.4.1
+    # via sphinx
+jinja2==3.1.3
+    # via sphinx
+markupsafe==2.1.5
+    # via jinja2
+packaging==23.2
+    # via sphinx
+pygments==2.17.2
+    # via
+    #   furo
+    #   sphinx
+requests==2.31.0
+    # via sphinx
+snowballstemmer==2.2.0
+    # via sphinx
+soupsieve==2.5
+    # via beautifulsoup4
+sphinx==7.2.6
+    # via
+    #   -r requirements/docs.in
+    #   furo
+    #   sphinx-basic-ng
+    #   sphinx-inline-tabs
+sphinx-basic-ng==1.0.0b2
+    # via furo
+sphinx-inline-tabs==2023.4.21
+    # via -r requirements/docs.in
+sphinxcontrib-applehelp==1.0.8
+    # via sphinx
+sphinxcontrib-devhelp==1.0.6
+    # via sphinx
+sphinxcontrib-htmlhelp==2.0.5
+    # via sphinx
+sphinxcontrib-jsmath==1.0.1
+    # via sphinx
+sphinxcontrib-qthelp==1.0.7
+    # via sphinx
+sphinxcontrib-serializinghtml==1.1.10
+    # via sphinx
+urllib3==2.2.1
+    # via requests

requirements/lint-requirements.txt

@@ -0,0 +1,36 @@
+#
+# This file is autogenerated by pip-compile with Python 3.11
+# by the following command:
+#
+#    pip-compile --no-build-isolation --output-file=requirements/lint-requirements.txt requirements/lint.in
+#
+docutils==0.20.1
+    # via restructuredtext-lint
+flake8==7.0.0
+    # via flake8-rst-docstrings
+flake8-rst-docstrings==0.3.0
+    # via -r requirements/lint.in
+markdown-it-py==3.0.0
+    # via rich
+mccabe==0.7.0
+    # via flake8
+mdurl==0.1.2
+    # via markdown-it-py
+pycodestyle==2.11.1
+    # via
+    #   -r requirements/lint.in
+    #   flake8
+pyflakes==3.2.0
+    # via flake8
+pygments==2.17.2
+    # via
+    #   flake8-rst-docstrings
+    #   rich
+pyyaml==6.0.1
+    # via relint
+relint==3.1.0
+    # via -r requirements/lint.in
+restructuredtext-lint==1.4.0
+    # via flake8-rst-docstrings
+rich==13.7.0
+    # via relint

requirements/requirements.txt

@@ -0,0 +1,211 @@
+#
+# This file is autogenerated by pip-compile with Python 3.11
+# by the following command:
+#
+#    pip-compile --no-build-isolation --output-file=requirements/requirements.txt pyproject.toml
+#
+alabaster==0.7.16
+    # via sphinx
+asttokens==2.4.1
+    # via stack-data
+babel==2.14.0
+    # via sphinx
+certifi==2024.2.2
+    # via requests
+charset-normalizer==3.3.2
+    # via requests
+comm==0.2.1
+    # via
+    #   ipykernel
+    #   ipywidgets
+contourpy==1.2.0
+    # via matplotlib
+conway-polynomials==0.9
+    # via sagemath-standard (pyproject.toml)
+cycler==0.12.1
+    # via matplotlib
+cypari2==2.1.4
+    # via sagemath-standard (pyproject.toml)
+cysignals==1.11.4
+    # via
+    #   cypari2
+    #   primecountpy
+    #   sagemath-standard (pyproject.toml)
+cython==3.0.8
+    # via
+    #   memory-allocator
+    #   primecountpy
+    #   sagemath-standard (pyproject.toml)
+debugpy==1.8.1
+    # via ipykernel
+decorator==5.1.1
+    # via ipython
+docutils==0.20.1
+    # via sphinx
+executing==2.0.1
+    # via stack-data
+fonttools==4.49.0
+    # via matplotlib
+fpylll==0.6.1
+    # via sagemath-standard (pyproject.toml)
+gmpy2==2.1.5
+    # via sagemath-standard (pyproject.toml)
+idna==3.6
+    # via requests
+imagesize==1.4.1
+    # via sphinx
+importlib-metadata==7.0.1
+    # via sagemath-standard (pyproject.toml)
+importlib-resources==6.1.1
+    # via sagemath-standard (pyproject.toml)
+ipykernel==6.29.2
+    # via sagemath-standard (pyproject.toml)
+ipython==8.22.1
+    # via
+    #   ipykernel
+    #   ipywidgets
+    #   sagemath-standard (pyproject.toml)
+ipywidgets==8.1.2
+    # via sagemath-standard (pyproject.toml)
+jedi==0.19.1
+    # via ipython
+jinja2==3.1.3
+    # via sphinx
+jupyter-client==8.6.0
+    # via
+    #   ipykernel
+    #   sagemath-standard (pyproject.toml)
+jupyter-core==5.7.1
+    # via
+    #   ipykernel
+    #   jupyter-client
+    #   sagemath-standard (pyproject.toml)
+jupyterlab-widgets==3.0.10
+    # via ipywidgets
+kiwisolver==1.4.5
+    # via matplotlib
+lrcalc==2.1
+    # via sagemath-standard (pyproject.toml)
+markupsafe==2.1.5
+    # via jinja2
+matplotlib==3.8.3
+    # via sagemath-standard (pyproject.toml)
+matplotlib-inline==0.1.6
+    # via
+    #   ipykernel
+    #   ipython
+memory-allocator==0.1.3
+    # via sagemath-standard (pyproject.toml)
+mpmath==1.3.0
+    # via
+    #   sagemath-standard (pyproject.toml)
+    #   sympy
+nest-asyncio==1.6.0
+    # via ipykernel
+networkx==3.2.1
+    # via sagemath-standard (pyproject.toml)
+numpy==1.26.4
+    # via
+    #   contourpy
+    #   matplotlib
+    #   sagemath-standard (pyproject.toml)
+    #   scipy
+packaging==23.2
+    # via
+    #   ipykernel
+    #   matplotlib
+    #   sphinx
+parso==0.8.3
+    # via jedi
+pexpect==4.9.0
+    # via
+    #   ipython
+    #   sagemath-standard (pyproject.toml)
+pillow==10.2.0
+    # via
+    #   matplotlib
+    #   sagemath-standard (pyproject.toml)
+platformdirs==4.2.0
+    # via jupyter-core
+pplpy==0.8.9
+    # via sagemath-standard (pyproject.toml)
+primecountpy==0.1.0
+    # via sagemath-standard (pyproject.toml)
+prompt-toolkit==3.0.43
+    # via ipython
+psutil==5.9.8
+    # via ipykernel
+ptyprocess==0.7.0
+    # via
+    #   pexpect
+    #   sagemath-standard (pyproject.toml)
+pure-eval==0.2.2
+    # via stack-data
+pygments==2.17.2
+    # via
+    #   ipython
+    #   sphinx
+pyparsing==3.1.1
+    # via matplotlib
+python-dateutil==2.8.2
+    # via
+    #   jupyter-client
+    #   matplotlib
+pyzmq==25.1.2
+    # via
+    #   ipykernel
+    #   jupyter-client
+requests==2.31.0
+    # via
+    #   sagemath-standard (pyproject.toml)
+    #   sphinx
+scipy==1.11.4
+    # via sagemath-standard (pyproject.toml)
+six==1.16.0
+    # via
+    #   asttokens
+    #   python-dateutil
+    #   sagemath-standard (pyproject.toml)
+snowballstemmer==2.2.0
+    # via sphinx
+sphinx==7.2.6
+    # via sagemath-standard (pyproject.toml)
+sphinxcontrib-applehelp==1.0.8
+    # via sphinx
+sphinxcontrib-devhelp==1.0.6
+    # via sphinx
+sphinxcontrib-htmlhelp==2.0.5
+    # via sphinx
+sphinxcontrib-jsmath==1.0.1
+    # via sphinx
+sphinxcontrib-qthelp==1.0.7
+    # via sphinx
+sphinxcontrib-serializinghtml==1.1.10
+    # via sphinx
+stack-data==0.6.3
+    # via ipython
+sympy==1.12
+    # via sagemath-standard (pyproject.toml)
+tornado==6.4
+    # via
+    #   ipykernel
+    #   jupyter-client
+traitlets==5.14.1
+    # via
+    #   comm
+    #   ipykernel
+    #   ipython
+    #   ipywidgets
+    #   jupyter-client
+    #   jupyter-core
+    #   matplotlib-inline
+typing-extensions==4.9.0
+    # via sagemath-standard (pyproject.toml)
+urllib3==2.2.1
+    # via requests
+wcwidth==0.2.13
+    # via prompt-toolkit
+widgetsnbextension==4.0.10
+    # via ipywidgets
+zipp==3.17.0
+    # via importlib-metadata

requirements/test-requirements.txt

@@ -0,0 +1,22 @@
+#
+# This file is autogenerated by pip-compile with Python 3.11
+# by the following command:
+#
+#    pip-compile --no-build-isolation --output-file=requirements/test-requirements.txt requirements/test.in
+#
+coverage==7.4.3
+    # via -r requirements/test.in
+execnet==2.0.2
+    # via pytest-xdist
+iniconfig==2.0.0
+    # via pytest
+packaging==23.2
+    # via pytest
+pluggy==1.4.0
+    # via pytest
+pytest==8.0.2
+    # via
+    #   -r requirements/test.in
+    #   pytest-xdist
+pytest-xdist==3.5.0
+    # via -r requirements/test.in