MAINT: Move the development configuration into pyproject.toml

.github/workflows/generate-documentation.yml

@@ -34,8 +34,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install -r requirements.txt
-        python -m pip install -r requirements-dev.txt
+        python -m pip install --group dev --group doc
 
     - name: Install arch
       run: |

.github/workflows/lint.yml

@@ -8,8 +8,8 @@ on:
 
 jobs:
   lint:
-    # The oldest and the newest supported Python. flake8 and black parse the code with
-    # the grammar of the Python that runs them.
+    # The oldest and the newest supported Python. black parses the code with the grammar
+    # of the Python that runs it.
     name: Lint, Python ${{ matrix.python-version }}
     runs-on: ubuntu-latest
     defaults:
@@ -27,19 +27,16 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
+      # The lint dependency group in pyproject.toml
       - name: Install the linters
         id: install
         run: |
           python -m pip install --upgrade pip
-          python -m pip install black flake8 isort ruff "numpydoc>=1.10"
+          python -m pip install --group lint
           python -m pip list
 
       # Every check runs even when an earlier one fails, so that the log shows all of
       # the problems
-      - name: flake8
-        if: ${{ !cancelled() && steps.install.outcome == 'success' }}
-        run: flake8 arch
-
       - name: ruff
         if: ${{ !cancelled() && steps.install.outcome == 'success' }}
         run: ruff check arch

.github/workflows/windows-arm.yml

@@ -64,17 +64,18 @@ jobs:
           python -c "import platform, sys; print(sys.version, platform.machine())"
           python -c "import sys, sysconfig; print(sysconfig.get_platform()); sys.exit(sysconfig.get_platform() != 'win-arm64')"
 
-      # Only wheels, so that the job fails if a dependency would have to be compiled
+      # Only wheels, so that the job fails if a dependency would have to be compiled. The
+      # test requirements are the test dependency group in pyproject.toml.
       - name: Install the dependencies
         env:
           NUMBA: ${{ matrix.numba }}
         run: |
-          packages=(numpy scipy pandas statsmodels matplotlib seaborn "pytest>=9,<10" pytest-xdist)
+          packages=(numpy scipy pandas statsmodels matplotlib seaborn)
           if [[ "${NUMBA}" == "true" ]]; then
             packages+=(numba)
           fi
           python -m pip install --upgrade pip
-          python -m pip install --only-binary=:all: "${packages[@]}"
+          python -m pip install --only-binary=:all: --group test "${packages[@]}"
 
       - name: Build the wheel
         run: |

README.md

@@ -266,14 +266,19 @@ Building the extensions from source needs the Visual Studio Build Tools
 
 ### Developing
 
-The development requirements are:
-
-- Cython (3.1+), meson-python and ninja, unless building without the binary
-  modules
-- pytest (9+, for tests)
-- sphinx (to build docs)
-- sphinx-immaterial (to build docs)
-- jupyter, notebook and nbsphinx (to build docs)
+The development requirements are dependency groups in `pyproject.toml`,
+which pip 25.1 or later installs. From a clone of the repository,
+
+```shell
+python -m pip install --group dev
+python -m pip install -e . --no-build-isolation
+```
+
+installs the tools to build (Cython 3.1+, meson-python and ninja), test
+(pytest 9+) and lint arch, and then arch itself. Adding `--group doc` to the
+first command also installs what the documentation needs (sphinx,
+sphinx-immaterial and nbsphinx). `doc/source/contributing.rst` lists the
+commands that check the code.
 
 ### Installation Notes
 

ci/azure/azure_template_posix.yml

@@ -212,7 +212,7 @@ jobs:
 
   - script: |
       echo "Testing editable install"
-      export COVERAGE_OPTS="--cov-config=.coveragerc --cov=arch --cov-branch --cov-report xml:coverage.xml --cov-report term"
+      export COVERAGE_OPTS="--cov=arch --cov-branch --cov-report xml:coverage.xml --cov-report term"
       echo pytest -m "${PYTEST_PATTERN}" --junitxml=junit/test-results.xml -n auto --durations=25 ${COVERAGE_OPTS} arch/tests
       pytest -m "${PYTEST_PATTERN}" --junitxml=junit/test-results.xml -n auto --durations=25 ${COVERAGE_OPTS} arch/tests
     displayName: 'Run tests (editable)'
@@ -230,7 +230,7 @@ jobs:
       echo "Testing with Cython coverage"
       # Uninstall xdist to avoid issues with coverage and Cython
       python -m pip uninstall pytest-xdist -y || true
-      export COVERAGE_OPTS="--cov-config=.coveragerc --cov=arch --cov-branch --cov-report xml:coverage.xml --cov-report term"
+      export COVERAGE_OPTS="--cov=arch --cov-branch --cov-report xml:coverage.xml --cov-report term"
       echo pytest --junitxml=junit/test-results.xml --durations=25 ${COVERAGE_OPTS} arch/tests/univariate/test_recursions.py arch/tests/bootstrap/test_samplers.py arch/tests/univariate/test_arch_in_mean.py
       pytest --junitxml=junit/test-results.xml --durations=25 ${COVERAGE_OPTS} arch/tests/univariate/test_recursions.py arch/tests/bootstrap/test_samplers.py arch/tests/univariate/test_arch_in_mean.py
     displayName: 'Run tests (cython coverage)'

ci/azure/azure_template_windows.yml

@@ -18,11 +18,14 @@ jobs:
   strategy:
     # The newest Python with the newest packages, and the oldest Python with numpy 1.x
     # (the default integer is 32 bits on Windows) and pandas 2.1. PACKAGES is installed
-    # in a single pip command with requirements.txt, so that pip also picks versions
-    # of the other packages that work with the pins.
+    # in a single pip command with the build and test dependency groups in
+    # pyproject.toml, so that pip also picks versions of the other packages that work
+    # with the pins. pip installs scipy, pandas and statsmodels with arch when PACKAGES
+    # does not list them.
     matrix:
       python314_win_latest:
         python.version: '3.14'
+        PACKAGES: 'matplotlib seaborn'
       python310_win_numpy126:
         python.version: '3.10'
         PACKAGES: 'numpy==1.26.4 scipy==1.11.4 pandas==2.1.4 statsmodels==0.14.1 matplotlib seaborn numba build'
@@ -40,9 +43,8 @@ jobs:
   - script: |
       python -m venv arch-test
       call arch-test\Scripts\activate.bat
-      python -m pip install --upgrade pip wheel
-      python -m pip install -r requirements-dev.txt -U
-      python -m pip install %PACKAGES% -r requirements.txt -U || exit /b 1
+      python -m pip install --upgrade pip
+      python -m pip install --group build --group test %PACKAGES% -U || exit /b 1
       python -m pip list
     displayName: 'Create Venv and Install dependencies'
 

ci/azure/install-posix.sh

@@ -1,5 +1,9 @@
 #!/usr/bin/env bash
 
+# The build tools, the test requirements and the packages that the example notebooks
+# need are dependency groups in pyproject.toml, which pip 25.1 or later installs
+DEP_GROUPS=(--group build --group test --group notebooks)
+
 if [[ ${USE_CONDA} == "true" ]]; then
   # Miniforge (conda-forge only) is installed by the pipeline and the env's bin
   # directory is on PATH, so no activation is needed.
@@ -13,16 +17,15 @@ if [[ ${USE_CONDA} == "true" ]]; then
   fi
   CMD="mamba install -n arch-test -y -c conda-forge numpy"
 else
-  CMD="python -m pip install numpy"
+  CMD="python -m pip install ${DEP_GROUPS[*]} numpy"
 fi
 
-python -m pip install --upgrade pip "setuptools>=61" wheel
-python -m pip install cython "pytest>=9,<10" pytest-xdist "coverage[toml]" pytest-cov ipython jupyter notebook nbconvert "property_cached>=1.6.3" nbconvert setuptools_scm colorama "meson-python>=0.18.0" meson ninja "numpydoc>=1.10"
-
+python -m pip install --upgrade pip
 
 # Versions are exact so that the job tests what its matrix entry says, and all of
-# the packages are installed in a single command so that the installer picks
-# versions of matplotlib, seaborn, ... that work with them
+# the packages (with pip, also the dependency groups) are installed in a single
+# command so that the installer picks versions of matplotlib, seaborn, ... that work
+# with them
 if [[ -n ${NUMPY} ]]; then CMD="$CMD==${NUMPY}"; fi;
 CMD="$CMD scipy"
 if [[ -n ${SCIPY} ]]; then CMD="$CMD==${SCIPY}"; fi;
@@ -47,6 +50,12 @@ CMD="$CMD $EXTRA"
 echo $CMD
 eval $CMD || exit 1
 
+if [[ ${USE_CONDA} == "true" ]]; then
+  # After the conda packages, so that pip keeps the numpy from conda-forge
+  echo python -m pip install "${DEP_GROUPS[@]}"
+  python -m pip install "${DEP_GROUPS[@]}" || exit 1
+fi
+
 if [[ ${NO_MATPLOTLIB,,} == true ]]; then
   # Fail if another package installed matplotlib, so that the job really tests without it
   if python -c "import importlib.util, sys; sys.exit(importlib.util.find_spec('matplotlib') is None)"; then

doc/source/changes/9.0.rst

@@ -1314,6 +1314,13 @@ Documentation and maintenance
   test suite, including the slow tests, on Python 3.13 to 3.15. Unlike the other jobs,
   it does not limit the number of BLAS threads, because NumPy's OpenBLAS on this
   platform crashes with one thread (see "Compatibility") (:issue:`1003`).
+- The development requirements are dependency groups in ``pyproject.toml``, which pip
+  25.1 or later installs, for example with ``python -m pip install --group dev`` (see
+  the contributing guide). They replace ``requirements.txt``, ``requirements-dev.txt``
+  and ``doc/requirements.txt``, and the ``test``, ``doc`` and ``dev`` extras, which have
+  been removed. The settings of coverage moved from ``.coveragerc`` to
+  ``pyproject.toml``, and ruff replaces flake8 in the style checks, with the same limit
+  of 99 characters on comments, docstrings and long strings (:issue:`1021`).
 
 Deprecations and removals
 ~~~~~~~~~~~~~~~~~~~~~~~~~

doc/source/contributing.rst

@@ -1,6 +1,47 @@
 Contributing
 ============
 
+Development environment
+-----------------------
+
+The development requirements are dependency groups (PEP 735) in ``pyproject.toml``,
+which pip 25.1 or later installs. From the root of a clone of the repository,
+
+.. code-block:: bash
+
+   python -m pip install --group dev
+   python -m pip install -e . --no-build-isolation
+
+installs the build tools, the test runner, the linters and the packages that the example
+notebooks need, and then builds and installs arch in place. Add ``--group doc`` to the
+first command to also build the documentation. The groups are:
+
+* ``build``: what ``python -m pip install -e . --no-build-isolation`` needs (Cython,
+  meson, meson-python, ninja, NumPy and setuptools-scm).
+* ``test``: pytest, pytest-xdist, pytest-cov and numpydoc.
+* ``notebooks``: jupyter and nbconvert, which the slow tests use to run the example
+  notebooks.
+* ``lint``: ruff, black, isort, numpydoc, mypy and the pandas and SciPy stubs.
+* ``docstrings``: numpydoc, which ``test`` and ``lint`` include.
+* ``dev``: ``build``, ``test``, ``lint`` and ``notebooks``, with matplotlib, seaborn and
+  pytest-randomly.
+* ``doc``: Sphinx, sphinx-immaterial and nbsphinx, in addition to ``dev``.
+* ``simulation``: the packages that the scripts in
+  ``arch/unitroot/critical_values/simulation`` need in addition to ``dev``.
+
+The groups do not include the dependencies of arch, which pip installs with arch. The
+tests and the checks that CI runs are
+
+.. code-block:: bash
+
+   python -m pytest arch/tests -n auto -m "not slow"
+   ruff check arch
+   black --check arch
+   isort --check arch
+   python -m numpydoc lint $(git ls-files "arch/*.py")
+
+and the settings of all of these tools are in ``pyproject.toml``.
+
 Docstrings
 ----------
 
@@ -115,8 +156,8 @@ The rules are configured in the ``[tool.numpydoc_validation]`` table of
    python -m numpydoc lint $(git ls-files "arch/*.py")
    python -m pytest arch/tests/test_docstrings.py
 
-Both need numpydoc 1.10 or later, which ``requirements-dev.txt`` and the ``dev`` extra
-install. The Lint workflow runs the first command, and the second is skipped when
+Both need numpydoc 1.10 or later, which the ``test``, ``lint`` and ``dev`` dependency
+groups install. The Lint workflow runs the first command, and the second is skipped when
 numpydoc is not installed.
 
 ``numpydoc lint`` reads the source files. It cannot see a docstring that a class