CI: run doctests on GH actions & CircleCI #11

Workflow file for this run

.github/workflows/linux_meson.yml at 43ecf92

	name: Linux Meson tests

	on:
	push:
	branches:
	- maintenance/**
	pull_request:
	branches:
	- main
	- maintenance/**

	permissions:
	contents: read # to fetch code (actions/checkout)

	env:
	CCACHE_DIR: "${{ github.workspace }}/.ccache"
	INSTALLDIR: "build-install"

	concurrency:
	group: ${{ github.workflow }}-${{ github.head_ref \|\| github.run_id }}
	cancel-in-progress: true

	jobs:
	get_commit_message:
	name: Get commit message
	uses: ./.github/workflows/commit_message.yml

	test_meson:
	name: Meson build
	needs: get_commit_message
	# If using act to run CI locally the github object does not exist and
	# the usual skipping should not be enforced
	if: >
	needs.get_commit_message.outputs.message == 1
	&& (github.repository == 'scipy/scipy' \|\| github.repository == '')
	runs-on: ubuntu-22.04
	strategy:
	matrix:
	python-version: ['3.10', '3.12'] # this run will use python dev versions when available
	maintenance-branch:
	- ${{ contains(github.ref, 'maintenance/') \|\| contains(github.base_ref, 'maintenance/') }}
	exclude:
	- maintenance-branch: true
	python-version: '3.12'

	steps:
	- uses: actions/[email protected]
	with:
	submodules: recursive

	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	cache: 'pip'
	cache-dependency-path: 'environment.yml'

	- name: Install Ubuntu dependencies
	run: \|
	# NOTE: not the same OpenBLAS version as in upstream CI (I'm being lazy here)
	sudo apt-get update
	sudo apt-get install -y libopenblas-dev libatlas-base-dev liblapack-dev gfortran libgmp-dev libmpfr-dev libsuitesparse-dev ccache libmpc-dev

	- name: Install Python packages
	if: matrix.python-version == '3.10'
	run: \|
	python -m pip install numpy cython pytest pytest-xdist pytest-timeout pybind11 mpmath gmpy2 pythran ninja meson click rich-click doit pydevtool pooch hypothesis

	- name: Install Python packages from repositories
	if: matrix.python-version == '3.12' # this run will use python dev versions when available
	run: \|
	python -m pip install git+https://github.com/numpy/numpy.git
	python -m pip install ninja cython pytest pybind11 pytest-xdist pytest-timeout click rich-click doit pydevtool pooch hypothesis "setuptools<67.3"
	python -m pip install git+https://github.com/serge-sans-paille/pythran.git
	python -m pip install git+https://github.com/mesonbuild/meson.git

	- name: Prepare compiler cache
	id: prep-ccache
	shell: bash
	run: \|
	mkdir -p "${CCACHE_DIR}"
	echo "dir=$CCACHE_DIR" >> $GITHUB_OUTPUT
	NOW=$(date -u +"%F-%T")
	echo "timestamp=${NOW}" >> $GITHUB_OUTPUT

	- name: Setup compiler cache
	uses: actions/cache@v3
	id: cache-ccache
	# Reference: https://docs.github.com/en/actions/guides/caching-dependencies-to-speed-up-workflows#matching-a-cache-key
	# NOTE: The caching strategy is modeled in a way that it will always have a unique cache key for each workflow run
	# (even if the same workflow is run multiple times). The restore keys are not unique and for a partial match, they will
	# return the most recently created cache entry, according to the GitHub Action Docs.
	with:
	path: ${{ steps.prep-ccache.outputs.dir }}
	# Restores ccache from either a previous build on this branch or on main
	key: ${{ github.workflow }}-${{ matrix.python-version }}-ccache-linux-${{ steps.prep-ccache.outputs.timestamp }}
	# This evaluates to `Linux Tests-3.10-ccache-linux-` which is not unique. As the CI matrix is expanded, this will
	# need to be updated to be unique so that the cache is not restored from a different job altogether.
	restore-keys: \|
	${{ github.workflow }}-${{ matrix.python-version }}-ccache-linux-

	- name: Setup build and install scipy
	run: \|
	python dev.py build --werror

	- name: Ccache performance
	shell: bash -l {0}
	run: ccache -s

	- name: Check installation
	run: \|
	pushd tools
	python check_installation.py ${{ env.INSTALLDIR }}
	./check_pyext_symbol_hiding.sh ../build
	popd

	- name: Mypy
	if: matrix.python-version == '3.10'
	run: \|
	# Packages that are only needed for their annotations
	python -m pip install mypy==1.0.0 types-psutil typing_extensions
	python -m pip install pybind11 sphinx

	python -u dev.py mypy

	- name: doctest_ng
	sudo apt-get install -y wamerican-small
	python -m pip install git+https://github.com/ev-br/scpdt.git
	python -m pip install matplotlib
	python dev.py doctest

	- name: Test SciPy
	run: \|
	export OMP_NUM_THREADS=2
	export SCIPY_USE_PROPACK=1
	python dev.py --no-build test -j2 -- --durations 10 --timeout=60

	#################################################################################
	test_venv_install:
	name: Pip install into venv
	needs: get_commit_message
	if: >
	needs.get_commit_message.outputs.message == 1
	&& (github.repository == 'scipy/scipy' \|\| github.repository == '')
	runs-on: ubuntu-22.04
	steps:
	- uses: actions/[email protected]
	with:
	submodules: recursive

	- name: Install Ubuntu dependencies
	run: \|
	# We're not running the full test suite here, only testing the install
	# into a venv is working, so leave out optional dependencies. That's
	# also why we can get away with an old version of OpenBLAS from Ubuntu
	sudo apt-get update
	sudo apt-get install -y python3-dev libopenblas-dev pkg-config gfortran

	- name: Create venv, install SciPy
	run: \|
	python -m venv ../venvs/scipy-venv
	source ../venvs/scipy-venv/bin/activate
	# Note that this uses build isolation. That's why we don't need build
	# dependencies to be installed in the venv itself.
	python -m pip install . -vv

	- name: Basic imports and tests
	run: \|
	source ../venvs/scipy-venv/bin/activate
	cd ..
	python -c "import scipy"
	python -c "import scipy.linalg"
	python -m pip install pytest hypothesis
	python -c "from scipy import cluster; cluster.test()"

	- name: Create venv inside source tree
	# This is a regression test for gh-16312
	run: \|
	python -m venv .venv
	source .venv/bin/activate
	# Install build dependencies. Use meson-python from its main branch,
	# most convenient to test in this job because we're using pip without
	# build isolation here.
	python -m pip install numpy pybind11 pythran cython pytest ninja hypothesis
	python -m pip install git+https://github.com/mesonbuild/meson-python.git
	# Non-isolated build, so we use dependencies installed inside the source tree
	python -m pip install -U pip # need pip >=23 for `--config-settings`
	python -m pip install . --no-build-isolation --config-settings=compile-args=-j2

	# Basic tests
	cd ..
	python -c "import scipy"
	python -c "import scipy.linalg"
	python -c "from scipy import cluster; cluster.test()"

	#################################################################################
	python_debug:
	# also uses the vcs->sdist->wheel route.
	name: Python-debug & ATLAS
	needs: get_commit_message
	if: >
	needs.get_commit_message.outputs.message == 1
	&& (github.repository == 'scipy/scipy' \|\| github.repository == '')
	runs-on: ubuntu-22.04 # provides python3.10-dbg
	steps:
	- uses: actions/[email protected]
	with:
	submodules: recursive
	- name: Configuring Test Environment
	run: \|
	sudo apt-get update
	sudo apt install python3-dbg python3-dev libatlas-base-dev liblapack-dev gfortran ccache libgmp-dev libmpfr-dev libmpc-dev
	python3-dbg --version # just to check
	python3-dbg -c 'import sys; print("Python debug build:", hasattr(sys, "gettotalrefcount"))'
	- name: Build SciPy
	run: \|
	python3-dbg -m pip install build
	python3-dbg -m build -Csetup-args=-Dbuildtype=debugoptimized -Csetup-args=-Dblas=blas-atlas -Csetup-args=-Dlapack=lapack-atlas -Ccompile-args=-j2
	python3-dbg -m pip install dist/scipy*.whl
	- name: Testing SciPy
	run: \|
	cd doc
	python3-dbg -m pip install pytest pytest-xdist pytest-timeout mpmath gmpy2 threadpoolctl pooch hypothesis
	python3-dbg -m pytest --pyargs scipy -n2 --durations=10 -m "not slow"

	#################################################################################
	gcc8:
	# Purpose is to examine builds with oldest-supported gcc and test with pydata/sparse.
	name: Build with gcc-8
	needs: get_commit_message
	if: >
	needs.get_commit_message.outputs.message == 1
	&& (github.repository == 'scipy/scipy' \|\| github.repository == '')
	runs-on: ubuntu-20.04 # 22.04 doesn't support gcc-8
	steps:
	- uses: actions/[email protected]
	with:
	submodules: recursive

	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.9"

	- name: Setup OS
	run: \|
	sudo apt-get -y update
	sudo apt install -y g++-8 gcc-8 gfortran-8
	sudo apt install -y libatlas-base-dev liblapack-dev libgmp-dev \
	libmpfr-dev libmpc-dev pkg-config libsuitesparse-dev liblapack-dev

	- name: Setup Python deps
	run: \|
	pip install "numpy==1.22.4" &&
	# build deps
	pip install build meson-python ninja pythran pybind11 cython
	# test deps
	pip install gmpy2 threadpoolctl mpmath pooch pythran pybind11 pytest pytest-xdist==2.5.0 pytest-timeout hypothesis
	pip install sparse

	- name: Build wheel and install
	run: \|
	set -euo pipefail
	export PYTHONOPTIMIZE=2

	# specify which compilers to use using environment variables
	CC=gcc-8 CXX=g++-8 FC=gfortran-8 python -m build --wheel --no-isolation -Csetup-args=-Dblas=blas-atlas -Csetup-args=-Dlapack=lapack-atlas -Ccompile-args=-j2
	python -m pip install dist/scipy*.whl

	- name: Run tests
	run: \|
	# can't be in source directory
	pushd $RUNNER_TEMP
	export PYTHONOPTIMIZE=2
	python -m pytest --pyargs scipy -n2 --durations=10
	popd

	#################################################################################
	prerelease_deps_coverage_64bit_blas:
	# TODO: re-enable ILP64 build.
	name: Prerelease deps, coverage and 64-bit BLAS
	needs: get_commit_message
	if: >
	needs.get_commit_message.outputs.message == 1
	&& (github.repository == 'scipy/scipy' \|\| github.repository == '')
	runs-on: ubuntu-latest
	strategy:
	matrix:
	# Both use numpy 2.0-dev at build time; 3.9 job then downgrades to
	# lowest supported NumPy version in order to test ABI compatibility.
	python-version: ['3.9', '3.11']

	steps:
	- uses: actions/[email protected]
	with:
	submodules: recursive

	- name: Setup Python
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}

	- name: Install Ubuntu dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install -y libgmp-dev libmpfr-dev libmpc-dev ccache gfortran

	- name: Caching Python dependencies
	uses: actions/cache@v3
	id: cache
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-prerelease

	- name: Install Python packages
	run: \|
	python -m pip install cython pythran ninja meson-python pybind11 click rich_click pydevtool
	# Note: matplotlib not installed here to avoid issues around numpy 2.0
	# (it can be put back after matplotlib has made a 2.0-compatible
	# release on PyPI.
	python -m pip install --pre --upgrade pytest pytest-cov pytest-xdist mpmath gmpy2 threadpoolctl pooch hypothesis
	# TODO: once the scipy_ symbol prefix issue is fixed, install
	# scipy-openblas32 from the pre-releases bucket again (see gh-19640)
	python -m pip install "scipy-openblas32<=0.3.23.293.2"
	# Install numpy last, to ensure we get 2.0.0-dev (avoid possible <2.0 constraints).
	python -m pip install --pre --upgrade --timeout=60 -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy

	- name: Prepare compiler cache
	id: prep-ccache
	shell: bash
	run: \|
	mkdir -p "${CCACHE_DIR}"
	echo "dir=$CCACHE_DIR" >> $GITHUB_OUTPUT
	NOW=$(date -u +"%F-%T")
	echo "timestamp=${NOW}" >> $GITHUB_OUTPUT

	- name: Setup compiler cache
	uses: actions/cache@v3
	id: cache-ccache
	with:
	path: ${{ steps.prep-ccache.outputs.dir }}
	# Restores ccache from either a previous build on this branch or on main
	key: ${{ github.workflow }}-${{ matrix.python-version }}-ccache-linux-prerelease-${{ steps.prep-ccache.outputs.timestamp }}
	restore-keys: \|
	${{ github.workflow }}-${{ matrix.python-version }}-ccache-linux-prerelease-

	- name: Build and install SciPy
	run: \|
	python dev.py build --gcov --with-scipy-openblas

	- name: Ccache performance
	shell: bash -l {0}
	run: ccache -s

	- name: Downgrade NumPy from 2.0-dev to lowest supported
	if: matrix.python-version == '3.9'
	run: \|
	python -m pip install "numpy==1.22.4"

	- name: Test SciPy
	run: \|
	export OPENBLAS_NUM_THREADS=1
	python dev.py --no-build test -j2 --mode full -- --cov --cov-report term-missing

	#################################################################################
	linux_32bit:
	name: Linux - 32 bit
	needs: get_commit_message
	if: >
	needs.get_commit_message.outputs.message == 1
	&& (github.repository == 'scipy/scipy' \|\| github.repository == '')
	runs-on: ubuntu-latest
	# I tried running directly in a container:, using the image: and options:
	# entries. Unfortunately at this time options: does not seem to listen to
	# --platform linux/i386.
	steps:
	- uses: actions/[email protected]
	with:
	submodules: recursive

	- name: build + test
	run: \|
	set -euo pipefail
	docker pull quay.io/pypa/manylinux2014_i686
	docker run -v $(pwd):/scipy --platform=linux/i386 quay.io/pypa/manylinux2014_i686 /bin/bash -c "cd /scipy && \
	uname -a && \
	basedir=\$(python3.9 tools/openblas_support.py) && \
	cp -r \$basedir/lib/* /usr/local/lib && \
	cp \$basedir/include/* /usr/local/include && \
	export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig && \
	python3.9 -m venv test && \
	source test/bin/activate && \
	python -m pip install doit click rich_click pydevtool meson ninja && \
	python -m pip install numpy==1.22.4 cython pybind11 pytest pytest-timeout pytest-xdist pytest-env 'Pillow<10.0.0' mpmath pythran pooch meson hypothesis && \
	LD_LIBRARY_PATH=/usr/local/lib python dev.py build && \
	LD_LIBRARY_PATH=/usr/local/lib python dev.py test"

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CI: run doctests on GH actions & CircleCI #11

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CI: run doctests on GH actions & CircleCI #11

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