tests

[Fix] CuBIC, SPADE with scipy 1.14.0, deprecated `.A` attribute in `s… #94

Workflow file for this run

	# This workflow will set up GitHub-hosted runners and install the required dependencies for elephant tests.
	# On a pull requests and on pushes to master it will run different tests for elephant.

	name: tests
	# define events that trigger workflow 'tests'
	on:
	workflow_dispatch: # enables manual triggering of workflow
	inputs:
	logLevel:
	description: 'Log level'
	required: true
	default: 'warning'
	type: choice
	options:
	- info
	- warning
	- debug

	pull_request:
	branches:
	- master
	types:
	#- assigned
	#- unassigned
	#- labeled
	#- unlabeled
	- opened
	#- edited
	#- closed
	- reopened
	- synchronize
	#- converted_to_draft
	#- ready_for_review
	#- locked
	#- unlocked
	#- review_requested
	#- review_request_removed
	#- auto_merge_enabled
	#- auto_merge_disabled

	push:
	branches:
	- master

	# Cancel previous workflows on the same pull request
	concurrency:
	group: ${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: true

	# jobs define the steps that will be executed on the runner
	jobs:

	# _
	# _ __ (_)_ __
	# \| '_ \\| \| '_ \
	# \| \|_) \| \| \|_) \|
	# \| .__/\|_\| .__/
	# \|_\| \|_\|

	# install dependencies and elephant with pip and run tests with pytest
	build-and-test-pip:
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	# python versions for elephant: [3.8, 3.9, "3.10", 3.11, 3.12]
	python-version: [3.9, "3.10", 3.11, 3.12]
	# OS [ubuntu-latest, macos-latest, windows-latest]
	os: [ubuntu-latest]
	# do not cancel all in-progress jobs if any matrix job fails
	fail-fast: false

	steps:
	# used to reset cache every month
	- name: Get current year-month
	id: date
	run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT

	- name: Get pip cache dir
	id: pip-cache
	run: \|
	echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT

	- uses: actions/checkout@v3

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	cache: 'pip'
	cache-dependency-path: '**/requirements.txt'

	- name: Cache test_env
	uses: actions/cache@v3
	with:
	path: ${{ steps.pip-cache.outputs.dir }}
	# Look to see if there is a cache hit for the corresponding requirements files
	# cache will be reset on changes to any requirements or every month
	key: ${{ runner.os }}-venv-${{ hashFiles('/requirements.txt') }}-${{ hashFiles('/requirements-tests.txt') }}
	-${{ hashFiles('/requirements-extras.txt') }}-${{ hashFiles('/CI.yml') }}-${{ hashFiles('setup.py') }}
	-${{ steps.date.outputs.date }}

	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install coveralls
	pip install -e .[extras,tests]

	- name: List packages
	run: \|
	pip list
	python --version

	- name: Test with pytest
	run: \|
	coverage run --source=elephant -m pytest
	coveralls --service=github \|\| echo "Coveralls submission failed"
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

	# ___ ____
	# _ __ ___ __ _ ___ / _ \/ ___\|
	# \| '_ ` _ \ / _` \|/ __\| \| \| \___ \
	# \| \| \| \| \| \| (_\| \| (__\| \|_\| \|___) \|
	# \|_\| \|_\| \|_\|\__,_\|\___\|\___/\|____/

	test-macOS:
	name: conda (${{ matrix.python-version }}, ${{ matrix.os }})
	runs-on: ${{ matrix.os }}
	strategy:
	# do not cancel all in-progress jobs if any matrix job fails
	fail-fast: false
	matrix:
	# OS [ubuntu-latest, macos-latest, windows-latest]
	os: [macos-12,macos-13]
	python-version: [3.11]
	steps:
	- name: Get current year-month
	id: date
	run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT

	- uses: actions/[email protected]

	- name: Cache conda
	uses: actions/cache@v3
	with:
	path: ~/conda_pkgs_dir
	key: ${{ runner.os }}-conda-${{hashFiles('requirements/environment.yml') }}-${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}

	- uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # corresponds to v3.0.4
	with:
	auto-update-conda: true
	python-version: ${{ matrix.python-version }}
	mamba-version: "*"
	channels: conda-forge,defaults
	channel-priority: true
	activate-environment: elephant
	environment-file: requirements/environment-tests.yml

	- name: Install dependencies
	shell: bash -l {0}
	run: \|
	python --version
	mamba install pytest pytest-cov coveralls
	pip install -e .[extras]

	- name: List packages
	shell: bash -l {0}
	run: \|
	pip list
	mamba list
	python --version

	- name: Test with pytest
	shell: bash -l {0}
	run: \|
	pytest --cov=elephant

	# __ ___ _
	# \ \ / (_)_ __ __\| \| _____ _____
	# \ \ /\ / /\| \| '_ \ / _` \|/ _ \ \ /\ / / __\|
	# \ V V / \| \| \| \| \| (_\| \| (_) \ V V /\__ \
	# \_/\_/ \|_\|_\| \|_\|\__,_\|\___/ \_/\_/ \|___/

	# install dependencies with pip and run tests with pytest
	test-pip:
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	# python versions for elephant: [3.8, 3.9, 3.10, 3.11]
	python-version: [3.11,]
	# OS [ubuntu-latest, macos-latest, windows-latest]
	os: [windows-latest]

	steps:
	- name: Get current year-month
	id: date
	run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT

	- uses: actions/checkout@v3

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}

	- name: Cache pip
	uses: actions/cache@v3
	with:
	path: ~\AppData\Local\pip\Cache
	# Look to see if there is a cache hit for the corresponding requirements files
	key: ${{ runner.os }}-pip-${{ hashFiles('/requirements.txt') }}-${{ hashFiles('/requirements-tests.txt') }}
	-${{ hashFiles('/requirements-extras.txt') }}-${{ hashFiles('setup.py') }} -${{ hashFiles('/CI.yml') }}-${{ steps.date.outputs.date }}

	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install pytest-cov coveralls
	pip install -e .[extras,tests]

	- name: List packages
	run: \|
	pip list
	python --version

	- name: Test with pytest
	run: \|
	pytest --cov=elephant

	# __ __ ____ ___
	# \| \/ \| _ \_ _\|
	# \| \|\/\| \| \|_) \| \|
	# \| \| \| \| __/\| \|
	# \|_\| \|_\|_\| \|___\|

	# install dependencies and elephant with pip and run MPI
	test-pip-MPI:
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	# python versions for elephant: [3.8, 3.9, 3.10, 3.11]
	python-version: [3.9]
	# OS [ubuntu-latest, macos-latest, windows-latest]
	os: [ubuntu-latest]

	# do not cancel all in-progress jobs if any matrix job fails
	fail-fast: false

	steps:
	- name: Get current year-month
	id: date
	run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
	- uses: actions/checkout@v3

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}

	- name: Get pip cache dir
	id: pip-cache
	run: \|
	echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT

	- name: Cache test_env
	uses: actions/cache@v3
	with:
	path: ${{ steps.pip-cache.outputs.dir }}
	# look to see if there is a cache hit for the corresponding requirements files
	# cache will be reset on changes to any requirements or every month
	key: ${{ runner.os }}-venv-${{ hashFiles('/requirements.txt') }}-${{ hashFiles('/requirements-tests.txt') }}
	-${{ hashFiles('/requirements-extras.txt') }}-${{ hashFiles('setup.py') }} -${{ hashFiles('/CI.yml') }}-${{ steps.date.outputs.date }}

	- name: Setup environment
	run: \|
	sudo apt-get update
	sudo apt install -y libopenmpi-dev openmpi-bin

	python -m pip install --upgrade pip
	pip install mpi4py
	pip install pytest-cov coveralls
	pip install -e .[extras,tests]

	- name: List packages
	run: \|
	pip list
	python --version

	- name: Test with pytest
	run: \|
	mpiexec -n 1 python -m mpi4py -m coverage run --source=elephant -m pytest
	coveralls --service=github \|\| echo "Coveralls submission failed"
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

	# ____ _
	# / ___\|___ _ __ __\| \| __ _
	# \| \| / _ \\| '_ \ / _` \|/ _` \|
	# \| \|__\| (_) \| \| \| \| (_\| \| (_\| \|
	# \____\___/\|_\| \|_\|\__,_\|\__,_\|

	# install dependencies with conda and run tests with pytest
	test-conda:
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	# python versions for elephant: [3.8, 3.9, 3.10, 3.11]
	python-version: [3.11]
	# OS [ubuntu-latest, macos-latest, windows-latest]
	os: [ubuntu-latest]

	# do not cancel all in-progress jobs if any matrix job fails
	fail-fast: false

	steps:
	- name: Get current year-month
	id: date
	run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT

	- uses: actions/checkout@v3

	- name: Get pip cache dir
	id: pip-cache
	run: \|
	echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT

	- name: Cache pip
	uses: actions/cache@v3
	with:
	path: ${{ steps.pip-cache.outputs.dir }}

	key: ${{ runner.os }}-pip-${{hashFiles('requirements/environment-tests.yml') }}-${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}

	- uses: conda-incubator/setup-miniconda@030178870c779d9e5e1b4e563269f3aa69b04081 # corresponds to v3.0.3
	with:
	auto-update-conda: true
	python-version: ${{ matrix.python-version }}
	mamba-version: "*"
	channels: conda-forge,defaults
	channel-priority: true
	activate-environment: elephant
	environment-file: requirements/environment-tests.yml

	- name: Install dependencies
	shell: bash -el {0}
	run: \|
	python --version
	conda install mpi4py openmpi
	mamba install pytest pytest-cov coveralls
	pip install -e .

	- name: List packages
	shell: bash -el {0}
	run: \|
	pip list
	mamba list
	python --version

	- name: Test with pytest
	shell: bash -el {0}
	run: \|
	pytest --cov=elephant

	# ____
	# \| _ \ ___ ___ ___
	# \| \| \| \|/ _ \ / __/ __\|
	# \| \|_\| \| (_) \| (__\__ \
	# \|____/ \___/ \___\|___/

	# install dependencies for the documentation and build .html
	docs:
	name: docs (${{ matrix.os }})
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	# python versions for elephant: [3.8, 3.9, 3.10, 3.11, 3.12]
	python-version: [3.12]
	# OS [ubuntu-latest, macos-latest, windows-latest]
	os: [ubuntu-latest]

	steps:

	- name: Get current year-month
	id: date
	run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT

	- uses: actions/checkout@v3

	- name: Get pip cache dir
	id: pip-cache
	run: \|
	echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT

	- name: Cache pip
	uses: actions/cache@v3
	with:
	path: ${{ steps.pip-cache.outputs.dir }}
	# Look to see if there is a cache hit for the corresponding requirements files
	key: ${{ runner.os }}-pip-${{ hashFiles('/requirements-docs.txt') }}-${{ hashFiles('/requirements-tutorials.txt') }}-${{ hashFiles('**/environment-docs.yml') }}
	-${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}

	- uses: conda-incubator/setup-miniconda@030178870c779d9e5e1b4e563269f3aa69b04081 # corresponds to v3.0.3
	with:
	auto-update-conda: true
	python-version: ${{ matrix.python-version }}
	mamba-version: "*"
	activate-environment: elephant
	environment-file: requirements/environment.yml

	- name: Install dependencies
	shell: bash -el {0} # enables conda incubator to activate environment
	run: \|
	sudo apt-get update
	sudo apt install -y libopenmpi-dev openmpi-bin

	conda install -c conda-forge openmpi pandoc libstdcxx-ng # fix libstdc++.so.6: version for new scipy versions > 1.9.1
	mamba env update --file requirements/environment-docs.yml --name elephant
	python -m pip install --upgrade pip
	pip install -e .[extras,tutorials,docs]
	# run notebooks
	sed -i -E "s/nbsphinx_execute =./nbsphinx_execute = 'always'/g" doc/conf.py

	- name: List packages
	shell: bash -el {0}
	run: \|
	pip list
	mamba list
	python --version

	- name: make html
	shell: bash -el {0}
	run: \|
	cd doc
	make html

	# install dependencies and elephant with pip and run tests with pytest
	doctests:
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	# python versions for elephant: [3.7, 3.8, 3.9, "3.10"]
	python-version: ["3.10"]

	# OS [ubuntu-latest, macos-latest, windows-latest]
	os: [ubuntu-latest]

	steps:
	# used to reset cache every month
	- name: Get current year-month
	id: date
	run: echo "::set-output name=date::$(date +'%Y-%m')"
	- uses: actions/checkout@v3

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}

	- name: Cache test_env
	uses: actions/cache@v3
	with:
	path: ~/test_env
	# Look to see if there is a cache hit for the corresponding requirements files
	# cache will be reset on changes to any requirements or every month
	key: ${{ runner.os }}-venv-${{ hashFiles('/requirements.txt') }}-${{ hashFiles('/requirements-tests.txt') }}
	-${{ hashFiles('/requirements-extras.txt') }}-${{ hashFiles('/CI.yml') }}-${{ hashFiles('setup.py') }}
	-${{ steps.date.outputs.date }}

	- name: Install dependencies
	run: \|
	# create an environment and install everything
	python -m venv ~/test_env
	source ~/test_env/bin/activate
	sudo apt install -y libopenmpi-dev openmpi-bin

	python -m pip install --upgrade pip
	pip install mpi4py
	pip install pytest-cov coveralls
	pip install -e .[extras,tests]

	- name: List packages
	run: \|
	source ~/test_env/bin/activate
	pip list
	python --version

	- name: Run doctests
	run: \|
	source ~/test_env/bin/activate
	pytest elephant --doctest-modules --ignore=elephant/test/

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[Fix] CuBIC, SPADE with scipy 1.14.0, deprecated `.A` attribute in `s… #94

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[Fix] CuBIC, SPADE with scipy 1.14.0, deprecated `.A` attribute in `s… #94

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[Fix] CuBIC, SPADE with scipy 1.14.0, deprecated .A attribute in `s… #94

Workflow file

Workflow file for this run

[Fix] CuBIC, SPADE with scipy 1.14.0, deprecated `.A` attribute in `s… #94