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Added a section in the documentation linking to Alpaca. (#607) #83

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Added a section in the documentation linking to Alpaca. (#607)

Added a section in the documentation linking to Alpaca. (#607) #83

Workflow file for this run

.github/workflows/CI.yml at dc3e65f
# 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
# 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: ${{ matrix.os }}
strategy:
matrix:
# python versions for elephant: [3.8, 3.9, "3.10", 3.11]
python-version: [3.8, 3.9, "3.10", 3.11]
# OS [ubuntu-latest, macos-latest, windows-latest]
os: [ubuntu-latest]
# do not cancel all in-progress jobs if any matrix job fails
fail-fast: false
steps:
# used to reset cache every month
- name: Get current year-month
id: date
run: echo "date=$(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 }}
cache: 'pip'
cache-dependency-path: '**/requirements.txt'
- name: Cache test_env
uses: actions/cache@v3
with:
path: /home/runner/.cache/pip
# 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 -r requirements/requirements-tests.txt
pip install -r requirements/requirements.txt
pip install -r requirements/requirements-extras.txt
pip install -e .
- name: List packages
run: |
pip list
python --version
- name: Test with pytest
run: |
coverage run --source=elephant -m pytest
coveralls --service=github
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
# ___ ____
# _ __ ___ __ _ ___ / _ \/ ___|
# | '_ ` _ \ / _` |/ __| | | \___ \
# | | | | | | (_| | (__| |_| |___) |
# |_| |_| |_|\__,_|\___|\___/|____/
test-macOS:
name: conda (${{ matrix.python-version }}, ${{ matrix.os }})
runs-on: ${{ matrix.os }}
strategy:
# do not cancel all in-progress jobs if any matrix job fails
fail-fast: false
matrix:
# OS [ubuntu-latest, macos-latest, windows-latest]
os: [macos-11,macos-12]
python-version: [3.9]
steps:
- name: Get current year-month
id: date
run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
- uses: actions/checkout@v3
- 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@3b0f2504dd76ef23b6d31f291f4913fb60ab5ff3 # corresponds to v2.2.0
with:
auto-update-conda: true
python-version: ${{ matrix.python-version }}
activate-environment: elephant
environment-file: requirements/environment-tests.yml
auto-activate-base: false
use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
- name: Install dependencies
shell: bash -l {0}
run: |
python --version
conda env list
conda install mpi4py openmpi
conda install pytest
conda install pytest-cov coveralls
pip install -e .[extras]
- name: List packages
shell: bash -l {0}
run: |
pip list
conda 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: ${{ matrix.os }}
strategy:
matrix:
# python versions for elephant: [3.8, 3.9, 3.10, 3.11]
python-version: [3.8,]
# OS [ubuntu-latest, macos-latest, windows-latest]
os: [windows-latest]
include:
# - os: ubuntu-latest
# path: ~/.cache/pip
# - os: macos-latest
# path: ~/Library/Caches/pip
- os: windows-latest
path: ~\AppData\Local\pip\Cache
# do not cancel all in-progress jobs if any matrix job fails
fail-fast: false
steps:
- name: Get current year-month
id: date
run: echo "date=$(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: Cache pip
uses: actions/cache@v3
with:
path: ${{ matrix.path }}
# 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 -r requirements/requirements-tests.txt
pip install -r requirements/requirements.txt
pip install -r requirements/requirements-extras.txt
pip install pytest-cov coveralls
pip install -e .
- 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: Cache test_env
uses: actions/cache@v3
with:
path: ~/.cache/pip
# 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 coveralls
pip install -r requirements/requirements-tests.txt
pip install -r requirements/requirements.txt
pip install -r requirements/requirements-extras.txt
pip install pytest-cov coveralls
pip install -e .
- 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
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
# ____ _
# / ___|___ _ __ __| | __ _
# | | / _ \| '_ \ / _` |/ _` |
# | |__| (_) | | | | (_| | (_| |
# \____\___/|_| |_|\__,_|\__,_|
# install dependencies with conda and run tests with pytest
test-conda:
runs-on: ${{ matrix.os }}
strategy:
matrix:
# OS [ubuntu-latest, macos-latest, windows-latest]
os: [ubuntu-latest]
python-version: [3.9]
# do not cancel all in-progress jobs if any matrix job fails
fail-fast: false
steps:
- uses: actions/checkout@v3
- name: Cache pip
uses: actions/cache@v3
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{hashFiles('requirements/environment-tests.yml') }}-${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}
- uses: conda-incubator/setup-miniconda@3b0f2504dd76ef23b6d31f291f4913fb60ab5ff3 # corresponds to v2.2.0
with:
auto-update-conda: true
python-version: ${{ matrix.python-version }}
activate-environment: elephant
environment-file: requirements/environment-tests.yml
auto-activate-base: false
use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
- name: Install dependencies
shell: bash -l {0}
run: |
python --version
conda env list
conda install mpi4py openmpi
conda install pytest
conda install pytest-cov coveralls
pip install -e .
- name: List packages
shell: bash -l {0}
run: |
pip list
conda list
python --version
- name: Test with pytest
shell: bash -l {0}
run: |
pytest --cov=elephant
# ____
# | _ \ ___ ___ ___
# | | | |/ _ \ / __/ __|
# | |_| | (_) | (__\__ \
# |____/ \___/ \___|___/
# install dependencies for the documentation and build .html
docs:
name: docs (${{ matrix.os }})
runs-on: ${{ matrix.os }}
strategy:
matrix:
# OS [ubuntu-latest, macos-latest, windows-latest]
os: [ubuntu-latest]
steps:
- name: Get current year-month
id: date
run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
- uses: actions/checkout@v3
- name: Add conda to system path
run: |
# $CONDA is an environment variable pointing to the root of the miniconda directory
echo $CONDA/bin >> $GITHUB_PATH
- name: Cache pip
uses: actions/cache@v3
with:
path: ~/.cache/pip
# 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 }}
- name: Install dependencies
run: |
conda config --add channels conda-forge # bugfix with scipy==1.8.1: libstdcxx-ng 12.1.0 required
sudo apt-get update
sudo apt install -y libopenmpi-dev openmpi-bin
conda update conda
conda install -c conda-forge openmpi pandoc libstdcxx-ng # fix libstdc++.so.6: version for new scipy versions > 1.9.1
conda env update --file requirements/environment-docs.yml --name base
activate base
python -m pip install --upgrade pip
pip install -r requirements/requirements-docs.txt
pip install -r requirements/requirements-tutorials.txt
pip install -e .[extras]
# run notebooks
sed -i -E "s/nbsphinx_execute *=.*/nbsphinx_execute = 'always'/g" doc/conf.py
- name: List packages
run: |
activate base
pip list
conda list
python --version
- name: make html
run: |
activate base
cd doc
make html
# install dependencies and elephant with pip and run tests with pytest
doctests:
runs-on: ${{ matrix.os }}
strategy:
matrix:
# python versions for elephant: [3.7, 3.8, 3.9, "3.10"]
python-version: ["3.10"]
# OS [ubuntu-latest, macos-latest, windows-latest]
os: [ubuntu-latest]
# do not cancel all in-progress jobs if any matrix job fails
fail-fast: false
steps:
# used to reset cache every month
- name: Get current year-month
id: date
run: echo "::set-output name=date::$(date +'%Y-%m')"
- uses: actions/checkout@v3
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
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 -r requirements/requirements-tests.txt
pip install -r requirements/requirements.txt
pip install -r requirements/requirements-extras.txt
pip install pytest-cov coveralls
pip install -e .
- 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/