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CI.yaml
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name: CI
on:
# GitHub has started calling new repo's first branch "main" https://github.com/github/renaming
# Existing codes likely still have "master" as the primary branch
# Both are tracked here to keep legacy and new codes working
push:
branches:
- "master"
- "main"
pull_request:
branches:
- "master"
- "main"
schedule:
# Nightly tests run on master by default:
# Scheduled workflows run on the latest commit on the default or base branch.
# (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
- cron: "0 0 * * TUE"
jobs:
test:
name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [macOS-latest, ubuntu-latest, windows-latest]
python-version: [3.7, 3.8, 3.9]
steps:
- uses: actions/checkout@v1
- name: Additional info about the build
shell: bash
run: |
uname -a
df -h
ulimit -a
# More info on options: https://github.com/conda-incubator/setup-miniconda
- uses: conda-incubator/setup-miniconda@v2
with:
python-version: ${{ matrix.python-version }}
environment-file: devtools/conda-envs/test_env.yaml
channels: conda-forge,defaults
activate-environment: test
auto-update-conda: false
auto-activate-base: false
show-channel-urls: true
- name: Install package
# conda setup requires this special shell
shell: bash -l {0}
run: |
python -m pip install . --no-deps
conda list
- name: Run package tests
# conda setup requires this special shell
shell: bash -l {0}
run: |
pytest -v --cov=kissim --cov-report=xml --cov-config=setup.cfg --color=yes kissim/tests/
- name: Run docs notebooks tests (on Linux only)
shell: bash -l {0}
run: |
if [ "$RUNNER_OS" == "Linux" ]; then
PYTEST_ARGS="--nbval-lax --current-env --nbval-cell-timeout=900"
pytest $PYTEST_ARGS docs/tutorials/*.ipynb -vvv
else
echo "Do not run notebooks under $RUNNER_OS"
fi
- name: CodeCov
uses: codecov/codecov-action@v1
with:
file: ./coverage.xml
flags: unittests
name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
lint-format-package:
runs-on: ubuntu-latest
env:
CI_OS: ubuntu-latest
PACKAGE: "kissim"
PYVER: "3.7"
steps:
- name: Checkout the code
uses: actions/checkout@v2
# More info on options: https://github.com/conda-incubator/setup-miniconda
- uses: conda-incubator/setup-miniconda@v2
with:
python-version: ${{ matrix.python-version }}
environment-file: devtools/conda-envs/test_env.yaml
channels: conda-forge,defaults,bioconda
activate-environment: test
auto-update-conda: true
auto-activate-base: false
show-channel-urls: true
# mamba-version: "*"
- name: Install linter and formatter
shell: bash -l {0}
run: |
conda install -y pylint black
- name: Run pylint
shell: bash -l {0}
run: |
pylint $PACKAGE/
- name: Run black check
shell: bash -l {0}
if: always()
run: |
black --check -l 99 $PACKAGE/
lint-format-notebooks:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
- name: Install notebook linter and formatter
run: |
python -m pip install black-nb
python -m pip install flake8-nb
- name: Run black-nb
shell: bash
run: |
black-nb -l 99 --check docs/tutorials/*ipynb
- name: Run flake8-nb
shell: bash
run: |
flake8-nb --config setup.cfg docs/tutorials/*ipynb
docs:
runs-on: ubuntu-latest
env:
CI_OS: ubuntu-latest
PACKAGE: "kissim"
PYVER: "3.7"
steps:
- name: Checkout the code
uses: actions/checkout@v2
# More info on options: https://github.com/conda-incubator/setup-miniconda
- uses: conda-incubator/setup-miniconda@v2
with:
python-version: ${{ matrix.python-version }}
environment-file: devtools/conda-envs/test_env.yaml
channels: conda-forge,defaults,bioconda
activate-environment: test
auto-update-conda: true
auto-activate-base: false
show-channel-urls: true
# mamba-version: "*"
- name: Install package
shell: bash -l {0}
run: |
python -m pip install . --no-deps
conda list
- name: Run sphinx
shell: bash -l {0}
run: |
cd docs
make clean
SPHINXOPTS="-W -T --keep-going" make html