fix #263: No module named 'pkg_resources' #306
Workflow file for this run
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name: CI | |
on: | |
# run every month on day 14 and 28 at 4:44 UTC | |
schedule: | |
- cron: "44 4 14,28 * *" | |
push: | |
branches: | |
- "main" | |
pull_request: | |
branches: | |
- "main" | |
concurrency: | |
group: "${{ github.ref }}-${{ github.head_ref }}" | |
cancel-in-progress: true | |
defaults: | |
run: | |
shell: bash -l {0} | |
jobs: | |
test: | |
runs-on: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [ubuntu-latest] | |
python-version: ["3.8", "3.9", "3.10", "3.11"] | |
gromacs-version: ["2023.1"] | |
# Test other GROMACS versions selectively on a recent Python. | |
# On macOS only test one GROMACS version and two Python versions | |
# to keep the testing matrix manageable. | |
include: | |
- os: ubuntu-latest | |
python-version: "3.11" | |
gromacs-version: "4.6.5" | |
- os: ubuntu-latest | |
python-version: "3.11" | |
gromacs-version: "2018.6" | |
- os: ubuntu-latest | |
python-version: "3.11" | |
gromacs-version: "2019.1" | |
- os: ubuntu-latest | |
python-version: "3.11" | |
gromacs-version: "2020.6" | |
- os: ubuntu-latest | |
python-version: "3.11" | |
gromacs-version: "2021.1" | |
- os: ubuntu-latest | |
python-version: "3.11" | |
gromacs-version: "2022.4" | |
# explicitly include a few macOS runners | |
# (conda-forge GROMACS >= 2021 is compiled to use rdtscp CPU instruction but these | |
# are not available in the macOS GitHub runner so we need to use a different GROMACS | |
# version. Try 2018.5 from bioconda. (2021.5 worked previously but not anymore.) | |
# Locally 2023.1 was successfully tested on Intel macOS 13.5.) | |
- os: macOS-latest | |
python-version: "3.11" | |
gromacs-version: "2018.6" | |
env: | |
MPLBACKEND: agg | |
steps: | |
- uses: actions/checkout@v3 | |
- name: micromamba environment and package installation (Python ${{ matrix.python-version }}) | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-file: ci/conda-envs/test_env.yaml | |
condarc: | | |
channels: | |
- conda-forge | |
- bioconda | |
channel_priority: flexible | |
cache-downloads: true | |
cache-environment: true | |
create-args: >- | |
python=${{ matrix.python-version }}.*=*_cpython | |
- name: Python version information ${{ matrix.python-version }} | |
run: | | |
python -c "import sys; print(sys.version)" | |
- name: micromamba environment information | |
run: | | |
micromamba info | |
micromamba list | |
cat /proc/cpuinfo || (/usr/sbin/system_profiler SPHardwareDataType; /usr/sbin/sysctl -a | grep machdep.cpu) | |
- name: Install pytest and plugins | |
run: | | |
micromamba install pytest pytest-pep8 pytest-cov codecov | |
- name: Install GROMACS (${{ matrix.gromacs-version }}) | |
# UGLY HACK/FIX (probably to issues with bioconda packages) | |
# - For 3.9, micromamba insists on using pypy 3.9 (and --py-pin does not help). | |
# We can't freeze because then it's not possible to install older GROMACS versions from bioconda. | |
run: | | |
micromamba install 'gromacs==${{ matrix.gromacs-version }}' pocl numkit python=${{ matrix.python-version }}.*=*_cpython | |
- name: Install package (with no dependencies) | |
run: | | |
python -m pip install --no-deps . | |
- name: Run tests | |
run: | | |
pytest -v --disable-pytest-warnings --durations=20 --low-performance --cov=gromacs --cov-report=xml --color=yes ./tests | |
- name: Codecov | |
uses: codecov/codecov-action@v3 | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} | |
file: ./coverage.xml | |
fail_ci_if_error: false |