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do not test deployed packages #406

do not test deployed packages

do not test deployed packages #406

Workflow file for this run

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: ["3.9", "3.10", "3.11", "3.12"]
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"
- os: ubuntu-latest
python-version: "3.11"
gromacs-version: "2023.4"
- os: ubuntu-latest
python-version: "3.11"
gromacs-version: "2024.2"
# explicitly include a few macOS runners; finding a version that works
# on the GH runners is tricky (eg some are compiled for rdtscp CPU instructions
# that are not available); 2018.6 (bioconda) worked for a while, but then stopped
# being resolved. 2024.2 (conda-forge) runs at the moment
- os: macOS-latest
python-version: "3.11"
gromacs-version: "2024.2"
- os: macOS-latest
python-version: "3.12"
gromacs-version: "2024.2"
env:
MPLBACKEND: agg
steps:
- name: git checkout
uses: actions/checkout@v4
with:
fetch-tags: true
- name: micromamba package and testing environment installation (Python ${{ matrix.python-version }}, GROMACS ${{ matrix.gromacs-version }})
uses: mamba-org/setup-micromamba@v1
with:
environment-file: ci/conda-envs/test_env.yaml
condarc: |
channels:
- conda-forge
- bioconda
channel_priority: flexible
cache-downloads: true
cache-environment: true
create-args: >-
python=${{ matrix.python-version }}.*=*_cpython
gromacs==${{ matrix.gromacs-version }}
- 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)
micromamba list | grep gromacs | grep ${{ matrix.gromacs-version }}
micromamba list | grep python | grep ${{ matrix.python-version }}
- 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@v4
with:
token: ${{ secrets.CODECOV_TOKEN }}
name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
file: ./coverage.xml
fail_ci_if_error: false