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Update IMDv3 support details for GROMACS, NAMD, and LAMMPS #328

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Update IMDv3 support details for GROMACS, NAMD, and LAMMPS

Update IMDv3 support details for GROMACS, NAMD, and LAMMPS #328

Workflow file for this run

.github/workflows/gh-ci.yaml at 4f2155d
name: GH Actions CI
on:
push:
branches:
- main
pull_request:
branches:
- main
- develop
schedule:
# Weekly tests at midnight on Sundays run on main 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 * * 0"
concurrency:
# Specific group naming so CI is only cancelled
# within same PR or on merge to main
group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
cancel-in-progress: true
defaults:
run:
shell: bash -l {0}
jobs:
environment-config:
if: github.repository == 'Becksteinlab/imdclient'
runs-on: ubuntu-latest
outputs:
stable-python-version: ${{ steps.get-compatible-python.outputs.stable-python }}
python-matrix: ${{ steps.get-compatible-python.outputs.python-versions }}
steps:
- uses: actions/setup-python@v4
with:
python-version: "3.11"
- id: get-compatible-python
uses: MDAnalysis/mdanalysis-compatible-python@main
with:
release: "latest"
main-tests:
if: github.repository == 'Becksteinlab/imdclient'
needs: environment-config
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: [macOS-latest, ubuntu-latest]
python-version: ["3.10", "3.11", "3.12", "3.13"]
steps:
- uses: actions/checkout@v4
- name: Build information
run: |
uname -a
df -h
ulimit -a
- name: Set architecture
id: set-arch
run: echo "ARCHITECTURE=$(if [[ '${{ matrix.os }}' == 'macOS-latest' ]]; then echo 'arm64'; else echo 'x64'; fi)" >> $GITHUB_ENV
# More info on options: https://github.com/conda-incubator/setup-miniconda
- name: Install conda dependencies
uses: conda-incubator/setup-miniconda@v2
with:
python-version: ${{ matrix.python-version }}
environment-file: devtools/conda-envs/test_env.yaml
add-pip-as-python-dependency: true
architecture: ${{ env.ARCHITECTURE }}
channels: conda-forge, defaults
activate-environment: imdclient-test
auto-update-conda: true
auto-activate-base: false
show-channel-urls: true
miniconda-version: latest
- name: Install imdclient
run: |
python --version
python -m pip install . --no-deps
- name: Python information
run: |
which python
which pip
pip list
conda info
conda list
- name: Run tests with merged coverage
run: |
pytest -n auto -v --cov=imdclient --cov-report=xml --color=yes imdclient/tests/test_imdclient.py imdclient/tests/test_utils.py
- name: codecov
if: github.event_name != 'schedule'
uses: codecov/[email protected]
with:
token: ${{ secrets.CODECOV_TOKEN }}
files: coverage.xml
name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
verbose: True
simulation_engine_tests:
if: github.repository == 'Becksteinlab/imdclient'
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
include:
- name: namd
image: ghcr.io/becksteinlab/streaming-namd-docker:main-common-cpu
script: imdclient/tests/test_namd.py
- name: gromacs
image: ghcr.io/becksteinlab/streaming-md-docker:main-common-cpu
script: imdclient/tests/test_gromacs.py
- name: lammps
image: ghcr.io/becksteinlab/streaming-md-docker:main-common-cpu
script: imdclient/tests/test_lammps.py
permissions:
contents: read
packages: read
steps:
- uses: actions/checkout@v4
- name: Build information
run: |
uname -a
df -h
ulimit -a
- name: Log in to the Container registry
uses: docker/login-action@v3
with:
registry: ghcr.io
username: ${{ github.actor }}
password: ${{ secrets.NAMD_DOCKER_TOKEN }}
- name: Install conda dependencies
uses: conda-incubator/setup-miniconda@v2
with:
python-version: "3.11"
environment-file: devtools/conda-envs/test_env.yaml
add-pip-as-python-dependency: true
architecture: x64
channels: conda-forge, defaults
activate-environment: imdclient-test
auto-update-conda: true
auto-activate-base: false
show-channel-urls: true
miniconda-version: latest
- name: Install package
run: |
python --version
python -m pip install . --no-deps
- name: Pull container
run: |
docker pull ${{ matrix.image }}
- name: Run simulation engine tests
run: |
pytest -v --cov=imdclient --cov-report=xml --color=yes ${{ matrix.script }}
- name: codecov
if: github.event_name != 'schedule'
uses: codecov/[email protected]
with:
token: ${{ secrets.CODECOV_TOKEN }}
files: coverage.xml
name: codecov-${{ matrix.name }}
verbose: True
pylint_check:
if: github.repository == 'Becksteinlab/imdclient'
needs: environment-config
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: ${{ needs.environment-config.outputs.stable-python-version }}
- name: Install Pylint
run: |
which pip
which python
pip install pylint mdanalysis
- name: Run Pylint
env:
PYLINTRC: .pylintrc
run: |
pylint imdclient
pypi_check:
if: github.repository == 'Becksteinlab/imdclient'
needs: environment-config
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ needs.environment-config.outputs.stable-python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ needs.environment-config.outputs.stable-python-version }}
- name: Install dependencies
run: |
pip install pipx twine
- name: Build package
run: |
python -m pipx run build --sdist
- name: Check package build
run: |
DISTRIBUTION=$(ls -t1 dist/imdclient-*.tar.gz | head -n 1)
test -n "${DISTRIBUTION}" || { echo "no distribution dist/imdclient-*.tar.gz found"; exit 1; }
echo "twine check $DISTRIBUTION"
twine check $DISTRIBUTION