Lattice dynamics workflow using Pheasy #5136
Workflow file for this run
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name: testing | |
on: | |
push: | |
branches: [main] | |
tags: ["v*"] | |
pull_request: | |
workflow_dispatch: | |
repository_dispatch: | |
types: [pymatgen-ci-trigger] | |
jobs: | |
lint: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: actions/setup-python@v5 | |
with: | |
python-version: "3.10" | |
cache: pip | |
cache-dependency-path: pyproject.toml | |
- uses: pre-commit/[email protected] | |
test-non-ase: | |
# prevent this action from running on forks | |
if: github.repository == 'materialsproject/atomate2' | |
services: | |
local_mongodb: | |
image: mongo:4.0 | |
ports: | |
- 27017:27017 | |
runs-on: ubuntu-latest | |
defaults: | |
run: | |
shell: bash -l {0} # enables conda/mamba env activation by reading bash profile | |
strategy: | |
matrix: | |
python-version: ["3.10", "3.11", "3.12"] | |
split: [1, 2, 3] | |
steps: | |
- name: Check out repo | |
uses: actions/checkout@v4 | |
- name: Set up micromamba | |
uses: mamba-org/setup-micromamba@main | |
- name: Create mamba environment | |
run: | | |
micromamba create -n a2 python=${{ matrix.python-version }} --yes | |
- name: Install uv | |
run: micromamba run -n a2 pip install uv | |
- name: Install conda dependencies | |
run: | | |
micromamba install -n a2 -c conda-forge enumlib packmol bader openbabel openff-toolkit==0.16.2 openff-interchange==0.3.22 --yes | |
- name: Install dependencies | |
run: | | |
micromamba activate a2 | |
python -m pip install --upgrade pip | |
mkdir -p ~/.abinit/pseudos | |
cp -r tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4 ~/.abinit/pseudos | |
uv pip install .[strict,strict-forcefields,tests,abinit] | |
uv pip install -i https://test.pypi.org/simple/ pheasy==0.0.1 # Install pheasy | |
uv pip install torch-runstats | |
uv pip install --no-deps nequip==0.5.6 | |
- name: Install ALA-Mode | |
run: | | |
micromamba activate a2 | |
micromamba install -n a2 -c conda-forge numpy scipy h5py compilers “libblas=*=*mkl” spglib boost eigen cmake ipython mkl-include openmpi --yes | |
git clone https://github.com/ttadano/ALM.git # do I need to modify this? | |
cd ALM # do I need to modify this? | |
cd python | |
python setup.py build # do I need to modify this? | |
uv pip install -e . # do I need to modify this? | |
- name: Install pymatgen from master if triggered by pymatgen repo dispatch | |
if: github.event_name == 'repository_dispatch' && github.event.action == 'pymatgen-ci-trigger' | |
run: | | |
micromamba activate a2 | |
uv pip install --upgrade 'git+https://github.com/materialsproject/pymatgen@${{ github.event.client_payload.pymatgen_ref }}' | |
- name: Test split ${{ matrix.split }} | |
env: | |
MP_API_KEY: ${{ secrets.MP_API_KEY }} | |
# regenerate durations file with `pytest --store-durations --durations-path tests/.pytest-split-durations` | |
# Note the use of `--splitting-algorithm least_duration`. | |
# This helps prevent a test split having no tests to run, and then the GH action failing, see: | |
# https://github.com/jerry-git/pytest-split/issues/95 | |
# However this `splitting-algorithm` means that tests cannot depend sensitively on the order they're executed in. | |
run: | | |
micromamba activate a2 | |
pytest --splits 3 --group ${{ matrix.split }} --durations-path tests/.pytest-split-durations --splitting-algorithm least_duration --ignore=tests/ase --cov=atomate2 --cov-report=xml | |
- uses: codecov/codecov-action@v1 | |
if: matrix.python-version == '3.10' && github.repository == 'materialsproject/atomate2' | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
name: coverage${{ matrix.split }} | |
file: ./coverage.xml | |
test-notebooks-and-ase: | |
# prevent this action from running on forks | |
if: github.repository == 'materialsproject/atomate2' | |
# It seems like anything torch-dependent and tblite can't be installed in the same environment | |
# without the tblite tests failing in CI, see, e.g.: | |
# https://github.com/tblite/tblite/issues/116 | |
# Outside of CI, having torch installed but not loaded seems not to affect tblite | |
# Set off ASE tests here, where tblite-dependent tests live | |
services: | |
local_mongodb: | |
image: mongo:4.0 | |
ports: | |
- 27017:27017 | |
runs-on: ubuntu-latest | |
defaults: | |
run: | |
shell: bash -l {0} # enables conda/mamba env activation by reading bash profile | |
strategy: | |
matrix: | |
python-version: ["3.10", "3.11", "3.12"] | |
steps: | |
- name: Check out repo | |
uses: actions/checkout@v4 | |
- name: Set up micromamba | |
uses: mamba-org/setup-micromamba@main | |
- name: Create mamba environment | |
run: | | |
micromamba create -n a2 python=${{ matrix.python-version }} --yes | |
- name: Install uv | |
run: micromamba run -n a2 pip install uv | |
- name: Install conda dependencies | |
run: | | |
micromamba install -n a2 -c conda-forge enumlib packmol bader openbabel openff-toolkit==0.16.2 openff-interchange==0.3.22 --yes | |
- name: Install dependencies | |
run: | | |
micromamba activate a2 | |
python -m pip install --upgrade pip | |
uv pip install .[strict,tests] | |
- name: Install pymatgen from master if triggered by pymatgen repo dispatch | |
if: github.event_name == 'repository_dispatch' && github.event.action == 'pymatgen-ci-trigger' | |
run: uv pip install --upgrade 'git+https://github.com/materialsproject/pymatgen@${{ github.event.client_payload.pymatgen_ref }}' | |
- name: Test Notebooks | |
run: | | |
micromamba activate a2 | |
pytest --nbmake ./tutorials --ignore=./tutorials/openmm_tutorial.ipynb | |
- name: Test ASE | |
env: | |
MP_API_KEY: ${{ secrets.MP_API_KEY }} | |
run: | | |
micromamba activate a2 | |
pytest --splits 1 --group 1 --cov=atomate2 --cov-report=xml tests/ase | |
- uses: codecov/codecov-action@v1 | |
if: matrix.python-version == '3.10' && github.repository == 'materialsproject/atomate2' | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
file: ./coverage.xml | |
docs: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: actions/setup-python@v5 | |
with: | |
python-version: "3.10" | |
cache: pip | |
cache-dependency-path: pyproject.toml | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip | |
pip install .[strict,strict-forcefields,docs] | |
- name: Build | |
run: sphinx-build docs docs_build | |
automerge: | |
needs: [lint, test-non-ase, test-notebooks-and-ase, docs] | |
runs-on: ubuntu-latest | |
permissions: | |
pull-requests: write | |
contents: write | |
steps: | |
- uses: fastify/github-action-merge-dependabot@v3 |