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PhononMaker add options to calculate_pdos and save force constant… #5021

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PhononMaker add options to calculate_pdos and save force constant…

PhononMaker add options to calculate_pdos and save force constant… #5021

Workflow file for this run

.github/workflows/testing.yml at 7add7ca
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=${{ matrix.python-version }} --yes
- name: Install uv
run: micromamba run -n a2 pip install uv
- name: Install conda dependencies
run: |
micromamba install -n a2 -c conda-forge enumlib packmol bader openbabel openff-toolkit==0.16.2 openff-interchange==0.3.22 --yes
- name: Install dependencies
run: |
micromamba activate a2
python -m pip install --upgrade pip
mkdir -p ~/.abinit/pseudos
cp -r tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4 ~/.abinit/pseudos
uv pip install .[strict,strict-forcefields,tests,abinit]
uv pip install torch-runstats
uv pip install --no-deps nequip==0.5.6
- name: Install pymatgen from master if triggered by pymatgen repo dispatch
if: github.event_name == 'repository_dispatch' && github.event.action == 'pymatgen-ci-trigger'
run: |
micromamba activate a2
uv pip install --upgrade 'git+https://github.com/materialsproject/pymatgen@${{ 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