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fix pip check for optional dependencies #13

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fix pip check for optional dependencies

fix pip check for optional dependencies #13

Workflow file for this run

.github/workflows/pipeline.yml at 5850d4a
name: Pipeline
on:
push:
branches: [ main ]
pull_request:
jobs:
black:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: psf/black@stable
with:
options: "--check --diff"
src: ./${{ github.event.repository.name }}
black_fix: # in most cases pre-commit is faster
needs: [black]
if: failure()
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
with:
token: ${{ secrets.DEPENDABOT_WORKFLOW_TOKEN }}
ref: ${{ github.event.pull_request.head.ref }} # Check out the head of the actual branch, not the PR
fetch-depth: 0 # otherwise, you will fail to push refs to dest repo
- name: format black
uses: psf/black@stable
with:
options: ""
src: "./${{ github.event.repository.name }}"
- name: commit
run: |
git config --local user.email "[email protected]"
git config --local user.name "pyiron-runner"
git commit -m "Format black" -a
- name: push
uses: ad-m/github-push-action@master
with:
github_token: ${{ secrets.DEPENDABOT_WORKFLOW_TOKEN }}
branch: ${{ github.event.pull_request.head.ref }}
coverage:
needs: [black]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Setup environment
shell: bash -l {0}
run: |
cp .ci_support/environment.yml environment.yml
tail --lines=+4 .ci_support/environment-lammps.yml >> environment.yml
tail --lines=+4 .ci_support/environment-qe.yml >> environment.yml
sed -i 's/- scipy =1.13.0/- scipy =1.12.0/g' environment.yml
echo -e "channels:\n - conda-forge\n" > .condarc
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v3
with:
python-version: '3.11'
miniforge-version: latest
condarc-file: .condarc
environment-file: environment.yml
- name: Test
shell: bash -l {0}
timeout-minutes: 30
run: |
pip install versioneer[toml]==0.29
pip install . --no-deps --no-build-isolation
coverage run --omit="atomistics/_version.py,tests/*" -m unittest discover tests
coverage xml
env:
ASE_ESPRESSO_COMMAND: "pw.x -in PREFIX.pwi > PREFIX.pwo"
ESPRESSO_PSEUDO: tests/static/qe
OMPI_MCA_plm: isolated
OMPI_MCA_btl_vader_single_copy_mechanism: none
OMPI_MCA_rmaps_base_oversubscribe: yes
- name: Upload coverage reports to Codecov
uses: codecov/codecov-action@v5
with:
token: ${{ secrets.CODECOV_TOKEN }}
minimal:
needs: [black]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Conda config
run: echo -e "channels:\n - conda-forge\n" > .condarc
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v3
with:
python-version: '3.12'
miniforge-version: latest
condarc-file: .condarc
environment-file: .ci_support/environment.yml
- name: Test
shell: bash -l {0}
timeout-minutes: 30
run: |
pip install versioneer[toml]==0.29
pip install . --no-deps --no-build-isolation
python -m unittest discover tests
notebooks:
needs: [black]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Merge Notebook environment
run: |
cp .ci_support/environment.yml environment.yml
tail --lines=+4 .ci_support/environment-notebooks.yml >> environment.yml
echo -e "channels:\n - conda-forge\n" > .condarc
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v3
with:
python-version: "3.12"
miniforge-version: latest
condarc-file: .condarc
environment-file: environment.yml
- name: Test
shell: bash -l {0}
run: |
pip install versioneer[toml]==0.29
pip install . --no-deps --no-build-isolation
cd notebooks
cp -r ../tests/static .
../.ci_support/build_notebooks.sh
pip_check:
needs: [black]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Conda config
run: |
cp .ci_support/environment.yml environment.yml
tail --lines=+4 .ci_support/environment-lammps.yml >> environment.yml
tail --lines=+4 .ci_support/environment-qe.yml >> environment.yml
tail --lines=+4 .ci_support/environment-gpaw.yml >> environment.yml
echo -e "channels:\n - conda-forge\n" > .condarc
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v3
with:
python-version: '3.12'
miniforge-version: latest
condarc-file: .condarc
environment-file: environment.yml
- name: Pip check
shell: bash -l {0}
run: |
pip install versioneer[toml]==0.29 tomlkit
python .ci_support/check.py
cat pyproject.toml
pip install . --no-deps --no-build-isolation
pip check
unittest_matrix:
needs: [black]
runs-on: ${{ matrix.operating-system }}
strategy:
matrix:
include:
- operating-system: macos-latest
python-version: '3.12'
- operating-system: ubuntu-latest
python-version: '3.12'
- operating-system: windows-latest
python-version: '3.12'
- operating-system: ubuntu-latest
python-version: '3.11'
- operating-system: ubuntu-latest
python-version: '3.10'
steps:
- uses: actions/checkout@v4
- name: Setup environment (windows)
if: matrix.operating-system == 'windows-latest'
shell: bash -l {0}
run: |
cp .ci_support/environment.yml environment.yml
echo -e "channels:\n - conda-forge\n" > .condarc
- name: Setup environment (unix)
if: matrix.operating-system != 'windows-latest'
shell: bash -l {0}
run: |
cp .ci_support/environment.yml environment.yml
tail --lines=+4 .ci_support/environment-lammps.yml >> environment.yml
echo -e "channels:\n - conda-forge\n" > .condarc
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v3
with:
python-version: ${{ matrix.python-version }}
miniforge-version: latest
condarc-file: .condarc
environment-file: environment.yml
- name: Test
shell: bash -l {0}
timeout-minutes: 30
run: |
pip install versioneer[toml]==0.29
pip install . --no-deps --no-build-isolation
python -m unittest discover tests
unittest_abinit:
needs: [black]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Merge Notebook environment
run: |
cp .ci_support/environment.yml environment.yml
tail --lines=+4 .ci_support/environment-abinit.yml >> environment.yml
echo -e "channels:\n - conda-forge\n" > .condarc
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v3
with:
python-version: '3.12'
miniforge-version: latest
condarc-file: .condarc
environment-file: environment.yml
- name: Test
shell: bash -l {0}
timeout-minutes: 30
run: |
pip install versioneer[toml]==0.29
pip install . --no-deps --no-build-isolation
python -m unittest tests/test_ase_interface/test_evcurve_ase_abinit.py
env:
ABINIT_PP_PATH: '/usr/share/miniconda3/envs/my-env/share/abinit/LDA_FHI'
ABI_PSPDIR: '/usr/share/miniconda3/envs/my-env/share/abinit/LDA_FHI'
ASE_ABINIT_COMMAND: 'abinit PREFIX.in > PREFIX.log'
unittest_gpaw:
needs: [black]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Merge Notebook environment
run: |
cp .ci_support/environment.yml environment.yml
tail --lines=+4 .ci_support/environment-gpaw.yml >> environment.yml
echo -e "channels:\n - conda-forge\n" > .condarc
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v3
with:
python-version: '3.12'
miniforge-version: latest
condarc-file: .condarc
environment-file: environment.yml
- name: Test
shell: bash -l {0}
timeout-minutes: 30
run: |
pip install versioneer[toml]==0.29
pip install . --no-deps --no-build-isolation
python -m unittest tests/test_ase_interface/test_evcurve_ase_gpaw.py
python -m unittest tests/test_ase_interface/test_elastic_ase_gpaw.py
python -m unittest tests/test_ase_interface/test_phonons_ase_gpaw.py
unittest_mace:
needs: [black]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Merge Notebook environment
run: |
cp .ci_support/environment.yml environment.yml
tail --lines=+4 .ci_support/environment-mace.yml >> environment.yml
echo -e "channels:\n - conda-forge\n" > .condarc
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v3
with:
python-version: '3.12'
miniforge-version: latest
condarc-file: .condarc
environment-file: environment.yml
- name: Test
shell: bash -l {0}
timeout-minutes: 60
run: |
pip install versioneer[toml]==0.29
pip install . --no-deps --no-build-isolation
python -m unittest tests/test_ase_interface/test_evcurve_ase_mace.py
python -m unittest tests/test_ase_interface/test_phonons_ase_mace.py
python -m unittest tests/test_ase_interface/test_quasiharmonic_ase_mace.py
python -m unittest tests/test_ase_interface/test_ase_md_mace.py
unittest_matgl:
needs: [black]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Merge Notebook environment
run: |
cp .ci_support/environment.yml environment.yml
tail --lines=+4 .ci_support/environment-matgl.yml >> environment.yml
echo -e "channels:\n - conda-forge\n" > .condarc
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v3
with:
python-version: '3.11'
miniforge-version: latest
condarc-file: .condarc
environment-file: environment.yml
- name: Test
shell: bash -l {0}
timeout-minutes: 60
run: |
pip install versioneer[toml]==0.29
pip install . --no-deps --no-build-isolation
python -m unittest tests/test_ase_interface/test_evcurve_ase_matgl.py
python -m unittest tests/test_ase_interface/test_phonons_ase_matgl.py
python -m unittest tests/test_ase_interface/test_quasiharmonic_ase_matgl.py
python -m unittest tests/test_ase_interface/test_ase_md_matgl.py
unittest_qe:
needs: [black]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Merge Notebook environment
run: |
cp .ci_support/environment.yml environment.yml
tail --lines=+4 .ci_support/environment-qe.yml >> environment.yml
echo -e "channels:\n - conda-forge\n" > .condarc
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v3
with:
python-version: '3.11'
miniforge-version: latest
condarc-file: .condarc
environment-file: environment.yml
- name: Test
shell: bash -l {0}
timeout-minutes: 60
run: |
pip install versioneer[toml]==0.29
pip install . --no-deps --no-build-isolation
python -m unittest tests/test_ase_interface/test_evcurve_ase_qe.py
env:
ASE_ESPRESSO_COMMAND: "pw.x -in PREFIX.pwi > PREFIX.pwo"
ESPRESSO_PSEUDO: tests/static/qe
OMPI_MCA_plm: isolated
OMPI_MCA_btl_vader_single_copy_mechanism: none
OMPI_MCA_rmaps_base_oversubscribe: yes
unittest_siesta:
needs: [black]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Merge Notebook environment
run: |
cp .ci_support/environment.yml environment.yml
tail --lines=+4 .ci_support/environment-siesta.yml >> environment.yml
echo -e "channels:\n - conda-forge\n" > .condarc
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v3
with:
python-version: '3.12'
miniforge-version: latest
condarc-file: .condarc
environment-file: environment.yml
- name: Test
shell: bash -l {0}
timeout-minutes: 30
run: |
pip install versioneer[toml]==0.29
pip install . --no-deps --no-build-isolation
python -m unittest tests/test_ase_interface/test_evcurve_ase_siesta.py
unittest_old:
needs: [black]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Conda config
run: echo -e "channels:\n - conda-forge\n" > .condarc
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v3
with:
python-version: '3.9'
miniforge-version: latest
condarc-file: .condarc
environment-file: .ci_support/environment-old.yml
- name: Test
shell: bash -l {0}
timeout-minutes: 30
run: |
pip install versioneer[toml]==0.29
pip install . --no-deps --no-build-isolation
python -m unittest discover tests
autobot:
needs: [unittest_old, unittest_siesta, unittest_qe, unittest_matgl, unittest_mace, unittest_gpaw, unittest_abinit, unittest_matrix, pip_check, notebooks, minimal, coverage]
permissions:
contents: write
pull-requests: write
runs-on: ubuntu-latest
if: (github.event.pull_request.user.login == 'dependabot[bot]' || github.event.pull_request.user.login == 'pre-commit-ci[bot]')
steps:
- name: Enable auto-merge for bot PRs
run: gh pr merge --auto --squash "$PR_URL"
env:
PR_URL: ${{github.event.pull_request.html_url}}
GH_TOKEN: ${{secrets.GITHUB_TOKEN}}