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fix pip check for optional dependencies #9

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fix pip check for optional dependencies

fix pip check for optional dependencies #9

Workflow file for this run

.github/workflows/pipeline.yml at 5a0383c
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 "pyiron@mpie.de"
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
run: |
cp .ci_support/environment.yml environment.yml
echo "- flux-core =0.59.0" >> 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: Install
shell: bash -l {0}
run: |
pip install versioneer[toml]==0.29
pip install . --no-deps --no-build-isolation
- name: Test
shell: bash -l {0}
run: >
flux start
coverage run --omit="pysqa/_version.py,tests/*" -m unittest discover tests
- name: Collect Coverage
shell: bash -l {0}
run: coverage xml
- 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: Setup environment
run: |
cp .ci_support/environment.yml environment.yml
sed -i '/defusedxml/d' environment.yml
sed -i '/paramiko/d' environment.yml
sed -i '/tqdm/d' environment.yml
echo -e "channels:\n - conda-forge\n" > .condarc
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v3
with:
python-version: '3.13'
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
python -m unittest discover tests
notebooks:
needs: [black]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Merge Notebook environment
run: |
cp binder/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: Install
shell: bash -l {0}
run: |
pip install versioneer[toml]==0.29
pip install . --no-deps --no-build-isolation
mkdir config
cp -r tests/config/flux config
- name: Notebooks with config
shell: bash -l {0}
run: >
flux start
papermill notebooks/example_config.ipynb example-config-out.ipynb -k "python3"
- name: Notebooks dynamic
shell: bash -l {0}
run: >
flux start
papermill notebooks/example_queue_type.ipynb example-queue-type-out.ipynb -k "python3"
pip_check:
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: '3.13'
miniforge-version: latest
condarc-file: .condarc
environment-file: .ci_support/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: '3.13'
- operating-system: windows-latest
python-version: '3.13'
- operating-system: ubuntu-latest
python-version: '3.13'
- operating-system: ubuntu-latest
python-version: '3.12'
- operating-system: ubuntu-latest
python-version: '3.11'
- operating-system: ubuntu-latest
python-version: '3.10'
- operating-system: ubuntu-latest
python-version: 3.9
steps:
- uses: actions/checkout@v4
- name: Conda config
shell: bash -l {0}
run: echo -e "channels:\n - conda-forge\n" > .condarc
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v3
with:
python-version: ${{ matrix.python-version }}
miniforge-version: latest
condarc-file: .condarc
environment-file: .ci_support/environment.yml
- name: Test
shell: bash -l {0}
run: |
pip install versioneer[toml]==0.29
pip install . --no-deps --no-build-isolation
python -m unittest discover tests
unittest_old:
needs: [black]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Conda config
run: echo -e "channels:\n - conda-forge\n" > .condarc
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v3
with:
python-version: '3.9'
miniforge-version: latest
condarc-file: .condarc
environment-file: .ci_support/environment-old.yml
- name: Test
shell: bash -l {0}
run: |
pip install versioneer[toml]==0.29
pip install . --no-deps --no-build-isolation
python -m unittest discover tests
autobot:
needs: [unittest_old, unittest_matrix, pip_check, notebooks, minimal, coverage]
permissions:
contents: write
pull-requests: write
runs-on: ubuntu-latest
if: (github.event.pull_request.user.login == 'dependabot[bot]' || github.event.pull_request.user.login == 'pre-commit-ci[bot]')
steps:
- name: Enable auto-merge for bot PRs
run: gh pr merge --auto --squash "$PR_URL"
env:
PR_URL: ${{github.event.pull_request.html_url}}
GH_TOKEN: ${{secrets.GITHUB_TOKEN}}