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name: Pylint | ||
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on: [push, pull_request] | ||
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jobs: | ||
build: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: actions/checkout@v3 | ||
- uses: mamba-org/setup-micromamba@main | ||
with: | ||
environment-file: ./HiCMatrix_env_ci.yml | ||
cache-downloads: true | ||
environment-name: HiCMatrix_env_ci | ||
- name: Analysing the code with pylint | ||
run: | | ||
micromamba activate HiCMatrix_env_ci | ||
# Disable | ||
# C0103: Invalid name | ||
# C0114: Missing module docstring | ||
# C0115: Missing class docstring | ||
# C0116: Missing function or method docstring | ||
# C0301: Line too long | ||
# C0302: Too many lines in module | ||
# R0801: Similar lines | ||
# R0902: Too many instance attributes | ||
# R0904: Too many public methods | ||
# R0912: Too many branches | ||
# R0913: Too many arguments | ||
# R0914: Too many local variables | ||
# R0915: Too many statements | ||
# R1702: Too many nested blocks | ||
# R1728: Consider using a generator | ||
pylint --disable C0103,C0114,C0115,C0116,C0301,C0302,R0801,R0902,R0904,R0912,R0913,R0914,R0915,R1702,R1728 $(git ls-files '*.py') |
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# This workflow will upload a Python Package using Twine when a release is created | ||
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries | ||
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# This workflow uses actions that are not certified by GitHub. | ||
# They are provided by a third-party and are governed by | ||
# separate terms of service, privacy policy, and support | ||
# documentation. | ||
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name: Upload Python Package | ||
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on: | ||
release: | ||
types: [published] | ||
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permissions: | ||
contents: read | ||
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jobs: | ||
deploy: | ||
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runs-on: ubuntu-latest | ||
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steps: | ||
- uses: actions/checkout@v3 | ||
- name: Set up Python | ||
uses: actions/setup-python@v3 | ||
with: | ||
python-version: '3.8' | ||
- name: Install dependencies | ||
run: | | ||
python -m pip install --upgrade pip | ||
pip install build | ||
- name: Build package | ||
run: python -m build | ||
- name: Publish package | ||
uses: pypa/gh-action-pypi-publish@v1.8 | ||
with: | ||
user: __token__ | ||
password: ${{ secrets.PYPI_API_TOKEN }} |
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name: Test | ||
on: [push, pull_request] | ||
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defaults: | ||
run: | ||
shell: bash -l {0} | ||
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jobs: | ||
test-linux: | ||
name: Test on Linux | ||
runs-on: ubuntu-latest | ||
strategy: | ||
matrix: | ||
python-version: | ||
- "3.8" | ||
- "3.9" | ||
- "3.10" | ||
steps: | ||
- uses: actions/checkout@v3 | ||
- name: Use python ${{ matrix.python-version }} | ||
run: echo " - python = ${{ matrix.python-version }}" >> ./HiCMatrix_env_ci.yml | ||
- uses: mamba-org/setup-micromamba@main | ||
with: | ||
environment-file: ./HiCMatrix_env_ci.yml | ||
cache-downloads: true | ||
environment-name: HiCMatrix_env_ci | ||
- name: pip install | ||
run: | | ||
micromamba activate HiCMatrix_env_ci | ||
python3 -m pip install . | ||
- name: Test HiCMatrix | ||
run: | | ||
micromamba activate HiCMatrix_env_ci | ||
py.test hicmatrix/test/ --capture=sys | ||
test-osx: | ||
name: Test on OSX | ||
runs-on: macOS-latest | ||
steps: | ||
- uses: actions/checkout@v3 | ||
- uses: mamba-org/setup-micromamba@main | ||
with: | ||
environment-file: ./HiCMatrix_env_ci.yml | ||
cache-downloads: true | ||
environment-name: HiCMatrix_env_ci | ||
- name: pip install | ||
run: | | ||
micromamba activate HiCMatrix_env_ci | ||
python3 -m pip install . | ||
- name: Test HiCMatrix | ||
run: | | ||
micromamba activate HiCMatrix_env_ci | ||
py.test hicmatrix/test/ --capture=sys |
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name: HiCMatrix_env_ci | ||
channels: | ||
- conda-forge | ||
- bioconda | ||
dependencies: | ||
- numpy >= 1.20 | ||
- scipy >= 1.2 | ||
- pandas >= 0.25 | ||
- pytables >= 3.5 | ||
- cooler >= 0.8.9 | ||
- intervaltree >= 3.0 | ||
- pytest | ||
- flake8 | ||
- pytest-xdist | ||
- pytest-forked | ||
- nose | ||
- pathlib | ||
- configparser | ||
- build # For the upload | ||
- twine # For the upload |
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