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chore(project): Python project skeleton dir tree
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‎.cookiecutterrc‎

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# This file exists so you can easily regenerate your project.
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# run:
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# (cd ..; cookiecutter -f --config-file=modacor/.cookiecutterrc gh:BAMresearch/yapy-cookiecutter)
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# or without answering questions:
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# (cd ..; cookiecutter -f --no-input --config-file=modacor/.cookiecutterrc gh:BAMresearch/yapy-cookiecutter)
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default_context:
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author_count: '3'
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full_names: 'Brian R. Pauw, Tim Snow, Ingo Breßler'
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emails: 'brian.pauw@bam.de, tim.snow@diamond.ac.uk, ingo.bressler@bam.de'
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websites: 'https://lookingatnothing.com, https://www.diamond.ac.uk/Instruments/Soft-Condensed-Matter/small-angle/I22/Staff/Tim-Snow.html,'
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project_name: 'MoDaCor'
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repo_name: 'modacor'
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repo_hosting: 'github.com'
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repo_hosting_domain: 'github.com'
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repo_userorg: 'BAMresearch'
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docs_url: 'https://BAMresearch.github.io/modacor'
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repo_main_branch: 'main'
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package_name: 'modacor'
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distribution_name: 'modacor'
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project_short_description: 'new modular data corrections for any neutron or xray technique that produces 1D or 2D scattering/diffraction/imaging data'
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release_date: 'today'
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year_from: '2025'
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year_to: '2025'
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version: '0.1.0'
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pypi_host: 'test.pypi.org'
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license: 'MIT license'
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sphinx_theme: 'furo'
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extra_context: {'exclude_existing': "['AUTHORS.rst', 'CHANGELOG.md', 'src/modacor/__init__.py']"}

‎.editorconfig‎

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# see https://editorconfig.org/
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root = true
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[*]
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# Use Unix-style newlines for most files (except Windows files, see below).
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end_of_line = lf
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trim_trailing_whitespace = true
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indent_style = space
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insert_final_newline = true
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indent_size = 4
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charset = utf-8
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[*.{bat,cmd,ps1}]
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end_of_line = crlf
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[*.{yml,yaml}]
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indent_size = 2
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[*.tsv]
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indent_style = tab

‎.github/workflows/build.yml‎

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name: Build
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# Controls when the action will run.
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on:
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workflow_call:
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jobs:
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build:
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# convert this to a matrix if builds differ between platforms
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: ['ubuntu-latest']
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steps:
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- name: Checking out the repo
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uses: actions/checkout@v4
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# see *py_ver* in ci/update.py
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- name: Setting up Python 3.12
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uses: actions/setup-python@v5
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with:
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python-version: '3.12'
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cache: pip
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cache-dependency-path: |
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ci/requirements.txt
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- name: Install dependencies
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shell: sh
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run: |
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[ -d "/c/miniconda" ] && /c/miniconda/condabin/activate.bat
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python -m pip install --upgrade pip
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python -m pip install --progress-bar=off -r ci/requirements.txt
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- name: Build
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run: tox -e build -v
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- name: Upload packages for publishing job
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uses: actions/upload-artifact@v4
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with:
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name: packages-${{ matrix.os }}
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path: |
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dist/*.whl
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dist/*.tar.gz
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publish:
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needs: [build]
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runs-on: 'ubuntu-latest'
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steps:
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- name: Checking out the repo
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uses: actions/checkout@v4
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- name: Install dependencies
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shell: sh
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run: |
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[ -d "/c/miniconda" ] && /c/miniconda/condabin/activate.bat
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python -m pip install --upgrade pip
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python -m pip install --progress-bar=off -r ci/requirements.txt
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- name: Download package artifacts
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uses: actions/download-artifact@v4
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with:
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pattern: packages-*
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merge-multiple: true
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path: dist
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- name: Check generated packages
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run: twine check dist/*.*
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- name: Upload packages
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env:
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TWINE_PASSWORD: "${{ secrets.TEST_PYPI_TOKEN }}"
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TWINE_NON_INTERACTIVE: 1
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run: |
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twine upload --disable-progress-bar --skip-existing -u __token__ -r testpypi dist/*.*

‎.github/workflows/ci-cd.yml‎

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name: CI-CD
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# Controls when the action will run.
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on:
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# Triggers the workflow on push or pull request events but only for the main branch
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push:
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branches: [main]
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pull_request:
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branches: [main]
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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jobs:
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# check if everything works first
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tests:
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uses: ./.github/workflows/tests.yml
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# make a new version next, release or prerelease
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release:
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needs: [tests]
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uses: ./.github/workflows/release.yml
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build:
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needs: [release, tests] # build only if all tests are successful
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uses: ./.github/workflows/build.yml
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secrets: inherit
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docs:
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needs: [release] # get (release) version number first
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uses: ./.github/workflows/docs.yml
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coverage:
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needs: [tests, docs] # coverage report is added to the docs webpage
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uses: ./.github/workflows/coverage.yml

‎.github/workflows/coverage.yml‎

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name: Coverage
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# Controls when the action will run.
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on:
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workflow_call:
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env:
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DOCS_URL: https://BAMresearch.github.io/modacor
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COV_REPORT_BASE_DIR: coverage-report
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jobs:
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combine:
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name: Combine coverage data
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runs-on: ubuntu-latest
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outputs:
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total: ${{ steps.total.outputs.total }}
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steps:
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- name: Checking out the repo
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uses: actions/checkout@v4
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# see *py_ver* in ci/update.py
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- name: Setting up Python 3.12
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uses: actions/setup-python@v5
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with:
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python-version: '3.12'
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cache: pip
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cache-dependency-path: |
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ci/requirements.txt
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- name: Install dependencies
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shell: sh
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run: |
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[ -d "/c/miniconda" ] && /c/miniconda/condabin/activate.bat
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python -m pip install --upgrade pip
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python -m pip install --progress-bar=off -r ci/requirements.txt
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- name: Download coverage data
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uses: actions/download-artifact@v4
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with:
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name: coverage
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- name: Combine and report
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id: combine
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shell: sh
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run: |
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set -x
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pwd && ls -la
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coverage combine coverage.*
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python3 -c 'import coverage,pprint; cov=coverage.Coverage(); cov.load();pprint.pprint(list(cov.get_data()._file_map.keys()))'
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coverage html --debug=pathmap
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- name: Upload HTML report
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uses: actions/upload-artifact@v4
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with:
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name: html_report
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path: htmlcov
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- name: Get total
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id: total
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shell: sh
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run: |
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echo "total=$(coverage report --format=total)" >> $GITHUB_OUTPUT
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publish:
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name: Publish coverage report
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needs: combine
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runs-on: ubuntu-latest
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steps:
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- name: Compute info for later steps
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id: info
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shell: sh
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run: |
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set -xe
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export SHA10=$(echo ${{ github.sha }} | cut -c 1-10)
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export SLUG=$(date +'%Y%m%d')_$SHA10
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export REPORT_DIR=$COV_REPORT_BASE_DIR/$SLUG
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export REF="${{ github.ref }}"
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echo "total=${{ needs.combine.outputs.total }}" >> $GITHUB_ENV
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echo "sha10=$SHA10" >> $GITHUB_ENV
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echo "slug=$SLUG" >> $GITHUB_ENV
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echo "report_dir=$REPORT_DIR" >> $GITHUB_ENV
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echo "branch=${REF#refs/heads/}" >> $GITHUB_ENV
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- name: Summarize
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shell: sh
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run: |
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echo '### Total coverage: ${{ env.total }}%' >> $GITHUB_STEP_SUMMARY
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- name: Checkout documentation pages branch
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if: ${{ github.ref == 'refs/heads/main' }}
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uses: actions/checkout@v4
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with:
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ref: gh-pages
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path: pages
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- name: Purge old documentation files
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shell: sh
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run: cd pages && git rm -rf . || true
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- name: Download previously generated documentation
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if: ${{ github.ref == 'refs/heads/main' }}
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uses: actions/download-artifact@v4
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with:
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name: docs
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path: pages
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- name: Download coverage HTML report
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if: ${{ github.ref == 'refs/heads/main' }}
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uses: actions/download-artifact@v4
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with:
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name: html_report
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path: pages/${{ env.report_dir }}
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- name: Push to report repo
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if: ${{ github.ref == 'refs/heads/main' }}
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shell: sh
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env:
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COMMIT_MESSAGE: ${{ github.event.head_commit.message }}
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REDIR_HTML: "pages/${{ env.COV_REPORT_BASE_DIR }}/index.html"
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BADGE_JSON: "pages/${{ env.COV_REPORT_BASE_DIR }}/cov.json"
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REPORT_URL: "${{ env.DOCS_URL }}/${{ env.report_dir }}"
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run: |
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set -xe
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# Make the redirect to the latest report.
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echo "<html><head>" > "$REDIR_HTML"
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echo "<meta http-equiv='refresh' content='0;url=$REPORT_URL' />" >> "$REDIR_HTML"
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echo "<body>Coverage report redirect..." >> "$REDIR_HTML"
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# Make the commit message.
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echo "${{ env.total }}% - $COMMIT_MESSAGE" > commit.txt
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echo "" >> commit.txt
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echo "$REPORT_URL" >> commit.txt
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echo "${{ env.sha10 }}: ${{ env.branch }}" >> commit.txt
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# Make badge json
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COL_MIN=10; COL_MAX=95;
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HUE=$(python3 -c "print(int((${{ env.total }} - $COL_MIN)/($COL_MAX - $COL_MIN) * 120))")
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echo "{\"schemaVersion\":1,\"label\":\"Coverage\",\"message\":\"${{ env.total }}%\",\"color\":\"hsl($HUE, 100%, 40%)\"}" > "$BADGE_JSON"
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# Commit.
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cd ./pages
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rm ${{ env.report_dir }}/.gitignore
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# ls -la ${{ env.report_dir }} # for debugging
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# ${{ env.report_dir }}/* "${REDIR_HTML#*/}" "${BADGE_JSON#*/}"
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git add -A
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git config user.name "${GITHUB_ACTOR}"
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git config user.email "${GITHUB_ACTOR}@users.noreply.github.com"
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git commit --file=../commit.txt
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git push
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echo "[$REPORT_URL]($REPORT_URL)" >> $GITHUB_STEP_SUMMARY

‎.github/workflows/docs.yml‎

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name: Docs
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# Controls when the action will run.
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on:
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workflow_call:
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jobs:
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docs:
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# defining this job separately allows to refer to it later as job.needs dependency
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runs-on: ubuntu-latest
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steps:
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- name: Checking out the repo
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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# see *py_ver* in ci/update.py
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- name: Setting up Python 3.12
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uses: actions/setup-python@v5
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with:
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python-version: '3.12'
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cache: pip
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cache-dependency-path: |
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ci/requirements.txt
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- name: Install required system packages
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shell: sh
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run: |
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PLATFORM="$(echo "$RUNNER_OS" | tr '[:upper:]' '[:lower:]')"
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REQFN="ci/requirements_$PLATFORM.txt"
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if [ "$PLATFORM" = "linux" ] && [ -f "$REQFN" ]; then
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sudo apt-get -y install $(sed -e '/^\s*#/d' "$REQFN")
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elif [ "$PLATFORM" = "windows" ] && [ -f "$REQFN" ]; then
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choco install $(sed -e '/^\s*#/d' "$REQFN")
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else
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echo "macro sys_install_req(): platform '$PLATFORM' not implemented yet."
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fi
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- name: Install dependencies
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shell: sh
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run: |
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[ -d "/c/miniconda" ] && /c/miniconda/condabin/activate.bat
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python -m pip install --upgrade pip
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python -m pip install --progress-bar=off -r ci/requirements.txt
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- name: Check
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shell: sh
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run: tox -e check -v
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- name: Generate documentation
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shell: sh
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run: tox -e docs -v
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- name: Upload docs for finalization later
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uses: actions/upload-artifact@v4
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with:
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name: docs
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path: dist/docs
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# - name: Upload generated documentation
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# uses: peaceiris/actions-gh-pages@v3
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# with:
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# github_token: ${{ secrets.GITHUB_TOKEN }}
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# publish_dir: ./dist/docs

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