Version propre du code sans les gros fichiers

Author: axelcournac

.coverage

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+name: build
+
+on: [push]
+
+
+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true  # ← ajouter ça
+  
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+
+    - name: Checkout repo
+      uses: actions/checkout@v4
+    
+    - name: Create micromamba env. for package
+      uses: mamba-org/setup-micromamba@v2
+      with:
+        generate-run-shell: true
+        environment-file: environment.yml
+        post-cleanup: none  # ← évite les erreurs de nettoyage
+
+    - name: Install package
+      run: |
+        pip install .
+      shell: micromamba-shell {0}
+
+    - name: Check installed package
+      run: |
+        hicberg --version
+        bowtie2 --version
+      shell: micromamba-shell {0}
+
+    - name: Lint and test
+      run: |
+        pip install pytest-pylint pytest pytest-cov pylint codecov mappy
+        pytest --pylint --pylint-error-types=EF --pylint-rcfile=.pylintrc --doctest-modules hicberg
+        coverage run --source=hicberg -m pytest -v tests
+        coverage report -m
+        coverage xml
+      shell: micromamba-shell {0}
+
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v5
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/build.yml

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+name: Build and deploy Github pages
+'on':
+  push:
+    branches:
+      - main
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+        with:
+          persist-credentials: false
+      - name: Set up Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.11
+      - name: Install Python dependencies
+        run: |
+          pip3 install setuptools
+          pip3 install sphinx sphinx-rtd-theme
+          pip install nbsphinx
+          sudo apt-get install -y pandoc
+
+      - name: Build Sphinx Doc
+        run: |
+            make -C docs clean
+            make -C docs html
+      - name: Deploy Github Pages
+        uses: JamesIves/github-pages-deploy-action@3.7.1
+        with:
+          GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
+          BRANCH: gh-pages
+          FOLDER: docs/_build/html/
+          CLEAN: true

.github/workflows/gh-pages.yml

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+
+name: Upload Python Package on PyPI
+
+on:
+  release:
+    types: [created]
+
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.11'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build package
+      run: python setup.py sdist bdist_wheel
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/publish.yml

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+name: Tests
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    
+    steps:
+      - uses: actions/checkout@v4
+      
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+          
+      - name: Install system dependencies (bowtie2, samtools)
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y bowtie2 samtools
+          
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .
+          pip install pytest pytest-cov
+          
+      - name: Run tests with coverage
+        id: pytest
+        continue-on-error: true
+        run: python -m pytest tests/ --cov=hicberg --cov-report=xml --cov-report=term-missing
+        
+      - name: Upload coverage to Codecov
+        if: always()
+        uses: codecov/codecov-action@v4
+        with:
+          files: ./coverage.xml
+          fail_ci_if_error: false
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/tests.yml

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+# Ignore logfiles
+*.log
+sandbox.py
+
+# Ignore hicberg/combined.bam
+*.bam
+hicberg/combined.bam