Merge pull request deeptools#48 from lldelisle/fix_pypi

Release 17.1

.github/workflows/pylint.yml

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+name: Pylint
+
+on: [push, pull_request]
+
+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: |
+        # 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')
+      shell: micromamba-shell {0}

.github/workflows/python-publish.yml

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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
+
+# 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.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    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 }}

.github/workflows/test.yml

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+name: Test
+on: [push, pull_request]
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+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 -e "\n   - 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: |
+        python3 -m pip install .
+      shell: micromamba-shell {0}
+    - name: Test HiCMatrix
+      run: |
+        py.test hicmatrix/test/ --capture=sys
+      shell: micromamba-shell {0}
+  test-osx:
+    name: Test on OSX
+    runs-on: macOS-latest
+    strategy:
+      matrix:
+        python-version:
+          - "3.8"
+          - "3.9"
+          - "3.10"
+    steps:
+    - uses: actions/checkout@v3
+    - name: Use python ${{ matrix.python-version }}
+      run: echo -e "\n   - 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: |
+        python3 -m pip install .
+      shell: micromamba-shell {0}
+    - name: Test HiCMatrix
+      run: |
+        py.test hicmatrix/test/ --capture=sys
+      shell: micromamba-shell {0}

HiCMatrix_env_ci.yml

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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
+   - pylint
+   - pytest-xdist
+   - pytest-forked
+   - nose
+   - pathlib
+   - configparser
+   - build # For the upload
+   - twine # For the upload