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Merge pull request #4 from breimanntools/my-local-changes
Update Workflows (add build_wheels, codeql, main, test_coverage)
2 parents fe7cef0 + c94c75d commit a4549d5

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‎.github/workflows/build_wheels.yml

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name: Build wheels
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on:
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release:
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types: [published]
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workflow_dispatch:
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jobs:
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generate-wheels-matrix:
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name: Generate wheels matrix
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runs-on: ubuntu-latest
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outputs:
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include: ${{ steps.set-matrix.outputs.include }}
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steps:
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- uses: actions/checkout@v3
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- name: Install cibuildwheel
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run: pipx install cibuildwheel==2.14.0
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- id: set-matrix
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run: |
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# ... (Keep this section as is in the original SHAP example)
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build_wheels:
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name: Build ${{ matrix.only }}
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needs: generate-wheels-matrix
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strategy:
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fail-fast: false
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matrix:
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include: ${{ fromJson(needs.generate-wheels-matrix.outputs.include) }}
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runs-on: ${{ matrix.os }}
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steps:
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- name: Check out the repo
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uses: actions/checkout@v3
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- name: Set up QEMU
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if: runner.os == 'Linux'
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uses: docker/setup-qemu-action@v2
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with:
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platforms: all
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- name: Build wheels
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uses: pypa/cibuildwheel@v2.14.0
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with:
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only: ${{ matrix.only }}
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- uses: actions/upload-artifact@v3
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with:
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path: ./wheelhouse/*.whl
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name: bdist_files
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build_sdist:
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name: Build source distribution
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runs-on: ubuntu-20.04
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steps:
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- name: Check out the repo
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uses: actions/checkout@v3
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- name: Set up Python 3.11
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uses: actions/setup-python@v4
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with:
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python-version: '3.11'
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- name: Build sdist (pep517)
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run: |
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python -m pip install build
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python -m build --sdist
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- name: Upload sdist
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uses: actions/upload-artifact@v3
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with:
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name: sdist_files
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path: dist/*.tar.gz
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publish_wheels:
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name: Publish wheels on pypi
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needs: [build_wheels, build_sdist]
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runs-on: ubuntu-latest
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if: startsWith(github.ref, 'refs/tags')
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steps:
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- uses: actions/download-artifact@v3
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with:
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name: bdist_files
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path: dist
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- uses: actions/download-artifact@v3
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with:
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name: sdist_files
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path: dist
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- name: Publish package to TestPyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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password: ${{ secrets.TEST_PYPI_TOKEN }}
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repository-url: https://test.pypi.org/legacy/
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- name: Publish package to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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password: ${{ secrets.PYPI_TOKEN }}

‎.github/workflows/codeql_analysis.yml

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name: CodeQL
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on:
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push:
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branches:
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- master
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pull_request:
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branches:
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- master
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schedule:
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- cron: '0 0 * * 0'
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jobs:
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analyze:
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name: Analyze
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Initialize CodeQL
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uses: github/codeql-action/init@v3
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with:
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languages: "python"
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- name: Perform CodeQL Analysis
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uses: github/codeql-action/analyze@v3
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code-quality:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: 3.9
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- name: Cache Python dependencies
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uses: actions/cache@v4
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-3.9-${{ hashFiles('**/requirements.txt') }}
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restore-keys: |
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${{ runner.os }}-pip-3.9-
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install flake8 mypy pylint
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- name: Run flake8 (check style)
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run: flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
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- name: Run mypy (check static typing)
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run: mypy xomics/__init__.py --follow-imports=skip

‎.github/workflows/main.yml

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name: Unit Tests
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on:
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push:
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branches:
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- master
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pull_request:
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branches:
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- master
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jobs:
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test:
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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, windows-latest]
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python-version: ['3.9', '3.10', '3.11', '3.12']
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steps:
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- uses: actions/checkout@v4
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- name: Cache Python dependencies
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uses: actions/cache@v4
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('**/requirements.txt') }}
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restore-keys: |
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${{ runner.os }}-pip-${{ matrix.python-version }}-
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r requirements.txt
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pip install pytest
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- name: Run Tests
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run: pytest tests
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env:
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HYPOTHESIS_DEADLINE: 10000000
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MPLBACKEND: Agg

‎.github/workflows/python-package.yml

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‎.github/workflows/test_coverage.yml

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name: Test Coverage
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on:
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push:
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branches:
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- master
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pull_request:
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branches:
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- master
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jobs:
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test:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.9'
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r requirements.txt
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pip install pytest pytest-cov
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- name: Run tests with coverage and generate XML report
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run: |
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pytest --cov=./ --cov-report=xml
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v3
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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file: ./coverage.xml
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fail_ci_if_error: true
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env:
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MPLBACKEND: Agg

‎xomics/__init__.py

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plot_enrich_map,
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plot_prank,
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plot_prank_scatter,
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plot_imput_histo,
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plot_settings,
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plot_legend,
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plot_get_clist,
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plot_gcfs)
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plot_imput_histo)
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__all__ = [
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"pRank",
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"plot_prank",
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"plot_prank_scatter",
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"plot_imput_histo",
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"plot_settings",
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"plot_legend",
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"plot_get_clist",
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"plot_gcfs"
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]

‎xomics/_utils/_utils.py

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"""This is a script for utility functions for utility functions."""
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# Helper functions
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# This function is only used in utility check function
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def add_str(str_error=None, str_add=None):
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"""Add additional error message 'str_add' to default error message ('add_str')"""
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if str_add:
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str_error += "\n " + str_add
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return str_error

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