Update Workflows (add build_wheels, codeql, main, test_coverage)

.github/workflows/build_wheels.yml

@@ -0,0 +1,92 @@
+name: Build wheels
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  generate-wheels-matrix:
+    name: Generate wheels matrix
+    runs-on: ubuntu-latest
+    outputs:
+      include: ${{ steps.set-matrix.outputs.include }}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install cibuildwheel
+        run: pipx install cibuildwheel==2.14.0
+      - id: set-matrix
+        run: |
+          # ... (Keep this section as is in the original SHAP example)
+
+  build_wheels:
+    name: Build ${{ matrix.only }}
+    needs: generate-wheels-matrix
+    strategy:
+      fail-fast: false
+      matrix:
+        include: ${{ fromJson(needs.generate-wheels-matrix.outputs.include) }}
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v3
+
+      - name: Set up QEMU
+        if: runner.os == 'Linux'
+        uses: docker/setup-qemu-action@v2
+        with:
+          platforms: all
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.14.0
+        with:
+          only: ${{ matrix.only }}
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./wheelhouse/*.whl
+          name: bdist_files
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v3
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+      - name: Build sdist (pep517)
+        run: |
+          python -m pip install build
+          python -m build --sdist
+      - name: Upload sdist
+        uses: actions/upload-artifact@v3
+        with:
+          name: sdist_files
+          path: dist/*.tar.gz
+
+  publish_wheels:
+    name: Publish wheels on pypi
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags')
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: bdist_files
+          path: dist
+      - uses: actions/download-artifact@v3
+        with:
+          name: sdist_files
+          path: dist
+      - name: Publish package to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.TEST_PYPI_TOKEN  }}
+          repository-url: https://test.pypi.org/legacy/
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/codeql_analysis.yml

@@ -0,0 +1,54 @@
+name: CodeQL
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+  schedule:
+    - cron: '0 0 * * 0'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v3
+        with:
+          languages: "python"
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v3
+
+  code-quality:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.9
+
+    - name: Cache Python dependencies
+      uses: actions/cache@v4
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-3.9-${{ hashFiles('**/requirements.txt') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-3.9-
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 mypy pylint
+
+    - name: Run flake8 (check style)
+      run: flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+
+    - name: Run mypy (check static typing)
+      run: mypy xomics/__init__.py --follow-imports=skip

.github/workflows/main.yml

@@ -0,0 +1,45 @@
+name: Unit Tests
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Cache Python dependencies
+      uses: actions/cache@v4
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('**/requirements.txt') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-${{ matrix.python-version }}-
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install pytest
+
+    - name: Run Tests
+      run: pytest tests
+      env:
+        HYPOTHESIS_DEADLINE: 10000000
+        MPLBACKEND: Agg

.github/workflows/test_coverage.yml

@@ -0,0 +1,40 @@
+name: Test Coverage
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.9'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install pytest pytest-cov
+
+    - name: Run tests with coverage and generate XML report
+      run: |
+        pytest --cov=./ --cov-report=xml
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: ./coverage.xml
+        fail_ci_if_error: true
+      env:
+        MPLBACKEND: Agg

xomics/__init__.py

@@ -7,11 +7,7 @@
                        plot_enrich_map,
                        plot_prank,
                        plot_prank_scatter,
-                       plot_imput_histo,
-                       plot_settings,
-                       plot_legend,
-                       plot_get_clist,
-                       plot_gcfs)
+                       plot_imput_histo)
 
 __all__ = [
     "pRank",
@@ -24,8 +20,4 @@
     "plot_prank",
     "plot_prank_scatter",
     "plot_imput_histo",
-    "plot_settings",
-    "plot_legend",
-    "plot_get_clist",
-    "plot_gcfs"
 ]

xomics/_utils/_utils.py

@@ -0,0 +1,10 @@
+"""This is a script for utility functions for utility functions."""
+
+
+# Helper functions
+# This function is only used in utility check function
+def add_str(str_error=None, str_add=None):
+    """Add additional error message 'str_add' to default error message ('add_str')"""
+    if str_add:
+        str_error += "\n  " + str_add
+    return str_error