Update README.rst badges and codeql_analysis

breimanntools · Jul 23, 2024 · b4f31e8 · b4f31e8
1 parent 7b54512
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diff --git a/.github/workflows/codeql_analysis.yml b/.github/workflows/codeql_analysis.yml
@@ -10,6 +10,10 @@ on:
   schedule:
     - cron: '0 0 * * 0'
 
+permissions:
+  contents: read
+  security-events: write
+
 jobs:
   analyze:
     name: Analyze
@@ -22,33 +26,33 @@ jobs:
         uses: github/codeql-action/init@v3
         with:
           languages: "python"
-      - name: Perform CodeQL Analysis
+      - name: Perform CodeQL xOmics
         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
+      - 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
diff --git a/README.rst b/README.rst
@@ -2,41 +2,63 @@ Welcome to the xOmics documentation
 ===================================
 .. Developer Notes:
     Please update badges in README.rst and vice versa
-.. image:: https://github.com/breimanntools/xomics/workflows/Build/badge.svg
-   :target: https://github.com/breimanntools/xomics/actions
-   :alt: Build Status
-
-.. image:: https://github.com/breimanntools/xomics/workflows/Python-check/badge.svg
-   :target: https://github.com/breimanntools/xomics/actions
-   :alt: Python-check
-
-.. image:: https://img.shields.io/pypi/status/xomics.svg
+.. Group 1: Package badges
+.. |PyPI Status| image:: https://img.shields.io/pypi/status/xomics.svg
    :target: https://pypi.org/project/xomics/
    :alt: PyPI - Status
 
-.. image:: https://img.shields.io/pypi/pyversions/xomics.svg
+.. |PyPI Version| image:: https://img.shields.io/pypi/v/xomics.svg
    :target: https://pypi.python.org/pypi/xomics
-   :alt: Supported Python Versions
+   :alt: PyPI - Package Version
 
-.. image:: https://img.shields.io/pypi/v/xomics.svg
+.. |Supported Python Versions| image:: https://img.shields.io/pypi/pyversions/xomics.svg
    :target: https://pypi.python.org/pypi/xomics
-   :alt: PyPI - Package Version
+   :alt: Supported Python Versions
 
-.. image:: https://anaconda.org/conda-forge/xomics/badges/version.svg
-   :target: https://anaconda.org/conda-forge/xomics
-   :alt: Conda - Package Version
+.. |Downloads| image:: https://pepy.tech/badge/xomics
+   :target: https://pepy.tech/project/xomics
+   :alt: Downloads
+
+.. |License| image:: https://img.shields.io/github/license/breimanntools/xomics.svg
+   :target: https://github.com/breimanntools/xomics/blob/master/LICENSE
+   :alt: License
 
-.. image:: https://readthedocs.org/projects/xomics/badge/?version=latest
+.. Group 2: Testing badges
+.. |Unit Tests| image:: https://github.com/breimanntools/xomics/actions/workflows/main.yml/badge.svg
+   :target: https://github.com/breimanntools/xomics/actions/workflows/main.yml
+   :alt: CI/CD Pipeline
+
+.. |CodeQL| image:: https://github.com/breimanntools/xomics/actions/workflows/codeql_analysis.yml/badge.svg
+   :target: https://github.com/breimanntools/xomics/actions/workflows/codeql_analysis.yml
+   :alt: CodeQL
+
+.. |Codecov| image:: https://codecov.io/gh/breimanntools/xomics/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/breimanntools/xomics
+   :alt: Codecov
+
+.. |Documentation Status| image:: https://readthedocs.org/projects/xomics/badge/?version=latest
    :target: https://xomics.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status
 
-.. image:: https://img.shields.io/github/license/breimanntools/xomics.svg
-   :target: https://github.com/breimanntools/xomics/blob/master/LICENSE
-   :alt: License
 
-.. image:: https://pepy.tech/badge/xomics
-   :target: https://pepy.tech/project/xomics
-   :alt: Downloads
+.. Group 3: Potential badges for future
+.. |Conda Version| image:: https://anaconda.org/conda-forge/xomics/badges/version.svg
+   :target: https://anaconda.org/conda-forge/xomics
+   :alt: Conda - Package Version
+
+
+..
+    Missing badges
+    |Conda Version|
+
+.. list-table::
+   :widths: 20 80
+   :header-rows: 1
+
+   * - **Package**
+     - |PyPI Status| |PyPI Version| |Supported Python Versions| |Downloads| |License|
+   * - **Testing**
+     - |Unit Tests| |CodeQL| |Codecov| |Documentation Status|
 
 **xOmics** (eXplainable Omics) is a Python framework developed for interpretable omics analysis,
 focusing on differential proteomics expression data. It introduces the following key algorithms: