Fix GitHub actions (#1)

Author: jkanche

.github/workflows/pypi-publish.yml

@@ -1,6 +1,3 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
 name: Publish to PyPI
 
 on:
@@ -9,43 +6,49 @@ on:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v5
-      with:
-        python-version: 3.11
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest tox
-    # - name: Lint with flake8
-    #   run: |
-    #     # stop the build if there are Python syntax errors or undefined names
-    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-    #     # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with tox
-      run: |
-        tox
-    - name: Build docs
-      run: |
-        tox -e docs
-    - run: touch ./docs/_build/html/.nojekyll
-    - name: GH Pages Deployment
-      uses: JamesIves/github-pages-deploy-action@4.1.3
-      with:
-        branch: gh-pages # The branch the action should deploy to.
-        folder: ./docs/_build/html
-        clean: true # Automatically remove deleted files from the deploy branch
-    - name: Build Project and Publish
-      run: |
-        python -m tox -e clean,build
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_PASSWORD }}
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest tox
+
+      - name: Setup git creds
+        run: |
+          git config --global user.email "gituser@biocpy"
+          git config --global user.name "Biocpy test user"
+
+      - name: Test with tox
+        run: |
+          tox
+
+      - name: Build docs
+        run: |
+          tox -e docs
+
+      - run: touch ./docs/_build/html/.nojekyll
+
+      - name: GH Pages Deployment
+        uses: JamesIves/github-pages-deploy-action@4.1.3
+        with:
+          branch: gh-pages # The branch the action should deploy to.
+          folder: ./docs/_build/html
+          clean: true # Automatically remove deleted files from the deploy branch
+
+      - name: Build Project and Publish
+        run: |
+          python -m tox -e clean,build
+
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/pypi-test.yml

@@ -1,40 +1,38 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
 name: Test the library
 
 on:
   push:
-    branches: [ master ]
+    branches: [master]
   pull_request:
-    branches: [ master ]
+    branches: [master]
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.9', '3.10', '3.11', '3.12' ]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     name: Python ${{ matrix.python-version }}
     steps:
-    - uses: actions/checkout@v4
-    - name: Setup Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-        cache: 'pip'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest tox
-    # - name: Lint with flake8
-    #   run: |
-    #     # stop the build if there are Python syntax errors or undefined names
-    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-    #     # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with tox
-      run: |
-        tox
+      - uses: actions/checkout@v4
+
+      - name: Setup git creds
+        run: |
+          git config --global user.email "gituser@biocpy"
+          git config --global user.name "Biocpy test user"
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest tox
+
+      - name: Test with tox
+        run: |
+          tox