Fix issues with Github pages action to publish docs (#2)

.github/workflows/pypi-publish.yml

@@ -19,12 +19,12 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install flake8 pytest tox
+          pip install tox
 
       - name: Setup git creds
         run: |
-          git config --global user.email "gituser@biocpy"
-          git config --global user.name "Biocpy test user"
+          git config --global user.name jkanche
+          git config --global user.email [email protected]
 
       - name: Test with tox
         run: |
@@ -37,7 +37,7 @@ jobs:
       - run: touch ./docs/_build/html/.nojekyll
 
       - name: GH Pages Deployment
-        uses: JamesIves/github-pages-deploy-action@4.1.3
+        uses: JamesIves/github-pages-deploy-action@v4
         with:
           branch: gh-pages # The branch the action should deploy to.
           folder: ./docs/_build/html
@@ -48,7 +48,7 @@ jobs:
           python -m tox -e clean,build
 
       - name: Publish package
-        uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+        uses: pypa/gh-action-pypi-publish@v1.12.2
         with:
           user: __token__
           password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/pypi-test.yml

@@ -31,7 +31,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install flake8 pytest tox
+          pip install tox
 
       - name: Test with tox
         run: |

CHANGELOG.md

@@ -10,4 +10,4 @@
   - Furo theme
   - Type hints documentation
 - Adds Ruff configuration for consistent code formatting
-- Creates standardized README with PyPI and CI badges
+- Creates standardized README with PyPI and CI badges

setup.py

@@ -1,10 +1,10 @@
 """
-    Setup file for biocsetup.
-    Use setup.cfg to configure your project.
+Setup file for biocsetup.
+Use setup.cfg to configure your project.
 
-    This file was generated with PyScaffold 4.6.
-    PyScaffold helps you to put up the scaffold of your new Python project.
-    Learn more under: https://pyscaffold.org/
+This file was generated with PyScaffold 4.6.
+PyScaffold helps you to put up the scaffold of your new Python project.
+Learn more under: https://pyscaffold.org/
 """
 
 from setuptools import setup

src/biocsetup/__init__.py

@@ -15,4 +15,4 @@
 finally:
     del version, PackageNotFoundError
 
-from .create_repository import create_repository
+from .create_repository import create_repository

src/biocsetup/templates/github_workflows/pypi-publish.yml

@@ -35,7 +35,7 @@ jobs:
       - run: touch ./docs/_build/html/.nojekyll
 
       - name: GH Pages Deployment
-        uses: JamesIves/github-pages-deploy-action@4.1.3
+        uses: JamesIves/github-pages-deploy-action@v4
         with:
           branch: gh-pages # The branch the action should deploy to.
           folder: ./docs/_build/html
@@ -46,7 +46,7 @@ jobs:
           python -m tox -e clean,build
 
       - name: Publish package
-        uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+        uses: pypa/gh-action-pypi-publish@v1.12.2
         with:
           user: __token__
           password: ${{ secrets.PYPI_API_TOKEN }}

tests/test_cli.py

@@ -18,7 +18,7 @@ def test_cli_basic():
     with runner.isolated_filesystem():
         result = runner.invoke(main, ["test-project"])
         assert result.exit_code == 0
-        
+
         # Check if project was created
         assert os.path.exists("test-project")
         assert os.path.exists(os.path.join("test-project", "src"))
@@ -29,23 +29,23 @@ def test_cli_with_options():
     runner = CliRunner()
     with runner.isolated_filesystem():
         result = runner.invoke(
-            main, 
+            main,
             [
                 "test-project",
                 "--description", "Test project description",
                 "--license", "BSD",
             ]
         )
         assert result.exit_code == 0
-        
+
         # Check if project was created
         project_dir = Path("test-project")
         assert project_dir.exists()
-        
+
         # Check if description was added to README
         readme_content = (project_dir / "README.md").read_text()
         assert "Test project description" in readme_content
-        
+
         # Check if license was set correctly
         setup_cfg = (project_dir / "setup.cfg").read_text()
         assert "BSD" in setup_cfg
@@ -57,7 +57,7 @@ def test_cli_invalid_path():
         # Create a file that will conflict with the project path
         with open("existing-file", "w") as f:
             f.write("test")
-            
+
         result = runner.invoke(main, ["existing-file"])
         assert result.exit_code != 0
 

tests/test_create.py

@@ -86,4 +86,4 @@ def test_create_repository_with_license(temp_dir):
     setup_cfg = Path(project_path) / "setup.cfg"
     with open(setup_cfg, "r") as f:
         content = f.read()
-        assert license in content
+        assert license in content