Minor changes to improve UX (#3)

Update tests, docstring, README etc.

CHANGELOG.md

@@ -1,5 +1,9 @@
 # Changelog
 
+## Version 0.1.1
+
+Minor changes to improve user experience.
+
 ## Version 0.1.0
 
 - Uses PyScaffold with Markdown extension for base project structure
@@ -10,4 +14,4 @@
   - Furo theme
   - Type hints documentation
 - Adds Ruff configuration for consistent code formatting
-- Creates standardized README with PyPI and CI badges
+- Creates README

README.md

@@ -44,6 +44,11 @@ create_repository(
 )
 ```
 
+## After setup
+
+- (Optional) Enable [pre-commit.ci](https://pre-commit.ci/) bot for your new repository.
+- (Optional) Install [ruff](https://docs.astral.sh/ruff/) for code formatting.
+
 <!-- pyscaffold-notes -->
 
 ## Note

docs/conf.py

@@ -171,7 +171,7 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = "alabaster"
+html_theme = "furo"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -301,4 +301,21 @@
     "pyscaffold": ("https://pyscaffold.org/en/stable", None),
 }
 
-print(f"loading configurations for {project} {version} ...", file=sys.stderr)
+print(f"loading configurations for {project} {version} ...", file=sys.stderr)
+
+# -- Biocsetup configuration -------------------------------------------------
+
+# Enable execution of code chunks in markdown
+extensions.append('myst_nb')
+
+# Less verbose api documentation
+extensions.append('sphinx_autodoc_typehints')
+
+autodoc_default_options = {
+    "special-members": True,
+    "undoc-members": True,
+    "exclude-members": "__weakref__, __dict__, __str__, __module__",
+}
+
+autosummary_generate = True
+autosummary_imported_members = True

docs/requirements.txt

@@ -1,3 +1,4 @@
+furo
 # Requirements file for ReadTheDocs, check .readthedocs.yml.
 # To build the module reference correctly, make sure every external package
 # under `install_requires` in `setup.cfg` is also listed here!

src/biocsetup/cli.py

@@ -9,10 +9,10 @@
 
 @click.command()
 @click.argument("project_path")
-@click.option("--description", "-d", help="Project description")
+@click.option("--description", "-d", help="Project description", default="Add a short description here!")
 @click.option("--license", "-l", default="MIT", help="License (default: MIT)")
 def main(project_path: str, description: str, license: str):
-    """Create a new Python package repository with consistent configuration."""
+    """Create a new BiocPy Python package."""
     create_repository(
         project_path=project_path,
         description=description,

src/biocsetup/create_repository.py

@@ -2,7 +2,7 @@
 from pathlib import Path
 from typing import Optional
 
-from pyscaffold import api
+from pyscaffold import api, file_system, shell
 from pyscaffoldext.markdown.extension import Markdown
 
 __author__ = "Jayaram Kancherla"
@@ -12,31 +12,37 @@
 
 def create_repository(
     project_path: str,
-    description: Optional[str] = None,
+    description: Optional[str] = "Add a short description here!",
     license: str = "MIT",
 ) -> None:
     """
     Create a new BiocPy Python package repository.
 
     Args:
         project_path:
-            Path where the new project should be created
+            Path where the new project should be created.
 
         description:
-            Optional project description
+            Optional project description.
 
         license:
-            License to use (default: MIT)
+            License to use.
+            Defaults to 'MIT'.
     """
     # Create project using pyscaffold with markdown extension
+    if description is None:
+        description = "Add a short description here!"
+
     opts = {
         "project_path": project_path,
-        "description": description or "Add a short description here!",
+        "description": description,
         "license": license,
         "extensions": [Markdown()],
     }
     api.create_project(**opts)
 
+    modified_files = []
+
     # Get absolute path to templates directory
     template_dir = Path(__file__).parent / "templates"
 
@@ -48,11 +54,13 @@ def create_repository(
         src = template_dir / "github_workflows" / workflow
         dst = gh_actions_dir / workflow
         shutil.copy2(src, dst)
+        modified_files.append(dst)
 
     # Add pre-commit config
     precommit_src = template_dir / "precommit" / "pre-commit-config.yaml"
     precommit_dst = Path(project_path) / ".pre-commit-config.yaml"
     shutil.copy2(precommit_src, precommit_dst)
+    modified_files.append(precommit_dst)
 
     # Modify sphinx conf.py
     conf_py_path = Path(project_path) / "docs" / "conf.py"
@@ -61,6 +69,7 @@ def create_repository(
 
     # Add myst-nb extension and configuration
     myst_config = """
+
 # -- Biocsetup configuration -------------------------------------------------
 
 # Enable execution of code chunks in markdown
@@ -77,24 +86,25 @@ def create_repository(
 
 autosummary_generate = True
 autosummary_imported_members = True
-
-html_theme = "furo"
 """
 
+    conf_content = conf_content.replace("alabaster", "furo")
+
     with open(conf_py_path, "w") as f:
         f.write(conf_content + myst_config)
+        modified_files.append(conf_py_path)
 
     # Update requirements.txt for docs
     docs_requirements = Path(project_path) / "docs" / "requirements.txt"
     with open(docs_requirements, "a") as f:
-        f.write("\nmyst-nb\nfuro\nsphinx-autodoc-typehints\n")
+        f.write("myst-nb\nfuro\nsphinx-autodoc-typehints\n")
+        modified_files.append(docs_requirements)
 
     # Modify README
     readme_path = Path(project_path) / "README.md"
     proj_name = Path(project_path).parts[-1]
 
-    new_readme = f"""
-[![PyPI-Server](https://img.shields.io/pypi/v/{proj_name}.svg)](https://pypi.org/project/{proj_name}/)
+    new_readme = f"""[![PyPI-Server](https://img.shields.io/pypi/v/{proj_name}.svg)](https://pypi.org/project/{proj_name}/)
 ![Unit tests](https://github.com/BiocPy/{proj_name}/actions/workflows/pypi-test.yml/badge.svg)
 
 # {proj_name}
@@ -121,6 +131,7 @@ def create_repository(
 
     with open(readme_path, "w") as f:
         f.write(new_readme)
+        modified_files.append(readme_path)
 
     # Modify ppyproject.toml to add ruff configuration
     pyprj_path = Path(project_path) / "pyproject.toml"
@@ -147,3 +158,12 @@ def create_repository(
 
     with open(pyprj_path, "w") as f:
         f.write(pyprj_content + ruff_config)
+        modified_files.append(pyprj_path)
+
+    with file_system.chdir(project_path):
+        for f in modified_files:
+            shell.git("add", str(f.relative_to(project_path)))
+
+        shell.git("commit", "-m", "BiocSetup configuration")
+
+    print("BiocSetup complete! 🚀 💥")

tests/test_cli.py

@@ -66,6 +66,6 @@ def test_cli_help():
     runner = CliRunner()
     result = runner.invoke(main, ["--help"])
     assert result.exit_code == 0
-    assert "Create a new Python package repository" in result.output
+    assert "Create a new BiocPy Python package" in result.output
     assert "--description" in result.output
     assert "--license" in result.output