feat: Initialize documentation #85
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WalkthroughThis pull request introduces significant enhancements to the Changes
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (6)
docs/index.md (1)
1-8: LGTM! Consider organizing documentation sections.The include-markdown directive is correctly configured. However, consider organizing the documentation into logical sections beyond just including the README.
Consider adding these common documentation sections:
- Getting Started Guide
- API Reference
- Examples/Tutorials
- Development Guide
- Troubleshooting
mkdocs.yaml (2)
1-5: Consider adding security-related configurations.The basic site configuration looks good, but consider adding security-related configurations.
Add these configurations for better security:
# Prevent XSS attacks strict: true # Add CSP headers extra: generator: false # Remove generator meta tag social: cards: true # Enable social cards
30-34: Consider adding useful documentation plugins.The current plugin selection is good, but could be enhanced.
Consider adding these useful plugins:
plugins: - minify: # Minifies HTML, JS and CSS minify_html: true minify_js: true minify_css: true - git-revision-date-localized # Shows last update date - mkdocstrings: # API documentation from docstrings handlers: python: paths: [src] # Path to your Python sourceREADME.md (2)
Line range hint
2-14: Consider organizing badges by category.While the badges provide excellent project status visibility, they could be better organized.
Consider grouping badges by category:
<!-- Status --> [![CI-CD][ci-badge]][ci-url] [![codecov][coverage-badge]][coverage-url] [![CodeFactor][codefactor-badge]][codefactor-url] <!-- Package --> [![PyPI - Version][pypi-version-badge]][pypi-url] [![PyPI - Python Version][python-version-badge]][pypi-url] [![PyPI - Format][pypi-format-badge]][pypi-url] <!-- Downloads --> [![Downloads][pepy-badge]][pepy-url] [![Docker Pulls][docker-badge]][docker-url]
98-102: Enhance documentation serving instructions.The documentation serving instructions could be more detailed.
Consider adding more context:
### Serve Documentation Locally The documentation is built using MkDocs. To serve it locally: ```bash pixi run -e docs doc-serveThe documentation will be available at http://127.0.0.1:8001
</blockquote></details> <details> <summary>pyproject.toml (1)</summary><blockquote> `92-111`: **Consider documentation migration strategy.** The shift from Sphinx to MkDocs is well-structured. However, consider the following recommendations: 1. Document the migration process in CHANGELOG.md 2. Ensure all existing documentation is properly converted from Sphinx format to MkDocs format 3. Update any documentation-related CI/CD workflows to use the new MkDocs commands </blockquote></details> </blockquote></details> <details> <summary>📜 Review details</summary> **Configuration used: CodeRabbit UI** **Review profile: CHILL** **Plan: Pro** <details> <summary>📥 Commits</summary> Reviewing files that changed from the base of the PR and between 0e868f6ffaf749fe1591d75215e1dcf00cca948b and 7de6f803bf8884091827ffb6f3a474ea1acb07de. </details> <details> <summary>⛔ Files ignored due to path filters (1)</summary> * `pixi.lock` is excluded by `!**/*.lock` </details> <details> <summary>📒 Files selected for processing (5)</summary> * `README.md` (5 hunks) * `docs/changelog.md` (1 hunks) * `docs/index.md` (1 hunks) * `mkdocs.yaml` (1 hunks) * `pyproject.toml` (1 hunks) </details> <details> <summary>✅ Files skipped from review due to trivial changes (1)</summary> * docs/changelog.md </details> <details> <summary>🧰 Additional context used</summary> <details> <summary>🪛 yamllint (1.35.1)</summary> <details> <summary>mkdocs.yaml</summary> [error] 35-35: trailing spaces (trailing-spaces) --- [error] 36-36: trailing spaces (trailing-spaces) --- [warning] 39-39: wrong indentation: expected 4 but found 2 (indentation) --- [error] 53-53: no new line character at the end of file (new-line-at-end-of-file) </details> </details> </details> <details> <summary>🔇 Additional comments (2)</summary> <details> <summary>pyproject.toml (2)</summary> `101-102`: **LGTM!** The PyPI dependency is well-configured with appropriate version constraints. --- `104-111`: **Verify mkdocs.yaml configuration file.** The tasks are well-defined, but let's ensure the referenced configuration file exists and is properly set up. <details> <summary>✅ Verification successful</summary> **mkdocs.yaml configuration is properly set up** The configuration file exists and contains all essential configurations: - Site name is defined as "READII" - Material theme is configured with appropriate features - Required plugins are set up (awesome-pages, search, git-authors, include-markdown) </details> <details> <summary>🏁 Scripts executed</summary> The following scripts were executed for the analysis: Script: ```shell #!/bin/bash # Description: Verify mkdocs.yaml exists and contains required configurations # Check if mkdocs.yaml exists if [ -f mkdocs.yaml ]; then echo "mkdocs.yaml exists" # Check for essential configurations rg -A 5 "^site_name:|^theme:|^plugins:" mkdocs.yaml else echo "mkdocs.yaml not found" fiLength of output: 754
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #85 +/- ##
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Coverage 44.51% 44.51%
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Files 16 16
Lines 739 739
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Hits 329 329
Misses 410 410 ☔ View full report in Codecov by Sentry. |
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (5)
mkdocs.yaml (5)
1-6: Consider adding additional metadata fields for better SEO and documentation.The basic configuration looks good, but consider adding these fields to enhance documentation discoverability and user experience:
site_url: The canonical URL where the documentation will be hostedcopyright: Copyright informationedit_uri: Path to edit pages on GitHubsite_name: READII repo_url: https://github.com/bhklab/readii repo_name: readii site_description: Package documentation for readii site_author: bhklab +site_url: https://bhklab.github.io/readii +copyright: Copyright © 2024 bhklab +edit_uri: edit/main/docs/
7-23: Consider expanding watch paths for comprehensive documentation updates.The build configuration is good, but consider adding these paths to the watch list for more comprehensive documentation updates:
README.md: To track changes in the main project documentationCHANGELOG.md: To track version history updates-watch: [docs, src, mkdocs.yaml] +watch: [docs, src, mkdocs.yaml, README.md, CHANGELOG.md]
26-28: Consider expanding navigation with common documentation sections.The current navigation structure is minimal. Consider adding these common sections to provide comprehensive documentation:
- API Reference
- Getting Started
- User Guide
- Contributing Guidelines
nav: - Home: index.md - Changelog: changelog.md + - Getting Started: getting-started.md + - User Guide: user-guide.md + - API Reference: api/ + - Contributing: contributing.md
30-34: Consider adding more plugins for enhanced documentation features.The current plugin setup is good, but consider these additional plugins to enhance the documentation:
mkdocs-material[imaging]: For image processing and optimizationmkdocstrings: For automatic API documentation from docstringsmkdocs-git-revision-date-localized-plugin: For showing last update datesplugins: - awesome-pages # simplifies configuring page titles and their order - search # necessary for search functionality to work - git-authors # adds authors to pages using git history - include-markdown # allows for including Markdown files into another Markdown file + - mkdocstrings: # automatic API documentation from docstrings + handlers: + python: + paths: [src] # path to your Python source code + - git-revision-date-localized # shows last update date on each page
36-53: Fix formatting issues in theme configuration.The theme configuration is comprehensive, but there are some formatting issues to address:
- Remove trailing spaces after
theme:on line 36- Add a newline at the end of the file
-theme: +theme: name: material # ... rest of configuration ... - toc.follow +🧰 Tools
🪛 yamllint (1.35.1)
[error] 36-36: trailing spaces
(trailing-spaces)
[error] 53-53: no new line character at the end of file
(new-line-at-end-of-file)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro
⛔ Files ignored due to path filters (1)
pixi.lockis excluded by!**/*.lock
📒 Files selected for processing (2)
mkdocs.yaml(1 hunks)pyproject.toml(2 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- pyproject.toml
🧰 Additional context used
🪛 yamllint (1.35.1)
mkdocs.yaml
[error] 35-35: trailing spaces
(trailing-spaces)
[error] 36-36: trailing spaces
(trailing-spaces)
[error] 53-53: no new line character at the end of file
(new-line-at-end-of-file)
Start of documentation, mostly copied the core dependencies and plugins from med-imagetools
this "core" would be the base of the main vs 2.0 branch
Summary by CodeRabbit
New Features
Documentation
Bug Fixes
Chores