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Claude/remove dev files 011 cuvl3 s1 usmt1 t xd wt6 bvx#11

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cafferychen777 merged 3 commits intomainfrom
claude/remove-dev-files-011CUVL3S1Usmt1TXdWT6Bvx
Oct 26, 2025
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Claude/remove dev files 011 cuvl3 s1 usmt1 t xd wt6 bvx#11
cafferychen777 merged 3 commits intomainfrom
claude/remove-dev-files-011CUVL3S1Usmt1TXdWT6Bvx

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Description

Brief description of the changes in this PR.

Type of Change

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to not work as expected)
  • Documentation update
  • Performance improvement
  • Code refactoring

Related Issues

Fixes #(issue number)

Changes Made

  • Added/modified spatial analysis methods
  • Updated MCP server functionality
  • Improved data preprocessing
  • Enhanced visualization capabilities
  • Updated documentation
  • Added tests
  • Other: ___________

Testing

  • All existing tests pass
  • Added new tests for new functionality
  • Tested with different data types (Visium, Slide-seq, etc.)
  • Tested MCP integration with Claude Desktop
  • Manual testing performed

Checklist

  • My code follows the project's style guidelines
  • I have performed a self-review of my code
  • I have commented my code, particularly in hard-to-understand areas
  • I have made corresponding changes to the documentation
  • My changes generate no new warnings
  • I have added tests that prove my fix is effective or that my feature works
  • New and existing unit tests pass locally with my changes

Screenshots (if applicable)

Add screenshots to help explain your changes.

Additional Notes

Any additional information that reviewers should know.

Removed mkdocs.yml as the project uses Jekyll with Just the Docs theme
for documentation, not MkDocs. This file was never used and could cause
confusion about the documentation system.

Evidence:
- .github/workflows/pages.yml uses Jekyll for building docs
- docs/_config.yml is the actual Jekyll configuration
- docs/Gemfile contains Jekyll dependencies

Updated .gitignore to prevent mkdocs.yml/mkdocs.yaml from being committed
in the future.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>
Removed custom color scheme and restored the default Just the Docs colors.

Changes:
- Deleted custom color scheme: docs/_sass/color_schemes/chatspatial.scss
- Updated docs/_config.yml to use default color scheme (removed custom theme reference)

The custom color scheme (teal/purple/orange) has been replaced with the
cleaner default Just the Docs blue theme for better readability.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>
Deleted docs/_sass/custom/custom.scss to completely restore the original
Just the Docs appearance without any custom styling enhancements.

Removed custom styles included:
- Enhanced typography and spacing
- Custom border-radius and shadows
- Hover animations and transitions
- Navigation and search enhancements
- Table and code block styling
- Custom button effects

The documentation now uses 100% vanilla Just the Docs theme for a
clean, professional, and consistent appearance.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>
@cafferychen777 cafferychen777 merged commit f698ff8 into main Oct 26, 2025
0 of 2 checks passed
cafferychen777 added a commit that referenced this pull request Dec 30, 2025
* Remove unused MkDocs configuration file

Removed mkdocs.yml as the project uses Jekyll with Just the Docs theme
for documentation, not MkDocs. This file was never used and could cause
confusion about the documentation system.

Evidence:
- .github/workflows/pages.yml uses Jekyll for building docs
- docs/_config.yml is the actual Jekyll configuration
- docs/Gemfile contains Jekyll dependencies

Updated .gitignore to prevent mkdocs.yml/mkdocs.yaml from being committed
in the future.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

* Restore Just the Docs default color scheme

Removed custom color scheme and restored the default Just the Docs colors.

Changes:
- Deleted custom color scheme: docs/_sass/color_schemes/chatspatial.scss
- Updated docs/_config.yml to use default color scheme (removed custom theme reference)

The custom color scheme (teal/purple/orange) has been replaced with the
cleaner default Just the Docs blue theme for better readability.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

* Remove all custom styles, use pure Just the Docs theme

Deleted docs/_sass/custom/custom.scss to completely restore the original
Just the Docs appearance without any custom styling enhancements.

Removed custom styles included:
- Enhanced typography and spacing
- Custom border-radius and shadows
- Hover animations and transitions
- Navigation and search enhancements
- Table and code block styling
- Custom button effects

The documentation now uses 100% vanilla Just the Docs theme for a
clean, professional, and consistent appearance.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

---------

Co-authored-by: Claude <noreply@anthropic.com>
@cafferychen777 cafferychen777 deleted the claude/remove-dev-files-011CUVL3S1Usmt1TXdWT6Bvx branch February 9, 2026 09:28
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2 participants