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Infrastructure improvements: DeepWiki, Traits, and documentation enhancements#438

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ocots merged 19 commits into
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Jun 11, 2026
Merged

Infrastructure improvements: DeepWiki, Traits, and documentation enhancements#438
ocots merged 19 commits into
mainfrom
develop

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@ocots ocots commented Jun 8, 2026 •
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Overview

This PR introduces the first step of a larger refactoring plan for CTBase.jl. The current change adds a DeepWiki badge to the documentation landing page with an appropriate disclaimer about AI-generated content.

Development Strategy

This PR establishes a develop branch that will serve as the integration point for multiple feature branches. Each feature will be developed in its own branch and merged into develop, following this workflow:

main
  ↑
develop (integration branch)
  ↑
feature/deepwiki ✓ (this PR)
feature/traits
feature/abstract-types
feature/exceptions-presentation ✓
feature/private-public-naming ✓
feature/jldoctest
feature/vitepress

Planned Features

The following features will be developed in separate branches and merged into develop:

  1. DeepWiki integration ✓ (this PR)

    • Add DeepWiki badge to documentation
    • Provide AI-assisted code exploration with appropriate disclaimers

  2. Traits module

    • Extract Traits module from CTFlows
    • Update philosophy documentation to explicitly state that traits should be in a separate module
    • This enables future consolidation of traits across the ecosystem in CTBase

  3. Abstract types module

    • Create dedicated module for abstract types
    • Update philosophy documentation to mirror the Traits pattern (separate module for abstract types)

  4. Private/public method naming and distribution ✓

    • Review and standardize naming conventions for private vs public methods
    • Ensure proper distribution across submodules

  5. Exception presentation ✓

  6. JLDocTest integration

    • Implement jldoctest functionality
    • Add label-based triggering mechanism for doctests

  7. VitePress documentation

    • Add VitePress as an alternative documentation system
    • Complement existing Documenter.jl setup

Current Changes

  • Added DeepWiki tip admonition to docs/src/index.md
  • Simplified badge link for cleaner presentation

Testing

Documentation builds successfully with julia --project=. docs/make.jl.

ocots added 3 commits June 8, 2026 18:22
@ocots
Merge branch 'main' into develop
27cb673
@ocots
foo
a2c5d45
@ocots
Standardize private/public method naming conventions
4e6555c 
- Add naming conventions to modules.md: symbol (public), _symbol (private helper), __symbol (default value)
- Rename private functions in Descriptions: compute_similarity → _compute_similarity, find_similar_descriptions → _find_similar_descriptions, format_description_candidates → _format_description_candidates
- Rename private functions in Exceptions: extract_user_frames → _extract_user_frames, format_user_friendly_error → _format_user_friendly_error, ansi_color → _ansi_color, ansi_reset → _ansi_reset, print_ansi_styled → _print_ansi_styled
- Update planning.md with improved checkpoint templates (MCP preferred, fallback commands)
- Fix extension tests to use fake types per testing-creation.md §6 (prevents flaky tests when extensions are loaded elsewhere)
@ocots ocots mentioned this pull request Jun 8, 2026
Merged
ocots and others added 8 commits June 8, 2026 19:06
@ocots
Merge pull request #439 from control-toolbox/feature/private-public-m…
bea4592 
…ethods

- Add naming conventions to modules.md: symbol (public), _symbol (private helper), __symbol (default value)
- Rename private functions in Descriptions: compute_similarity → _compute_similarity, find_similar_descriptions → _find_similar_descriptions, format_description_candidates → _format_description_candidates
- Rename private functions in Exceptions: extract_user_frames → _extract_user_frames, format_user_friendly_error → _format_user_friendly_error, ansi_color → _ansi_color, ansi_reset → _ansi_reset, print_ansi_styled → _print_ansi_styled
- Update planning.md with improved checkpoint templates (MCP preferred, fallback commands)
- Fix extension tests to use fake types per testing-creation.md §6 (prevents flaky tests when extensions are loaded elsewhere)
@ocots
foo
a3cc692
@ocots
Merge branch 'feature/private-public-methods' into develop
19c9ca9
@ocots
Refactor: Restructure extensions and Unicode modules following module…
12de0d3 
… philosophy

- Move extensions from ext/*.jl to ext/ExtensionName/ subdirectories with proper entry_point.jl pattern
- Move extension implementations to src/Extensions/ submodules (coverage_postprocessing.jl, documenter_reference.jl, test_runner.jl)
- Split Unicode module into subscripts.jl and superscripts.jl submodules
- Update all imports to use qualified paths (CTBase.Extensions.run_tests, Unicode.ctindices, etc.)
- Update documentation to reflect new qualified import paths
- Restructure test files to follow new module organization
- Remove redundant test files (test_utils.jl, test_display.jl) and consolidate into enriched test files
@ocots
Merge pull request #440 from control-toolbox/feat/module-philosophy
5139714 
- Move extensions from ext/*.jl to ext/ExtensionName/ subdirectories with proper entry_point.jl pattern
- Move extension implementations to src/Extensions/ submodules (coverage_postprocessing.jl, documenter_reference.jl, test_runner.jl)
- Split Unicode module into subscripts.jl and superscripts.jl submodules
- Update all imports to use qualified paths (CTBase.Extensions.run_tests, Unicode.ctindices, etc.)
- Update documentation to reflect new qualified import paths
- Restructure test files to follow new module organization
- Remove redundant test files (test_utils.jl, test_display.jl) and consolidate into enriched test files
@ocots
Update API reference and fix documentation cross-references
84ed889 
- docs/api_reference.jl: Add all missing source files to each module's documentation (Core, Unicode, Extensions, and all extensions)
- docs/src/guide/test-runner.md: Remove invalid @ref to TestRunner.TestRunInfo (not accessible in documentation context)
- ext/TestRunner/entry_point.jl: Remove invalid @ref to TestRunner.TestRunInfo from docstring
- src/Core: Rename utils.jl to default.jl for clarity
@ocots
Refactor test suite for orthogonality
636f0c9 
Split large monolithic test files into smaller, focused test files:
- Core: test_core.jl → test_core_types.jl, test_utils.jl
- Exceptions: test_types.jl → test_exception_types.jl, test_extension_error.jl
- Extensions: test_extensions_enriched.jl → test_extension_stubs.jl
- Extensions: test_coverage_edge_cases.jl → test_coverage_helpers.jl
- Extensions: test_documenter_reference.jl → 7 focused files (api, config_helpers, page_building, pipeline, symbol_helpers, type_formatting, types)
- Extensions: test_testrunner.jl → 6 focused files (arg_parsing, execution, progress, selection, types)
- Unicode: test_unicode_enriched.jl, test_unicode_utils.jl → test_subscripts.jl, test_superscripts.jl

Enhanced exception display tests with new branches for IncorrectArgument and AmbiguousDescription.
Added Descriptions import to test_display_description.jl.
@ocots
Merge pull request #441 from control-toolbox/feat/test-orthogonality
6f4c4e3 
Refactor test suite for orthogonality
@ocots ocots mentioned this pull request Jun 9, 2026
Merged
@ocots

ocots commented Jun 9, 2026

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Status Update

Progress on the planned features:

  1. DeepWiki integration ✓ (completed in this PR)
  2. Traits module - pending
  3. Abstract types module - pending
  4. Private/public method naming and distribution ✓ (completed in Refactor test suite for orthogonality #441, merged into develop)
  5. Exception presentation ✓ (completed in Refactor test suite for orthogonality #441, merged into develop)
  6. JLDocTest integration - pending
  7. VitePress documentation - pending

The develop branch now includes the DeepWiki integration plus the private/public method naming and exception presentation improvements from #441.

@ocots ocots mentioned this pull request Jun 9, 2026
Closed
ocots added 2 commits June 9, 2026 12:20
@ocots
Add placeholder for exception presentation review work
3e20120
@ocots
Differentiate error messages in ctindice() and ctupperscript() for ne…
992656f 
…gative vs multi-digit values

- Split error condition in ctindice(): i < 0 now shows "must be positive" (expected: ≥ 0), i > 9 shows "must be a single digit" with suggestion to use ctindices()
- Split error condition in ctupperscript(): same pattern with ctupperscripts() suggestion
- Updated tests to verify new error messages
- All 90 tests in test/suite/unicode/ pass
@ocots ocots mentioned this pull request Jun 9, 2026
Merged
5 tasks
ocots added 4 commits June 9, 2026 12:21
@ocots
Remove placeholder file
43ccfb6
@ocots
Redesign exception display with improved formatting and structure
40fbfcc 
- Refactored display.jl to use modular rendering functions
- Added structured exception context display with sections
- Improved error message formatting with clear hierarchy
- Updated tests to cover new display behavior
- Updated documentation in exceptions.md and index.md
@ocots
Merge pull request #444 from control-toolbox/feat/exception-display-r…
d29535a 
…edesign

Redesign exception display with improved formatting and structure
@ocots
Merge pull request #443 from control-toolbox/exception-presentation-r…
7e443df 
…eview

Review and improve exception presentation
@ocots

ocots commented Jun 11, 2026

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Scope update: Parts 2, 6, and 7 from the planned features are postponed to a later date. Part 3 (Abstract types module) is cancelled. The current focus remains on the completed items (1, 4, and 5) and the DeepWiki integration.

@ocots
ocots merged commit 01aff2b into main Jun 11, 2026
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@ocots
ocots deleted the develop branch June 11, 2026 20:16
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