Copilot

Implement CodeFixer for PH2089: Avoid assignment in condition with comprehensive test coverage

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This PR implements a CodeFixer for the PH2089 diagnostic "Avoid assignment in condition" that automatically refactors problematic code patterns, with comprehensive test coverage for complex real-world scenarios. The CodeFixer transforms...

Investigate RegexNeedsTimeoutAnalyzer: Identify Roslyn 3.6.0 compatibility limitation with C# 9 target-typed new expressions

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Investigation of failing RegexNeedsTimeoutAnalyzer tests revealed a fundamental compatibility issue between the project's Roslyn 3.6.0 dependency and C# 9+ target-typed `new` expressions. ## Problem The RegexNeedsTimeoutAnalyzer was failing to detect...

Fix user creation not updating configuration field automatically

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The Hue adapter was not automatically updating the `user` field in the configuration after successfully creating a new user on the bridge. Users had to manually copy the username from...

Configurable attachment blocks for email with mutator interface

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Implements configurable attachment blocks for the Blockly email block with a mutator interface that allows dynamic management of multiple attachments. The implementation follows the older Blockly API patterns compatible with...

Migrate all Mondo-EFO mappings: obsolete EFO terms and analyze metadata

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- [x] Explore repository structure and understand the mapping file format - [x] Parse all 2,655 terms from mondo_efo_mappings.tsv - [x] **Import Mondo terms** - Added 25 missing terms to...

GWAS catalog contains 93 associations under "response to xenobiotic stimulus" where reported traits specify drugs (e.g., "Response to carboplatin in ovarian cancer") but map only to generic GO:0009410. This adds...

Add 7 drug response terms from GWAS Catalog analysis

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GWAS Catalog contains associations where reported traits mention specific drugs (e.g., "response to mesalamine") but are mapped to generic parent terms like "response to xenobiotic stimulus". This adds precise drug...

Optimize phpcs CI execution and improve output clarity

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The phpcs GitHub Action was slow (~2m 31s) and provided ambiguous output ("No fixable errors were found" doesn't indicate if violations exist). ## Changes **Performance optimization (~50% faster)** - Skip...

Upgrade to Tailwind CSS 4.1

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- [x] Update package.json to use Tailwind CSS 4.1 and remove PostCSS dependencies - [x] Convert all // comments to /* */ format in CSS files - [x] Convert tailwind.config.js...

Migrates CI/CD from Travis CI to GitHub Actions using `ddev/github-action-setup-ddev`. Removes all Travis dependencies with no backward compatibility layer. ## Workflows - **lint.yml** - PhpStan, PHPCS, shellcheck on PRs and...