Copilot

> can you add a test that targets this fix Added comprehensive tests that validate the fix in commit 14190d8. The tests cover 4 key scenarios: 1. **Files within BuildDropPath**...

> @copilot fix the tests please. Fixed the SSM test pollution issue in commit d305d70. The test suite now passes with 153/153 examples passing (excluding 2 pre-existing Debian image selection...

> @copilot > Fix those pre-existing errors, too. > You can do it! Fixed in commit 9310e02! All 234 tests now pass. The issue was that the test expectations were...

> @copilot Make a list of the obsoleted PR terms and suggest replacements from the Protein Ontology. Here's the list of obsoleted PRO terms with replacement suggestions: | OBA Term...

> @copilot I added 4 OBA terms to the issue. Make a list of the obsoleted PR terms and suggest replacements from the Protein Ontology. I'd be happy to check...

> @copilot These are the OBA IDs I added to the issue. Make a list of the obsoleted PR terms and suggest replacements from the Protein Ontology. > > OBA:1000220...

> @copilot These 4 GO terms have been obsoleted. Check again and suggest appropriate replacement terms from GO. You're correct - I apologize for the confusion. The GO import in...

> @copilot: Merge `main`, resolve conflicts, and follow updated `AGENTS.md` . Merged main and resolved conflicts in commit 780619b9. Updated `make_tri_lattice()` to follow the new AGENTS.md guidelines: - Added experimental...

> @copilot add tests that test this behavior Added test `TOPP_MapAlignerPoseClustering_5` that verifies exception handling with blank mzML files. The test ensures the tool doesn't crash when encountering files with...

> @copilot We will want to tell people they will need .NET 10 and Visual Studio 2026 or Visual Studio Code with the C# Dev Kit. Visual Studio 2022 isn't...