Carafe Integration #3549
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Carafe Integration #3549
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dshteyn
commented
Jul 18, 2025
dshteyn
commented
- Integrate carafe.
- Add a test to run carafe.
- Expose some basic user options for AlphaPeptDeep.
…support' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support
…yline/work/20240816_pythoninstaller_with_virtual_env_support
…yline/work/20240816_pythoninstaller_with_virtual_env_support Merge branch 'Skyline/work/20240816_pythoninstaller_with_virtual_env_support' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support Fix test for nodes where Long Paths is not set and alert with appropriate message if insufficient privileges to set it. try #2 Fix hang on simulating Nvidia GPU hardware when not available on computer physically Revert last commit Fix hang on simulating Nvidia GPU hardware when not available on computer physically Move AlphapeptdeepBuildLibraryTest test data to TestPerf. Add answer sheet to AlphapeptdeepBuildLibraryTest test data. Compare answers with allowance for small rounding differences. Merge branch 'Skyline/work/20240816_pythoninstaller_with_virtual_env_support' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support Improve canceling. Should only have to Cancel once to stop. Merge branch 'Skyline/work/20240816_pythoninstaller_with_virtual_env_support' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support Address ReSharper complaints Merge branch 'master' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support Simplify user experience for enabling GPU installation with required elevation. Combine the separate GPU setup steps in one simple batch that can get run if user has permissions. Make Cancellations more robust. Update Test to reflect simpler UI. Simplify Nvidia dialog and give better user directions. Disable "OK" button on Nvidia admin message when not running elevated. Adjust the test to reflect the simpler interface. AlphaPeptDeep test moved to TestPerf and associated bugfixes and simulated modes for Nvidia components dealing with tasks when installing and configuring Python + Nvidia Progress with Testing and Nvidia batch file to set PATH to point to CuDNN Fix issue with canceling long jobs. Move AlphapeptdeepBuildLibraryTest.cs to TestPerf Fix build issues caused by last commit Correct a bug with simulated states move Nvidia installation resource to correct a TC code inspection issue. Merge branch 'master' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support Simplify code. Increase test coverage. Write bat script to install Nvidia libraries and instruct the user and administrator what to do. Installation script to for NVIDIA Libraries Fix bug with Path change not checking if already contains a new target. Fix a merge issue Merge branch 'Skyline/work/20250207_TestingCancellationTokens' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support # Merged Conflicts: # pwiz_tools/Skyline/Model/AlphaPeptDeep/AlphapeptdeepLibraryBuilder.cs # pwiz_tools/Skyline/Model/Lib/Library.cs # pwiz_tools/Skyline/TestFunctional/AlphapeptdeepBuildLibraryTest.cs # pwiz_tools/Skyline/TestUtil/PythonTestUtil.cs Test with and without iRT, summary comments. Merge branch 'master' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support # Resolved Conflicts: # .gitignore # pwiz_tools/Skyline/SettingsUI/BuildLibraryDlg.resx
…support' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support
…ified" error reported on TeamCity
…training document and predicts a library for a protein FASTA input using Bo's latest development code. Other changes to make the Skyline interface work better with Carafe.
…yline document as the target or tuning document when employing Carafe.
… certain why the directory goes missing on AWS node but let's create it if necessary.
…_virtual_env_support
…er Skyline document.
…ary if unknown modifications are present.
…yline/work/20240816_pythoninstaller_with_virtual_env_support
…support' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support
…ilder interface to return the SrmDocument and Build Library Toolname.
…support' of https://github.com/ProteoWizard/pwiz into pwiz-CarafeSupport-Feb262025 # Merged Conflicts: # pwiz_tools/Skyline/Model/AlphaPeptDeep/AlphapeptdeepLibraryBuilder.cs # pwiz_tools/Skyline/Model/Carafe/CarafeLibraryBuilder.cs # pwiz_tools/Skyline/Model/Koina/KoinaLibraryBuilder.cs # pwiz_tools/Skyline/Model/Lib/Midas/MidasBlibBuilder.cs
…ring by ProcessRunner for Immediate Window output cleanliness.
…ported mods GetWarningMods when building a library.
…es predicted by AlphaPeptDeep run by Skyline. Fix problem when using paths with bad legacy character combos. Code cleanup.
…nd IM. Multiply AlphaPeptDeep NORMALIZED_RT by 100 for scaling as suggested by Brendan
…illed in on the Properties tab of the wizard. Add tests with APD and Carafe with empty Name and empty Path.
…n breaks CUDA dependencies and prevents running on GPU.
…edMods' of https://github.com/ProteoWizard/pwiz into Skyline/work/20250226_CarafeSupport
…s Warning due to lack of Ccs model.
…ectra. Remove unused code in CarafeBuildLibraryTest.
…o mismatch in spectral libraries
…gle is different from that computed by NormalizedContrastAngleSqrt
… associated changes. Update email address to a more permanent option.
…com/ProteoWizard/pwiz into Skyline/work/20250226_CarafeSupport
…com/ProteoWizard/pwiz into Skyline/work/20250226_CarafeSupport
…orial tests to address Team City cleanup of test area issue.
…k/20250226_CarafeSupport
…yline/work/20250226_CarafeSupport
…yline/work/20250226_CarafeSupport
…com/ProteoWizard/pwiz into Skyline/work/20250226_CarafeSupport
…com/ProteoWizard/pwiz into Skyline/work/20250226_CarafeSupport
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