Carafe Integration #3549
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Carafe Integration #3549
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Contributor
dshteyn
commented
Jul 18, 2025
dshteyn
commented
- Integrate carafe.
- Add a test to run carafe.
- Expose some basic user options for AlphaPeptDeep.
…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
…uildLibraryDlg, Dispose dialog instead in PythonInstallerUI. Bugfix CPU fallback for running library build when user answers "No" to Nvidia Libraries. Make variable name more descriptive for tracking user's answer to Nvidia admin elevation requirement.
…support' of https://github.com/ProteoWizard/pwiz into pwiz-CarafeSupport-Feb262025 # Resolved Conflicts: # pwiz_tools/Shared/CommonUtil/SystemUtil/ProcessRunner.cs # pwiz_tools/Skyline/Model/AlphaPeptDeep/AlphapeptdeepLibraryBuilder.cs # pwiz_tools/Skyline/Model/Carafe/CarafeLibraryBuilder.cs # pwiz_tools/Skyline/SettingsUI/BuildLibraryDlg.resx
…support' of https://github.com/ProteoWizard/pwiz into pwiz-CarafeSupport-Feb262025 # Resolved: # pwiz_tools/Skyline/SettingsUI/BuildLibraryDlg.cs # pwiz_tools/Skyline/ToolsUI/PythonInstallerUI.cs
…support' of https://github.com/ProteoWizard/pwiz into pwiz-CarafeSupport-Feb262025
…released file locks after running APD build library test.
…yline/work/20240816_pythoninstaller_with_virtual_env_support
… comparisons as these number are now multiplied by 10^2 before writing, adjust the tolerance from 10^-3 to 10^-1
…_virtual_env_support
… APDBuildLibraryTest
…support' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support
…a test directory.
…support' of https://github.com/ProteoWizard/pwiz into pwiz-CarafeSupport-Feb262025 # Merged Conflict: # pwiz_tools/Skyline/Model/Tools/PythonInstaller.cs
…on Mobility predictions with AlphaPeptDeep
…yline/work/20250226_CarafeSupport
…com/ProteoWizard/pwiz into Skyline/work/20250226_CarafeSupport
…com/ProteoWizard/pwiz into Skyline/work/20250226_CarafeSupport
…yline/work/20250226_CarafeSupport
Zip file now has separate folders for expected files and rawdata.
…yline/work/20250226_CarafeSupport
…com/nickshulman/pwiz into Skyline/work/20250226_CarafeSupport
…yline/work/20250226_CarafeSupport
…yline/work/20250226_CarafeSupport
…yline/work/20250226_CarafeSupport
…yline/work/20250226_CarafeSupport
…yline/work/20250226_CarafeSupport
…k/20250226_CarafeSupport
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