Alphapeptdeep Integration #3123
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nickshulman
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Aug 18, 2024
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Something went wrong with the merge here. It shouldn't show changes from other PRs. Maybe try fetching latest master and rebasing your branch on it. Do you need help doing that?. |
My guess is that pushing "Update branch" will fix everything. |
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Yeah. Thanks for asking. I did a rebase which treated the updated changes and anything in between as new commits. I rolled back those changes and added the updates as a new commit. That fixed this branch. I will do a merge from master later on. |
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On TeamCity the TestData test runs from an installed directory (installed with the WIX-based installer). Any non-vendor DLLs have to be added into |
…IResources into ToolsResources
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…ry with alphapeptdeep" This reverts commit 5c487ab. Tempororily remove this commit to make TeamCity build succeeds
…om skyline document
…alphapeptdeep cli to build library
… library file to be skyline compatible
…support' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support
…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.
…yline/work/20240816_pythoninstaller_with_virtual_env_support
…support' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support
…support' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support
…sheet to AlphapeptdeepBuildLibraryTest test data. Compare answers with allowance for small rounding differences.
…on computer physically
…yline/work/20240816_pythoninstaller_with_virtual_env_support
…iate message if insufficient privileges to set it.
…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
… certain why the directory goes missing on AWS node but let's create it if necessary.
…_virtual_env_support
…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
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PythonInstallertoPythonInstallerLegacyDlgPythonInstallerimplementation to support Python virtual environmentPythonInstallerimplementation