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Alphapeptdeep Integration#3123

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xgwang-uw wants to merge 198 commits intomasterProteoWizard/pwiz:masterfrom Skyline/work/20240816_pythoninstaller_with_virtual_env_supportProteoWizard/pwiz:Skyline/work/20240816_pythoninstaller_with_virtual_env_supportCopy head branch name to clipboard

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Commits on Apr 4, 2024

• PeakTotalIonCurrentArea

  

  Nicholas Shulman

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Commits on Aug 26, 2024

• Rename PythonInstaller to PythonInstallerLegacyDlg

  xgwang-uw

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• Add PythonInstaller that supports virtual environment

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• Update to add OneOf dependency with PackageReference

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• Add RuntimeIdentifier win to Skyline.csproj to fix nuget restore error

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• Fix scaling issue and enable locatable for PythonInstallerDlg form

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• Fix AutoScaleDimensions value in PythonInstallerDlg.resx

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• Add more verbose logging if "CheckForMissingResources" fails.

  

  Nicholas Shulman

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• Fix CodeInspection test by moving PythonInstaller strings from ToolsUIResources into ToolsResources

  

  Nicholas Shulman

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• Added OneOf.dll to Product-template.wxs

  

  chambm

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• Fix PythonInstallerTest by consuming strings from ToolsResources

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• Setup python virtual environment and implement building library with alphapeptdeep

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Commits on Aug 27, 2024

• Remove unused exception vars

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• Revert "Setup python virtual environment and implement building library with alphapeptdeep"

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Commits on Aug 28, 2024

• Setup python virtual environment and add empty AlphapeptdeepLibraryBuilder class

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• Add top level logic for BuildLibrary in AlphapeptdeepLibrarybuilder

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Commits on Sep 3, 2024

• AlphapeptdeepLibraryBuilder - prepare input file for alphapeptdeep from skyline document

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Commits on Sep 4, 2024

• AlphapeptdeepLibraryBuilder - prepare settings.yaml file and execute alphapeptdeep cli to build library

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Commits on Sep 5, 2024

• AlphapeptdeepLibraryBuilder - transform alphapeptdeep output spectral library file to be skyline compatible

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• AlphapeptdeepLibraryBuilder - build transformed alphapeptdeep output to .blib and import into skyline

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Commits on Sep 9, 2024

• Setup python and java environments for Carafe

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Commits on Sep 10, 2024

• Update carafe UI to match existing functionalities

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Commits on Sep 12, 2024

• Implement CarafeLibraryBuilder to make carafe work end to end in Skyline

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Commits on Nov 8, 2024

• Merge remote-tracking branch 'remotes/origin/master' into Skyline/work/20240403_PeakTotalIonCurrentArea

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Commits on Nov 15, 2024

• Add "PeakIonMetrics"

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• Merge remote-tracking branch 'remotes/origin/master' into Skyline/work/20240403_PeakTotalIonCurrentArea

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• Remove TotalIonCurrentArea from TransitionGroupChromInfo

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• Mark PeakIonMetrics as "[Expensive]" so that they cannot be sorted or filtered on.

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Commits on Nov 16, 2024

• Merge branch 'master' into Skyline/work/20240403_PeakTotalIonCurrentArea

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Commits on Nov 18, 2024

• Merge remote-tracking branch 'remotes/origin/master' into Skyline/work/20240403_PeakTotalIonCurrentArea

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• Merge branch 'Skyline/work/20240403_PeakTotalIonCurrentArea' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240403_PeakTotalIonCurrentArea

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• Add MBI_SDK.dll to ClickOnce installed files

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Commits on Nov 20, 2024

• Merge branch 'master' into Skyline/work/20240403_PeakTotalIonCurrentArea

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Commits on Dec 3, 2024

• Merge remote-tracking branch 'remotes/origin/master' into Skyline/work/20240403_PeakTotalIonCurrentArea

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• Add "Injection Time" to Full Scan spectrum property sheet.

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• Merge branch 'Skyline/work/20240403_PeakTotalIonCurrentArea' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240403_PeakTotalIonCurrentArea

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Commits on Dec 4, 2024

• Merge branch 'master' into Skyline/work/20240816_pythoninstaller_with_virtual_env_support

  

  David Shteynberg

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  David Shteynberg

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Commits on Dec 5, 2024

• Changed filename from DocumentHash to base64 string encoding to avoid

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  David Shteynberg

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  David Shteynberg

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• Switch to a FolderBrowserDialog since user selects the Library Filename and a

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  dshteyn

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• Adjust warning for skipped peptides, don't show modification name since it is unknown/blank

  dshteyn

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• Merge remote-tracking branch 'remotes/origin/master' into Skyline/work/20240403_PeakTotalIonCurrentArea

  nickshulman

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• Divide injection time by 1000 before multiplying by Intensity so that ion count is accurate when Intensity is ions per second.

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Commits on Dec 6, 2024

• Merge branch 'master' into Skyline/work/20240403_PeakTotalIonCurrentArea

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• (1) Backout FolderBrowserDialog and place back SaveFileDialog (2) When the user selects a file using Browse and then gives the library a name, honor the user's chosen save file name and don't rewri…

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• Alphapeptdeep integration test to verify no duplicate accessions exist in the list of modifications

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• AlphaPeptDeep potential Warnings with modifications, these are localizable.

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• AlphaPeptDeep interface corrections

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• Updated resx with localizable strings

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• Adding a new function to combine the Unimod accession (aka ID) with amino acids that it applies to, because UnimodId alone is not unique in the UniModData class

  dshteyn

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• Test to verify unique accessions in the unimod modification list used by AlphapeptdeepLibraryBuilder

  dshteyn

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• Clarify message

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• Clarify message

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Commits on Dec 7, 2024

• Address PR comment on extraneous code

  dshteyn

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• Implement AlphaPeptDeepLibraryBuilder ability to read all Unimod modifications defined by UniModData class

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• Address PR comment on extraneous code

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• Localizable strings for Python installation message for AlphaPeptDeep

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• Switch to MultiButtonMsgDlg to alert need to install python.

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Commits on Dec 9, 2024

• Fix typo which caused "Spectrum Ion Count" to have the wrong value.

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• Merge branch 'Skyline/work/20240403_PeakTotalIonCurrentArea' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240403_PeakTotalIonCurrentArea

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• Merge remote-tracking branch 'remotes/origin/master' into Skyline/work/20240403_PeakTotalIonCurrentArea

  nickshulman

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Commits on Dec 10, 2024

• Address TC code inspection warnings in code I added and merge master into branch.

  dshteyn

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• Addressing more TC code inspection concerns

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• Another TC Code Inspection warning addressed.

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• Switch Unimod accession setting to use {unimod_accession}:{name} to avoid collisions of accessions identified by failing test on TC

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Commits on Dec 11, 2024

• Merge branch 'master' into 'Skyline/work/20240909_carafe_integration'

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• Use default Directory.CreateDirectory and quiet down ReSharper

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• Quiet ReSharper Warnings by removing unnecessary using statements

  dshteyn

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• Address ReSharper inspection issues

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Commits on Dec 12, 2024

• Merge branch 'master' of github.com:ProteoWizard/pwiz into Skyline/work/20240909_carafe_integration

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• Merge branch 'Skyline/work/20240816_pythoninstaller_with_virtual_env_support' of github.com:ProteoWizard/pwiz into Skyline/work/20240909_carafe_integration

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• Python installation for Carafe, dialog

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Commits on Dec 13, 2024

• Merge remote-tracking branch 'remotes/origin/master' into Skyline/work/20240403_PeakTotalIonCurrentArea

  nickshulman

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• Moving towards getting carafe to function in skyline

  dshteyn

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• Got installation of python and modules working so Carafe can be used in Skyline

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Commits on Dec 14, 2024

• Change names of columns to include "LcPeak" and "Analyte"

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Commits on Dec 16, 2024

• Merge branch 'master' into Skyline/work/20240403_PeakTotalIonCurrentArea

  nickshulman

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Commits on Dec 17, 2024

• Changes for installing python for ALPHAPEPTDEEP and CARAFE. Modifications for ALPHAPEPTDEEP updated to match the program's expectation. Testing of python installation for ALPHAPEPTDEEP revealed the…

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Commits on Dec 18, 2024

• Merge branch 'master' of github.com:ProteoWizard/pwiz into Skyline/work/20240909_carafe_integration

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• Merge [master] into [20240909_carafe_integration] and changes related to running AlphapeptDeep and Carafe via Skyline

  dshteyn

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• - skip peptides containing unsupported modifications in Carafe and AlphapeptDeep

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• Merge branch 'master' of github.com:ProteoWizard/pwiz into Skyline/work/20240909_carafe_integration

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• - address ReSharper warnings

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• Merge branch 'Skyline/work/20240909_carafe_integration' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240909_carafe_integration

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Commits on Dec 19, 2024

• Correct typo calling wrong function

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• Address ReSharper concerns

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• Merge branch 'master' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240909_carafe_integration

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Commits on Dec 20, 2024

• - Create a modification index to track supported modifications by Carafe

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Commits on Dec 21, 2024

• - Report the name of the tool in the Immediate Window when encountering unsupported modifications by AlphapeptDeep or Carafe

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• Merge branch 'master' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240909_carafe_integration

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Commits on Dec 22, 2024

• Merge 20240909_carafe_integration branch changes into 20240816_pythoninstaller_with_virtual_env_support branch

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Commits on Dec 25, 2024

• Allow SpectrumMetadata TotalIonCurrent and InjectionTime to be null

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• Merge branch 'Skyline/work/20240403_PeakTotalIonCurrentArea' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240403_PeakTotalIonCurrentArea

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• Merge remote-tracking branch 'remotes/origin/master' into Skyline/work/20240403_PeakTotalIonCurrentArea

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• Add "ApexSpectrumId" because Bo asked for it.

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• Fix Flags enum in SpectrumMetadata

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Commits on Dec 27, 2024

• Merge branch 'master' of github.com:ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support

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Commits on Dec 28, 2024

• Code refactoring for Python environment set up and optional setting of Windows LongPathsEnabled registry key using SkylineProcessRunner with elevated privilege. Gives the user notice about LongPath…

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• Merge branch 'master' of github.com:ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support

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• Code inspection correction.

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• Refactor move InstallPythonVirtualEnvironment function from PythonInstaller to BuildLibraryDlg to address failing test due to: "(Skyline model code must not depend on UI code)"

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• Changes to address TeamCity testing concerns

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• Move function InstallPythonVirtualEnvironment from BuildLibraryDlg to ToolInstallUI

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• Removed extraneous using statements identified by ReSharper

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• Move InstallPythonVirtualEnvironment function to its own class in ToolsUI/PythonInstallerUI.cs

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• Attempt to address System.NullReferenceException reported by TeamCity on this line

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Commits on Jan 5, 2025

• + Improve PythonInstaller

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• Merge branch 'master' of github.com:ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support

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• Address TC code inspection issue:

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Commits on Jan 6, 2025

• Attempt to run PythonInstallerUI in TestFunctional without enabling Windows LongPathsEnabled setting, which requires elevation and unlikely to work in an automated test where this is not available.

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• Correct problem with Python installation for future Carafe BuildLibraryDlg functionality. Disable failing TestFunctional tests until python installation failures on TC test nodes can be resolved.

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• Undo last change to TestFunctional.csproj

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• Disable failing TestFunctional tests for now.

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• Merge branch 'master' into Skyline/work/20240403_PeakTotalIonCurrentArea

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• Merge branch 'master' into Skyline/work/20240816_pythoninstaller_with_virtual_env_support

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Commits on Jan 7, 2025

• Improve Error messages.

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Commits on Jan 8, 2025

• Remove unnecessary using statements found by ReSharper

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• Merge branch 'master' of github.com:ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support

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• Merge branch 'Skyline/work/20240816_pythoninstaller_with_virtual_env_support' of github.com:ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support

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• Additional messages to help to the log

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• Merge branch 'master' into Skyline/work/20240403_PeakTotalIonCurrentArea

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Commits on Jan 9, 2025

• fix TestResultFileMetaData

  

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• Merge branch 'master' of github.com:ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support

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• Changes to address issue with spaces in filenames discovered by running tests locally with TestRunner. Clarify function name that detects elevation level of the running process (as opposed to the u…

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• TEST CODE: this is to be reverted after the test!!! Code to catch the AWS test node in the act of failing to install/configure python.

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• Merge remote-tracking branch 'remotes/origin/master' into Skyline/work/20240403_PeakTotalIonCurrentArea

  

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• Fix TestIgnoreSimScans

  

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• Remove bogus "PauseTest()"

  

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Commits on Jan 10, 2025

• Merge branch 'master' of github.com:ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support

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• Fix MS tutorial test

  

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• Remove unnecessary code in the test

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• Merge branch 'master' of github.com:ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support

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• Fix LC Peak Analyte Ion Count

  

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• Merge remote-tracking branch 'remotes/origin/master' into Skyline/work/20240403_PeakTotalIonCurrentArea

  

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• Merge branch 'Skyline/work/20240403_PeakTotalIonCurrentArea' of github.com:ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support

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Commits on Jan 13, 2025

• Apply button for Customized Reports. Need some help saving TreeState so expanded paths don't collapse after each click on Apply.

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Commits on Jan 14, 2025

• Clarify error message and direct user/developer to wiki page which explains how to set EnableLongPaths. Also set this for testing purposes in SkylineNightly after buddy review suggestion.

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• Improve comments for developers and messages displayed to users. Simplify user directed messages and options. Clean up directories used for virtual environments and python installs upon failure. Do…

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Commits on Jan 17, 2025

• Improved validation of python tasks using hash signatures. Move clean up of python installation functions to PythonInstaller. Prevent crash if trying to build library from an empty document.

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• Merge branch 'master' of github.com:ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support

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• Merge branch 'Skyline/work/20240816_pythoninstaller_with_virtual_env_support' of github.com:ProteoWizard/pwiz into 20250113_Carafe_CUDA_Apply

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Commits on Jan 18, 2025

• Disable cuda in this branch.

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• Merge branch 'master' of github.com:ProteoWizard/pwiz into 20250113_Carafe_CUDA_Apply

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• GPU support for NVIDIA cards. Improve flexibility and validation of Python install for AlphapeptDeep and Carafe. Run python installation with terminal closed.

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Commits on Jan 22, 2025

• Switch for device gpu in Alphapeptdeep. Minor corrections.

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• Merge branch 'master' of github.com:ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support

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• Improve messages, improve Python install user experience, download and install Cuda/CuDNN when NVIDIA hardware, upgrade to Python 3.9.13, run AlphapeptDeep on GPU.

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• Test should only wait for Cuda related elevation permissions message when Nvidia GPU is detected

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• Emulate what is possible in the UI better as suggested by Brian Pratt

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• If Nvidia card is not detected don't add Cuda/CuDNN tasks to the process.

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• 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

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• Merge changes

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• Make names more consistent to match the original AlphaPeptDeep publication

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• Merge branch 'Skyline/work/20240816_pythoninstaller_with_virtual_env_support' of github.com:ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support

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• Test using retries to read a file that might be used by another process.

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• Refactor and improve code in the process of fixing problem discovered during testing. Also changes to the PythonTestUtil related to order of Message Dialogs presented during Python Install and Nvid…

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• Address some issue with failing tests.

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• Merge branch 'master' of github.com:ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support

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• Decrement expected number of failures 'Skyline model code must not depend on UI code'

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Commits on Jan 28, 2025

• Implement changes to TestAlphaPeptDeepBuildLibrary and related fixes to PythonInstaller revealed by BPratt's buddy testing

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• Merge branch 'master' of github.com:ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support

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Commits on Jan 29, 2025

• Merge branch 'master' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support and address

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• Implement suggested changes

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Commits on Jan 31, 2025

• Changes in response to bpratt comments on PR3123

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• Implement suggestion from bpratt to improve user experience: output from running AlphaPeptDeep will be logged to the Immediate Window

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• Merge branch 'master' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support

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Commits on Feb 4, 2025

• Incorporate bpratt's suggested changes.

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• Merge branch 'master' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support

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Commits on Feb 5, 2025

• Clean-up some code cruft. Allow SkylineProcessRunner to Kill a process when "Cancel" is pressed. Update to Python installer to improve user experience.

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• cruft

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• Merge branch 'master' of github.com:ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support

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Commits on Feb 6, 2025

• Make cancellations easier by preventing blocking on reader.ReadLine in SkylineProcessRunner. Refactor PythonInstallerUI a to improve readability. ProcessRunner will not report message to the dialog…

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• Implement Brian's suggestions to improve user experience.

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• Output Alphapeptdeep result in timestamped directories to prevent collision or files between runs. Implement longValidate options for PythonInstaller to enable thorough validation including hash co…

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• Add check of Python installation to the test after Python is installed and configured to verify that this was done properly by the test.

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• Add a function in PythonInstaller to delete Tools/Python and call it in AlphapeptdeepBuildLibraryTest that cleans the slate for a more thorough test.

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Commits on Feb 7, 2025

• Switch to standard SafeDeleteLongPath for consistency.

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• Testing branch for using CancellationToken to cancel and removing second thread in SkylineProcessRunner for Nick

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Commits on Feb 8, 2025

• Make the LongWaitDlg cancel button work responsively using CancellationToken with Nick's help.

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Commits on Feb 9, 2025

• Improve the library building organization with timestamps. Create library builders only when needed for building (not for verifying.) This to allows testing library build products by hashes, which …

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• Merge branch 'master' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support

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Commits on Feb 10, 2025

• Test with and without iRT, summary comments.

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Commits on Feb 11, 2025

• Merge branch 'Skyline/work/20250207_TestingCancellationTokens' of https://github.com/ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support

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