Alphapeptdeep Integration #3123
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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
…to .blib and import into skyline
…taller to BuildLibraryDlg to address failing test due to: "(Skyline model code must not depend on UI code)"
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Let’s review this change carefully. The code certainly looks poorly designed for inclusion in the Model space. You can’t bring up a form inside Model. On the other hand a function to install a virtual environment in Python seems better placed in a PythonInstaller class than the BuildLibraryDlg… or in necessary, PythonInstalllerUI out in the UI space.
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I moved the InstallPythonVirtualEnvironment function to ToolInstallUI, which is more appropriate than either Model space or BuildLibraryDlg. |
…lsUI/PythonInstallerUI.cs
+ disable Carafe BuildLibraryDlg user-facing option for now + add test to exercising BuildLibraryDlg with AlphapeptDeep + add test for future exercising of BuildLibraryDlg with Carafe
…rk/20240816_pythoninstaller_with_virtual_env_support
"Assert.Fail failed. 1 code inspection failures found:
Found prohibited use of
"using.*(pwiz\.Skyline\.(Alerts|Controls|.*UI)|System\.Windows\.Forms|pwiz\.Common\.GUI)"
(Skyline model code must not depend on UI code) at
Z:\pwiz\pwiz_tools\Skyline\Model\Tools\PythonInstaller.cs(14)
using pwiz.Skyline.Alerts;"
…indows LongPathsEnabled setting, which requires elevation and unlikely to work in an automated test where this is not available.
…ryDlg functionality. Disable failing TestFunctional tests until python installation failures on TC test nodes can be resolved.
…_virtual_env_support
Centralize InstallPython test routine in PythonTesUtil class. Check if running as Administrator in InstallPython and throw error if not Administrator and need to set LongPathsEnabled. Initial stubs for future Nvidia GPU support via Cuda Library.
…rk/20240816_pythoninstaller_with_virtual_env_support
…support' of github.com:ProteoWizard/pwiz into Skyline/work/20240816_pythoninstaller_with_virtual_env_support
…rk/20240816_pythoninstaller_with_virtual_env_support
…ng tests locally with TestRunner. Clarify function name that detects elevation level of the running process (as opposed to the user being admin.) Add functionality that undoes changes to the registry done by python installation as part of a test.
… AWS test node in the act of failing to install/configure python.
…rk/20240816_pythoninstaller_with_virtual_env_support
…rk/20240816_pythoninstaller_with_virtual_env_support
…plains how to set EnableLongPaths. Also set this for testing purposes in SkylineNightly after buddy review suggestion.
…rk/20240816_pythoninstaller_with_virtual_env_support
…lify user directed messages and options. Clean up directories used for virtual environments and python installs upon failure. Do not continue further tasks for python installation on Cancel.
PythonInstallertoPythonInstallerLegacyDlgPythonInstallerimplementation to support Python virtual environmentPythonInstallerimplementation