Alphapeptdeep Integration #3123
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pwiz_tools/Skyline/packages.config
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| <?xml version="1.0" encoding="utf-8"?> | |||
| <packages> | |||
| <package id="OneOf" version="3.0.271" targetFramework="net472" /> | |||
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This works on my development machine, but the build on TeamCity seems to be failing because it does not see this dll.
So far we have been adding all of the dll's that we need to:
pwiz_tools/Shared/lib
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For modern Nuget we use PackageReference, like this for Ardia in the Skyline.csproj file:
<ItemGroup>
<PackageReference Include="Microsoft.Web.WebView2">
<Version>1.0.2420.47</Version>
</PackageReference>
</ItemGroup>
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Sounds good. Thanks for the suggestion here. I've updated OneOf to use PackageReference. It works locally. Let's see if the teamcity test can pass now
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Everything builds fine on TeamCity, but now it looks like "OneOf.dll" is not getting copied to where it needs to go.
The test "CheckForMissingResources" is failing to load "Skyline-daily.exe":
System.IO.FileNotFoundException: Could not load file or assembly 'OneOf, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null' or one of its dependencies. The system cannot find the file specified.
File name: 'OneOf, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null'
Does anyone know how to fix something like this?
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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
…rk/20240909_carafe_integration
…thub.com/ProteoWizard/pwiz into Skyline/work/20240909_carafe_integration
…yline/work/20240909_carafe_integration
- Install python modules of specific versions used by carafe - Make name of variable for storing modifications plural
…ng unsupported modifications by AlphapeptDeep or Carafe
…yline/work/20240909_carafe_integration
…installer_with_virtual_env_support branch
…rk/20240816_pythoninstaller_with_virtual_env_support
…f Windows LongPathsEnabled registry key using SkylineProcessRunner with elevated privilege. Gives the user notice about LongPathsEnabled and attempts set up without LongPathsEnabled if user clicks 'Cancel' Verified that LongPathsEnabled is now set as expected when user clicks 'OK.' Python installation tasks list prerequisite changes to prevent pip packages re-installation if the only task is setting 'LongPathsEnabled.' Preparation for a functional PythonInstallerTest, still to be implemented.
…rk/20240816_pythoninstaller_with_virtual_env_support
…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
PythonInstallertoPythonInstallerLegacyDlgPythonInstallerimplementation to support Python virtual environmentPythonInstallerimplementation