Updated mzMLb to current pwiz #4
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* removed Console.WriteLine left in Koina code by mistake * fixed GrpcChannel leak (but not unmanaged code leak, still tracking that down)
Change BullseyeSharp so that instead of being a dependency of Skyline, Skyline just includes the .exe from the bin folder
…fference because it's only called once though) * temporarily removed cancelability testing from EncyclopeDiaSearchTest because it may be leading to non-deterministic results
Skyline: Implement --import-pep-list command-line argument - Added --import-pep-list command-line argument (requested by Dan)
Changed to exclude reporter ions when calculating library dot products and detecting peaks (requested by Philip)
* made TestEncyclopeDiaSearch tolerance of 1/1/1/4 difference in document counts until problem with repeating EncyclopeDIA results can be resolved * added code-only option for outputting log files for parallel EncyclopeDIA jobs --------- Co-authored-by: Nicholas Shulman <[email protected]>
Fix incorrect code in Skyline.Designer.cs which broke design view in Visual Studio Fixed rare unhandled error displaying chromatograms (reported a few times anonymously on exception web)
(Hardklor.exe had already been added with the main feature finding commit) Also, remove "hardklor_logo.png" from set of files that Skyline ships with since it is just supposed to be a resource.
- now works more like the UI finding pre-defined mods and using Unimod - fixed --pep-add-mod to add to Settings.Default and default to variable mods - added operator+ to Argument to make using for name-value pairs easier in tests
* fixed leak with EncyclopeDIA MultiProgressControl
This should prevent the cascade of test failures beginning with "TestLibraryBuild" that happened last night.
… not having access to root certificates needed; at some point I will fix this by exporting those root certs on the host, copying them to the runner, and having Skyline read them from a file
Fixed graphs are sometimes blank when displaying more than 100 precursors at the same time (reported by Q)
* changed temp directory logic for EncyclopeDIA in an attempt to fix nightly failures (I have not been able to reproduce, but I suspect the failure to find sqlite files is due to some collision in temp directories when multiple ED processes run at the same time) * changed ProcessRunner.SetTmpDirForCleanup to use ProcessStartInfo's TMP variable if set
* added M+16 to test peptide
* added SkipTestUntil for UniquePeptides perf tests (until 5-29-24)
The following line no longer appears in the audit logs. Removed suffix = ".mzML" Import Peptide Search wizard no longer includes the filename extension as part of the suggested replicate name as a result of part of the feature finding commit on May 6th. In "ShowRemovePrefixDialog" it was changed to use "Path.GetFileNameWithoutExtension".
Fixed unhandled error if network failure at the end of chromatogram extraction (reported on exception web)
…ta with plain integer scan numbers in the spectrumNativeID attribute (reported by Saicharan)
…r non-columnar files such as audit logs (#2985) Internal test issue only.
…ecking the RunPerfTests flag (#2986) internal test issue only
…2983) * Skyline: Implement --pep-add-mod-variable=<true|false> for FragPipe - Also made StaticMod class IValidating which got tricky - some old sloppiness creating invalid mods - Also made LabelAtoms cache masses when only for one AA - Includes improved documentation of "Dot Product" columns in reports
…etes (#2989) Bug fix in PanoramaClient - if there is an error during asynchronous file upload, trying to access the Result property on UploadFileCompletedEventArgs throws an exception. Check the Error and Cancelled properties first to determine if the upload request completed correctly.
Make BackgroundScanProvider communicate with GraphFullScan through BeginInvoke instead of Invoke to avoid the case where GraphFullScan tries to Join the background thread just as it is trying to Invoke to the UI thread.
* Skyline: Various fixes and improvements for tutorial screenshots - Fixed layout in ViewEditor for Japanese and Chinese - Fixed to VolcanoPlotFormattingDlg for failure in IsPauseForScreenShots mode - Removed screenshotlist argument from TestRunner and SkylineTester - Fixed issue with auto-screenshot mode not saving to non-existent language folders - Fixed ScreenshotPreviewForm startup placement in auto-size mode on 2nd monitor - Added console output for each screenshot - Cleaned up unnecessary Thread.Sleep() code in ScreenshotPreviewForm - Cleaned up a bit inside ScreenshotManager and add code to ForceOnScreen() the frame to be screenshot - Added keyboard commands (Ctrl-C and Ctrl-Shift-C) to copy new and old bitmaps respectively. - Removed Thread.Sleep() in auto-screenshot mode for more testing - Improved commenting in several places
…torialTest (#3251) * Skyline: First drafts of AuditLogTutorialTest and SmallMolLibrariesTutorialTest - Moved ScreenshotManager instantiation to where SkylineWindow is not null - Added support for showing Undo and Redo dropdowns - Improved and centralized support for showing Reports dropdown - Removed left over ZIP files from .csproj files - Improved and centralized code to keep screenshot forms on screen
…sitory dirty (#3240) * added check in tcbuild.bat that clean script does not make the repository dirty * fixed removing WIFF auxiliary files for Unicode testing * changed timstof_prm_scheduler.prmsqlite to be written to test directory instead of repo root * updated .gitignore for SearchControlLog.txt and UserSettings.data (from WIFF2 SDK) * added error message immediately after clean script for dirty repo * added Thermo/x64 subdir to .gitignore * added CleanBumbershoot.bat * added src_subset to .gitignore (automatically cleaning it when the build is successful would be an alternative, but then if the build fails, it would be dirty for subsequent builds of different configs) * added files to .gitignore either created by TeamCity or by older versions of the code (e.g. without the fixes to delete WIFF auxiliary files for Unicode testing)
- Wait for calculator regression to appear in the UI before adding a second regression from the functional test thread
…ple/binaries location to gitignore * added artifact_xml directory to gitignore and changed TeamCity artifact upload script to create artifact XMLs in that directory (I considered using an out-of-repo location but that would require the Windows path separators to be escaped in the Python script)
* Switch peak area screenshot from graph to graph form. * Set specific location for peak area graph and results grid view. Make results grid form available to tests. * Set data grid column widths for Screenshot #20 that accommodate EN, ZH, JP with 2 line column titles and 8 visible columns. Widened floating pane a bit to comfortably accommodate single set of widths. * Screenshot 20: Use RunUIForScreenshot to avoid resizing table during normal test runs * Screenshot 22: position floating windows relative to Skyline's bottom-right corner * Update data grid column widths in screenshot #17 to support localization in EN, ZH, JP. Refactor floating window size and column widths to share them with other screenshots.
…raryImportAsSmallMolecules (#3259) Also adds WaitForMultiButtonMsgDlg(string messageFormat, int millis = WAIT_TIME) to wait for a MultiButtonMsgDlg to be shown with a message that could have been created with the given messageFormat Internal test issue, not reported by any user
…cesswide lock in the ctor to ensure only one thread is in use at a time (#3253) For the record, this is a design call made by MattC and myself, in anticipation of Mobilion resolving the issue eventually. Not worth the effort to build a "not suitable for parallel use" sense into the UI of either application. Looks a bit funny when parallel processing multiple .mbi files in Skyline and MSConvertGUI, as only one proceeds at a time, but it does complete. Matt notes: "Eventually I should add an IterationListener parameter for Reader::read() so the user can be informed why it's paused. Could be useful for other readers as well if/when the fillInMetadata() function is a little slower than we'd like. Skyline isn't set up to listen and report those messages, but MSConvertGUI is." Co-authored-by: Matt Chambers <[email protected]>
…3256) * Skyline: First draft of TestDdaTutorial and TestPeakPickingTutorial for auto-screenshots - fixed a gap in file locking testing that cause TestDdaTutorial to fail with a strange message
* Checkpoint PRM Tutorial progress * Automate screenshot #20 which was manually created. * Add a new .zip file containing .sky/d files with data used to generate screenshot #20's 5-point calibration curve. * Minor fixes in other screenshots explicitly set active replicate and use labels to show dot products
… skipped when being run as small molecules. (#3265) Internal test issue, not reported by any user
Fixed duplicate entries on Calibration Curve legend when first shown (reported by Brendan) The line "this.calibrationGraphControl1.Options" was not supposed to be in CalibrationForm.Designer.cs, and was causing "Settings_OnPropertyChanged" to get called in the middle of "Update" which resulted in two sets of curves being added. Also, added "[Browsable(false)]" to a few properties that were not supposed to be seen in the property sheet. And changed a few "[EditorBrowsable(EditorBrowsableState.Never)]" to "[Browsable(false)]" because "EditorBrowsable" was the wrong attribute to be using to hide something from the property sheet. "EditorBrowsable" is use for IntelliSense.
* changed build-nt-x86 rule in .gitignore to work at any path level * disabled problematic section of Ardia functional test (currently test is 100% broken though due to apparent server-side change, still working on it) * disabled Mac GitHub Action build * added -q to CleanBiblioSpec.bat's git clean calls * moved TestConnected testing in Skyline Jamfile.jam from TestFunctional target to its own TestConnected target * added TestOrbiPrmArdia test to TC skiplist * added post-build git status check to ensure no non-ignored files were created * added SkylineWithTestConnected target to vcs_trigger_and_paths_config.py - updated msconvert-help.txt * added Bruker manifests to .gitignore * made install_pwiz_vendor_api_bruker_stub explicit target - fixed option description for BlibFilter -b (closes #3263)
* fixed code inspection (hidden because the new TestConnected config used an overridden string for its GitHub status report feature instead of the default based on the build config name)
* Skyline: Cleanup persistent folder before and after test runs - Helps avoid the case where a prior failure causes an echo failure in the next run because cleanup deletes left over files in the persistent folder
…er_Shimadzu_Test files do not have it, but I have manually tested on DIA files that do
- Fix Skyline icon displaying on control-box forms - Always WaitForGraphs it taking a screenshot in PauseForScreenShot
… BUILD This commit DOES NOT BUILD. Separate GIT commit so rename of files works. Rename Form OpenDataSourceDialog to BaseFileDialogNE. Following commits will add new subclasses OpenFileDialogNE and OpenDataSourceDialog
As part of previous commit and this commit: Rename OpenDataSourceDialog to BaseFileDialogNE Add new empty classes OpenFileDialogNE and OpenDataSourceDialog New inheritance path: BaseFileDialogNE > OpenFileDialogNE > OpenDataSourceDialog Move Open() method to class OpenFileDialogNE
Note in particular the new "UsageOfDefaultStructEquality" warning has been reduced to a suggestion - it wants equality members for structs, because the ones generated automatically are probably inefficient. Worth thinking about when looking at performance issues but not worth a general change to many dozens of files.
…hread, as detected in a debug build. (#3276) Fix a handful of tests which were accessing UI elements on the test thread, as detected in a debug build. Note in particular the new convenience function in TestUtil.AbtractFunctionalTest /// <summary> /// Convenience function for getting a value on the UI thread /// e.g. var value = CallUI(() => control.Value); /// </summary> public T CallUI<T>([InstantHandle] Func<T> func)
Fixed scrollbar thumb position after pasting into Document Grid (reported by Brendan)
* Skyline: Improvements to tutorial screenshots based on testing - Created ScreenshotProcessingExtensions to hold bitmap processing functions - Added diff coloring to the old image in ScreenshotPreviewForm - Added labels and a picture-box to ScreenshotPreviewForm for improved diffing - Improved code to decide when to use the skyline icon as Form.Icon - New DigitalRune.Windows.Docking.dll with better LArrow cursor - Hid Source tab in DocumentGridViewContext for screenshots in debug builds - Initial attempt to freeze the AllChromatogramsGraph for a screenshot - Added function to ImportFastaControl to scroll FASTA file path text to show the file - Hid the GPF checkbox in ImportResultsDIAControl in screenshot mode for 24.1 screenshots - Better normalization of language names in SkylineTester and TestRunner - Show context menu selection in s-09 for TestHiResMetabolomicsTutorial - Fixed SkylineTester issue with test selection when "Tutorials" starts selected - Fixed column widths in library build tab in DIA/SWATH tutorial for screenshot - Fixed forcing SkylineWindow on screen in DIA/SWATH tutorial during docking screenshots before docking starts - Fixed waits in auto-screenshot mode to avoid blurry screenshots - Fixed a number issues with border calculations between normal Windows forms, floating dockable forms, and docked dockable forms in Document and non-Document states. - Fixed screenshot numbers in URLs to match the what is currently in https://skyline.ms/tutorials/24-1/ - Fixed some necessary border clean-up in cases where image processing is implemented
per https://skyline.ms/announcements/home/support/thread.view?rowId=40366 it appears that the MassLynx reader DLL throws an exception when it encounters an empty chromatogram (or "channel", in API-speak). With this change we catch and ignore the exception, with the assumption that if there's an actual problem then attempts to get channel name etc with throw too, and we'll let that one pass through. reported by user Warham
While chasing down memory issues, I noticed that there seemed to be some proximity to tests that involved asking for lockmass correction on data that isn't actual Waters raw. I'm not 100%% convinced that this is the issue, but it does seem just as well to simplify this code so that the data processing chain is left completely untouched when spurious requests are made. If nothing else it makes for a more accurate set of CVParams. not reported by any user
#3287) * Skyline: More improvements towards auto-screenshots for 24.1 tutorials - annotate image in DriftTimePredictorTutorialTest - added new helpers to ScreenshotProcessingExtensions to support text, arrows, and brackets - restore shorter SkylineWindow in HiResMetabolomicsTutorial
…e it's actually the remote API causing the unreliability)
* Skyline: More tutorial screenshot improvements - added the ability to us the Git HEAD PNG file as the old image - added rectangle annotation to ScreenshotProcessingExtensions - made ANNOTATION_COLOR public and used as the default for grid highlight annotations - tweaks to annotation and scaling in TestLibraryExplorerTutorial and TestMs1Tutorial - implemented MultiFormActivator for Skyline and the ScreenshotPreviewForm
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