Updated mzMLb to current pwiz #4
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* Stellar method export implementation * Stellar isolation list exporter isolated into a separate class. * Tests for isolation list export added.
Fixed blank message box when no FASTA file for import EncyclopeDIA search (not reported by anyone, introduced with Koina refactor) Also remove a few unused strings from Resources.resx which did not exist in Resources.designer.cs Add "ResourcesTest" which verifies that none of the .Designer.cs files have any missing resources.
Fixed error adding decoys to a document with high resolution MS1 and sulfur containing amino acids (reported on exception web)
Thermo Stellar method export code review for PR 2954. Adding missing xml schema file.
* Make UI changes to add new Search menu and split Import > Peptide Search into two menu items * Remove input file type dropdown list and fix its producer logic and rewire its consumers to use new logic
"Settings.Designer.cs" had been manually edited and "Settings.settings" was not up to date with the Prosit -> Koina rename.
Auto Layout Labels in group comparison volcano and peak areas relative abundance plots Co-authored-by: Brendan MacLean <[email protected]> Co-authored-by: RitaCh <[email protected]> Co-authored-by: Nicholas Shulman <[email protected]>
Fixed the negative RT export for all Agilent instruments
…e 243) (#2708) * Implemented tooltips for the replicated peak area comparison plot
…3011) Co-authored-by: brendanx67 <[email protected]>
When the document has mixed polarity, csv files get created with names ending in "_negative_0001.csv" and "_positive_0001.csv" so those files need to be verified instead.
* added dotCover support to parallel testing mode (coverage=on/off and dotcoverexe path relative to pwiz root) * changed host worker to run as a child process instead of an extra thread in the main TestRunner process * changed ReportExceptionForRetry() to not do a delay on the first retry * added TestRunner checkdocker parameter to allow skipping the check that the current always_up_runner image can actually be run * added coverage checkbox to SkylineTester * added default value for dotcoverexe (should work if you extract the zip file attached to the PR to the pwiz root directory) * tweaked worker count adjustment when not enough parallelizable tests * cleaned up program exit logic when cancellation is requested
…some transitions are truncated (#3009) Changed so values such as "Normalized Area", "Calculated Concentration" still have a value even when some peaks are missing or truncated. Warning messages are displayed in Document Grid. Old behavior is available with "Normalized Area Strict" sub-property in Document Grid (requested by Mike and others)
Changed to remember peak area relative abundance formatting settings in the Skyline document. Changed protein abundance value on relative abundance plot to be sum of transitions instead of average (requested by Mike)
…f(unknownInstrumentIsError) throw; else print warning" logic (#3023) - made failures reading WIFF metadata optionally fatal (depending on ignoreUnknownInstrumentError setting) - fixed ignoreUnknownInstrumentError default value to be false - fixed reading CE from WIFF file spectra - added fallback handling for when calling centroiding or framing zeros on WIFF2 spectra throws exceptions but the profile/unframed spectra are available
* fixed Reader_Bruker_TSF not being included in FullReaderList (so its supported file extensions did not get enumerated by SeeMS and MSConvertGUI)
…ageComparer (#3303) Skyline: Some last improvements to the SkylinePreviewForm based on ImageComparer - implement git revert function - make ImageSource.disk show the modified state of the file on disk - avoid drawing curved borders on PopupPickLists in Windows 11 - fixed race condition in RemoveAnnotationTest
The first time the Statement Completion Form came up during TestMethodEditTutorial, its height would incorrectly be too large.
Fixed so that log scale can be used with "Ratio to Standard" normalization methods on Peak Area Replicate Comparison bar graph.
Fixed unhandled error on Edit Linked Peptides dialog (reported by Caroline)
- Hide blinking caret in ComboBoxes with an edit control - Hide RTF control in ScreenshotPreviewForm and ImageComparerWindow as soon as it is not appropriate - Fixed FullScanSettingsControl radio button layout from bug introduced with feature finding - Fixed GroupedStudies1TutorialTest to not maximize the SkylineWindow which produces a monitor dependent screenshot - Fixed GroupedStudies1TutorialTest to reliably AutoResize the FoldChangeResult column - Tweaked MethodRefinementTutorialTest with FocusDocument and some sizing fixes - Tweaked Ms1FullScanFilteringTutorial with FocusDocument and JiggleSelection - Fixed MultiFormActivator to check for IsHandleCreated before Handle which can cause HWND creation, and clear MultiFormActivator before restarting a test. - Connected Revert toolstrip button in ScreenshotPreviewForm to its event handler - Tweaked ScreenshotProcessingExtensions.CleanupBorder to use lighter gray for interior borders of docked DockableForms - Fixed AbstractFunctionalTest to only change a window icon when it has Resources.Skyline but that does not match SkylineWindow.Icon.
- Made several MS1 graph screenshots slightly wider in Japanese - Fixed detection of modified files in Git for new output format - Fixed ImageComparerWindow behavior when no modified files are found
… to better match existing screenshots (#3309)
- Fixed ability to use a screenshot of an error message in AllChromatogramsGraph (TargetedMsmsTutorialTest) - Added short-circuit for auto-screenshot mode in non-en languages to untranslated tutorials - Final tweaks to LibraryExplorerTutorialTest for auto-screenshot update
…taken (Draft 1) (#3311)
Introduce a new library for using P/Invoke. This makes Skyline's use of Win32 APIs more transparent and reduces code duplication. APIs for production code are in CommonUtil under namespace pwiz.Common.SystemUtil.PInvoke. Test-only use of P/Invoke goes in TestRunnerLib under namespace TestRunnerLib.PInvoke. New code inspections check for P/Invoke use outside these locations (with limited exceptions). New or modified uses of P/Invoke should follow conventions described in PInvokecommon and go in the correct namespace. Also update the expected values used during code inspection to check the size and shape of the P/Invoke APIs in CodeInspectionTest. New project dependencies: * Test depends on TestRunnerLib * TestFunctional depends on TestRunnerLib * TestRunnerLib depends on System.Windows.Forms
- Fixed ScreenshotInfo Regex to recognize all tutorial folders - Improved BaseFileDialogNE Look in field to hopefully be consistent and better laid out - Fixed DiaUmpireTutorialTest to scroll FASTA paths to the end and other fixes - Added suffixes to tests ending in Tutorial that were not associated with folders in Documentation/Tutorials
…shots (#3316) - Fixed MultiFormActivator for ScreenshotPreviewForm
…ition Settings > Full Scan dialog (#3313)
…f tutorials (#3315) * Skyline: Update Perf tutorial screenshots to current auto-screenshot taken - update all previously updated tutorials for: - docking larrow cursor - combo box caret - peptide search full-scan settings layout * - update screenshots for IMSFiltering to auto-screenshot taken * - update screenshots for SmallMoleculeIMSLibraries tutorial to auto-screenshot taken * - update screenshots for DIA-Umpire-TTOF tutorial to auto-screenshot taken * - update screenshots for TestAuditLogTutorial to fixed auto-screenshot * - update Import Results Files form screenshots with fixes * - update screenshots for OpenDataSourceDialog in Perf tutorial tests * - update MethodEdit statement completion screenshot * - update PeptideSettingsUI.QuantificationTab screenshots to 24.1
- Add a Paste function to the Image Comparer to simplify pasting screenshots from a 24.1 build to current master
…de isn't included in coverage stats - it's only the code that's being tested that we're concerned about (#3317) Note that TeamCity has its own exclusion list, I've updated that too but this is necessary for local use.
- Added test mode that very quickly checks audit logs are named correctly
* Skyline: Fixes for consistent screenshots on Windows 11 - Fixed ColorDepth on ImageLists to match the files they include. - Fixed CleanupBorder to set corner radius to zero for interior docked DockableForms. - More CleanupBorder fixes for Windows 11
* Skyline: Refactor to remove references to pausing at page numbers in tutorials - with the move to HTML we no longer track page numbers the way we did for Word docs and PDFs
… color ImageList.ColorDepth
* Skyline: More fixes for screenshot consistency - Add back annotation screenshot in TestGroupedStudies1Tutorial removed with page number refactoring - Reduce the size of the maximized Skyline window in TestGroupedStudies1Tutorial to work for both Windows 10 and 11 * - switch back to constant size for "maximized" window, but one that works for all test screens - Fix Regex for screenshot naming in ImageComparer/ScreenshotInfo.cs
… property sheet in "ViewMenu" form. (#3322) Prevent properties like "SelectedResultsIndex" from showing up in the property sheet in "ViewMenu" form. In the form designer for classes that are derived from "SkylineControl", such as "ViewMenu" or "EditMenu", some properties from the base class were showing up in the property sheet.
…3325) * Skyline: Fix tutorial screenshots related to dotp annotation changes - Remove code in TestExistingExperimentsTutorial to hide the rdotp line in Peak Areas graphs - Add an instruction to DIA and PRM tutorials to switch from dotp line to labels
Fix a naming issue in DwmapiTest that caused EntryPointNotFound exceptions and broke screenshots in SkylineTester's Quality tab. (#3326)
… renamed (TODO: refactor TestRunner's test listing feature to avoid this potential source of error; e.g. skip ones with NoNightlyTesting attribute, or perhaps a new one like NoCITesting which would be more aggressive than NoNightly)
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