SmartPeak Changelog¶
v1.6.0 (2020-05-25)¶
Features¶
Display progress information (#367)
Ability to export Sequence (#368)
Advanced explorer views part 2 (#344)
Adding search functionality to ParametersTable
Sorting functionalities for ParametersTable
Plot-Stepper for chromatograms and feature line plots
Plot/Unplot All
App wide tooltip info
Adding quick help for various UI elements
v1.4.0 (2020-04-26)¶
Features¶
Changes¶
Feat/aut722 Rework for a more modular GUI (#355)
Moved Run Workflow window in its own widget
Moved About dialog box in its own widget
Moved Log into its own widget
Added visible_ flag in Widget
Moved SetWindowsize in Widget
Made CalibratorsPlotWidget and LinePlot2DWidgets retainable.
Report: removed draw_ and use Widget’s visible_ instead
RunworkflowWidget is resizable
v1.3.0 (2020-04-09)¶
Features¶
Advanced Explorer Views 1 (#324)
Advanced Explorer Views - adding sorting functionality and viewing of File Name
Updated about popup [skip ci]
Adding searching functionality
Sorting and searching for injection/transition/feature tables
Selective searching for tables with dropdown menu
Disallow sorting for all-checked/all-unchecked columns
Sorting and searching for various tables in main window
Final enhancements to FilePicker, ExplorerTables and MainTables
Preventing filenames from being appended twice when opening via button click
Adding reusable table functions for searching/sorting
Adding unittest for Widget
Make parameters editable (#337)
Enhancing FilePicker entries to be displayed in human readable format (#339)
Added Statistics and more informations in the info panel (#341)
Added SmartPeak documentation
Adding working examples for calculating MDVs (#326)
Fix¶
Fix formatting of changelog for emails and github releases (#340)
Fixed crash when launching workflow with no injection (#332)
Fixed Windows SmartPeak install: executable is not available from start menu (#338)
Add cmake nsis configuration for creating application links
Add icon to executable on windows
Update cmake nsis config to include icon to installer and launch the application when installation complete
Configure default CPACK_GENERATOR for windows
v1.2.0 (2020-03-15)¶
Features¶
Provide smartpeak tool python package for continuous integration. (#324)
Peak picking for MS2 RawDataProcessor method. (#315)
Include/Pass version tag to SmartPeak code. (#320)
Add Utilities::getSmartPeakVersion() static method.
Include version information in gui and logs.
Description of the workflow steps displayed to the user. (#321)
Description of the workflow steps displayed to the user.
Disabled edition when workflow is running. Update application handler in main thread when workflow finished to run.
Add getID, getName and getDescription to SequenceProcessor (#304)
Ability to save and load previous workflows. (#307)
Move commands to SequenceHandlers, remove the workflow modal dialog. Save/Load in menu.
Remove unused format check.
Improve error handling, avoid supplicate creations of commands.
Use BuildCommandsFromNames, fixed const signed parameter.
Implementation of SpectraPlotWidget, split Widgets in their own files.
SmartPeak support for isotopic labeling experiments. (#283)
Fix single entries not shown w/ file Picker.
Parse isotopic_purity_values from a dedicated field.
Add param for CalculateMDVAccuracies.
Finalise SmartPeak support for isotopic labeling experiments.
Update TRAML file with SumFormula.
Update RawDataProcessor with modified OpenMS::IsotopeLabelingMDVs.
Advanced plotting. (#298)
Fix Sliders. Disable/Enable legend. Lines and scatter use same colors.
More stability to display while running workflow.
Sliders along with legend checkbox are now part of the chromatogram widget.
Add compact view.
Allow for resizing the GUI bottom, left and upper panes. (#297)
Signing SmartPeak with DTU-issued certificate. (#296)
Add exporter to GUI and remove previously generated sequences in examples data. (#288)
Add Xcalibur writer to sequence parser.
Add new application processor for XCalibur.
Add makeSequenceFileMasshunter. (#287)
Fix bug in directory and add to the gui export menu.
Add method for making and writing an analyst sequence file along with tests. (#285)
Add exporter to the GUI.
Change member naming convention in SequenceProcessor classes.
Change filenames to use an explicit param for the mzML filename using the filename member of the raw data metadata.
Change sequenceParser to insert the injection name if no original filename value is provided.
Update to SequenceParser to reflect change in filenaming semantics for mzML.
Add addition of filename to featureMap when loading the featureMap. (#294)
Changes¶
Switch to ImGui v1.81 Release. (#328)
MergeFeatures (#295)
Refactor SearchAccurateMass into two methods for searching the accurate mass and the other for making the consensus features from the individual adducts.
Change weighted average to sum in MakeConsensusFeatures.
Change FeatureMap creation step of Search accurate mass to make subordinates instead of features for compatibility with downstream quantitation and filtering.
Rename MakeConsensusFeatures to MergeFeatures and updated the FIA-MS default workflow.
Update MergeInjections to set the subordinate even merging at the Feature level.
Migrate all ImGui::columns to ImGui::tables in the GUI. (#286)
Switch to imgui v1.79, Boost to 1.73.
Various adjustments to the current ImGui tables API.
Resolve fatal error: reference is not a tree when checking out ImGui’s specific commit.
ImGui::Tables - removing inner borders in FilePicker.
Update ImGui::Tables API. (#281)
Append missing include for OpenSwathAlgo.
Update GUI to latest ImGui API tables.
Refresh parameters table only when parameters change. (#317)
Refresh parameters table only when user parameters or workflow change
Use notification to update the view.
Move ParametersTableWidget to its own File.
Move observers to sequenceHandlers.
Refactor handling user parameters (#302)
Parameter do not use anymore map/vectors/maps, but ParameterSet, container of FunctionParameter, containers of Parameter.
It’s still possible to initialize with the old structure of map/vector/map.
Parameter can be initialized from an OpenMS Parameter (to create the schema).
Parameter can be assigned to another Parameter, the schema, allowing validation.
Commands return the list of Parameter they need to run (getParameterSchema()), allowing validation when setting up the workflow, not when running it.
Parameter Panel show different colors: user overridden parameters, the default parameters (schema), and the unused (not appearing from the schema).
Parameter Panel colors invalid values in red. Mouse over it shows some indication: constraint, expected Type.
Fix¶
Fix Chromatogram stops updating after having selected all plots.
Not specifying some user parameters will not prevent processors to run. (#329)
Fix HPLC UV Unknowns preset. (#325)
Log not written when GUI is launched from folder that requires Admin privileges to write to (#301)
Add static method SmartPeak::Utilities::getLogFilepath() for dynamic path to log.
Redirect logging path for GUI.
Handle errors and log message to console.
Fixed chromatogram and spectra range reset when selecting different components. (#314)
File name not shown when selected. (#312)
Displaying selected file name in the designated field & adding double-click-to-open feature.
Add possibility to create new file from FilePicker.
Extra warnings in FIA-MS workflow. (#311)
Prioritize the use of subordinate metadata when choosing between feature level and subordinate level.
Add extra logging to warn the user when the extract_spectra step for FIA-MS fails due to missing the RT that the spectra was acquired.
Fixed Compilation issue with Commands, set LoadRawData parameter constraint to “ChromeleonFile” instead of “Chromeleon”. (#308)
Exception handling in QuantitationMethods. (#306)
Add additional exception to catch misc OpenMS exceptions that interupt the workflow.
Changed racked code to match ideosyncrocy in numbers less than 10.
Replaced sample_name with injection_name in Analyst conversion.
Bug in HPLC data processing (#284)
Artificially scale the chromatograms when loading HPLC data derived from a .txt file.
Small/minor aesthetic fix to tables. (#282)
SequenceSegmentProcess exporters. (#280)
Update Estimation methods to use filter templates as the template.
Bad values copy in EstimateFeaturesRSD.
Add extra debug info to SelectFeatures.
Add sections in Filename for new store/load pairs in sequenceSegmentProcessor.
Add new store/load pairs to sequenceSegmentProcessor for estimations of RSDs and Background.
Update SharedProcessors with new sequenceSegmentProcessor store/load pairs.
Bad GC-MS full scan workflow presets.
Add views for filter and qc tables to the SessionHandler.
Other¶
Refactor initialization of shared pointers.
Set FeatureMetadataSize dynamically.
Update SessionHandler_test for the new entries in metadataToString and metadataToString.
Update metadataToString and metadataToString with average_accuracy & absolute_difference.
v1.1a (2020-08-30)¶
Features¶
Add support for computing more accurate peak area metrics that will be used for downstream analysis and filtering in FIA-MS to pickms1features.
Add consensus calculations to SearchAccurateMass.
Add support for sample group handler in add sample to sequence.
Add SampleGroupProcessor.
Add MergeInjections with test for the case of subordinates.
Add option to record the convex hull during PickMS1Features.
Add hull points and best left/right widths to PickMS1Features.
Add support for spectra explorer.
Support for plotting spectra and additional support for defining the ranges of chromatograms and spectra as well as plotting features wtihout raw data and vice versa.
Example data and preliminary code for FIA-MS workflow.
Add documentation for ReadtheDocs with Sphinx/Doxygen.
Working NSIS setup but it is missing all of the dependency libraries and executables.
Implement SequenceProcessorMultithread.
Top and bottom windows follow host’s window resize.’
Integrate recent changes from AppWindow to GUI: Changes to AppWindow were lost after the AppWindow files removal.
Ask for pathnames before running workflow.
Implement class WorkflowManager: workflow is copied back to the main app.
Clear FilePicker’s filter on entering a directory.
Implement Info tab functionality, related to QuickInfo menu.
Add widget Report to store a csv file with FeatureSummary or SequenceSummary.
Changes¶
Update FIAMS parameters and TraML templates.
Packaging for macOS (dmg), Linux (deb), Windows (exe), CI for macOS and CI for Windows.
Add support for feature level feature table and matrix reporting along with optimization of feature table and feature matrix updating in the GUI.
Update PickMS1Features and SearchAccurateMass so that all necessary feature metadata needed for downstream filtering, QC, and analytics is captured in the FeatureMap and saved to the FeatureMapHistory.
Fix¶
Prioritize the use of subordinate metadata when choosing between feature level and subordinate level.
Expand MergeInjections tests and isolated/corrected several bugs.
Major bugs in SampleGroupProcessor; Add makeFeatureMapFromHistory for better handling of input FeatureXML files.
Bug in UpdateFEatureMapHistory.
Bug in mergeInjections where missing injection data caused the feature to be removed prematurely.
Bug in FeatureMatrix.
Bug in filtering by injection name or sequence segment name.
Add options for running sequence processor with specified injections or segments.
EMG processor and app state fixes.
About window not using a popup/modal because it relies on hacks/workarounds.
v1.0a (2020-07-16)¶
Features¶
GUI can load a session from a sequence.
Implement processor LoadSessionFromSequence.
Add FilePicker
Add AppStateProcessor logic to FilePicker
getPathnameContent uses class Table, fetches name, size, type and date of entries
File type filter.
Navigate directories, show their content.
Add AppState to AppWindow.
Drag and Drop steps.
Add Workflow widget to the application.
Add processor class BuildCommandsFromIds to AppStateProcessor.
Use single-pane navigation.
Add “go up” directory button.
Do not insert “.” and “..” to folder content.
Navigate directories, show their content.
Add to gui: Report, Run workflow.
Add validation check on Report checkboxes. At least one of both column should be selected.
Add widget Report to store a csv file with FeatureSummary or SequenceSummary.
Add Workflow widget to the application.
Implement class GuiAppender.
CLI and pivot export.
Load files in a separate thread, and disable buttons until it’s done.
Add EMGProcessor.
Add in features line and heatmap plots.
Feature explorer pane.
CLI can export integration start/end for FeatureSummary.csv and SequenceSummary.csv.
Changes¶
Install dependency libboost-filesystem-dev apt package.
Improve AppStateProcessor hierarchy, remove unnecessary structs, make them private methods.
AppStateProcessor’s methods become structs/classes.
Separate CLI functionalities into AppState and AppStateProcessor.
AppState does not keep info about selected metadata and sample types.
Simplify CLI menu entries.
Fix¶
Implicit conversion from char to plog::util::nstring.
Indentation in AppWindow::HelpMarker().
Avoid shadowing menu item with text below/under (level, z-index wise) it in workflow steps. Use Button instead of Text.
FilePicker does not call OpenPopup at every frame.
Add support for OpenMS shared data and removing fixed path names.
Enable selecting all metadata in CLI app,
Main arguments in GUI.
Cmake configuration for OpenGL (Linux).
CommandLine: reset fetures and raw data directories after loading a new sequence file.
v0.1.0 (2019-04-08)¶
First release of SmartPeak