Releases: AutoFlowResearch/SmartPeak
Releases · AutoFlowResearch/SmartPeak
v1.7.0
v1.6.0
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
v1.5.0
v1.4.0
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
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)
Changes
- Refactor of Feature line and heatmap plots (#349)
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
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.
Version 1.1.0 alpha
Features
- Various GUI updates for visualization including sliders to specify the chromatographic and mz ranges
- Support for specifying the number of processors to use
- Supporting for plotting spectra data resulting from non-targeted metabolomics experiments
- Flow injection analysis mass spectrometry (FIA-MS) workflow
Fixes
- Various GUI bug fixes
- Major bug fix in the underlying library call to
SelectFeaturesresulting in segmentation faults in multi-thread environments
Version 1.0.0 alpha
Features
- All targeted/semi-targeted/quantitative workflows are included for metabolomics
- All minimal GUI features needed to support the workflows are included for metabolomics
- Logging, input checking, and reporting are also included
- Unit test coverage for all core business logic
- Integration tests with examples for LC-MS/MS, HPLC, and GC-MS (SIM and full scan)
- installation and packaging on windows only