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@smartpeak-ci smartpeak-ci released this 15 Mar 21:10
v1.2.0
428f9dd

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.
Assets 5
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