v0.12.1-beta

Merge #1397 from ElucidataInc/alpha_fixes

Alpha fixes

v0.12.1-alpha

[CI/CD] Directly place auth token in deployment section

v0.12.0

Major changes:

• Rewrote isotope and adduct detection logic to
  • handle absence of unlabelled parents ions and optional filtering based on parents
  • enable manual integration of any/all isotopologues using the compound widget
• A uniform visual appearance across platforms along with many small UI/UX changes and fixes

Minor changes:

• Improve emDB save behaviour (proper threading, safety checks, etc.)
• Ability to save raw chromatogram and base peak spectra in emDB
• Make auto-save optional and disabled by default
• Update application session to reflect filtered samples (when filtering using sample search box)
• Further improvement in peak-group deletion performance (from tables)

CLI-specific changes:

• Allow saving peakdetector analyses as emDB files
• Fix neural-net based quality assignment

Code changes/refactors:

• Merged Database and Databases classes, added tests and moved to core
• Removed isotope and adduct detection modules in favor of reusing the same peak-detection logic for both manual automated integration
• Removed libpillow as dependency

v0.12.0-beta

Merge #1331 from ElucidataInc/alpha_fixes

Alpha fixes

v0.12.0-alpha

Merge #1330 from sakshikukreja14/fix_deleteAllWarning

[fix] Fix 'deleteAll' warning for bookmark table

v0.11.0

Features

• Enable editing of chromatogram area and baseline of integrated peak-groups in a table, using the new "Peak Editor" #556 #1290
• Peak-groups having consensus fragmentation spectra can be exported as a spectral library (MSP only) #1291

Enhancements

• Enable non-blocking export for EICs as PDF and allow exporting all/selected groups #1261
• Give each peak-group its own set of integration parameters and view them using the new "Settings Log"
• Link isotopologue peak integration x-ranges #1271
• Estimate possibility of RAM exhaustion and warn user with appropriate alternatives
• Notify users about memory exhaustion during sample load step, without crashing #1136

UI/UX

• Removed the default state from the “Use Default Parameters” button in the "Options" dialog #1251
• Sample order for OBI-Warp drop-down will be alphabetically sorted #1250
• Refactored and improved efficiency on single/multiple group deletions in large peak tables #573
• Adjusted bar-plot font size based on bar width #565
• Highlight individual peak area of a peak-group and not everything above the red line
• Values in "Isotope Widget" will show peak-group's actual distribution and not recalculate from global settings #1225
• Moved "Exclude unfragmented groups" to "Match Fragmentation" options and allow it whenever applicable
• Prohibit closing peak-detection dialog when detection is in progress
• Sync and freeze isotope bar-plot for integrated groups
• Allow adjusting the compound name column's size, in peak tables
• Duplicate peak prompts will now appear liberally allowing the user to make a call instead of employing fancy logic underneath
• Removed the console appearing with Windows GUIs

Bug fixes

• Fixed "nan" values when "Sum" EIC type was selected on Windows #1259
• Defined behavior for chromatograms for same transition (precursor-product m/z pair) but different CE #1273
• Fixed the issue where peak bubbles are floating when alignment is performed after peak detection #1257
• Fixed incorrect baseline calculated for RT constrained slices
• Handle carriage-return character as newlines while reading compound CSV files
• Fixed retention time line disappearing on zoom out #1266
• Fixed enabled/disabled state for match retention time window if corresponding option is checked
• Fixed detection of compounds having only m/z #1282
• Fixed "crashserver.exe" not exiting even after application is terminated, on Windows #1295
• Fixed fragmentation events disappearing, if mass tolerance lock is on #1234
• Fixed CSV reports not editable while app is running, on Windows
• Fixed groups from last detection being populated in current peak-table when current detection is cancelled

Miscellaneous

• Refactored and fresh set of tests for mzUtils class
• Refactored Compound class and added tests
• Refactored isotope detection and make the effects of each parameter more straightforward #1255
• Removed "Train" neural net button
• Removed the "Notes" widget
• Removed the "Gallery" widget
• Reverted commit that removed "adductName" column from Polly exports
• Added "adductName" column to peaks file
• Read more information from MoNA spectral libraries.
• CD - prevent pre-release tags from creating an update repository
• Use smart pointers for shared peak-groups among central widgets (table, EIC, etc.), eliminating a whole class of crashes
• Removed "FirstView" app from EPI dialog

v0.11.0-beta.1

Merge #1308 from ElucidataInc/beta_fixes

Beta fixes

v0.11.0-beta

Merge #1302 from ElucidataInc/alpha_fixes

Alpha fixes

v0.11.0-alpha

Merge #1297 from saifulbkhan/ftr_modify_peaks

[Ftr] Modify integrated peaks #1290

v0.10.0

Features:

• Improve untargeted detection #152 #313 #616 #1053
• Enable detection of common adducts #475
• Allow pushing session data directly to Polly projects
• Enable automatic notification and updates from within the application
• Visualize integrated area under peak-groups #782
• Export sample metadata file template #1171

UI/UX:

• Replaced icons new ones
• Add close buttons to all widgets #939
• Warn user about sample load failure #676
• Update isotope plot on peak-group selection #703
• Allow ignoring close event (with a “No” response)
• Make "Peak Detection" dialog more compact #1161
• Allow “unmarking” peak-groups #171
• Show “NA” for absent sample number in tooltip #358
• Add “Sample Number” column to samples widget #358
• View abundance in user-set quant type in isotope widget #571
• Draw baseline in-front of corresponding EIC #960

Bug fixes:

• Prevent CLI crash on invalid sample strings
• Perform time unit conversion for mzML scans #1176
• Incorrect peak count in results table
• Missing mz-intensity pairs from scans
• Mark C12 PARENT peak-group as same as parent #537
• Filter formula string for special characters #1168
• Export isotope labels in peak-detailed format
• Use double for Isotope object constructor #393
• Prevent updates to weights of neural network with subsequent detections
• Fix RT delta values not shown for untargeted+DB detection #1204
• Re-enable running concurrent sessions #1215
• Fix crash on switching tolerance sync button with empty EIC #1230
• Resolve compound suffixes over sessions #1003
• Fix internet connectivity check #1239
• Fix incorrect report of good peak count #1142

Misc:

• Read El-MAVEN's settings file in CLI #1163
• Add an option to export non-bad peak-groups #171
• Read normalisation factor from sample metadata
• Refactored and added doctest-based testing for JsonReports and CSVReports
• Replace random number generation with std library-based utilities
• Remove optional “user selected isotope” export
• Read neutral masses from compound DB (“mass” column)
• Allow RT-restriction for untargeted+DB matching #1203
• Parallelize mass-slicing step #250
• Remove “Getting Started” dialog