Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[4.8.2] - 2024-03-20

Changed

#319: GEO Datasets: Move GDSInfo initialization in a worker thread

[4.8.1] - 2024-01-10

Changed

#345: Raise the required resdk package version

Fixed

#346: Fix OWDifferentialExpression data inputs and outputs

[4.8.0] - 2023-09-01

Changed

#338: Bioinformatics add-on now has improved documentation.
#344: GEO Data Sets now outputs metas as discrete and not as string variables.
#343: OWdictyExpress now outputs 'Time' as continuous and not as string variable.

Fixed

#340: Delaunay attribute vertices was deprecated since Scipy version 0.12.0 in favour of simplices and it was finally removed in version 1.11.0.
#344: fixes sorting that did not work when you clicked on the column in Gene Set Enrichment widget.

[4.7.2] - 2023-07-06

Changed

#335: Time is now column name for Dicty express data

[4.7.1] - 2023-02-06

[4.7.0] - 2023-02-06

[4.6.0] - 2022-11-24

Changed

#311: Add QC data to Genialis Expression widget
#322: (OWGeneSetEnrichment) Export gene sets enrichment report
#311: Add QC data to Genialis Expression widget

Fixed

#308: Annotate Projection: Fix commit invoke
#313: Fix compatibility with Python 3.10
#314: Replace colorpalette and other necessary fixes
#316: kegg: Fix kegg.from_taxid mapping due to change in api search results
#320: QtCore.Qt.ItemIsTristate is deprecated. Use ItemIsUserTristate instead
#323: (OWGenialisExpressions) fix sign in dialog, remove info box, use defered commit

[4.5.0] - 2021-10-07

Changed

#290: (OWAnnotateProjection) follow widget UI style guidelines
#289: Refactor GUI components of resolwe widgets
#286: Change the documentation theme

Fixed

#289: Fix for breaking changes in requests-cache package
#288: Fix for issues that occurred after changes in widget auto-summary were introduced

[4.4.0] - 2021-06-08

Changed

#282: (OWGenialisExpressions) use CollectionTables to fetch data

[4.3.1] - 2021-03-01

Fixed

#281: (OWKEGGPathwayBrowser) Fix selection.

Changed

#282: (OWdictyExpress) use CredentialManager and ConcurrentWidgetMixin.

[4.3.0] - 2020-12-23

Added

#278: (OWGenialisExpressions) Metadata now includes Relations and optional Clinical data.

[4.2.0] - 2020-10-27

Fixed

#267: (OWGenialisExpressions) Fixed animation toggle.

Changed

#269: (OWGenialisExpressions) Changed default window size.
#274: (OWGenialisExpressions) Use number of samples/genes as quantiles in Quantile transformation.

Added

#268: (OWGenialisExpressions) Use Orange.widgets.credentials.CredentialManager to securely store user password.
#270: (OWGenialisExpressions) Additionally, filter data objects by process type and input annotations.
#272, #276: (OWGenialisExpressions) Rename table attributes when matching genes and display report.

Other

The release includes some other minor bug fixes and project maintenance.

[4.1.0] - 2020-08-27

Fixed

#214: Fixed a problem in OWGEODatasets with filter component, related isue.
#233: Fixed output summary and stop showing links if they are not available, related isue.
#231: Properly use gene matcher in dictyExpress widget.
#237: Fixed a problem with enrichment. Results from Gene Set Enrichemnt and GOBrowser widgets are now consistent, related isue.
#241: OWGEODatasets: Remove wrap reimplementation.
#242: Marker genes settings migration.

Changed

#215: Bump minimum version of point-annotator module.
#216: Update icon for Gene Set Enrichment widget.
#221: Update icons for Volcano plot and Annotate Projection widgets.
#260: Update icon for dictyExpress widget.
#219: Complete redesign of Marker Genes widget.
#244: Unify add-on descriptions, related isue.

Added

#215: Add support for sparse data in Annotation module.
#245: setup Github Actions and tox.
#252: Add GenialisExpressions widget, project status.

[4.0.0] - 2019-09-05

Fixed

#203: Correct column data in GeneSets widget.
#205: Fix issue where GeneSets widget crashed on network error. Display friendly warning that cached files are used.
#206: Fix issue where GEODatasets widget crashed on network error. Display friendly warning that cached files are used.

Changed

#168: Overhaul of gene module. We no longer use pickled dictionaries to map gene names to their corresponding Entrez Ids. We use SQLite tables that are indexed using FTS5 SQLite extension.
#204: Package cellannotation replaced with point-annotator

Added

13b54e7: HomoloGene module (Wrapper around NCBI HomoloGene database)
#178: add Homology widget.

Removed

a713abe: removed legacy serverfiles update scripts in favor of bioinformatics-serverfiles.

[3.5.0] - 2019-07-19

Did not keep a changelog...