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Release 0.14.0

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@seve seve released this 28 Jan 01:14
0.14.0
3dd50e5

Summary: 0.14.0 adds ontology-based autosuggestions to the experimental annotation feature, category labeling in the main graph/embedding, and a number of bug fixes and incremental improvements.

Added:

  • The experimental annotations feature is augmented with the ability to autosuggest labels from an ontology. Ontology is specified from an .obo file. See the --experimental-annotations-ontology command line flag.
  • Main embedding (graph) display enhanced with the ability to display category names over the center of the constituent cells. Enabled/disabled by a new UI button in the button bar.
  • When launched, cellxgene will inform users when a new version is available on PyPi.org. This check may be bypassed with the new --no-upgrade-check command line option.

Changed:

  • Labels / names in the user interface will now display in a sorted order, including embedding names, annotation names, and categorical annotation values.
  • Various internal build updates and improvements.
  • Fonts needed by the application are now served by the internal web server, rather than relying on internet connectivity.
  • Javascript and Python package dependencies updated.
  • FAQ link removed from Info menu
  • All large histograms will now have a consistent number of bins (PR #1086)
  • User-created annotations may now contain additional characters (now allow alphanumeric, plus -_.() and single spaces. Fixes issue #1113.
  • The recent 0.7.* release of the anndata module is incompatible with cellxgene. This release pins the anndata dependency to 0.6.22post1 (the most recent compatible version).

Fixed:

  • A significant number of bug fixes to experimental annotations, including #1050, #1057, #1036, #1055 and others.
  • Annotation file name, specified by --experimental-annotations-file, will now allow file names containing a hyphen. Fixes issue #1072
  • Fixed bug which would cause user-created annotations to lose the (mandatory) unassigned category. Fixes issue #1090
  • Various layout and whitespace improvements throughout the app.
  • Added missing python requests package to requirements.
  • Fixed bug that would crash if the user created an annotation name which was the same as another existing annotation name. Fixes issue #1112
  • Ensure that all user-created annotation labels are correctly saved, without transformation, to the annotations CSV file. There were several labels (eg, 'nan') which would not be saved correctly to the annotations CSV file. Fixes issue #1111.
  • Some sequences of actions caused the undo button to behave unpredictably. This is fixed by #1099
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