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CHANGELOG.md

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Changelog

[0.4.1] - 2019-11-08

Fixed

  • #434 Fixed FornaContainer selector issue, in which FornaContainer styles were being applied to all svg elements on the page.

[0.4.0] - 2019-11-05

Added

  • #430 Async AlignmentChart, Circos, Ideogram, Molecule2dViewer, Molecule3dViewer, NeedlePlot, OncoPrint, SequenceViewwer and Speck components

[0.3.0] - 2019-10-22

Added

  • Added FornaContainer component for RNA secondary structure analysis.

[0.2.0] - 2019-10-18

Fixed

  • Fixed AlignmentChart error in which colorscale being undefined caused rendering to fail.
  • Fixed AlignmentChart PropType for eventDatum to string (which is what gets returned).
  • Fixed Circos error in which tracks variable being undefined caused rendering to fail.
  • Fixed Clustergram error in which display_ratio (a float or a list) was used as a list instead of self._display_ratio, which always has the type list.
  • Fixed Molecule2dViewer error in which modelData being undefined caused rendering to fail.
  • Fixed Molecule2dViewer PropType for source and target atoms within the links property to also include PropTypes.shape.
  • Fixed Molecule3dViewer error in which there was no re-rendering upon a change in the selectionType prop.
  • Fixed SequenceViewer error in which the component initially rendered with coverage that had no defined onClick behavior.

Added

  • Added re-rendering for Molecule2dViewer and Molecule3dViewer upon the selectedAtomIds prop being updated. (This lets the user write to the selectedAtomIds prop through a Dash component.)
  • Added re-rendering for SequenceViewer upon the coverageClicked prop being updated.

Removed

  • Removed AlignmentViewer component (#414)

[0.1.4] - 2019-08-02

Changed

  • Updated core dependency to dash>=1.0.0.

[0.1.3] - 2019-07-31

Changed

  • Renamed Clustergram parameters hide_labels and symmetric_value into hidden_labels and center_values respectively.

Fixed

  • Fixed issue with Molecule2dViewer not displaying triple bonds.

[0.1.2] - 2019-07-13

Changed

  • Made Speck component compatible with refactored Speck library.
  • Optimized Speck component further to increase performance.

Added

  • Added default props to Molecule3dViewer component.
  • Added zoom/pan and export SVG capabilities to Circos.

[0.1.1] - 2019-06-06

Added

  • Added Molecule2dViewer component.

Changed

  • Refactored Speck component and implemented general bug fixes.

Fixed

  • Fixed issue with Speck not responding to preset changes.

[0.1.0] - 2019-05-27

Removed

  • Removed all parsing tools in dash_bio.utils to a separate package, dash_bio_utils.

[0.0.11] - 2019-05-09

Added

  • Added to xyz_reader the ability to handle whitespace at the beginning and end of a line (in data file).
  • Added a working link to the JS distribution, so serving scripts locally is no longer necessary.

[0.0.10] - 2019-04-30

Fixed

  • Fixed homepage link in package metadata.

[0.0.9] - 2019-04-29

Fixed

  • Fixed issue with Clustergram rows and columns reordering incorrectly on the heatmap when precomputed traces are used to generate the figure.
  • Fixed issue with Speck not rendering unless it is attached to a callback.
  • Prevented Speck from trying to calculate a system with no atom.
  • Let Clustergram render even when row and column labels are not specified, by adding default values.
  • Allowed multiple SequenceViewer components to render on the same application.

Changed

  • Changed Clustergram to only return a figure by default, so that values no longer need to be unpacked.
  • Changed Molecule3dViewer's selectionType prop to accept all- lowercase values.

Added

  • Added to Clustergram the ability to generate a "curve dictionary" to translate curve number (available in hoverData/clickData) to the row or column cluster it represents on the graph.

[0.0.8] - 2019-01-04

Fixed

  • Fixed issue with Clustergram not reordering rows and columns after clustering.

Removed

  • Removed mentions of Dash events in OncoPrint component.
  • Removed properties which weren't used in Ideogram component.

Changed

  • Changed property fullChromosomeLabels so that it can be updated using dash callbacks.
  • Changed Imputer (deprecated) to SimpleImputer in Clustergram component.
  • Changed property name impute_function to imputer_parameters in Clustergram component.
  • Changed install requirement to Dash version 0.40.0 or greater.

Added

  • Added ability to define custom colors in style parser for Molecule3D.

[0.0.7] - 2019-26-02

Changed

  • Changed unicode right arrow to greater-than sign in Circos for compatibility with Python 2.7.

[0.0.6] - 2019-22-02

Added

  • Added requirements from files in utils, as well as from pure-Python components, to setup install requirements.
  • Added more descriptive prop descriptions for Dash Ideogram.

[0.0.5] - 2019-15-02

Changed

  • Changed filenames in dash_bio/utils/ folder to be snake case instead of camel case.

[0.0.4] - 2019-11-02

Added

  • Added recent update to Speck library to fix jumpy behavior on click-and-drag.

[0.0.3] - 2019-06-02

Added

  • Added variables to define strings used in _volcano.py graph labels.

[0.0.2] - 2019-05-02

Fixed

  • Fixed incompatibility issues with Dash 0.36.0.

Removed

  • Removed all mentions of fireEvent and anything else that used Dash events (which have been removed).