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CHANGELOG.md

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Changelog

[1.0.2] - 2022-03-18

Fixed

  • #675 Fixed an issue with the JS resource files in the npm release of dash-bio. As pointed out in this community post some of the dependencies have not been resolved at their external unpkg URL.
  • #671 Fixed Onco-Print range property description.

[1.0.1] - 2022-01-19

Changed

  • #667 Added support for dash-bio-utils stub package and deprecation warning.
  • #667 Updated Ideogram version, props and removed support for old versions of ideogram (for more info see #393).

[1.0.0] - 2022-01-17

Changed

  • #589 Merged dash-bio-utils into the dash bio package namespace.

Fixed

  • #646 Fixed dendrogram domain whitespaces for Clustergram when dendrogram property is not set for either axis (for more info see #644).

[0.9.0] - 2021-12-14

Fixed

  • #629 Fixed an issue where IGV would generate duplicate tracks in the browser when a reload of the module was triggered through dcc.Tabs (for more info see #572).

Added

  • #587 Added JSME component.
  • #628 Added option to add colored labels to rows and columns on Clustergram.
  • #640 Added loading states to each component to support custom loading css with dash-data-is-loading.
  • #642 Added scrollZoom property to Molecule2dViewer.
  • #641 Added showLegend property to Speck viewer, which allows users to show a color legend for atoms shown on the canvas.
  • #641 Added style property to Speck and Molecule3dViewer to enable generic style overrides on the plot div.

Changed

  • #589 Removed hardcoded clustergram linkage method, added parameter link_method instead.
  • #592 Changed default plot colors of Clustergram to color vision deficiency friendly colormap (for more info see #450).

[0.8.0] - 2021-09-27

Fixed

  • #576 Fixed abnormal memory consumption with Molecule3dViewer component when selecting residues or rotating the molecule (for more info see #511).
  • #575 Bumped Ideogram version to 1.6.0 to fix erratic annotations behavior (for more info see #524).

Added

  • #567 Added VariantMap component (see #504 for original PR).
  • #573 Added the ability to configure the FornaContainer hover info with hoverPattern prop and interpolated node keys (for more info see #519).
  • #579 Added ability to resize the NeedlePlot component (for more info see #545).
  • #583 Added the ability to manually set Sequence ID's for AlignmentChart component (for more info see #421).

[0.7.1] - 2021-07-26

Fixed

  • #562 Repeated re-rendering of the Molecule3dViewer component caused the viewer zoom to decrease multiplicatively. This fix also exposes the zoom and zoomTo props for this component.
  • #565 Fixed major domain annotation positioning for the NeedlePlot component and exposed textangle prop to allow domain annotation text to be angled relative to the horizontal axis.

Changed

  • #563 Changed package scripts to 3 main build scripts: build:js, build:backends, and build to combined them. This brings the dash-bio build process in-line with the process for other Dash component libraries. As part of this change, __init__.py now also uses relative imports to load components (for more info, see #534).

Added

  • #564 Added component generation support for Dash Julia.
  • #565 Added margins and clickData props to NeedlePlot to expose event data for callbacks.

[0.7.0] - 2021-04-19

Fixed

  • #547 sideByside prop fix for NglMoleculeViewer component when ALL chains are visualized.

Added

  • #543 Added Dash Pileup component.
  • #547 Added shapes and isosurfaces props to 3dMoleculeViewer to enable rendering additional features on the molecule.
  • #553 Added source mapping.
  • #554 Added additional props and arbitrary layout arguments to VolcanoPlot.

Changed

  • #550 Updated CONTRIBUTING.md andbasic demo app structure. In addition, removed residual code and pre-deploy scripts associated with now-discontinued Dash Bio gallery.

[0.6.1] - 2021-02-15

Fixed

  • #544 Miscellaneous fixes for NglMoleculeViewer component.

[0.6.0] - 2021-01-28

Added

  • #537 Added Dash-IGV component.

[0.5.1] - 2020-12-27

Fixed

  • #536 Fixed abandoned resource vulnerability with CircosJS fork.

[0.5.0] - 2020-10-05

Added

  • #496 Added Dash-NGL-Moleculeviewer component.

Fixed

  • #512 Fixed bug involving clustergrams not being visible in dendograms.

[0.4.8] - 2020-03-16

Changed

  • #489 Renamed async modules with hyphen - instead of tilde ~
  • #494 Update from React 16.8.6 to 16.13.0

Added

  • #492 Added working support of labels in Clustergram.

[0.4.7] - 2020-02-21

Added

  • #478 Added support of DataFrame as Clustergram input.

[0.4.6] - 2020-01-07

Fixed

  • #458 Fixed reordering bug of row and column indices following clustering in Clustergram component.

[0.4.5] - 2019-11-26

  • #452 Fix issue finding CDN resources when using serve_locally=False

[0.4.4] - 2019-11-21

Fixed

  • #423 Fixed internal method call in Clustergram component.

[0.4.3] - 2019-11-18

Changed

  • #438 Updated FornaContainer dependency to a version without extraneous console.log calls.

[0.4.2] - 2019-11-15

Fixed

  • #437 Fix IE11 compatibility issues and ES5 compatibility and validation

[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).