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CHANGELOG.md

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Changelog

0.1.0 - In progress

Changed

  • Changed the bundling process so that subsets of components are bundled into separate JS files by targeting the src/components/{name}/index.js files.

0.0.25 - 2020-03-26

Added

  • Removed nwb, added custom webpack configuration.
  • Added glossary.
  • Added theme props, with support for "light" and "dark". Added a URL theme parameter for the demo.

Changed

  • Upgrade vitessce-image-viewer to 0.1.3 & use data loaders.
  • Rename "LayerPublisher" to "SourcePublisher".
  • Converted the polygon tool to a lasso tool.
  • Loosened assumptions about cell info object properties when rendering cell hover messages to fix a TypeError bug.

0.0.24 - 2020-03-02

Added

  • Check that HTTP status is good before trying to parse response.
  • Please-wait only applies to component.
  • Make scatterplot dot size a constant 1px, and molecules 3px.
  • Friendlier error if mapping in config doesn't match data.
  • Test error handling in Cypress.
  • Log a data-URI for the viewconf on load.
  • Restore dark background to homepage.

Changed

  • No more missing spaces when we spell out the acronym.

Removed

  • Remove vestigial gh-pages.

0.0.23 - 2020-02-06

Added

  • HTTP headers to pass can be specified in the layers of the viewconf.

Changed

  • Fix merge-to-master builds on Travis.
  • Upgrade vitessce-grid to v0.0.6 to support pane closing.
  • Removed bootstrap and moved the small set of bootstrap styles being used into an SCSS mixin.
  • Fixed broken rectangular selection tool (broke due to a nebula.gl upgrade from v0.12.0 to v0.17.1), but switched the interaction from dragging to clicking.

0.0.22 - 2019-01-22

Added

  • Now, a plain scatterplot will also clear the please-wait.

0.0.21 - 2019-01-21

Added

  • Until UI is available, dump viewconf to console.
  • Added styles to prevent unintentional text selection during grid item resize in Safari.

Changed

  • Loosen the cells schema to accommodate data from HuBMAP.

0.0.20 - 2019-01-06

changed

  • Removed OpenSeadragon in favor of deckgl

0.0.19 - 2019-12-10

Removed

  • Removed Docz and .mdx files and update package.json.

Added

  • Travis checks that changelog was updated.
  • Links to component demos.
  • Top-level CSS rule to keep component styles from leaking out.

Changed

  • CSS filename in UMD no longer contains hash.
  • Update to NodeJS 10 on Travis.

0.0.18 - 2019-11-18

Added

  • Initial zoom can be specified for scatterplots.
  • Allow background imagery to be translated horizontally and vertically.
  • Close cell set tabs.
  • Color cell sets.
  • Split long menu of cell operations into smaller menus from icons.
  • Cell sets can be exported and imported as JSON.
  • Union, intersection, and complement of cell sets.
  • View all set descendants at a particular level.
  • More public demos.
  • Export validateAndRender for use as component.

Changed

  • Gave up on CSS modules. We'll still split out CSS into separate files, but the extra name-munging was just confusing.
  • Crosshairs are now full height and width.
  • S3 data is now organized by dataset.

0.0.17 - 2019-07-19

Added

  • Polygon selection tool leveraging the Nebula.gl package.
  • Tooltip in heatmap.
  • WIP: Using CSS modules.
  • Hierarchical cell set manager component with save, name, rename, delete, rearrange, and view functionality.

Changed

  • PubSubVitessceGrid is now exported, and the registry lookup function is a parameter.
  • A HiGlass demo no longer requires HiGlass to be checked in as part of this project.

0.0.16 - 2019-06-26

Added

  • Linked hover effect between spatial, scatterplot, and heatmap.
  • Tooltip for cell status text upon hover in spatial and scatterplot views.

Changed

  • Using Deck.gl's built in picking instead of quadtree.

0.0.15 - 2019-06-07

Added

  • The <TitleInfo> component now takes children, and our JSX is tidier.
  • Using docz for documentation, and add to the push script.
  • Each JSON schema now checks that we are getting all and only the expected fields... and we have a sort-of schema for the schema to make sure these checks are in place.
  • Handle arbitrary mappings, not just t-SNE. Now computing PCA in vitessce-data.
  • Flexible configuration: load components by name, or have multiple instances of the same type of component.
  • Half-baked proof-of-concept integration with HiGlass.
  • Separate registry that holds Name -> Component mappings.
  • Easy deployment to vitessce.io.
  • Friendlier error page on AWS deployment.
  • Display current version info in deployed demo.
  • Can now specify the URL of a JSON config to load.

Changed

  • Make Heatmap more usable as a standalone.
  • Fix (?) the scrollbars which had spontaneously appeared.
  • Factor out the grid machinery into a separate package, vitessce-grid.
  • More information on the Welcome page, so changed it to a two-column layout.

0.0.14 - 2019-04-29

Added

  • Add Cypress.io tests.
  • Thank-you to NIH on the front page.
  • Add Google Analytics to all pages.
  • "Please wait" now waits for all layers.
  • Use react-grid-layout for draggable panes; Layouts can be specified either responsively, or with fixed grid positions. Grid height is based on window height at load.
  • Script (push-demo.sh) to push demo to S3, without making a new release.
  • Use OpenSeadragon for tiled imagery.

Changed

  • Spatial viewport is part of the initial FAKE_API_RESPONSE, instead of being hardcoded.
  • Neighborhoods are enabled, but hidden by default.

0.0.13 - 2019-03-26

Changed

  • Lots of display tweaks to create a consistent dark color scheme.

0.0.12 - 2019-03-26

Added

  • Heatmap is row-normed. (This is a change in vitessce-data.)
  • Borders on heatmap components... but this will be reverted.
  • Cells are visible on initial load.

Changed

  • Dark color scheme, with better contrast when colored
  • Heatmap spans the entire bottom.

0.0.11 - 2019-03-20

Added

  • Roll up the layers list when not hovered.
  • Component titles give summary stats about data.

Changed

  • Change color scales, styling of unselected cells, and marquee rendering, to improve contrast.
  • Only update selected set at end of drag.

0.0.10 - 2019-03-19

Added

  • Heatmap: Gene expression levels occupy most of the space; Above, there are bands showing the currently selected cell set, and the current cell coloring.

Changed

  • Spatial and t-SNE backgrounds are now black.
  • Move the Factor radio buttons to their own component, above Genes.

0.0.9 - 2019-03-17

Added

  • Neighborhoods layer: no interactivity, and it's obvious that the source data has some problems.

Changed

  • Got the image registration right, finally.
  • Initial viewport is hardcoded: Data is no longer centered on (0, 0) origin.

0.0.8 - 2019-03-16

Added

  • Load and validate JSON for clusters, categorical factors, gene expression levels, and cell neighborhoods.
  • Toggle between factor values: Spatial and t-SNE categorical colors are updated.
  • Toggle between gene expression levels: Spatial and t-SNE continuous colors are updated.
  • Toggle between multiple imagery layers.

Changed

  • The stained imagery is positioned and scaled better, but still slightly off.
  • No outlines on cell polygons.

0.0.7 - 2019-03-07

Added

  • Component diagram and minimal documentation of library.
  • Make space for a brief description of the dataset on the welcome page.
  • Load background imagery.
  • More unit tests.
  • Label each component, and identify the current dataset.
  • Replace global selection tools with in-component tools.
  • Toggle visibility of each layer.
  • "Please wait" while molecules load.
  • Add placeholder for genes component.

Changed

  • Use a quadtree to identify the cells in the selected region.

0.0.6 - 2019-02-25

Added

  • Welcome screen where user picks dataset.
  • All the cells are selected on start.

Removed

  • No longer supports drag and drop to add file.

0.0.5 - 2019-02-20

Added

  • Distinguish pan and single-select mode from drag-to-select.
  • Drag-to-select supported for both Spatial and Tsne: Selection state is linked.
  • Set of selected cells is updated during drag; there is also a grey overlay.
  • Add the strict AirBNB linting rules.
  • Load Linnarsson cell data by default, rather than starting from a blank screen.

Changed

  • Assume data has been scaled to fit a 2000 pixel-wide window, centered on the origin, and adjust line widths and dot sizes accordingly.

0.0.4 - 2019-02-08

Added

  • Drag and drop JSON files representing cells and molecules.
  • There is a helpful link to the sample data download.
  • JSON files are validated against schema, and detailed errors go to console.
  • Flexbox CSS for clean columns.