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Merge and cleanup Heatmap visualisation #35

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Merge and cleanup Heatmap visualisation #35

wants to merge 256 commits into from
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Commits on Dec 20, 2018

  1. Some documentation

    @pverscha
    pverscha committed Dec 20, 2018
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  2. Width of squares is now dynamically calculated

    @pverscha
    pverscha committed Dec 20, 2018
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  3. Titles of rows ans columns are also rendered right now

    @pverscha
    pverscha committed Dec 20, 2018
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  4. Visualization implemented a bit more

    @pverscha
    pverscha committed Dec 20, 2018
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  5. Fixed exporting as jQuery function

    @pverscha
    pverscha committed Dec 20, 2018
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  6. Replaced text-nodes by foreign objects to be able to use ellipsis

    @pverscha
    pverscha committed Dec 20, 2018
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Commits on Dec 25, 2018

  1. Implement functions for displaying and styling tooltip

    @pverscha
    pverscha committed Dec 25, 2018
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  2. Basic tooltip is now working

    @pverscha
    pverscha committed Dec 25, 2018
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  3. Generated random data for better debugging of heatmap

    @pverscha
    pverscha committed Dec 25, 2018
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  4. Start implementation of clustering for Heatmap

    @pverscha
    pverscha committed Dec 25, 2018
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  5. A Tree is now constructed during clustering of the Heatmap

    @pverscha
    pverscha committed Dec 25, 2018
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  6. Clustering actually seems to work

    @pverscha
    pverscha committed Dec 25, 2018
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Commits on Dec 27, 2018

  1. Animations after clustering the heatmap

    @pverscha
    pverscha committed Dec 27, 2018
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  2. Column and row labels are now also animated

    @pverscha
    pverscha committed Dec 27, 2018
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Commits on Dec 30, 2018

  1. Updated tooltips to be more comprehensive and choice for animation speed

    @pverscha
    pverscha committed Dec 30, 2018
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Commits on Jan 2, 2019

  1. Restructured metrics class

    @pverscha
    pverscha committed Jan 2, 2019
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Commits on Mar 7, 2019

  1. Ava is initialized

    @pverscha
    pverscha committed Mar 7, 2019
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  2. Add tests for clustering

    @pverscha
    pverscha committed Mar 7, 2019
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Commits on Mar 10, 2019

  1. More work on writing test cases

    @pverscha
    pverscha committed Mar 10, 2019
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  2. Fix some problems with typings on Windows

    @pverscha
    pverscha committed Mar 10, 2019
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  3. Changed directory structure

    @pverscha
    pverscha committed Mar 10, 2019
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  4. Implemented MOLO heuristics for reordering dendrogram

    @pverscha
    pverscha committed Mar 10, 2019
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Commits on Mar 12, 2019

  1. Minor changes

    @pverscha
    pverscha committed Mar 12, 2019
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Commits on Mar 16, 2019

  1. Start cleaning up code and overload of generics

    @pverscha
    pverscha committed Mar 16, 2019
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  2. Start fixing tests

    @pverscha
    pverscha committed Mar 16, 2019
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  3. Refactoring workt

    @pverscha
    pverscha committed Mar 16, 2019
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  4. Fixed tests

    @pverscha
    pverscha committed Mar 16, 2019
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  5. Newick Tree generator is working now

    @pverscha
    pverscha committed Mar 16, 2019
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Commits on Mar 19, 2019

  1. Resturctured code

    @pverscha
    pverscha committed Mar 19, 2019
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Commits on Mar 26, 2019

  1. Cleanup console.logs

    @pverscha
    pverscha committed Mar 26, 2019
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  2. Fixed options

    @pverscha
    pverscha committed Mar 26, 2019
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  3. Work on package.json

    @pverscha
    pverscha committed Mar 26, 2019
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  4. Update gitignore

    @pverscha
    pverscha committed Mar 26, 2019
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  5. Removed redundant files

    @pverscha
    pverscha committed Mar 26, 2019
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  6. Update gitignore

    @pverscha
    pverscha committed Mar 26, 2019
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  7. Removed .idea

    @pverscha
    pverscha committed Mar 26, 2019
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  8. Remove jQuery

    @pverscha
    pverscha committed Mar 26, 2019
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  9. Fix typings

    @pverscha
    pverscha committed Mar 26, 2019
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Commits on Mar 27, 2019

  1. Fix NPM package upload

    @pverscha
    pverscha committed Mar 27, 2019
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  2. Examples are working now

    @pverscha
    pverscha committed Mar 27, 2019
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  3. Trying to emit es5 libraries

    @pverscha
    pverscha committed Mar 27, 2019
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Commits on Mar 28, 2019

  1. Fixed publishing npm packages for real

    @pverscha
    pverscha committed Mar 28, 2019
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  2. Fixed invalid tree topology

    @pverscha
    pverscha committed Mar 28, 2019
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Commits on Mar 31, 2019

  1. Minor changes

    @pverscha
    pverscha committed Mar 31, 2019
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  2. Fixed issue #1

    @pverscha
    pverscha committed Mar 31, 2019
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  3. Remove console.logs

    @pverscha
    pverscha committed Mar 31, 2019
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  4. Width and height are calculated dynamically now

    @pverscha
    pverscha committed Mar 31, 2019
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  5. Fixed some exports

    @pverscha
    pverscha committed Mar 31, 2019
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Commits on Apr 1, 2019

  1. Remove CSS width restriction

    @pverscha
    pverscha committed Apr 1, 2019
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Commits on Apr 3, 2019

  1. Add toFullScreen() method

    @pverscha
    pverscha committed Apr 3, 2019
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Commits on Apr 10, 2019

  1. Fixed possible reflected XSS

    @pverscha
    pverscha committed Apr 10, 2019
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  2. Writing readme

    @pverscha
    pverscha committed Apr 10, 2019
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  3. Updated example image

    @pverscha
    pverscha committed Apr 10, 2019
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  4. More work on README

    @pverscha
    pverscha committed Apr 10, 2019
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  5. More work on readme

    @pverscha
    pverscha committed Apr 10, 2019
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  6. Add README-content

    @pverscha
    pverscha committed Apr 10, 2019
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  7. Nicer tooltip

    @pverscha
    pverscha committed Apr 10, 2019
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Commits on Jun 13, 2019

  1. Fixing clustering options

    @pverscha
    pverscha committed Jun 13, 2019
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Commits on Aug 29, 2019

  1. Set up automatic code formatting 

    Attempting to mimic current style
    @MaybeJustJames
    MaybeJustJames committed Aug 29, 2019
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  2. Extract color palettes from src-old/sunburst/sunburst.js

    @MaybeJustJames
    MaybeJustJames committed Aug 29, 2019
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  3. Script re-implementation of src-old/sunburst/sunburstNode.js

    @MaybeJustJames
    MaybeJustJames committed Aug 29, 2019
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  4. Correct formatting

    @MaybeJustJames
    MaybeJustJames committed Aug 29, 2019
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  5. Initial generic settings implementation

    @MaybeJustJames
    MaybeJustJames committed Aug 29, 2019
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  6. Remove dist/ from the git index 

    Transpiled output should not be in git
    @MaybeJustJames
    MaybeJustJames committed Aug 29, 2019
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  7. Ignore dist/ files and backup files

    @MaybeJustJames
    MaybeJustJames committed Aug 29, 2019
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  8. Fix type error (by casting) in maxCountHeap

    @MaybeJustJames
    MaybeJustJames committed Aug 29, 2019
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  9. Complete initial implementation of SunburstSettings and begin tests

    @MaybeJustJames
    MaybeJustJames committed Aug 29, 2019
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  10. Initial template implementation of sunburst class

    @MaybeJustJames
    MaybeJustJames committed Aug 29, 2019
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Commits on Aug 30, 2019

  1. Ensure tests for SunburstSettings pass

    @MaybeJustJames
    MaybeJustJames committed Aug 30, 2019
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  2. Mark rerootCallback as optional

    @MaybeJustJames
    MaybeJustJames committed Aug 30, 2019
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  3. Implement custom Optional<> type 

    - Also change parameter name for sunburstNode.createNodes from node to nodes
    @MaybeJustJames
    MaybeJustJames committed Aug 30, 2019
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  4. Add tslint configuration

    @MaybeJustJames
    MaybeJustJames committed Aug 30, 2019
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  5. Reduce SunburstSettings implementation complexity

    @MaybeJustJames
    MaybeJustJames committed Aug 30, 2019
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Commits on Sep 2, 2019

  1. Correct import

    @MaybeJustJames
    MaybeJustJames committed Sep 2, 2019
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  2. Correct some tslint warnings

    @MaybeJustJames
    MaybeJustJames committed Sep 2, 2019
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  3. Test SunburstNode

    @MaybeJustJames
    MaybeJustJames committed Sep 2, 2019
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  4. Extra type checking

    @MaybeJustJames
    MaybeJustJames committed Sep 2, 2019
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  5. Trying to make sunburst compile

    @MaybeJustJames
    MaybeJustJames committed Sep 2, 2019
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Commits on Sep 3, 2019

  1. Fix some type warnings

    @MaybeJustJames
    MaybeJustJames committed Sep 3, 2019
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  2. Sunburst now compiles

    @MaybeJustJames
    MaybeJustJames committed Sep 3, 2019
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Commits on Sep 4, 2019

  1. Example displays an SVG 

    * Now jquery plugin is not going to be ported
    @MaybeJustJames
    MaybeJustJames committed Sep 4, 2019
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  2. Clean up package.json

    @MaybeJustJames
    MaybeJustJames committed Sep 4, 2019
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  3. Fix build 

    Also remove yarn lock file
    @MaybeJustJames
    MaybeJustJames committed Sep 4, 2019
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Commits on Sep 5, 2019

  1. Typescript version now displays a sunburst image

    @MaybeJustJames
    MaybeJustJames committed Sep 5, 2019
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  2. Implement some useful mathematical functions

    @MaybeJustJames
    MaybeJustJames committed Sep 5, 2019
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Commits on Sep 6, 2019

  1. Fix a logic bug in Optional::isPresent

    @MaybeJustJames
    MaybeJustJames committed Sep 6, 2019
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  2. Create a Color manipulation library 

    Also refactor color manipulation code from util into color
    @MaybeJustJames
    MaybeJustJames committed Sep 6, 2019
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  3. Fix Optional class of() factory method

    @MaybeJustJames
    MaybeJustJames committed Sep 6, 2019
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  4. Add tests and fix bugs and linter warnings in color and math

    @MaybeJustJames
    MaybeJustJames committed Sep 6, 2019
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  5. Correctly colour the sunburst

    @MaybeJustJames
    MaybeJustJames committed Sep 6, 2019
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  6. Quality of life working with tslint

    @MaybeJustJames
    MaybeJustJames committed Sep 6, 2019
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Commits on Sep 9, 2019

  1. Small fix for the optional type and add some tests

    @MaybeJustJames
    MaybeJustJames committed Sep 9, 2019
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  2. Introduce extra tests for a bug fix in Optional

    @MaybeJustJames
    MaybeJustJames committed Sep 9, 2019
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  3. Clean up Utils and add more tests 

    Also implement new function: generateId()
    @MaybeJustJames
    MaybeJustJames committed Sep 9, 2019
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  4. Make ColorPalette a sub-module of colors

    @MaybeJustJames
    MaybeJustJames committed Sep 9, 2019
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Commits on Sep 10, 2019

  1. Initial implementation of breadcrumbs

    @MaybeJustJames
    MaybeJustJames committed Sep 10, 2019
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Commits on Sep 12, 2019

  1. Only color nodes based on first 2 children

    @MaybeJustJames
    MaybeJustJames committed Sep 12, 2019
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  2. Breadcrumbs working reasonably

    @MaybeJustJames
    MaybeJustJames committed Sep 12, 2019
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  3. Fix softing comparison function

    @MaybeJustJames
    MaybeJustJames committed Sep 12, 2019
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Commits on Sep 16, 2019

  1. Implement tooltips

    @MaybeJustJames
    MaybeJustJames committed Sep 16, 2019
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  2. Fix remaining linter warnings

    @MaybeJustJames
    MaybeJustJames committed Sep 16, 2019
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  3. Fix tslint config indentation

    @MaybeJustJames
    MaybeJustJames committed Sep 16, 2019
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Commits on Sep 17, 2019

  1. Start working on text labels

    @MaybeJustJames
    MaybeJustJames committed Sep 17, 2019
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Commits on Sep 19, 2019

  1. Initial implementation of text labels

    @MaybeJustJames
    MaybeJustJames committed Sep 19, 2019
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Commits on Sep 20, 2019

  1. Small cleanup for text labels

    @MaybeJustJames
    MaybeJustJames committed Sep 20, 2019
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  2. Minor changes to text label

    @MaybeJustJames
    MaybeJustJames committed Sep 20, 2019
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Commits on Sep 25, 2019

  1. Fight typescript to get animation building -- still not working corre… 

    …ctly
    @MaybeJustJames
    MaybeJustJames committed Sep 25, 2019
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Commits on Sep 26, 2019

  1. Got animation somewhat working

    @MaybeJustJames
    MaybeJustJames committed Sep 26, 2019
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Commits on Sep 30, 2019

  1. Trying to work out rescaling

    @MaybeJustJames
    MaybeJustJames committed Sep 30, 2019
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  2. Initial animation working

    @MaybeJustJames
    MaybeJustJames committed Sep 30, 2019
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  3. Small fix for parentNode in animation

    @MaybeJustJames
    MaybeJustJames committed Sep 30, 2019
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  4. Add some tests for Data

    @MaybeJustJames
    MaybeJustJames committed Sep 30, 2019
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Commits on Oct 2, 2019

  1. Animate text labels correctly

    @MaybeJustJames
    MaybeJustJames committed Oct 2, 2019
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  2. Fix for color tests

    @MaybeJustJames
    MaybeJustJames committed Oct 2, 2019
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Commits on Oct 3, 2019

  1. Scale the radius correctly even when animating

    @MaybeJustJames
    MaybeJustJames committed Oct 3, 2019
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  2. Now have label display based on node size correct

    @MaybeJustJames
    MaybeJustJames committed Oct 3, 2019
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  3. Hide labels that do not fit

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  4. Compute reasonable text label sizes

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Commits on Oct 11, 2019

  1. Extract breadcrumb logic

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Commits on Oct 14, 2019

  1. Extract generic tooltip logic

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Commits on Oct 15, 2019

  1. Extract styling functions

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  2. Extracted all label styliung functions

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  3. Extract the only node styling function

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  4. A bit of code organising and documentation for styles

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  5. Add some documentation

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Commits on Oct 16, 2019

  1. Minor reorganisation

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  2. Keep tslint as happy as can be

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  3. Code cleanup

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Commits on Oct 17, 2019

  1. Small reorganisation and docs

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Commits on Oct 18, 2019

  1. Basic example showing multiple sunburst visualisations 

    And minor quality of life improvements
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Commits on Oct 21, 2019

  1. Reorganise files so that they can be merged into visualisations tree

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Commits on Oct 23, 2019

  1. Move test directory to same location as unipept-visualisations

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  2. Merged unipept-heatmap repository

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  3. npm audit fix

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Commits on Oct 25, 2019

  1. Start implementing a rudimentary DataFrame interface 

    To make dealing with the heatmap data easier.
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Commits on Oct 28, 2019

  1. Remove unnecessary SanitizeHTML dependency

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  2. Define a new HeatmapNode

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Commits on Oct 29, 2019

  1. Flesh out DataFrame type a little

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  2. Simplify setttings handling

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Commits on Oct 31, 2019

  1. Simplify a lot of data handling with Ramda lenses

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Commits on Nov 4, 2019

  1. Users shouldn't have to know about ramda. 

    Remove ramda lens interface from settings
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  2. Initial working import of the heatmap. 

    Just the visualisation working. No labels yet.
    @MaybeJustJames
    MaybeJustJames committed Nov 4, 2019
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  3. Tooltips now working

    @MaybeJustJames
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Commits on Nov 6, 2019

  1. Displaying labels for the heatmap and dev server setup

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  2. Update examples

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  3. Small fixes

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Commits on Nov 7, 2019

  1. Add reordering to DataFrame and Series classes

    @MaybeJustJames
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Commits on Dec 31, 2019

  1. Node data is now a sum type

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  2. Initialize gitignore

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    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  3. Initialize repository

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  4. Updated gitignore

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  5. Initialized empty repository for visualizations

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  6. Preprocessing data

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  7. Some documentation

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  8. Width of squares is now dynamically calculated

    @pverscha @MaybeJustJames
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  9. Titles of rows ans columns are also rendered right now

    @pverscha @MaybeJustJames
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  10. Visualization implemented a bit more

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  11. Replaced text-nodes by foreign objects to be able to use ellipsis

    @pverscha @MaybeJustJames
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  12. Implement functions for displaying and styling tooltip

    @pverscha @MaybeJustJames
    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  13. Basic tooltip is now working

    @pverscha @MaybeJustJames
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  14. Generated random data for better debugging of heatmap

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  15. Start implementation of clustering for Heatmap

    @pverscha @MaybeJustJames
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  16. A Tree is now constructed during clustering of the Heatmap

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  17. Clustering actually seems to work

    @pverscha @MaybeJustJames
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  18. Animations after clustering the heatmap

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  19. Column and row labels are now also animated

    @pverscha @MaybeJustJames
    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  20. Updated tooltips to be more comprehensive and choice for animation speed

    @pverscha @MaybeJustJames
    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  21. Restructured metrics class

    @pverscha @MaybeJustJames
    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  22. Ava is initialized

    @pverscha @MaybeJustJames
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  23. Add tests for clustering

    @pverscha @MaybeJustJames
    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  24. More work on writing test cases

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    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  25. Fix some problems with typings on Windows

    @pverscha @MaybeJustJames
    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  26. Changed directory structure

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    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  27. Implemented MOLO heuristics for reordering dendrogram

    @pverscha @MaybeJustJames
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  28. Minor changes

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    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  29. Start cleaning up code and overload of generics

    @pverscha @MaybeJustJames
    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  30. Start fixing tests

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    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  31. Refactoring workt

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  32. Fixed tests

    @pverscha @MaybeJustJames
    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  33. Newick Tree generator is working now

    @pverscha @MaybeJustJames
    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  34. Resturctured code

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  35. Cleanup console.logs

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    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  36. Fixed options

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    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  37. Removed redundant files

    @pverscha @MaybeJustJames
    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  38. Removed .idea

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  39. Remove jQuery

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    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  40. Fix typings

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    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  41. Fix NPM package upload

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    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  42. Examples are working now

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  43. Trying to emit es5 libraries

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  44. Fixed invalid tree topology

    @pverscha @MaybeJustJames
    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  45. Minor changes

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  46. Fixed issue #1

    @pverscha @MaybeJustJames
    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  47. Remove console.logs

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  48. Width and height are calculated dynamically now

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  49. Fixed some exports

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    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  50. Remove CSS width restriction

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  51. Add toFullScreen() method

    @pverscha @MaybeJustJames
    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  52. Fixed possible reflected XSS

    @pverscha @MaybeJustJames
    pverscha authored and MaybeJustJames committed Dec 31, 2019
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  53. Writing readme

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  54. Updated example image

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  55. More work on README

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  56. More work on readme

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  57. Add README-content

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  58. Nicer tooltip

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  59. Fixing clustering options

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  60. Reorganise files so that they can be merged into visualisations tree

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  61. Move test directory to same location as unipept-visualisations

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  62. Start implementing a rudimentary DataFrame interface 

    To make dealing with the heatmap data easier.
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  63. Remove unnecessary SanitizeHTML dependency

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  64. Define a new HeatmapNode

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  65. Flesh out DataFrame type a little

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  66. Simplify setttings handling

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  67. Simplify a lot of data handling with Ramda lenses

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  68. Users shouldn't have to know about ramda. 

    Remove ramda lens interface from settings
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  69. Initial working import of the heatmap. 

    Just the visualisation working. No labels yet.
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  70. Tooltips now working

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  71. Displaying labels for the heatmap and dev server setup

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  72. Update examples

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  73. Small fixes

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  74. Add reordering to DataFrame and Series classes

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  75. Start cleanup and simplification of clustering code

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  76. Merge branch '2.0_heatmap' of github.com:unipept/unipept-visualizatio… 

    …ns into 2.0_heatmap
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  77. Attempt to clean up and simplify clustering code

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Commits on Jun 2, 2020

  1. Rework and simplify distance matrix computation

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Commits on Jun 3, 2020

  1. Add idxmin and idxmax functions to Series and DataFrame

    @MaybeJustJames
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  2. Simplify the DataFrame ctor

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  3. DataFrame idxmax() and idxmin() now return a single max/min

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    MaybeJustJames committed Jun 3, 2020
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Commits on Jun 10, 2020

  1. Add drop() function to Series

    @MaybeJustJames
    MaybeJustJames committed Jun 10, 2020
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Commits on Jun 17, 2020

  1. Working UPGMA and distance matrix tests

    @MaybeJustJames
    MaybeJustJames committed Jun 17, 2020
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  2. Clean up the UPGMA implementation

    @MaybeJustJames
    MaybeJustJames committed Jun 17, 2020
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  3. Add clustering documentation

    @MaybeJustJames
    MaybeJustJames committed Jun 17, 2020
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Commits on Jun 23, 2020

  1. Add more cluster tests for UPGMA clustering

    @MaybeJustJames
    MaybeJustJames committed Jun 23, 2020
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Commits on Jun 25, 2020

  1. Implement and test the dendsort algorithm 

    Based on R code from:
https://bitbucket.org/vda-lab/dendsort/src/master/R/sort_smallest.R
    @MaybeJustJames
    MaybeJustJames committed Jun 25, 2020
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  2. Remove files that are no longer used

    @MaybeJustJames
    MaybeJustJames committed Jun 25, 2020
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  3. Add extendedDiagnostics to tsconfig

    @MaybeJustJames
    MaybeJustJames committed Jun 25, 2020
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Commits on Jun 29, 2020

  1. Finalise necessary items for clustering implementation on Heatmap

    @MaybeJustJames
    MaybeJustJames committed Jun 29, 2020
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  2. Likewise

    @MaybeJustJames
    MaybeJustJames committed Jun 29, 2020
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  3. Correct a typing siiue on typescript upgrade

    @MaybeJustJames
    MaybeJustJames committed Jun 29, 2020
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  4. Add and fix tests

    @MaybeJustJames
    MaybeJustJames committed Jun 29, 2020
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  5. Clustering implementation

    @MaybeJustJames
    MaybeJustJames committed Jun 29, 2020
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  6. Update dependencies and integrate eslint/prettier

    @MaybeJustJames
    MaybeJustJames committed Jun 29, 2020
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  7. Lint and Prettier all code

    @MaybeJustJames
    MaybeJustJames committed Jun 29, 2020
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Commits on Jun 30, 2020

  1. Revert "Lint and Prettier all code" 

    This reverts commit 8501d5a.
    @MaybeJustJames
    MaybeJustJames committed Jun 30, 2020
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  2. Dependency and config changes

    @MaybeJustJames
    MaybeJustJames committed Jun 30, 2020
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  3. Working heatmap example

    @MaybeJustJames
    MaybeJustJames committed Jun 30, 2020
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  4. Implement animated clustering

    @MaybeJustJames
    MaybeJustJames committed Jun 30, 2020
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  5. Heatmap has full animations working and same data as v1 example

    @MaybeJustJames
    MaybeJustJames committed Jun 30, 2020
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  6. Add documentation

    @MaybeJustJames
    MaybeJustJames committed Jun 30, 2020
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  7. Add more documentation

    @MaybeJustJames
    MaybeJustJames committed Jun 30, 2020
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