fix plotlyviz colors; fix agglomerative clustering; change searchbar default

2.0.1

Fixed

• min_cluster_samples now only accepts an int -- now AgglomerativeClustering works (#224)
• plotlyviz.scomplex_to_graph no longer casts color_values to a 2d array, and visuals._tooltip_components now generates
  either 1d or 2d member_histogram depending on dimensionality of color_values (#225)

Fixed/Changed

• The AND and OR searchbar queries no longer multiplies the base size of a node by the ratio of how many of its items match. Rather,
  the base size of the node is simply multiplied by how many of its items match the query. With this change, the size of a node
  during an AND or OR search query again directly reflects the number of items within the node. (#227)
• The default search mode is now AND -- because that's the expected behavior, because that's how the google works (#227)

Brand new visualizations with color picker!

Visualization

All of the below changes apply to kmapper's D3 html visualization.

• added searchbar functionality (see documentation for include_searchbar in kmapper.visualize())
• upgraded d3 from v3 to v6 -- one huge benefit of the new d3-force library is that it is [deterministic](https:// twitter.com/mbostock/status/725124754701717504?lang=en), so a given graph will always render the same visually, across browsers and reloads.
• clicking on a node will set it as the "focus node" (the node for which details are shown in the details pane). until the user clicks off of the node. That is to say, click-focus is not lost if another node is moused-over. Click-focus is released if (1) another node is clicked on, or (2) if the user clicks on the blank canvas.
• hovering over a node will "freeze" it in place until no longer hovering over that node. This makes it easier to grab the node. If no node is currently set as the "focus node" via a click, then hovering over a node will also make it the focus node.
• once a node is dragged, it stays ("freezes") where it was dragged
• added the ability to freeze (and unfreeze) all nodes with keystrokes f and x,
• the focus node visually "pulses" in the display
• added the ability to "save" the positioning of all nodes in the display. Saves to a .json file. Node positioning can be re-loaded via providing the json save file.
• multiple color_values arrays can be passed, and switched between interactively in the display.
• the node color function can be specified, as a string, to any function available on the numpy base class (e.g., 'mean', 'median', 'max', 'min'. (Before, the only available function was np.mean.
  • Multiple node color functions can be specified, and toggled between interactively in the display.
• The toolbar display now uses css flexbox, which avoids overlap-problems on smaller viewports.

Kmapper

• change several visualize-related functions to be private
• only support python >= 3.6

CI/CD revamp

New release process requires a new release!

Bug fixes and visualization improvements

:D

JOSS Release

Adds JOSS paper title and description to zenodo metadata release information

JOSS Release (v3)

• Fix formatting in .zenodo.json

JOSS Release (v2)

• correct zenodo author metadata

JOSS Release (v1)

• Use sphinx-gallery for documentation examples (#164)
• Removed mutable arguments (#165)
• Minor JOSS edits (#166)
• Allow sparse matrices in map function (PR #163)

Cover fix, docs revamp

• New implementation of the cover API makes it consistent with the literature.
• New documentation website (kepler-mapper.scikit-tda.org).

Visualization revamps

This release contains lots of updates to visualization interfaces. We include a new plotly visualization system, an adapter to networkx graphs, cleaned up documentation website, and small bug fixes.