Hiveplotlib Change Log

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog,

As of January, 2024, this project adheres to Semantic Versioning.

Version 0.25.1 (released Jul 5, 2024)

Fixed

  • Compatibility with numpy 2.0.0.

Version 0.25.0 (released Mar 23, 2024)

Added

Version 0.24.0 (Released Feb 18, 2024)

Added

  • hiveplotlib.datasets.example_nodes_and_edges() added for generating random nodes, node splits, and edges for an arbitrary number of axes.

  • hiveplotlib.HivePlot.connect_axes() now allows users to specify control_rho_scale and control_angle_shift, which allow users to modify the positioning of the control point for the Bézier curve of each edge. By default, the control point for an edge between two nodes is the polar midpoint of the two curves, but users can now scale the polar distance from the origin (control_rho_scale) or shift the angle counterclockwise (control_angle_shift) for each control point relative to its default median polar position.

Changed

Fixed

Removed

  • hiveplotlib.HivePlot.to_json() revised to generate a more D3-friendly JSON structure. The "curves" key originally contained multiple lines in a single list of [x, y] values separated by [null, null] values. The lines are now split into their own lists. This proved more compatible for plotting in JavaScript. The original JSON structure could still be created for now by running with deprecated_version=True in versions 0.22.0 and 0.23.0. The old JSON structure was deprecated in version 0.22.0 and has been removed in this version.

Many thanks to:

  • @besiansejdiu for ideas, discussion, and code review for exposing the changing of control points of edge Bézier curves.

  • @michael.catanzaro for assistance on migrating to ruff.

  • @abrahamdavidsmith for assistance on automating Gitlab releases.

Version 0.23.0 (released Feb 2, 2024)

Added

Changed

  • All occurances of mpl_axes_off in hiveplotlib.viz.matplotlib and hiveplotlib.viz.datashader renamed to axes_off for consistency between different viz back ends.

  • Many redundant viz warnings used for all viz back ends pulled out of individual viz functions into hiveplotlib.viz.input_checks.input_check() to avoid redundant code, especially as the repository expands support for more visualization packages. User experience will not be changed by this.

  • Other redundant, viz package-agnostic code pulled out from individual viz functions into the hiveplotlib.viz.base sub-module as well as into private _fig_setup methods. User experience will not be changed by either of these revisions.

  • For all occurances of axes_labels_fontsize in hiveplotlib.viz.bokeh, the default value has been raised from "13px" to "16px".

  • For all occurances of buffer in hiveplotlib.viz.bokeh, the default value has been raised from "0.2" to "0.3" (to compensate for the larger default font for axes labels).

  • For all occurances of center_plot in hiveplotlib.viz, if the provided hive plot / P2CP has no axes, then no centering will run. (This would previously trigger an error.)

  • hiveplotlib.datasets.example_hive_plot() no longer defaults to putting the kwarg alpha=1 on all edges for viz, as this does not generalize to the hiveplotlib.viz.plotly use case. Kwargs now exposed for the underlying hiveplotlib.hive_plot_n_axes() call.

Version 0.22.0 (released Jan 23, 2024)

Added

Changed

  • hiveplotlib.HivePlot.to_json() revised to generate a more D3-friendly JSON structure. The "curves" key originally contained multiple lines in a single list of [x, y] values separated by [null, null] values. The lines are now split into their own lists. This proved more compatible for plotting in JavaScript. The original JSON structure can still be created for now by running with deprecated_version=True. Running this way will raise a DeprecationWarning and will be removed in version 0.24.0.

  • Moving to full semantic versioning (e.g. x.y.z) this release and onward.

Version 0.21 (released Mar 20, 2023)

Enhancements

  • hiveplotlib.hive_plot_n_axes() now accepts a None value as one of the values in the axes_assignments input. The None axis takes all otherwise-unassigned nodes from the node_list input and assigns them to that axis.

  • Restructure hiveplotlib.__init__.py to split out capabilities into submodules. Now have hiveplotlib.node, hiveplotlib.axis, hiveplotlib.hiveplot, and hiveplotlib.p2cp modules. High-level imports have been left unchanged.

  • split_nodes_on_variable(), a node-specific utility function, moved from hiveplotlib.utils moved into hiveplotlib.node.

  • The two P2CP-specific utility functions in hiveplotlib.p2cp_utils – split_df_on_variable() and indices_for_unique_values() – have been moved into hiveplotlib.p2cp. The hiveplotlib.p2cp_utils module has been deleted.

  • Added hiveplotlib.node.dataframe_to_node_list() for converting rows of a dataframe into a list of Node instances.

  • Added hiveplotlib.viz.datashader.datashade_hive_plot_mpl() for higher-level call to do fully-datashaded hive plots (node and edges plus the standard axes_viz()).

  • Add a buffer parameter to the datashading calls to have their extent go slightly beyond axis extents by default (and can be increased further by the user as desired).

  • Add some international trade network data to the package, and a reader function hiveplotlib.datasets.international_trade_data(). Also added generalized runner with instructions for how to make additional trade datasets from the Harvard Growth Lab dataset in the hiveplotlib repository under ./runners/make_trade_network_dataset.py.

  • Improved type hinting throughout the package.

  • Fix / clarify some of the hiveplotlib.viz.datashader function docstrings.

  • Formally add seaborn to dependencies for hiveplotlib[datashader]. Switch default edge colormap for hiveplotlib.viz.datashader.datashade_edges_mpl() from "viridis" to the seaborn colormap used in the “Hive Plots for Large Networks” example notebook.

  • All remaining np.random.seed() removed from repository (some of this was still in the test suite). These have all been replaced with rng = np.random.default_rng(0).

  • Added notebook called “Hive Plots with More Than 3 Groups,” documenting examples of the new None axis capability as well as other 4+ group hive plot options, specifically a multi-layered axes hive plots, and a Hive Plot Matrix (HPM).

  • Major refurbishment of the “Bitcoin Trader Network” notebook.

Bug Fixes

  • Fix to the hiveplotlib.viz.datashader functions, which did not correctly compose. If datashading onto an existing figure and axis without any hive plot axes, the image did not span the correct extent. Now, when datashading onto an existing figure and and axis, the datashader images will now always auto-scale to the extent of the hive plot axes.

Removed Deprecations

  • The _mpl named viz functions, which raised a DeprecationWarning in version 0.20, have been removed in version 0.21. For example, hiveplotlib.viz.hive_plot_viz_mpl() is now called hiveplotlib.viz.hive_plot_viz. Although the matplotlib backend is available by default, different backends can be accessed within the hiveplotlib.viz module. For example an explicit matplotlib backend hive plot visualization can now be called via hiveplotlib.viz.matplotlib.hive_plot_viz(), and a bokeh backend hive plot visualization can now be called via hiveplotlib.viz.bokeh.hive_plot_viz().

    Note

    hiveplotlib.viz.datashader.datashade_edges_mpl() and hiveplotlib.viz.datashader.datashade_nodes_mpl have been left with their _mpl naming for now, as datashading could eventually be done via multiple backends.

Version 0.20 (released Jan 19, 2023)

Enhancements

  • hiveplotlib.viz.bokeh submodule of bokeh-backend viz functions for hive plots and P2CPs added.

  • hiveplotlib.viz default matplotlib-backend viz functions have been renamed without the _mpl ending. matplotlib-backend viz code is now contained in the hiveplotlib.viz.matplotlib sub-module, making the _mpl redundant. Default viz called under hiveplotlib.viz, however, will still use the matplotlib backend.

  • Improvements to hiveplotlib.viz docstrings.

  • Exposed kwargs that allow the modification of axes labels in the hiveplotlib.viz module.

  • hiveplotlib now being checked against flake8-docstrings. (flake8 and documentation-building checks also incorporated into the CI pipeline). Many subtle documentation revisions from this change.

  • hiveplotlib.viz functions that are exposed to both HivePlot and P2CP instances now use the hiveplotlib.viz.input_checks.input_check() call to validate proper inputs. This will scale better if the code ever supports additional instances or further checks on said instances. In the least, this made the viz code a little more DRY.

Note

The _mpl named viz functions will raise a DeprecationWarning in version 0.20, with support to be removed in version 0.21.

hiveplotlib.viz.datashader.datashade_edges_mpl() and hiveplotlib.viz.datashader.datashade_nodes_mpl have been left with their _mpl naming for now, as datashading could eventually be done via multiple backends.

Bug Fixes

  • pytest warnings in the CI about a coming deprecation resolved.

Version 0.19 (released Sept 6, 2022)

Enhancements

  • Added hiveplotlib.viz.datashader module added, plus documentation explaining and demonstrating datashading capabilities for both hive plots and P2CPs.

  • hiveplotlib.viz.edge_viz_mpl(), hiveplotlib.viz.hive_plot_viz_mpl() and hiveplotlib.viz.p2cp_viz_mpl() now have an exposed tags parameter that allows plotting a subset of tags (with default behavior to plot all tags).

  • Improved type hints for hiveplotlib.viz module.

  • hiveplotlib.viz.p2cp_legend_mpl() revised tags_to_include parameter to tags to be more consistent with the rest of the API.

  • License revised from GNU AGPL to BSD License (BSD-3-Clause).

Bug Fixes

  • Major bug fix in hiveplotlib.viz.edge_viz_mpl(), which made incorrect assumptions about how one can compose lines in matplotlib. Revised to use LineCollection on the backend.

  • Incorrect assumptions also found in notebooks demonstrating viz in other packages. These have been corrected.

  • Fixed hiveplotlib.viz.axes_viz_mpl() not responding to mpl_axes_of=False use case.

Version 0.18 (released Aug 17, 2022)

Enhancements

  • HivePlot.to_json() and P2CP.to_json() implemented.

  • Documentation notebook showing how to visualize hive plots and P2CPs with other viz libraries off of the JSON output.

  • Started this change log (and filled in a little bit of it looking back at some previous versions).

  • Switched the spacers between discretized edges in the (n, 2) numpy arrays to being np.nan instead of None. This allows us to preserve float-typed arrays instead of being forced to switch to Object-typed arrays, which speeds up the code and improves memory usage.

Bug Fixes

  • HivePlot.add_edge_kwargs() doesn’t need to be run with a2_to_a1=False to avoid errors with axis <-> repeat axis anymore.

  • Generally more case control / useful warnings for HivePlot.add_edge_kwargs() when trying to put kwargs on impossible edge sets.

  • Revised DeprecationWarning issues that were arising from using pytest.warns(None) throughout the test suite.

  • Revised random draws in hiveplotlib.datasets.four_gaussian_blobs_3d() to use np.random.default_rng() instead of np.random.seed().

Version 0.17 (released Feb 8, 2022)

  • A couple of bug fixes in hive_plot_n_axes(), additional utility functions, pandas futurewarning resolved, lots more documentation.

Enhancements

  • Additional Utility Functions

Bug Fixes

  • A couple of bug fixes in hive_plot_n_axes().

Version 0.16 (released Dec 21, 2021)