Version 2.7.0: REUSE, install and backend updates

Support graph-tool >= 2.4.6
Support networkx >= 3
Move to pyproject.toml
Make project REUSE compliant

Fix bug for igraph node attributes

Version 2.5.2: improve Shapely and GraphML support

This bugfix version upgrades the geometry submodule to make it ready for the upcoming 2.0 version of Shapely.
It also improves the GraphML IO functions so that they support graphs with missing attributes.

Version 2.5.1: bugfixes, improved documentation and plots (with annotations)

This is mostly a bugfix version but it also introduces harmonic centrality support with igraph and node annotations on plots.

New features

• Support for harmonic centrality with igraph (52aec27).
• Node annotations when hovering on nodes in plots (81c7da0)

Enhancement

Circular self-loops on network plots (81c7da0).

Bugfixes

• Fix curved edges and sizes (81c7da0)
• improved spatial support (to_undirected and Graph init, e83fd6a)
• Fix spectral radius for unweighted graphs (f2dc429)
• Fix save_spikes and receptor port support with NEST (f2dc429)

Version 2.5.0: sparse clustered graphs and improved backend support

This new version adds support for NetworkX 2.6+, introduces a new network model, improves IO and plotting modules, and extends the list of functions that are supported by the default backend (if networkx, igraph, and graph-tool are not installed on the system).

New features

• sparse_clustered: it is now possible to generate sparse graphs with a desired clustering coefficient, this comes with an associated rewiring scheme (f45d0a9b)
• support for GraphML file format (a9f8710d)
• support for NetworkX 2.6+ (f4e5002e)

Enhancements

• More efficient edge attribute access (speed and memory improvements, c8f29951)
• Improved plots (color and size support for nodes and edges, visible arrows for directed networks..., 7f5340b8 & ccdd627f)
• Add connectedness test with nngt default backend (d3979a15)

Bugfixes

Correct delete_edges for nngt backend that did not update the node degrees (b1ca08df).

Version 2.4.0: Geospatial data and NEST3 support

This new release brings the possibility to plot graph together with geospatial data and adds support for the new NEST 3 release.

New features

• the geospatial module and its draw_map function.
• support for NEST 3

Enhancements

• faster and more versatile get_edges function
• improved support of undirected graphs with non-positive weight attributes
• check for ununsed keywords arguments when creating Graph objects

Bugfixes

• Correct SWP if deviations are negative
• default NeuralGroup is excitatory
• fix Structure.create_meta_group
• fix error in new_edges for empty edge list

NNGT 2.3.0: improved (undirected) analysis and plots

This new release includes a lot of bugfixes and under-the-hood improvements as well as a set of new tools for better analysis, especially with undirected measures.

All testing and main code hosting has been moved to SourceHut and the documentation has been updated and now includes an automatic dark theme for all browser requesting it.

New features

• to_undirected method, to create undirected counterparts from directed (even weighted) networks (patch 20376)
• local_closure as a complementary tool for clustering (#155), see [Yin2019]
• Zhang--Horvath method for weighted clustering (#146), see [Zhang2005]

Enhancements

• improved support for positions/structures (#149)
• improved from_matrix class method to support all Graph arguments (#149)
• improved plots: positional layout and opacity (#149):
  • layout can now be a list of custom positions.
  • added ealpha and nalpha support for edge and node transparency.
• shortest path and path length method can be used in "undirected" mode on directed weighted networks (patch 20470)

Bugfixes

• corrected calculation of weighted path length for SWP (patch 20470)
• fixed circular graph and lattice reciprocity (patch 20412)
• corrected spatial plots with networkx (#154)
• fixed IO issue with non-string node attributes (#152)
• fixed nonstring_container import for RNGs (#151)
• fixed edge deletion with nngt backend (#149)

Breaking change

Default mode for SWP is now to use the average local clustering instead of the global clustering.

NNGT 2.2.1: bugfixes for edge deletion, addition of Price network

This release fixes several issues with edge deletion on all backends except networkx (see #137 and #141).
It also corrects several issues with the connector functions (#145).
Finally, it also shows the addition of the Price connectivity scheme with some generalizations (#138 and #139).

Most of all, it will fix the PyPi issue regarding the plot module, since I forgot to add the new mpl_chord_diagram submodule in the previous release, making the plot module unusable.

NNGT 2.2.0: hive plots, chord diagrams and improved graph structuring

This new release of NNGT brings about a set of new plotting functions and better functionalities for non-neuronal structured graphs through the Structure and Group classes and the get_structure_graph function.

New features:

• Addition of hive plots (#108)
• Add chord diagrams from mpl_chord_diagram (#107)
• Add Structure/Group classes for non-neuronal ensembles and structure graph to analyze connections between groups (#105 & #107)
• (Neural)Groups get an add_nodes method (#110)

Enhancements:

• Speedup get_edges (#132)
• Added edge and node deletion methods (#129)
• Improved plots and created documentation gallery (#109)

Bugfixes:

• correct "eid" attribute issue when copying graphs (#134)
• correct global clustering for unweighted directed networks (#131)
• fix io string issue for node/edge attributes and node/edge deletion (#103 & #130)
• fix returned degrees and clustering for a subset of nodes (#126)
• proper copy of returned attributes with graph-tool (#125)
• correct save_spikes (#122)
• fix delays setting (#121)
• correct graph loading with 0-out-degree neighbour lines (#118)
• fix undirected clustering for weighted directed networks (#112)
• fix loading with from_matrix (#112)
• get_edges with source/target node for undirected graphs (#102)

NNGT 2.1.0: introducing partial clustering for directed graphs

Version 2.1 further extends the normalized graph analysis methods with the addition of partial clustering coefficient for directed graphs.
It also notably improves plotting and support of undirected networks.

New features:

• Added cycle, middleman, fan-in and fan-out clustering versions for directed graphs.

Enhancements:

• connect_* functions now return only the newly created edges when some edges are dropped due to ignore_invalid argument
• make_spatial now works properly when only positions are provided during graph initialization.
• improved graph drawings:
  • corrected restrict nodes
  • add restrict_edges
  • improved fast plot (markers)
  • add colorbar label
  • improved color support (html, vectors)

Bugfixes:

• lattice_rewire now works for undirected networks for any number of edges (and not only when the edge number matches that of a regular lattice)
• correct weight initialization with distributions and loading
• Fixed the copy method:
  • correct initialization of edge attributes upon graph copy
  • solved issue with copy of undirected graphs becoming directed upon copy
  • use of copy is now forbidden with MPI

2.0.1 patch: install and RNGs on windows

This patch simply fixes the installation on Windows as well as random generators seeding on this platform.
For an overview of the latest changes associated to the move to major version 2.0, please see the 2.0.0 release.