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NNGT 2.5.0: sparse clustered graphs and improved backend support

Tanguy Fardet


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  <identifier identifierType="DOI">10.5281/zenodo.3552708</identifier>
  <creators>
    <creator>
      <creatorName>Tanguy Fardet</creatorName>
    </creator>
  </creators>
  <titles>
    <title>NNGT 2.5.0: sparse clustered graphs and improved backend support</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2021</publicationYear>
  <subjects>
    <subject>nngt</subject>
    <subject>neuron</subject>
    <subject>network</subject>
    <subject>graph</subject>
    <subject>topology</subject>
    <subject>python</subject>
    <subject>nest</subject>
    <subject>graph-tool</subject>
    <subject>networkx</subject>
    <subject>igraph</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2021-08-18</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3552708</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsDerivedFrom" resourceTypeGeneral="Text">https://git.sr.ht/~tfardet/NNGT</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsReferencedBy" resourceTypeGeneral="Text">https://nngt.readthedocs.io/en/latest</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3402493</relatedIdentifier>
  </relatedIdentifiers>
  <version>v2.5.0</version>
  <rightsList>
    <rights rightsURI="https://opensource.org/licenses/GPL-3.0">GNU General Public License v3.0 only</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;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).&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;New features&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;sparse_clustered: it is now possible to generate sparse graphs with a desired clustering coefficient, this comes with an associated rewiring scheme (&lt;a href="https://git.sr.ht/~tfardet/NNGT/commit/f45d0a9b8c895066bb59b2d1ee150b452fb7cfd5"&gt;f45d0a9b&lt;/a&gt;)&lt;/li&gt;
	&lt;li&gt;support for GraphML file format (&lt;a href="https://git.sr.ht/~tfardet/NNGT/commit/a9f8710da727dd51fdc01a31e7b8a2dc7d13188a"&gt;a9f8710d&lt;/a&gt;)&lt;/li&gt;
	&lt;li&gt;support NetworkX 2.6+ (&lt;a href="https://git.sr.ht/~tfardet/NNGT/commit/f4e5002ec6f409eb8f2b1af4f70ba8e49877650c"&gt;f4e5002e&lt;/a&gt;)&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;strong&gt;Enhancements&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;More efficient edge attribute access (speed and memory improvements, &lt;a href="https://git.sr.ht/~tfardet/NNGT/commit/c8f29951207274ba830d490e0ebc1361540a5eec"&gt;c8f29951&lt;/a&gt;)&lt;/li&gt;
	&lt;li&gt;Improved plots (color and size support for nodes and edges, visible arrows for directed networks..., &lt;a href="https://git.sr.ht/~tfardet/NNGT/commit/7f5340b8dbd20789d47a8e6a58a80a3cf026a921"&gt;7f5340b8&lt;/a&gt; &amp;amp; &lt;a href="https://git.sr.ht/~tfardet/NNGT/commit/ccdd627f240b43e32ffe8cbce409186fddfc4865"&gt;ccdd627f&lt;/a&gt;)&lt;/li&gt;
	&lt;li&gt;Add connectedness test with nngt default backend (&lt;a href="https://git.sr.ht/~tfardet/NNGT/commit/d3979a1526793df2419368675f3f21a1e7556938"&gt;d3979a15&lt;/a&gt;)&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;&lt;strong&gt;Bugfixes&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;Correct delete_edges for nngt backend that did not update the node degrees (&lt;a href="https://git.sr.ht/~tfardet/NNGT/commit/b1ca08dfa968978a022026c413382b287bf723aa"&gt;b1ca08df&lt;/a&gt;).&lt;/p&gt;</description>
  </descriptions>
</resource>
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