HyperNetX - v2.4.1

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.4.0...v2.4.1

Hotfix for #169

Scientific Software - Peer-reviewed - Python
Published by ryandanehy 8 months ago

HyperNetX - v2.4.0

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.3.11...v2.4.0

Main changes are our brand new visualizations.

Scientific Software - Peer-reviewed - Python
Published by ryandanehy 10 months ago

HyperNetX - v2.3.13

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.3.11...v2.3.13

Updating factory dict method to deepcopy dict updates to documentation

Scientific Software - Peer-reviewed - Python
Published by ryandanehy 11 months ago

HyperNetX - v2.3.12

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.3.10...v2.3.12

moving request into methods to simplify hnx import

Scientific Software - Peer-reviewed - Python
Published by ryandanehy 11 months ago

HyperNetX - v2.3.11

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.3.10...v2.3.11

fixed the link to documentation in Long Description and README updated contributor lists on both documents.

Scientific Software - Peer-reviewed - Python
Published by ryandanehy 11 months ago

HyperNetX - v2.3.10

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.3.9...v2.3.10

Changes by made by @brendapraggastis

HIF.py addition

Scientific Software - Peer-reviewed - Python
Published by ryandanehy about 1 year ago

HyperNetX - v2.3.9

Hotfixes

• changes submitted by @brendapraggastis

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.3.8...v2.3.9

Scientific Software - Peer-reviewed - Python
Published by ryandanehy about 1 year ago

HyperNetX - v2.3.8

Hotfixes

• changes submitted by @myersau3

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.3.7...v2.3.8

Scientific Software - Peer-reviewed - Python
Published by ryandanehy about 1 year ago

HyperNetX - v2.3.7

Hotfixes

• changes submitted by ft on 7.25 by @brendapraggastis in https://github.com/pnnl/HyperNetX/pull/161

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.3.6...v2.3.7

Scientific Software - Peer-reviewed - Python
Published by ryandanehy over 1 year ago

HyperNetX - v2.3.6

Hotfixes

• Fixes failing test_hypergraph.py test

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.3.5...v2.3.6

Scientific Software - Peer-reviewed - Python
Published by ryandanehy over 1 year ago

HyperNetX - HNX v2.3.5

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.3.4...v2.3.5

Scientific Software - Peer-reviewed - Python
Published by ryandanehy over 1 year ago

HyperNetX - HNX v2.3.4

Hotfixes

• Fixes #151

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.3.3...v2.3.4

Scientific Software - Peer-reviewed - Python
Published by bonicim over 1 year ago

HyperNetX - HNX v2.3.3

What's New

• Added capability to run HyperNetX in a Docker container; see HyperNetX repo at DockerHub

What's Changed

• Updated CI scripts
• Added pushing to DockerHub upon new release to CD scripts

Fixes

• Fixed typos in README
• Fixed typos and image URL in Sphinx documentation
• Fixed versioning tool configuration

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.3.2...v2.3.3

Scientific Software - Peer-reviewed - Python
Published by bonicim over 1 year ago

HyperNetX - HNX v2.3.2

What's Changed

• Fix typos in documenatation
• Update (readthdocs) documentation scripts to use poetry
• Remove unnecessary documentation Workflow
• Update core dependencies to be more loosely constrained
• Remove CI/CD scripts from Makefile
• Remove CI/CD instructions from Readme
• Update requirements.txt
• Bump werkzeug from 3.0.2 to 3.0.3 by @dependabot in https://github.com/pnnl/HyperNetX/pull/153
• Bump jinja2 from 3.1.3 to 3.1.4 by @dependabot in https://github.com/pnnl/HyperNetX/pull/152

New Contributors

• @dependabot made their first contribution in https://github.com/pnnl/HyperNetX/pull/153

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.3.1...v2.3.2

Scientific Software - Peer-reviewed - Python
Published by bonicim over 1 year ago

HyperNetX - HNX v2.3.1

Hotfixes

• Add decorator dependency
• Update poetry.lock
• Fix publish pypi workflow

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.3.0...v2.3.1

Scientific Software - Peer-reviewed - Python
Published by bonicim over 1 year ago

HyperNetX - HNX v2.3.0

HyperNetX 2.3

HyperNetX 2.3. is the latest, stable release. The core library has been refactored to take better advantage of Pandas Dataframes, improve readability and maintainability, address bugs, and make it easier to change. New features have been added, most notably the ability to add and remove edges, nodes, and incidences. Updating is recommended.

Version 2.3 is not backwards compatible. Objects constructed using earlier versions can be imported using their incidence dictionaries and/or property datafames.

What's New

• We've added new functionality to Hypergraphs; you can add and remove nodes, edges, and incidences on Hypergraph.
• Arithmetic operations have also been added to Hypergraph: sum, difference, union, intersection
• We've also added a new tutorial on basic hypergraph arithmetic operations
• Under the hood, the EntitySet has been replaced by HypergraphView, new factory methods have been created to support the Hypergraph constructor, and internal classes such as IncidenceStore and PropertyStore help maintain the structure and attributes of a Hypergraph

What's Changed

• Documentation has received a major update; the Glossary and docstrings of Hypergraph have been updated.
• HNX now requires Python ^3.10,<=3.12
• We've upgraded all the underlying core libraries to the latest versions.

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.2.0...v2.3.0

Scientific Software - Peer-reviewed - Python
Published by bonicim over 1 year ago

HyperNetX - HNX v2.2.0p

This is release for the HyperNetX paper to be reviewed and published under the Journal of Open Source Software (JOSS).

The main difference between v2.2.0 and v2.2.0p is that this release contains documents, images, and scripts related to the HyperNetX paper. There are no source code changes.

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.2.0...v2.2.0p

Scientific Software - Peer-reviewed - Python
Published by bonicim almost 2 years ago

HyperNetX - HNX v2.2.0

Improvements

• Update drawing submodule
• Reorganize tutorials
• Update documentation, README
• Update dependencies
• Update CI/CD scripts, Makefile
• Updated tests

Fixes

• Fixes minor bugs in Hypergraph constructor and helper method

What's Changed

• dependencies: change python-igraph to igraph by @szhorvat in https://github.com/pnnl/HyperNetX/pull/117

New Contributors

• @szhorvat made their first contribution in https://github.com/pnnl/HyperNetX/pull/117

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.1.4...v2.2.0

Scientific Software - Peer-reviewed - Python
Published by bonicim almost 2 years ago

HyperNetX - HNX v.2.1.4

Fixes

• Addresses JOSS-paper related issues: #142, #143, #144, and #145.
• Updates optional dependencies

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.1.3...v2.1.4

Scientific Software - Peer-reviewed - Python
Published by bonicim almost 2 years ago

HyperNetX - HNX v2.1.3

Fixes

• Addresses issues #133, #132, #130, #129, and #128.

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.1.2...v2.1.3

Scientific Software - Peer-reviewed - Python
Published by bonicim about 2 years ago

HyperNetX - HNX v2.1.2

Improvements

• Make LICENSE.rst OSI compliant; resolves #127

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.1.1...v2.1.2

Scientific Software - Peer-reviewed - Python
Published by bonicim about 2 years ago

HyperNetX - HNX v.2.1.1

Improvements

• Update modularity docs

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.1.0...v2.1.1

Scientific Software - Peer-reviewed - Python
Published by bonicim about 2 years ago

HyperNetX - HNX v2.1.0

Improvements, Enhancements

• Refactor hypergraph_modularity; add tutorial; thank you @ftheberge
• Add conductance, tests; thank you @NicolBuratti @uninicol

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.0.5...v2.1.0

Modularity module updates

Unchanged functions:

• dict2part(D)
• part2dict(A)
• linear(d, c)
• majority(d, c)
• strict(d, c)
• two_section(HG)
• kumar(HG, delta=0.01, verbose=False)

No longer required

• precompute_attributes(H)
• computepartition_probas(HG, A)
• degreetax(HG, Pr, wdc)
• edgecontribution(HG, A, wdc)
• deltaec(HG, P, v, a, b, wdc)
• binppmf(d, c, p)
• deltadt(HG, P, v, a, b, wdc)

New version

• modularity(HG, A, wdc=linear)
• last_step(HG, L, wdc=linear, delta=0.01, verbose=False)

New (hidden) functions

• laststep_unweighted
• laststep_weighted

Scientific Software - Peer-reviewed - Python
Published by bonicim about 2 years ago

HyperNetX - HNX v2.0.5

Fixes

• Updates docstrings and documentation examples for Hypergraph.collapse_nodes and Hypergraph.collapse_nodes_and_edges methods
• Enables deprecation warnings for Hypergraph class to be displayed on REPL, Jupyter Notebooks

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.0.4...v2.0.5

Scientific Software - Peer-reviewed - Python
Published by bonicim about 2 years ago

HyperNetX - HNX v2.0.4

Fixes

• Fixes errors in Jupyter where H.dataframe and H.dual().dataframe had common references.

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.0.3...v2.0.4

Scientific Software - Peer-reviewed - Python
Published by bonicim over 2 years ago

HyperNetX - HNX v2.0.3

Fixes

• Fix bug on remove method Hypergraph class

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.0.2...v2.0.3

Scientific Software - Peer-reviewed - Python
Published by bonicim over 2 years ago

HyperNetX - HNX v2.0.2

Fixes:

• Fix import statements in Collab tutorials
• Update CD workflow

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.0.1...v2.0.2

Scientific Software - Peer-reviewed - Python
Published by bonicim over 2 years ago

HyperNetX - HNX v2.0.1

Fixes

• Fix search capability in documentation
• Update and reorganize tutorials
• Update centrality tutorial
• Cleanup Makefile; fix and update README and tutorial 1

Full Changelog: https://github.com/pnnl/HyperNetX/compare/v2.0.0...v2.0.1

Scientific Software - Peer-reviewed - Python
Published by bonicim over 2 years ago

HyperNetX - HNX v2.0.0

New Features in Version 2.0

HNX 2.0 now accepts metadata as core attributes of the edges and nodes of a hypergraph. While the library continues to accept lists, dictionaries and dataframes as basic inputs for hypergraph constructions, both cell properties and edge and node properties can now be easily added for retrieval as object attributes.

The core library has been rebuilt to take advantage of the flexibility and speed of Pandas Dataframes. Dataframes offer the ability to store and easily access hypergraph metadata. Metadata can be used for filtering objects, and characterize their distributions by their attributes.

Version 2.0 is not backwards compatible. Objects constructed using version 1.x can be imported from their incidence dictionaries.

What's New

1. The Hypergraph constructor now accepts nested dictionaries with incidence cell properties, pandas.DataFrames, and 2-column Numpy arrays.
2. Additional constructors accept incidence matrices and incidence dataframes.
3. Hypergraph constructors accept cell, edge, and node metadata.
4. Metadata available as attributes on the cells, edges, and nodes.
5. User-defined cell weights and default weights available to incidence matrix.
6. Meta data persists with restrictions and removals.
7. Meta data persists onto s-linegraphs as node attributes of Networkx graphs.
8. New hnxwidget available using pip install hnxwidget.

What's Changed

1. The static and dynamic distinctions no longer exist. All hypergraphs use the same underlying data structure, supported by Pandas dataFrames. All hypergraphs maintain a state_dict to avoid repeating computations.
2. Methods for adding nodes and hyperedges are currently not supported.
3. The nwhy optimizations are no longer supported.
4. Entity and EntitySet classes are being moved to the background. The Hypergraph constructor does not accept either.

Scientific Software - Peer-reviewed - Python
Published by bonicim over 2 years ago

HyperNetX - HNX v1.2.5 Hotfix

• Fixes factory method of hypergraph constructor
• Fixes ModuleNotFoundError on decorator dependency
• Adds automated test tool
• Updates tests

Scientific Software - Peer-reviewed - Python
Published by bonicim over 3 years ago

HyperNetX - HNX 1.2.4 hotfix/hyp-254

Fixed bug for Hypergraph.size(). Gave incorrect value when nodeset was empty set.

Scientific Software - Peer-reviewed - Python
Published by brendapraggastis over 3 years ago

HyperNetX - HNX 1.2.3 Hotfix

fixes bug in dist_stats, which did not handle dynamic hypergraphs properly.

Scientific Software - Peer-reviewed - Python
Published by brendapraggastis almost 4 years ago

HyperNetX - HNX 1.2.2 Hotfix

Updated setup.py to include celluloid and igraph as required modules during install.

Scientific Software - Peer-reviewed - Python
Published by noah-farris about 4 years ago

HyperNetX - New Modularity and Clustering Module

Added module and tutorial for hypergraph modularity and clustering. Several Bug fixes

Scientific Software - Peer-reviewed - Python
Published by brendapraggastis about 4 years ago

HyperNetX - HNX 1.1.3 bugfix

• fixed size and degree bugs in hypergraph
• updated Tutorial 8 to work without nwhy
• fixed bug in Tutoral 10

Scientific Software - Peer-reviewed - Python
Published by brendapraggastis over 4 years ago

HyperNetX - Bugfix for Adjacency Matrix

Bugfix for adjacency matrix. Cell weighting is currently only supported for incidence matrices. User will need to determine appropriate use of weights for adjacency matrix according to their application for now. Static nodes and edges can have attributes set through the StaticEntity class. Use s-parameter to generate s-linegraph adjacency matrix and networkx generated graph with node and edge attributes read from data.

Scientific Software - Peer-reviewed - Python
Published by brendapraggastis over 4 years ago

HyperNetX - HNX v1.1

1. Static Hypergraph refactored to improve performance across all methods.
2. Added modules and tutorials for Contagion Modeling, Community Detection, Clustering, and Hypergraph Generation.
3. Cell weights for incidence matrices may be added to static hypergraphs on construction.
4. Changed nodes and edges to UserLists with the option to add properties in Static Hypergraph.
5. Static Hypergraph nodes has membership property for fast look up of edges incident to a node.

Scientific Software - Peer-reviewed - Python
Published by brendapraggastis over 4 years ago

HyperNetX - HNX 1.0.4 bugfix

removed merge conflict that was pushed by accident

Scientific Software - Peer-reviewed - Python
Published by brendapraggastis over 4 years ago

HyperNetX - Correcting imports for colab tutorials - bugfix

Scientific Software - Peer-reviewed - Python
Published by brendapraggastis over 4 years ago

HyperNetX - HNX 1.0.4

Linked data for tutorials to github files for use with colab.

Scientific Software - Peer-reviewed - Python
Published by brendapraggastis over 4 years ago

HyperNetX - Bug fix

Bug fix, import missing

Scientific Software - Peer-reviewed - Python
Published by brendapraggastis over 4 years ago

HyperNetX - HNX 1.0.0

New Features of Version 1.0:

1. Hypergraph construction can be sped up by reading in all of the data at once. In particular the hypergraph constructor may read a Pandas dataframe object and create edges and nodes based on column headers. The new hypergraphs are given an attribute static=True.
2. A C++ addon called NWHy can be used in Linux environments to support optimized hypergraph methods such as s-centrality measures.
3. A JavaScript addon called Hypernetx-Widget can be used to interactively inspect hypergraphs in a Jupyter Notebook.
4. We've added four new tutorials highlighting the s-centrality metrics, static Hypergraphs, NWHy, and Hypernetx-Widget.

Scientific Software - Peer-reviewed - Python
Published by brendapraggastis over 4 years ago

HyperNetX - s_centrality_module

• add 3 methods for computing s-centrality plus tests
• updated documentation
• optimized homology to leverage boolean operations

Scientific Software - Peer-reviewed - Python
Published by brendapraggastis over 5 years ago

HyperNetX - updated setup

• fixed errors in setup file, algorithms were not added in
• fixed bug in tutorial

Scientific Software - Peer-reviewed - Python
Published by brendapraggastis almost 6 years ago

HyperNetX - documentation update

• fixed bug in tutorial
• regenerated documentation with correct version number

Scientific Software - Peer-reviewed - Python
Published by brendapraggastis almost 6 years ago

HyperNetX - optimization for homology mod2

updated homology mod2 to run faster

Scientific Software - Peer-reviewed - Python
Published by brendapraggastis almost 6 years ago

HyperNetX - upgrade for homology

Homology mod 2 using Smith Normal Form available for small examples Constructors for numpy matrix and pandas dataframe added

Scientific Software - Peer-reviewed - Python
Published by brendapraggastis almost 6 years ago

HyperNetX - hotfix/hyp-109

updated code to be compatible with NetworkX 2.4. removed untested code that should not have been pushed

Scientific Software - Peer-reviewed - Python
Published by brendapraggastis almost 6 years ago

HyperNetX - hotfix/hyp-43

fixed drawing/rubber_band.py so edge labels won't disappear

Scientific Software - Peer-reviewed - Python
Published by brendapraggastis almost 6 years ago

HyperNetX - fixed Hypergraph.restrict_to_nodes

The Hypergraph.restricttonodes function was deleting memberships of nodes. We updated the method. now the new restricted hypergraph does not share edges or nodes with the original hypergraph, although the reference uids will remain the same.

Scientific Software - Peer-reviewed - Python
Published by brendapraggastis over 6 years ago

HyperNetX -

Scientific Software - Peer-reviewed - Python
Published by brendapraggastis almost 7 years ago

HyperNetX - First PYPI release

Scientific Software - Peer-reviewed - Python
Published by brendapraggastis almost 7 years ago

HyperNetX - HyperNetX v.0.2

Scientific Software - Peer-reviewed - Python
Published by devcentral-pnnl almost 7 years ago