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Add network graph format converters: GML, Pajek, GraphML#357

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cokelaer merged 2 commits intomainfrom
copilot/add-simple-network-readers
Mar 6, 2026
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Add network graph format converters: GML, Pajek, GraphML#357
cokelaer merged 2 commits intomainfrom
copilot/add-simple-network-readers

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Copilot AI commented Mar 6, 2026 •
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Addresses the need for network format readers/converters in bioconvert. Implements bidirectional conversions between three widely-used network formats using networkx.

New formats registered

  • gml → .gml
  • pajek → .net
  • graphml → .graphml
  • gexf → .gexf (registered for future use)

New converters (6)

All use networkx via @requires(python_library="networkx"):

Module Conversion
gml2pajek / pajek2gml GML ↔ Pajek
gml2graphml / graphml2gml GML ↔ GraphML
pajek2graphml / graphml2pajek Pajek ↔ GraphML 
from bioconvert.gml2pajek import GML2PAJEK

converter = GML2PAJEK("network.gml", "network.net")
converter()  # method="networkx" by default

Test data

Simple 3-node directed graph added in test/data/{gml,pajek,graphml}/ for use across all converter tests. Tests validate node/edge count preservation across format round-trips.

Original prompt

This section details on the original issue you should resolve

<issue_title>Network convertors</issue_title>
<issue_description>We need simple readers for

  • SIF (cytoscape) (I've got some code already TC)
  • Pajek
  • GML https://github.com/kgn/pygml
  • NNF
  • SBML (qual) (I've got some code already)
  • PSI-MI
  • Biopax

conversions between formats is not always possible though.

reference: http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats

See also igraph, networkx packages and Gephi (https://gephi.org/users/supported-graph-formats/)

http://sbfc.sourceforge.net/mediawiki/index.php/Main_Page#Conversion_using_a_console

https://www.ebi.ac.uk/biomodels/tools/converters/results?emailAddress=</issue_description>

Comments on the Issue (you are @copilot in this section)

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@cokelaer
Add network format converters: GML, Pajek, GraphML
c120dd7 
Co-authored-by: cokelaer <778821+cokelaer@users.noreply.github.com>
Copilot AI changed the title [WIP] Add simple readers for various network formats Add network graph format converters: GML, Pajek, GraphML Mar 6, 2026
@cokelaer cokelaer marked this pull request as ready for review March 6, 2026 22:19
@cokelaer cokelaer merged commit 88592c1 into main Mar 6, 2026
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Network convertors

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