v0.6.0

0.6.0 (2024-08-19)

Features

• Allow user to ask for cytoscape compatible json files so they can load the network directly into cytoscape if they want. Default remains the html visualisation. (aeee623)
• Created a style file which can be loaded into cytoscape. This will colour nodes and label edges like in the html visualisations plasnet produces by default. To be used in conjugtion with json files directly in cytoscape. Does not include a layout. Is not outputted by plasnet at any point, as it doesn't change between datasets and only needs to be loaded into cytoscape once. (db36474)

Bug Fixes

• adding output_type to add_sample_hits() (792774f)
• Remove weights from asynchronuous label propagation algorithm (e7cccfc)
• removing unused variable relative_json_path (eab515e)

v0.5.1

0.5.1 (2024-02-27)

Bug Fixes

• fix bug: key error exception when building RH PLSDB DB (3175ca5)

v0.5.0

0.5.0 (2023-12-21)

Features

• now creating a hub_plasmids.csv file when running the plasnet type command explicitly listing each hub plasmid (214fb9e)

v0.4.2

0.4.2 (2023-12-21)

Code Refactoring

• switching terminology from blackhole to hub (c0edfca)

v0.4.1

0.4.1 (2023-12-19)

Bug Fixes

• add parameter use_cached to BlackholeGraph._get_blackhole_plasmids(), solving the slowdown introduced in releases v0.3.3 and v0.3.4 (fc7685e)

v0.4.0

0.4.0 (2023-12-15)

chore

• release 0.4.0 (a6b7441)

Features

• now we can provide metadata to plasmids (param --plasmids-metadata in plasnet split) (46df1b5)

v0.3.4

0.3.4 (2023-12-12)

Bug Fixes

• iteratively removing blackholes until convergence (976c8d1)

v0.3.3

0.3.3 (2023-12-12)

Continuous Integration

• just running coverage if python version is 3.11 (2084763)

Bug Fixes

• fix a bug where plasnet was not correctly recognising blackholes in type command (92bbefa)

v0.3.2

0.3.2 (2023-11-27)

Bug Fixes

• now setting the default colour for blackhole plasmids instead of erroring out with KeyError (fa966d2)

v0.3.1

0.3.1 (2023-11-17)

Continuous Integration

• re-enabling python versions 3.8, 3.9 and 3.10 in the CI tests (c30c2a0)

Documentation

• small fix to the link of add-sample-hits output in README.md (ef945bf)