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)

v0.3.0

0.3.0 (2023-11-17)

Documentation

• updating README.md with add-sample-hits subcommand documentation (2df8bc5)

Features

• adding ListOfSampleGraphs class (0b29530)
• adding SampleGraph class (e673f36)
• adding subcommand add-sample-hits (34c25b9)

Bug Fixes

• adding SampleGraph.from_subcommunity_graph() (398d863)
• fixing BaseGraph.get_induced_components() (d9e277c)
• fixing HTML sample filters production (8db01bc)
• fixing OutputProducer.produce_subcommunities_visualisation() typing (90875c4)
• fixing SampleGraph constructor (f5edfb0)
• removing unused tag in index_template.html (33d9690)

Code Refactoring

• adding attribute description to BaseGraph instead of computing it when producing visualiation (a2496fc)
• adding attribute path to BaseGraph instead of computing it when producing the visualisation (4367bc0)
• adding method ListOfGraphs.get_graphs_sorted_by_size() instead of computing this during visualisation (69d1db7)
• big refactor in OutputProducer, using the previous changes to produce visualisation (750a8de)
• graph parameter in BaseGraph classes and its subclasses is now properly typed as Optional (09f92cf)
• ListOfSampleGraphs -> SampleGraphs (9062ca2)
• removing old code to add sample hits from BaseGraph (4445907)

Tests

• adding add-sample-hits integration test (f700e88)
• adding subcommunities pickle to test data (d216dcc)
• updating test data (6e33af4)