Skip to content

Latest commit

 

History

History
341 lines (198 loc) · 22.1 KB

CHANGELOG.md

File metadata and controls

341 lines (198 loc) · 22.1 KB

Changelog

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)

0.5.1 (2024-02-27)

Bug Fixes

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

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)

0.4.2 (2023-12-21)

Code Refactoring

  • switching terminology from blackhole to hub (c0edfca)

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)

0.4.0 (2023-12-15)

chore

Features

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

0.3.4 (2023-12-12)

Bug Fixes

  • iteratively removing blackholes until convergence (976c8d1)

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)

0.3.2 (2023-11-27)

Bug Fixes

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

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)

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)

0.2.0 (2023-11-14)

Continuous Integration

  • removing conventional-prs.yaml (ef78901)
  • temporarily removing pylint from pre-commit and ci (d821f19)

Features

  • edges now show the split and type distance in their labels (51c5c00)

Bug Fixes

  • colouring the original communities, pre-typing, in the type command (0fc3821)
  • removing redundant attribute BlackholeGraph._original_graph (4e622e0)

Tests

  • updating tests/data/communities.pkl (11c4588)

0.1.7 (2023-11-14)

Continuous Integration

  • now correctly making release-pypi deploy to pypi once a release is published (f05f764)

0.1.6 (2023-11-13)

Continuous Integration

  • allowing release-pypi workflow to be manually triggered (38b8edc)

0.1.5 (2023-11-13)

Continuous Integration

  • running release-pypi when release is published (442bdb6)

0.1.4 (2023-11-13)

Continuous Integration

  • release-pypi now triggered when a release is created (8bcb724)

0.1.3 (2023-11-13)

Continuous Integration

  • automatically uploading plasnet results to gh-pages (97a434e)
  • just generating new visualisations with pushes to the main branch (3babbcb)
  • setting up poetry before installing (e345f4b)

Documentation

  • adding links to the latest visualisations to README (4af8669)

0.1.2 (2023-11-13)

Build System

  • adding coverage to dev deps (263646d)
  • adding test command to Makefile (6b20632)
  • removing tag command from Makefile (9a7f562)
  • updating make coverage (eecb53f)

Continuous Integration

Miscellaneous Chores

  • updating readme with badges (aa4e700)

Documentation

  • updating README installation and usage (29acd34)

Tests

  • adding integration test data (e718a7b)
  • adding split and type command integration tests (191c049)

0.1.1 (2023-11-13)

Continuous Integration

  • adding release-pypi workflow for tagged commits (4b9df0e)

0.1.0 (2023-11-13)

Build System

  • adding mypy to dev deps (5cac9e6)

Continuous Integration

  • adding convetional-prs action (75015ff)
  • adding release-please action (0cb02c8)
  • improving CI script and installing plasnet (8377b7d)
  • temporarily using python version 3.11 to save resources (cd99d2f)
  • testing ci fail (3c32e95)
  • using the correct default branch (790fd34)

Miscellaneous Chores

  • adding Makefile (b9381ce)
  • adding pylint to dev-deps (45931e5)
  • pre-commit now failing fast and adding commented out pylint hook (dd64f2a)
  • pylint now runs but pre-commit does not fail if it fails (e00ee75)

Features

  • adding colours to subcommunities visualisation (730bcc5)
  • adding commitlint to the repo (b719203)
  • adding conventional commit checking through pre-commit (273d9df)
  • adding flake8, black and isort to dev deps (a192108)
  • adding initial Makefile with pre_commit rule (2b9b32d)
  • adding remove_plasmids() to BaseGraph (be7e729)
  • adding seed-isort-config to auto config known_third_party (42d8879)
  • now adding subcommunity colours to the community vis. in the type subcommand (9f7fe62)
  • now creating objects/communities.tsv file describing the community clustering in the split subcommand (511d677)
  • outputting an objects/typing.tsv file describing the typing for the type subcommand (690fc84)
  • outputting binary objects in the type subcommand (49f0c4c)
  • running pre-commit during CI (3c930e5)

Bug Fixes

  • adding --version to the CLI (7c8aee9)
  • adding more logging to the type subcommand (9168ff9)
  • adding the main import back to plasnet/init.py (1b87f48)
  • addint stubs to mypy and making it strict (dbba7b3)
  • all_subcommunities in the type subcommand is now Subcommunities instead of list[Subcommunities] (ff00cde)
  • BaseGraph.get_induced_components() now actually retruning a BaseGraph (a3e390f)
  • casting Communities to itself (9719792)
  • doing pre-commit linting/formatting properly now (a9f16e4)
  • explicitly exporting attribute 'main' in plasnet package (d8f00d8)
  • fixing BaseGraph and ListOfGraphs typings (8e41e76)
  • fixing BaseGraph constructor and all the hierarchy constructors and adding the label attribute (a3e7916)
  • fixing implementation of CommunityGraph.split_graph_into_subcommunities (6fdacc7)
  • fixing implementation of OutputProducer.produce_subcommunities_visualisation() (6e455f8)
  • fixing small import issue in community_graph.py (83474cd)
  • fixing type subcommand description (7ef7dcf)
  • fixing type subcommand implementation (b99a412)
  • improving linting (bb7fd3a)
  • improving pre-commit config (b066a0f)
  • improving Subcommunities inheritance (345c31f)
  • Improving SubcommunityGraph inheritance and implementing required methods (45e18b4)
  • managing pre-commit configs through .pre-commit-config.yaml (27587a7)
  • now keeping mypy and flake8 logs when pre-committing (7f00712)
  • now outputting subcommunities and refactoring communities outputting (b5b7d68)
  • PlasmidGraph.build() now actually returning a PlasmidGraph (a739a58)
  • plasnet.main() does not return anything (206ea6a)
  • reducing max line length from 120 to 100 (72d8f76)
  • removing husky and commitlint config - all done through pre-commit now (061b5b8)
  • removing redundant noqa (0ccb383)
  • removing verbosity from pre-commits (a82c582)
  • updating pre-commit deps (acae5f6)
  • updating readme (081610d)
  • using the graph label for filename and label instead of generating them on the fly (6a98166)

Code Refactoring

  • adding a comment to Makefile (7fad449)
  • adding an important comment to .pre-commit-config.yaml (5db6074)
  • black (a4d8aa2)
  • black reformatting (a470b9f)
  • extracting class BlackholeGraph from CommunityGraph (0706794)
  • flake8 (0178225)
  • improving overall typing (59ff4e0)
  • isort (8a1a0c6)
  • linting (87cb9f2)
  • OutputProducer.produce_subcommunities_visualisation() now receives Subcommunities instead of list[Subcommunities] (0bfd9e7)
  • removing unused import pickle (5206a38)
  • small typing refactor: List -> list (32d240b)
  • type of our nodes is str (d7fac0b)
  • typing: improving ListOfGraphs.load() typing (68b60ae)
  • unused methods cleanup (223fc13)