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)

v0.2.0

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)

v0.1.7

0.1.7 (2023-11-14)

Continuous Integration

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

v0.1.6

0.1.6 (2023-11-13)

Continuous Integration

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

v0.1.5

0.1.5 (2023-11-13)

Continuous Integration

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

v0.1.4

0.1.4 (2023-11-13)

Continuous Integration

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

v0.1.3

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)

v0.1.2

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

• adding coverage badge (584b9cc)
• CI debugging (72c1b53)
• CI debugging (64d083c)
• now running make coverage (fd0d2c1)
• now running tests in CI (95bc22a)
• trying to fix Coverage Push changes step in CI (44a77cb)

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)

v0.1.1

0.1.1 (2023-11-13)

Continuous Integration

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

v0.1.0

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 clean...