0.4.2

Fixed

• TypeClassifier.predict_types using inverse type probabilities when
  given several clusters to process.

0.4.1

Fixed

• gecco run command crashing on input sequences not containing any genes.

0.4.0

Added

• gecco.model.ProductType enum to model the biosynthetic class of a BGC.

Removed

• pandas interaction from internal data model.
• ClusterCRF code specific to cross-validation.

Changed

• pandas, fisher and statsmodels dependencies are now optional.
• gecco train command expects a cluster table in addition to the feature
  table to know the types of the input BGCs.

0.3.0

Changed

• Replaced Nearest-Neighbours classifier with Random Forest to perform type
  prediction for candidate BGCs.
• gecco.knn module was renamed to implementation-agnostic name gecco.types.

Fixed

• Extraction of domain composition taking a long time in gecco train command.

Removed

• --metric argument to the gecco run CLI command.

0.2.2

Changed

• Domain and Gene can now carry qualifiers that are used when they
  are translated to a sequence feature.

Added

• InterPro names, accessions, and HMMER e-value for each annotated domain
  in GenBank output files.

0.2.1

Fixed

• Various potential crashes in ClusterRefiner code.

Removed

• Uneeded feature dictionary filtering in ClusterCRF for models with
  Fisher Exact Test feature selection.

0.2.0

Fixed

• pandas warning about unsorted columns in gecco run.

Removed

• Gene.probability property, replaced by Gene.maximum_probability and
  Gene.average_probability properties to be explicit.

Changed

• Internal model now uses Pfam and Tigrfam with the top 35% features
  selected with Fisher's Exact Test.
• ClusterRefiner now removes genes on Cluster edges if they do not
  contain any domain annotation.

0.1.1

Added

• ClusterCRF.predict_probabilities to annotate a list of Gene.

Changed

• BGC probability is now stored at the Domain level instead of at the Gene
  level, independently of the feature extraction level used by the CRF.
• ClusterKNN will use the model path provided to gecco run if any.

Docs

• Added this changelog file to document changes in the code.
• Added documentation to gecco submodules missing some.
• Included the CHANGELOG.md file to the generated docs.

0.1.0

Initial release.

0.0.1

Proof-of-concept.