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CHANGELOG.rst

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1.1.0

  • Adds newick output format, available on the build and search CLI commands
  • Adds progress reporting powered by tqdm for taxonomy download, reading, building and searching
  • Adds CLI tests, improves tree tests and increases test coverage overall
  • Some other improvements and updates to README.rst

1.0.0

0.3.2

  • Updates README

0.3.1

  • Fixed the 'publishing to PyPI' action

0.3.0

  • Moved to use pyproject.toml and Poetry for packaging
  • Improved type hint annotations

0.2.1

  • Re-added the "filter" option to the TaxonResolver class and CLI
  • Several improvements in usability and consistency

0.2.0

  • Improved performance with Nested Sets
  • Added new pandas dependency
  • Tree "schema" stored as a pandas DataFrame
  • Modified Preorder Tree Traversal markup is used for quick tree search
  • Improved search times by reducing the number of subtrees searched
  • Additional optimisations by using Python sets
  • Updated description in the README.rst

0.1.0

  • Removed the "Any Python Tree" anytree dependency
  • Large refactoring and rewrite of the TaxonResolver class
  • Removed TaxonResolverFast and fast mode
  • New test cases based on a mock tree testdata/nodes_mock.dmp
  • Simplified usage of the class and CLI
  • Only currently working with pickle format for writing and loading
  • Searching takes included, excluded and filter lists of TaxIDs
  • Validation only takes included TaxIDs
  • CLI search and validate can take multiple TaxIDs at once

0.0.6

  • Additional fixes and improvements for missing and invalid TaxIDs

0.0.5

  • Brought TaxonResolverFast in line with the functionality of TaxonResolver
  • Searching and validation based on lists of TaxIDs (instead of relying only on files)
  • Updated CLI to take multiple filter files
  • Updated CLI to take comma-separated values for search and validation
  • CLI writes to STDOUT by default for search and validation
  • Capturing a list TaxIDs used for filter, which allows searching and validation without having to provide them again

0.0.4

  • Fixed the logic under validation and searching
  • Added TaxonResolverFast class for faster searching and validation (but it requires a built Tree)
  • Added --mode 'fast' mode to the CLI

0.0.3

  • Improved filtering and searching functions
  • Searching performs validation to prevent searching exceptions/errors
  • Added search/validate 'by taxid' methods
  • Added cached search as an option

0.0.2

  • Added wrapper class and methods to work with the Taxonomy Resolver
  • Added functions to build a Tree and converting it to anytree Tree (with re-parenting)
  • Added command-line interface (CLI) with sub-commands for common functions

0.0.1

  • Started development