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CHANGELOG.md

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Changelog

To-do

  • Fix documentation issues [ ]
    • Add subpackage docstrings [ ]
  • Create methods for Sample and Project
    • .describe []
    • .write_paths_to_file, .copy_files_to_dir(), .link_files_to_dir()

v0.1.18a

  • Patch file deserializer bug [x]

v0.1.18

  • Add support for ProvStore API (#23) [x]
  • Add subparsers for CLI commands [x]
  • Add Directories class to Files module [x]
    • Support globbing Directory outputs [x]
  • Increase test coverage [x]
  • Added more example data [x]
  • Make config.threads an integer to support operations [x]

v0.1.17

  • Add more database methods [x]
  • Improver error handling for JSON methods [x]
  • Add Project.run_programs method [x]
  • Create ProvEntity and ProvActivity for Project.files and .programs [x]
    • Create Project Bundle for .files and .programs [x]

v0.1.16

  • Update README [x]
  • Add Project.add_files() and add_programs() method [x]
  • Improve Project deserializer [x]
  • Add Project steps to Workflow class [x]

v0.1.15

  • Improve Sample.to_series() and Project.to_csv() methods [x]
  • Add Project.to_csv() calls to tests [x]
  • Add database commands to CLI options [x]
  • Remodel environment as Agent rather than Entity [x]
  • Improve output PROVN documents [x]
  • Add Diamond preset and tests [x]

v0.1.14

  • Add blastdb example data [x]
  • Add BLASTn preset and workflow and respective tests [x]
  • Improve BioProvDB tests [x]
  • Improve Project.auto_update and Project.sha1 behaviour and tests [x]
  • Improve Workflow behaviour for custom Workflow arguments [x]

v0.1.13

  • Add BioProvDB class [x]
  • Add database methods to Project class [x]
  • Add BioProvDB tests [x]
  • Add dot attribute to BioProvDocument [x]
  • Update W3C-PROV tutorial [x]
  • Improve test coverage [x]
  • Debug Program deserializer [x]

v0.1.12

  • Patching errors for JSON IO [x]
    • Create File, Program, Run deserializers [x]
  • Implement path replacing methods for multi-user support [x]

v0.1.11

  • Fix Run.start_time and Run.end_time testing [x]
  • Improve Program tests [x]
  • Allow users to have multiple environments [x]
  • Improving internal PROV relationships [x]

v0.1.10

  • Refactoring hashes using hashlib [x]
  • Removing EnvProv.env_set attribute [x]
  • Implementing file hashes [x]
  • Debug EnvProv JSON deserializer [x]
  • Updating introductory tutorial [x]

v0.1.9

  • Improve Env constructor in Project deserializer [x]
  • Improve Program behaviour when dealing with not found Programs [x]
  • Implement utils.serializer_filter function [x]
  • Improve pretty printing of commands [x]

v0.1.8

  • Improve BioProvDocument constructor [x]
  • Improve Sample and Program serializers [x]
  • Improve internal PROV relationships [x]

v0.1.7

  • Fix documentation build [x]
  • Refactor f-strings [x]
  • Draft of complete Prov document (all relationships) [x]

v0.1.6

  • Add more Provenance classes [x]
  • Improve Provenance graph [x]
  • Add contributing guidelines [x]
  • Refactor config and prov modules [x]
  • Add CLI options to show config [x]
  • Rename src.program to src.main [x]
  • Refactoring tests: joining src.program and src.sample tests into src.main [x]

v0.1.5

  • Add W3C-PROV tutorial [x]
  • Small tweaks to default arguments in Program and File module [x]

v0.1.4

  • Fix PresetProgram.add_parameter bug [x]
  • Add basic Tutorial [x]
  • Refactor SeqStats data class [x]
  • Improve Provenance classes [x]

v0.1.3

  • Patching more JSON IO bugs [x]

v0.1.2

  • Refactor functions in src.files module [x]
  • Add support for BioPython AlignIO module [x]
  • Patching src.program module [x]
  • Improving JSON serializers [x]