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CHANGELOG.md

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Release history

1.2.3 (2023-02-13)

  • fix: rptools version restriction

1.2.2 (2023-02-08)

  • fix: numpy version restriction

1.2.1 (2023-01-06)

  • chore(test_Construct.py): compare based on Component URIs
  • chore(test.yml): transition to mamba for GA
  • chore: fix github action workflows

1.2.0 (2022-12-05)

  • chore(Designer): add type hint
  • fix(Designer): prevent StopIteration exception
  • fix(Designer): follow csv writer end of line recommandation

1.1.1 (2022-08-23)

  • fix(test_Construct.py): update hash probably due to a new version of lxml library
  • test(test_get_sbol_new.txt): add an output test file for debugging (function test_get_sbol)

1.1.0 (2022-05-05)

  • feat(cli): expose max number of gene to CLI args
  • docs(README): update
  • chore: remove deprecated code

1.0.1 (2022-03-25)

  • fix(test_Construct.py): update hash for sbol output

1.0.0 (2022-03-23)

  • feat(cli.py): SBOL output dir is now optional
  • fix(cli.py): update default number of constructs
  • docs(README): update
  • build(meta.yaml): remove unneeded library

0.3.4 (2021-10-25)

  • docs: add README about the lycopene file
  • feat: get enzyme IDs from selenzy annotation
  • chore: update example with new selenzy output file
  • build: make use of rptools library

0.3.3 (2021-10-22)

  • fix: handle correctly multiple UniProt IDs per reaction
  • fix: ID based workaround to generate duplicate parts in SBOL

0.3.2 (2021-10-15)

  • fix: generate plate coordinates by columns
  • fix: output up to 88 constructs, not 96
  • docs: provide example for the lycopene pathway

0.3.1 (2021-07-22)

  • style(cli): show default values in help
  • feat(cli): add cds_permutation arg
  • feat(Designer): export the biolegio plate file

0.3.0 (2021-07-20)

  • docs(README): update info on RBS naming pattern
  • docs: provides an example of the --parts_file option
  • fix(Designer): fix the way combinatorics is built
  • !fix: constructs are always polycistronic

0.2.2

  • fix(Designer): raise exception if no linkers / parts provided

0.2.1

  • fix(Designer): _parts_files not defined

0.2.0

  • feat: single argument for all part files (linker, user)
  • feat: remove the need for the linker plate file
  • fix(Designer): uniprot ID extraction
  • docs(README): update input section
  • docs(README): update command line example

0.1.1

  • test(test_designer.py): fix unsuccessful test (output file renamed)
  • build(environment.yaml): fix sbol2 package not found (due to package new name)
  • fix(designer): fix spelling in output files
  • build(recipe): update dependencies
  • build: no longer need brsynth conda channel, pysbol2 is in conda-forge

0.1.0

  • fix(designer): fix random generation not "reproductible" with a fixed seed
  • refactor: separate classes
  • fix: fix loading of default data
  • docs(readme): add developer section
  • fix: update dependancies to sbol2 as pysbol is deprecated
  • refactor(cli): build polycistronic constructs by default
  • feat: refine part and linker attributes, predict linker suffix and prefix

0.0.2

  • Packaged version

0.0.1

  • Hello, world