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CHANGELOG.md

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Change Log

Unreleased

  • nothing yet

v0.8.1

Changed

  • primer scheme and associated fields are now optional
  • .fastq.gz files now work correctly for paired samples
  • reports (during ncbi_submit check) now come out in numerical rather than alphabetical order
  • submission title uses subdir if plate not provided

v0.8.0

Added

  • can now edit how fastq files are discovered for each sample in config

Changed

  • fixed previously untested ability to submit paired reads

v0.7.0

Added

  • can now prepare/submit BioProject portion of XML (not yet tested with biosample/sra in the same submission, but it works alone)

Changed

  • updated readme

v0.6.0

Added

  • can now submit only the samples being updated based on what appears in spuid_endings, with the flag --update_only

v0.5.0

Changed

  • readme reflects new behavior
  • example files can be produced
  • ftp now has subparsers for check/submit rather than --check/--submit arguments
  • fixed bug filling empty bs attributes with bp accession
  • handles sample names contained in other sample names - assumes name will always be separated from the rest of the filename by one of ".", "-", "_"

Added

  • can compile all biosample accessions from lab's ftp submissions
  • can now prepare xml for read updates alongside regular submissions
  • can now resubmit xml (in case of errors in original submission)

v0.4.6

Changed

  • --fastq_dir not required if checking on submission
  • verifies existance of any provided filenames or raises FileNotFound
  • fixed primer scheme determination
  • various minor syntax edits

Removed

  • unused imports

v0.4.5

Changed

  • fastq.gz files are allowed (instead of just fastq files)

v0.4.4

Changed

  • fixed check for excludables
  • fixed filling na as bioproject
  • minor printout adjustments
  • minor cleanup

v0.4.3

Changed

  • fixed readme
  • fixed missing text with unimplemented _offer_skip_option

v0.4.2

Changed

  • Readme reflects new behavior
  • Readme improved
  • improved setup.py
  • fixed a helper function

v0.4.1

Changed

  • ./example dir is actually included, now

v0.4.0

Added

  • Made config.py/template.sbt accessible
    • Can now create (semi-)generic config & template files via ncbi_submit example
  • ./example dir should now be part of package

Changed

  • Now check that outdir is not a file and create before doing much else

Removed

  • ./config directory - merged contents into ./example

v0.3.2 (First fully-functional version)

Changed

  • Fixed some issues with logging
  • Edited to README to fit with recent changes
  • Fixed some field name access issues (how config variable sars_cov_2_diag_pcr_ct_values is used)

v0.3.1

Changed

  • Reconfigured a few arguments in arguments.py for better command line usage

v0.3.0

Added

  • Can get version from within scripts
  • Logging

Changed

  • How version number was accessed

v0.2.2 - v0.2.8

Changed

  • Dependency edits because PyPI and test.PyPI had me confused

v0.2.0 / v0.2.1

Changed

  • Restructured code to fit poetry's typical packaging format

v0.1.0

Added

  • First attempt at reconfiguring and packaging this project
    • All features exist within the main code
    • Still plenty of bugs
  • Versioning