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Release 0.3.0

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@kblin kblin released this 18 Jun 19:29
· 35 commits to master since this release
0.3.0

This is release 0.3.0 of ncbi-genome-download.

This is a release breaking backwards compatibility a bit, hence the new minor
relase number. If you are just using the command line tool, everything should
still work, but note that some of the options have changed to their plural
forms. If you are using the API, you need to update your code to use the new
plural forms of the option names.

This version also no longer supports Python 2.7.

In addition, this version also contains some contributed features or bugfixes:

  • gimme_taxa.py now is installable, thanks Istvan (@ialbert)
  • We no longer break on FTP entries without an FTP path, thanks Paul (@openpaul)
  • We now raise an error if you try to download metagenomes from RefSeq.
    Thanks again, Paul (@openpaul)
  • Updated Chinese README file, thanks James (@jamesyangget)
  • We no longer leak pool workers when running parallel downloads, thanks
    Gerrit (@Wrzlprmft)

Detailed changes:

Gerrit Ansmann (2):
      Using context manager for pool. This should at least partially fix Issue #120.
      Restructuring to avoid excessively long and complicated line.

Istvan Albert (1):
      made gimme_taxa.py an installable script

James Yang (3):
      fix and update translation
      Update README-CN.md
      Update README-CN.md

Kai Blin (18):
      core: Make get_name_and_checksum not skip the wrong files
      config: Init section before group
      main: Print nicer error messages on invalid arguments
      config: Add tests for new 'no metagenomes in refseq' check
      chore: Update contributor map
      chore: Drop python2 compatibility code
      chore: Style pass to make flake8 happy
      chore: Update supported Python versions in README
      chore: set up GitHub workflow for testing and publishing
      chore: Add vim config directory to gitignore
      core: Make acceptable --refseq-categories a list
      chore: Use py3 to test in drone as well
      core: Fix default for new list-based --refseq-category parameter
      core: Split strain parsing from strain label generation
      core: Also allow to filter by strain
      core: Also show strain in the dry-run listing
      core: Break the API so all list types now use the plural form.
      Bump version number to 0.3.0

Paul Saary (2):
      move na check into filter function
      raise warning if refseq metagenome is requested, as there is no such thing at the moment