Release 0.2.7

This is release 0.2.7 of ncbi-genome-download.
Highlights of this version include:

• Input options that supported a comma-separated list can now also read from
  files.
• Support for downloading files in RNA FASTA format (thanks, @bluegenes).
• Contributed script to get taxids for all children of a parent taxon (thanks
  @jrjhealey and @nick-youngblut).

Detailed changes:

Joe Healey (2):
added contrib dir and script for queriying NCBI Taxa names/nums
Added gimme_taxa to README

Kai Blin (20):
core: Add a dry-run option
core: Add a cache for the assembly summary files
core: Move configuration/input validation to a config object
core: Fix caching code for python 2.7
core: Remove unused SUPPORTED_TAXONOMIC_GROUPS import
tests: Remove a useless print call
core: Add print_function import for python 2.7 compatibility
config: refactor command line list parameter handling
core: Add a test for os.makedirs error handling
config: Add the option of reading list from a file for _create_list
config: Allow passing file-based lists for genus, taxid, and species taxid parameters
core: Split out the entry filtering logic
core: refactor iterating over taxonomic groups into _download function
core: Refactor to split _download into two separate, distinct functions
tests: Remove outdated comment
core: Allow multiple assembly levels
core: Allow filtering by assembly accessions
chore: Add Joe to .mailmap for correct attribution in the release notes
chore: setup.py finally understands markdown natively
Bump version number to 0.2.7

Nicholas Youngblut (3):
major alterations to gimme_taxa.py
removed --name parameter; now name can be used in taxid list
updated README section on gimme_taxa; fixed gimme_taxa header bug

Tessa Pierce (2):
add support for *rna.fna.gz file download
add test for download rna-fna

Release 0.2.6

This is release 0.2.6 of ncbi-genome-download.
Highlights of this version include:

• Multiple formats, taxids, species, etc. can now be downloaded as once, see
  README for how to use this. Thanks to Ruben (@rhpvorderman).
• You can now save information on downloaded files in a tab-separated table
  similar to the assembly_summary.txt file NCBI provides. Thanks to Ryan
  (@rrwick).

Detailed changes:

Kai Blin (22):
      chore: Add slack notifications to drone build
      core: Always return a boolean in worker()
      core: Make table an optional parameter for download_entry
      core: Make table an optional argument for download_file_job() and move to back
      chore: Add a 'lint' target to run pylint
      chore: Configure CI to run slack notifications only on push, but regardless of success/failure
      core: Disable a couple of pylint warnings
      jobs: Spin out the DownloadJob to be a proper object
      config: Move all configuration into an extra module
      jobs: get full test coverage
      core: Detect if no downloads matched the specified filter
      core: Don't use multiprocessing if only a single thread should be used
      core: Don't cover function to generate the argument parser
      core: Metadata table code needs refactoring, snooze coverage warnings
      chore: Make pycodestyle happy and update outdated docstrings
      chore: No pycodestyle warnings anymore.
      chore: Ignore ropeproject output for git
      core: Rename download_entry to create_downloadjob, as it doesn't download anything anymore
      metadata: Split out handling of the metadata table to a separate module
      README: Python 3.3 has reached end-of-life, drop support
      chore: Add mailmap to fix Ruben's name for git-shortlog
      Bump version number to 0.2.6

Ruben Vorderman (25):
      use args object
      update docstring
      allow multiple formats to be downloaded
      remove redundant is not none. Add description
      enabled multiple download of much things
      improve efficiency by relocating the loops
      minor spell mistakes
      separated argument_parser from main
      fixed quite a few tests
      fixed some other tests
      fixed all tests
      updated readme
      backwards compatibility
      eliminated version problem
      restore old test for backwards compatibility
      speed up algorithm immensely
      cleanup
      revert test to original
      revert removal in method call section
      typo
      review style additions
      use pylint to check for style errors
      add test to check all logic
      add test to check all logic
      remove 'unknown' from 'SUPPORTED_TAXONOMIC_GROUPS'

Ryan Wick (2):
      Runner script for convenience
      New option for saving metadata table

Release 0.2.5

This is release 0.2.5 of ncbi-genome-download.

Highlights of this version include:

• Enable specifically downloading reference and representative genomes.
• New 'ngd' command alias saves you from having to type 'ncbi-genome-download' all the time.

Detailed changes:

Kai Blin (3):
      core: Allow filtering by RefSeq category
      setup: Also add short alias 'ngd' for the CLI script
      Bump version to 0.2.5

Release 0.2.4

This is release 0.2.4 of ncbi-genome-download.

Highlights of this version include:

• Enable using ncbi-genome-download as API from your own scripts, thanks to Marc Bourqui (@mbourqui).
• Also allow downloading the _assembly_report.txt and _assembly_stats.txt files, thanks to Peter Cock (@peterjc).
• Better handle interrupting with Ctrl-C while downloading in multiple threads.

Detailed changes:

Kai Blin (6):
      core: More gracefully abort on Ctrl-C
      core: Silence some pylint style warnings I disagree with
      chore: Update drone CI config for drone 0.7
      README: Switch CI links to HTTPS.
      publish.sh: Switch to using twine and build universal binary wheel
      Bump version to 0.2.4

Marc Bourqui (27):
      Update gitignore for PyCharm
      Replace args with kwargs in download signature
      Merge _download and download
      Update tests to previous commits
      Bug fixes in Enums, some renamings, more doc
      Update packaging related stuff     * Version number     * Requirements     * README
      Move tests folder (were not finding package files otherwise)
      Fix AttributeError
      Fix Enum related issues
      Fix issues and tests
      Update imports
      Fix tests     * Bring back _download() for testing purposes
      WIP preserve enum order
      Update EMap to avoid usage of dict which does not preserve order
      Move test folder for drone testing
      Minor performance improvement
      Fix README
      Remove __init__.py in tests/ and revert test_parse_checksums() auto line breaks
      Fix unreachable code
      Unbump version number
      Fix undesired new line
      Rename var to _download_mock when dealing with _download()
      Fix SystemError: Parent module '' not loaded, cannot perform relative import
      Fix TypeError and AssertionErrors
      Fix Enum ordering for Pyhton 2
      Move comment line
      Fix AttributeError

Peter Cock (3):
      Download XXX_assembly_report.txt and XXX_assembly_stats.txt
      Use strict bash mode in publish.sh
      Include PyPI version badge in README

This is release 0.2.3 of ncbi-genome-download.

This is release 0.2.3 of ncbi-genome-download.

Highlights of this version include:

• Properly deal with existing human-readable symlinks when re-running a download, thanks to An Phung (@anphung).
• Support creating human-readable symlinks without reloading the genome data
• Work around formatting issues in NCBI's viral assembly_summary.txt files

Detailed changes:

An Phung (1):
      core: Check symlink existence, fix #20

Kai Blin (6):
      create_readable_dir: Special case viral entries, because they are special snowflakes
      core: Make sure invalid checksum lines are skipped.
      core: Allow creating human-readable links for already downloaded files
      summary: Skip invalid assembly_summary.txt lines
      summary: Try to fix invalid viral assembly_summary.txt lines instead of skipping them
      Bump version to 0.2.3