Release 0.2.9

This is release 0.2.9 of ncbi-acc-download.

This release is a bugfix release to fix an issue in the tests happening with requests 2.31.

Thanks to GitHub user Benjamin Drung (@bdrung) for providing an initial PR for this.

Detailed changes:

Kai Blin (3):
      tests: requests 2.31 seems to need ContentType set to work, so add that
      chore: Update supported python versions
      chore: Bump version to 0.2.9

Release 0.2.8

This is release 0.2.8 of ncbi-acc-download.

Major features of this release are:

• The ability to download a genomic range instead of the full record (thanks
  to Zach Kurtz @zdk123)
• A validation step that removes partial features from both ends of a record
  after the --range option was used (thanks again to Zach Kurtz @zdk123)
• Biopython 1.79 support

Detailed changes:

Kai Blin (5):
      chore: Ignore some more IDE-related stuff
      wgs: Biopython 1.79 changed the dance to detect WGS master records without sequence
      chore: update pytest test fixture setup
      README: Add documentation for --range and -e correct
      chore: Bump version to 0.2.8

Zachary Kurtz (3):
      add range parameter to download
      add correct validator to filter out of range proteins
      add data correction test

Release 0.2.7

This is release 0.2.7 of ncbi-acc-download.

The biggest change of this release is the addition of multiple strategies to
handle the Entrez API rate limiting requests. Darian Hole (@DarianHole)
contributed a new --api-key parameter that allows users to specify their
NCBI API key. Additionally, ncbi-genome-download now properly detects that
requests are being rate limited, and retries the download after the wait
period requested by the server.

Additionally, this release drops support for Python versions that hit their
end of life, namely 2.7 and 3.5.

Detailed changes:

Darian Hole (1):
      Add support for API key input (#17)

Kai Blin (10):
      chore: use a dash instead of an underscore in the --api-key option
      download: Error code 429 is special, so handle it that way
      wgs: Handle TooManyRequests error during recursive download by waiting
      core: Handle TooManyRequests error by waiting
      chore: Remove Python 2 compatibility code
      chore: Make sure the code passes flake8 checks
      chore: Add automated tests via GitHub Actions
      chore: Add GitHub action to publish releases to pypi
      chore: Make sure to install all deps
      chore: Bump version to 0.2.7

Release 0.2.6

This is a bugfix release of ncbi-acc-download.

The main changes are:

• Support for recursively downloading transcriptome shotgun assembly files.
• More user-friendly error messages when downloading fails.

This is the last version to support Python 2.7.

Detailed changes:

Kai Blin (4):
      wgs: Support transcriptome shotgun assembly files
      main: More user-friendly error reporting
      chore: Bump version to 0.2.6
      core: Adjust tests for new InvalidIdError

Release 0.2.5

This is a bug fix release to address Python 2.7 support.
You really should be switching to Python 3, though.

Detailed changes:

Kai Blin (3):
      download: Python 2.7 compatibility
      wgs: Python 2.7 compatibility
      chore: Bump version to 0.2.5

Release 0.2.4

This is mainly a bugfix release making sure an additional download error is
raised correctly.

Detailed changes:

Kai Blin (3):
      core: Make ENTREZ/SVIEWER URLs configurable
      download: Also catch ChunkedEncodingErros during the actual download
      chore: Bump version to 0.2.4

WGS/WGS_SCAFLD/CONTIG support

Allow downloading the full record for entries with WGS/WGS_SCAFLD/CONTIG
entries. You can use the --recursive option from the command line to enable
this.

Detailed changes:

Kai Blin (2):
      wgs: Add support for recursive download of WGS/WGS_SCAFLD/CONTIG entries
      chore: Bump version to 0.2.1

Release 0.2.0

More updates to the ncbi-acc-download script.

Major new features are:

• Added support for featuretable and GFF3 formats for nucleotide downloads.
• Moved the functionality of the --out flag to --prefix
• Added a new --out flag that keeps the output filename intact

Thanks to Shaun Jackman (@sjackman) for the feature suggestions.

Detailed changes:

Kai Blin (4):
      core: Add support for featuretable format
      core: Add support for GFF3 format by going to sviewer API instead of Entrez
      core: Keep filename intact for --out, move old meaning to --prefix
      chore: Bump version to 0.2.0

Initial release

Initial release of the NCBI download-by-acc script.

It still is very rudimentary and just downloads genome data in GenBank format
or Protein data in FASTA forma