Ncbi-acc-download

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

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

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

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

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

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