Ncbi-acc-download

Latest version: v0.2.7

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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

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

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

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

0.2.1

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

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

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