Ncbi-genome-download

This is release 0.3.3 of ncbi-genome-download.

This release has no new features on top of 0.3.2 but adds some information on how to cite the software.

Detailed changes:

Kai Blin (5):
README: Add citation information
CITATION: Add a citation metadata file
CITATION: Second attempt at generating a valid CITATION.rff file
CITATION: use the correct file name for the citation metadata file
Bump version to 0.3.3


0.3.2.zenodo-init
This is a re-release 0.3.2 of ncbi-genome-download, to get a Zenodo DOI generated. It's functionally identical to the existing 0.3.2 release.

Major changes of this release are:
* Add support for the new format assembly info headers, fixing downloads.
* Support for the translated-cds format (thanks SwiftSeal)
* Allow fuzzy searches for accessions
* Cache the MD5SUMS files for a day as well, to make re-starting the
download easier.

Detailed changes:

Kai Blin (9):
core: Actually expose the --fuzzy-accessions logic built back in 2019 on the command line
core: Improve the --refseq-categories tooltip
core: Only re-download MD5SUMS if they're more than a day old
core: Show progress bar both for downloading MD5SUMS and data files
chore: update the python versions for the CI workflow
chore: Remove old drone CI integration
chore: Reformat README.md to fix markdownlint errors
summary: Support the new format summary files
Bump version to 0.3.2

Moray Smith (1):
Update config.py

This is release 0.3.2 of ncbi-genome-download.

Major changes of this release are:
* Add support for the new format assembly info headers, fixing downloads.
* Support for the translated-cds format (thanks SwiftSeal)
* Allow fuzzy searches for accessions
* Cache the MD5SUMS files for a day as well, to make re-starting the
download easier.

Thanks also to chasemc and twelvesummer for submitting patches for the header format.

Detailed changes:

Kai Blin (9):
core: Actually expose the --fuzzy-accessions logic built back in 2019 on the command line
core: Improve the --refseq-categories tooltip
core: Only re-download MD5SUMS if they're more than a day old
core: Show progress bar both for downloading MD5SUMS and data files
chore: update the python versions for the CI workflow
chore: Remove old drone CI integration
chore: Reformat README.md to fix markdownlint errors
summary: Support the new format summary files
Bump version to 0.3.2

Moray Smith (1):
Update config.py

This is release 0.3.1 of ncbi-acc-download.

Main features of this release are:
* support for progress bars (thanks to 444thLiao)
* various bug fixes (thanks peterjc and jrjhealey)

Detailed changes:


Joe Healey (1):
remove unused function and update email

Kai Blin (8):
core: Change the progress bar shorthand to -P, default to no progress bar
chore: Use pytest.fixture instead of deprecated pytest.yield_fixture
core: Don't attempt to download metagenome info from refseq even if group is all
chore: Ignore more IDE files
chore: Fix all linter errors reported by flake8
Makefile: switch linting to flake8 to match CI setup
chore: Update mailmap
Bump version number to 0.3.1

Peter Cock (1):
Fixed typo in command line API help

Tianhua Liao (2):
add progress bar
fix repeat bars

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

This is release 0.2.12 of ncbi-genome-download.

Highlights of this release are:

* Parallel downloads of checksum files (Thanks to Adelme Bazin (axbazin))
* New --flat-output option to dump all downloaded files into a single directory
* We now have a Chinese translation of the README (Thanks James Yang (jamesyangget))

Detailed changes:

Adelme Bazin (5):
core : Checking MD5SUM in parallel when more than one process is allowed
add integration test to check if metadata table was filled properly. Expected failure when using multiprocessing.
fill metadata table in config_download instead of download_file_job to avoid problems with multiprocessing
modify the metadata_fill test functions so that they follow the same logic than the current code
fix the call to Pool with the 'with' statement for python2

Kai Blin (13):
core: Allow keeping the downloaded files in a flat hierarchy
chore: Break long help text lines
core: Fix the --flat-output description
README: Update install documentation
core: Add tests for type material downloads
chore: Add docstring and coverage skip to `downloadjob_creator_caller`
config: Test `is_compatible_assembly_accession()` in fuzzy_accession mode
core: Add a docstring to new fill_metadata function
core: Acquire the metadata table object outside of the download loops
config: Also support downloading metagenomes
core: Check for exact match on genus name before trying to capitalise it
chore: Update README to note that 0.2.12 is the last version to support Python 2
Bump version number to 0.2.12

James Yang (1):
translate README.md into Chinese (97)

This is release 0.2.11 of ncbi-genome-download which fixes two logging issues.

Thanks to David Morgan (Cptmorgan27) for providing a patch.

Detailed changes:


David Morgan (1):
core: remove print statement for type material

Kai Blin (4):
chore: Use a named logger instead of the root logger
README: Make it clearer that more than just bacteria and viral groups are available
chore: Remove landscape.io link, as that service seems dead
Bump version number to 0.2.11