Scripts to download genomes from the NCBI FTP servers
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
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:
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:
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:
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)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:
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
This is a bugfix release to ncbi-genome-download also adding two convenience features.
Major changes are:
Detailed changes:
Chris Gulvik (1):
create_symlink func modified to create relative rather than absolute symbolic links; resolves #62
Kai Blin (5):
core: Allow for fuzzy matching for specified organism names
core: Allow for fuzzy matching of specified accessions
chore: Fix two whitespace issues
core: Deal with organism names that don't contain a species part
Bump version number to 0.2.10
This release adds the "relation to type material filter" contributed by Jason Davis-Cooke. Thanks for that.
Detailed changes:
Jason Davis-Cooke (1):
feat(core): add 'relation to type material' as as filtering option (#82)
Kai Blin (2):
README: Document the type material filter option
Bump version number to 0.2.9
This is mainly a bugfix release fixing a UnicodeEncodeError when writing to a --metadata-table file with non-ASCII entries like in record GCF_000234725.1.
Thanks to @danudwary and @jananiravi for the error reports.
Also thanks to Tessa Pierce and Joe Healey for their contributions.
Detailed changes:
Joe Healey (1):
update readme with conda install
Kai Blin (3):
config: Change a tab indent to spaces
core: Open metatable file with utf-8 encoding
Bump version number to 0.2.8
Tessa Pierce (1):
add support for rm (repeat masked) eukaryotic genomes