Ncbi-genome-download

This is a bugfix release to ncbi-genome-download also adding two convenience
features.

Major changes are:
* Use realtive instead of absolute symlinks for human-readable output (thanks
chrisgulvik)
* No longer crash on abnormal organism names (thanks to andrewsanchez for the
initial pull request)
* Allow for fuzzy matching of both organism name and accessions

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

This is release 0.2.7 of ncbi-genome-download.
Highlights of this version include:

* Input options that supported a comma-separated list can now also read from
files.
* Support for downloading files in RNA FASTA format (thanks, bluegenes).
* Contributed script to get taxids for all children of a parent taxon (thanks
jrjhealey and nick-youngblut).

Detailed changes:

Joe Healey (2):
added contrib dir and script for queriying NCBI Taxa names/nums
Added gimme_taxa to README

Kai Blin (20):
core: Add a dry-run option
core: Add a cache for the assembly summary files
core: Move configuration/input validation to a config object
core: Fix caching code for python 2.7
core: Remove unused SUPPORTED_TAXONOMIC_GROUPS import
tests: Remove a useless print call
core: Add print_function import for python 2.7 compatibility
config: refactor command line list parameter handling
core: Add a test for os.makedirs error handling
config: Add the option of reading list from a file for _create_list
config: Allow passing file-based lists for genus, taxid, and species taxid parameters
core: Split out the entry filtering logic
core: refactor iterating over taxonomic groups into _download function
core: Refactor to split _download into two separate, distinct functions
tests: Remove outdated comment
core: Allow multiple assembly levels
core: Allow filtering by assembly accessions
chore: Add Joe to .mailmap for correct attribution in the release notes
chore: setup.py finally understands markdown natively
Bump version number to 0.2.7

Nicholas Youngblut (3):
major alterations to gimme_taxa.py
removed --name parameter; now name can be used in taxid list
updated README section on gimme_taxa; fixed gimme_taxa header bug

Tessa Pierce (2):
add support for *rna.fna.gz file download
add test for download rna-fna

This is release 0.2.6 of ncbi-genome-download.
Highlights of this version include:

* Multiple formats, taxids, species, etc. can now be downloaded as once, see
README for how to use this. Thanks to Ruben (rhpvorderman).
* You can now save information on downloaded files in a tab-separated table
similar to the assembly_summary.txt file NCBI provides. Thanks to Ryan
(rrwick).

Detailed changes:


Kai Blin (22):
chore: Add slack notifications to drone build
core: Always return a boolean in worker()
core: Make table an optional parameter for download_entry
core: Make table an optional argument for download_file_job() and move to back
chore: Add a 'lint' target to run pylint
chore: Configure CI to run slack notifications only on push, but regardless of success/failure
core: Disable a couple of pylint warnings
jobs: Spin out the DownloadJob to be a proper object
config: Move all configuration into an extra module
jobs: get full test coverage
core: Detect if no downloads matched the specified filter
core: Don't use multiprocessing if only a single thread should be used
core: Don't cover function to generate the argument parser
core: Metadata table code needs refactoring, snooze coverage warnings
chore: Make pycodestyle happy and update outdated docstrings
chore: No pycodestyle warnings anymore.
chore: Ignore ropeproject output for git
core: Rename download_entry to create_downloadjob, as it doesn't download anything anymore
metadata: Split out handling of the metadata table to a separate module
README: Python 3.3 has reached end-of-life, drop support
chore: Add mailmap to fix Ruben's name for git-shortlog
Bump version number to 0.2.6

Ruben Vorderman (25):
use args object
update docstring
allow multiple formats to be downloaded
remove redundant is not none. Add description
enabled multiple download of much things
improve efficiency by relocating the loops
minor spell mistakes
separated argument_parser from main
fixed quite a few tests
fixed some other tests
fixed all tests
updated readme
backwards compatibility
eliminated version problem
restore old test for backwards compatibility
speed up algorithm immensely
cleanup
revert test to original
revert removal in method call section
typo
review style additions
use pylint to check for style errors
add test to check all logic
add test to check all logic
remove 'unknown' from 'SUPPORTED_TAXONOMIC_GROUPS'

Ryan Wick (2):
Runner script for convenience
New option for saving metadata table

This is release 0.2.5 of ncbi-genome-download.

Highlights of this version include:

* Enable specifically downloading reference and representative genomes.
* New 'ngd' command alias saves you from having to type 'ncbi-genome-download' all the time.


Detailed changes:


Kai Blin (3):
core: Allow filtering by RefSeq category
setup: Also add short alias 'ngd' for the CLI script
Bump version to 0.2.5