Releases | Open Source Science

What's Changed

[MRG] update versions of sourmash, screed, and snakemake by @ctb in https://github.com/spacegraphcats/spacegraphcats/pull/479
[MRG] enable dependabot by @ctb in https://github.com/spacegraphcats/spacegraphcats/pull/472
Bump snakemake from 7.3.8 to 7.18.2 by @dependabot in https://github.com/spacegraphcats/spacegraphcats/pull/476
Bump codecov/codecov-action from 1 to 3 by @dependabot in https://github.com/spacegraphcats/spacegraphcats/pull/475
Bump actions/checkout from 2 to 3 by @dependabot in https://github.com/spacegraphcats/spacegraphcats/pull/474
Bump actions/setup-python from 2 to 4 by @dependabot in https://github.com/spacegraphcats/spacegraphcats/pull/473
[MRG] update when GitHub actions run: on PRs, on merge to latest, and daily by @ctb in https://github.com/spacegraphcats/spacegraphcats/pull/478

New Contributors

@dependabot made their first contribution in https://github.com/spacegraphcats/spacegraphcats/pull/476

Full Changelog: https://github.com/spacegraphcats/spacegraphcats/compare/v2.1.1...v2.1.2

- Standard ML
Published by ctb over 3 years ago

What's Changed

[MRG] add fixes in #294 to the right branch by @ctb in https://github.com/spacegraphcats/spacegraphcats/pull/468
[MRG] update sourmash req to 4.5.0 by @ctb in https://github.com/spacegraphcats/spacegraphcats/pull/466

Full Changelog: https://github.com/spacegraphcats/spacegraphcats/compare/v2.1...v2.1.1

- Standard ML
Published by ctb almost 4 years ago

What's Changed

[ MRG] fix command typo in documentation by @taylorreiter in https://github.com/spacegraphcats/spacegraphcats/pull/419
Fix sanity check in rdomset.domination_graph() by @mogproject in https://github.com/spacegraphcats/spacegraphcats/pull/424
[MRG] add cdbg node annotations to multifasta query output by @taylorreiter in https://github.com/spacegraphcats/spacegraphcats/pull/422
[MRG] remove unnecessary bcalm_unitigs cli arg by @ctb in https://github.com/spacegraphcats/spacegraphcats/pull/432
[MRG] switch 'master' refs over to 'latest' in docs by @ctb in https://github.com/spacegraphcats/spacegraphcats/pull/431
[MRG] close databases and files appropriately by @ctb in https://github.com/spacegraphcats/spacegraphcats/pull/438
[MRG] clean up some unused code in indexcdbgby_multifasta.py by @ctb in https://github.com/spacegraphcats/spacegraphcats/pull/442
[MRG] some trial scripts for protein search of unitigs by @ctb in https://github.com/spacegraphcats/spacegraphcats/pull/379
[MRG] add dominator abundance counting, per sample. by @ctb in https://github.com/spacegraphcats/spacegraphcats/pull/303
[MRG] add mamba as a conda dependency, b/c snakemake wants it. by @ctb in https://github.com/spacegraphcats/spacegraphcats/pull/459
[MRG] Remove kmer size argument from rule build_multifasta_index in spacegraphcats/conf/Snakefile by @taylorreiter in https://github.com/spacegraphcats/spacegraphcats/pull/460

Full Changelog: https://github.com/spacegraphcats/spacegraphcats/compare/v2.0...v2.1

- Standard ML
Published by ctb about 4 years ago

With this v2.0 release, we've fixed several significant bugs, added thorough documentation, added several major new features and a variety of scripts, cleaned up the code base a fair bit, decreased memory usage by about 25%, and added many tests!

If you've been using spacegraphcats v1.x, the command line has changed - the main difference is that you now must specify at least one target before the config file. That is, instead of python -m spacegraphcats <config file> <target> [<more targets>...] you now run python -m spacegraphcats <target> <config file> [<more targets>...]

We don't have a migration guide per se, but you can see the set of changes for the base pipeline in our paper here.

Please note that the file formats and locations have changed, so you'll need to rebuild any and all of your indexes.

Major new features:

add paired read indexing and retrieval (#344, #356)
improve BCALM input handling & sorting; reduce memory usage ~25% (#310)

Bug fixes:

Fix pendant removal bug #299 (#310)
Fix assignment bug in rdomset.domination_graph (fixes #390) (#394)

Major refactoring and new internal functionality:

support randomizing unitig order via config parameter. (#391)
handle duplicate hashes in input cDBG. (#375)
add shadow annotations to support --shadow-prefix (#365)
Make default spacegraphcats interface use the click API (#353)
use contigs sqlite DB, rather than contigs.fa.gz, for contig retrieval (#345, #350, #361)
remove python 2 support (#328)
add default config via defaults.conf (#410)

Documentation enhancements:

add documentation and mkdocs site for spacegraphcats (#392)

Refactoring and cleanup:

relocate cDBG files to cDBG directory (#407)
store ksize in MPHF index (#406)
properly close output files in bcalmtogxt (#402)
update rule makecontigskmer_index with contigs.sizes output (#401)
update sourmash version requirements (#395)
remove bcalm install test (#396)
rename bcalmtogxt2 to bcalmtogxt (#397)
update sourmash versions in environment.yml (#367, #385, #389)
Update test markers for pytest (#386)
Update dib-lab software dependencies; fix warnings (#385)
update citation info (#381)
use less yield, more memory (#361)
adjust output messages (#359)
move tests under tests/ (#343)
add json2yaml script
update tests to include buggy behavior
add some shorter test files based on twofoo; automate tests
ci: add flake to tests, format with black, and add precommit hooks (#326)
chore: update click (#327)
ci: switch to github actions, fix some linting issues (#323)
Fix catlas checkpointing (#412)
add thread/cores parameter to bcalm in the Snakefile (#415)

- Standard ML
Published by ctb about 5 years ago

spacegraphcats - v2.0rc1

Many cleanups and format changes:

relocate cDBG files to cDBG directory (#407)
store ksize in MPHF index (#406)
add documentation and mkdocs site for spacegraphcats (#392)
properly close output files in bcalmtogxt (#402)
update rule makecontigskmer_index with contigs.sizes output (#401)
update sourmash version requirements (#395)
remove bcalm install test (#396)
rename bcalmtogxt2 to bcalmtogxt (#397)
Fix assignment bug in rdomset.domination_graph (fixes #390) (#394)
support randomizing unitig order via config parameter. (#391)
update sourmash to >=4 in environment.yml (#389)
Update test markers for pytest (#386)
Update dib-lab software dependencies; fix warnings (#385)
update citation info (#381)
handle duplicate hashes in input cDBG. (#375)

- Standard ML
Published by ctb about 5 years ago

spacegraphcats - v2.0b11

There are no changes to file formats in this release vs v2.0b10, merely speed improvements and code cleanup.

Revert change in release v2.0b10 that made read indexing slower
add shadow annotations to support --shadow-prefix (#365)
update version of sourmash to 4.0.0a3 (#367)