4.1.0 (2022-10-26)

Features

kmer: Add k-mer counting. (7b1d556)
kmer: Add k-mer counting. (b7e7136)
magna.gtdb: Add previous release metadata files. (14f2c93)

Reverts

magna.foo: Remove test file. (ee425d7)

4.0.1 (2022-09-27)

Bug Fixes

ci: Bump. Fix issue where bumped version is not included. (013cdb4)

4.0.0 (2022-09-27)

Features

rust: Added PYO3 rust bindings and updated CI/CD. (7d28848)

BREAKING CHANGES

rust: Rust is required.

3.5.0 (2022-07-15)

Features

gtdb/metadata: Added R207 metadata files. (5c5a075)
gtdb/ssu: Added R207 SSU files. (051ca48)
gtdb/tree: Added R207 tree. (24b2377)

3.4.1 (2022-05-12)

Bug Fixes

rq: Update typer config. (1c62416)

3.4.0 (2022-05-12)

Features

rq: Add generalised commands for redis-queue. (aee6e67)

3.3.0 (2022-05-11)

Features

util.collection.get_batches: Generator to create batches of a sized collection. (8f19427)

3.2.0 (2022-05-10)

Features

util.disk.get_file_size_fmt: Add human-readable formatter for file size. (d421cae)

3.1.1 (2022-05-10)

Bug Fixes

util.web.download_file: Remove line used for testing. (61ee7af)

3.1.0 (2022-05-10)

Features

util.web.download_file: Add silent option for download. (b2b8fea)

3.0.1 (2022-05-10)

Bug Fixes

ncbi.web.get_ncbi_assembly_id: Ensure that the correct ID is returned. (a2d88f5)

3.0.0 (2022-05-10)

Features

3.0.0: Docs / Refactor / NCBI / CLI (71df0e5)

BREAKING CHANGES

3.0.0: Refactored util.io -> util.web

2.8.0 (2022-05-07)

Features

PFAM/TIGRFAM: Add TopHit file. (eff81d2)

2.7.1 (2022-05-05)

Bug Fixes

PFAM/TIGRFAM: Adjust columns in tophit file, fix data type. (c63fc52)

2.7.0 (2022-05-04)

Bug Fixes

util.pandas.optimise_df: Remove error if integer data type cannot be matched. (34daffd)

Features

PFAM/TIGRFAM: Include a set containing markers at specific releases. (62387d7)

2.6.2 (2022-04-17)

Bug Fixes

util.pandas.optimise_df: Stricter processing for float data types. (3f4aadb)

2.6.1 (2022-04-17)

Bug Fixes

util.pandas.optimise_df: Stricter processing for unsigned data types. (64063ff)

2.6.0 (2022-04-15)

Features

util.pandas: Add optimise_df to reduce dataframe size. (706baff)

2.5.1 (2022-04-11)

Bug Fixes

tree: Force rd=False. (67087e6)

2.5.0 (2022-04-11)

Features

tree: Add distance matrix to newick conversion method. (9146bbb)

2.4.1 (2022-03-29)

Bug Fixes

gunc: Fixed path to feather for concatenated assignment file. (5f48c1b)

2.4.0 (2022-03-29)

Features

gtdb markers: Added sets of BAC120/AR53/AR122 markers. (30e66c3)
gunc: Add method to parse contig_assignments file. (625c597)
pfam/tigrfam: Add PFAM/TIGRFAM output parsers. (35c0755)

2.3.0 (2022-03-29)

Features

diamond: Added diamond file handler. (6dd18a5)

2.2.0 (2022-03-17)

Features

gunc: Updated GUNC paths. (8306b31)

2.1.1 (2022-03-11)

Bug Fixes

gunc: TSV extension instead of feather for gunc file. (5d0e84f)

2.1.0 (2022-03-11)

Features

io: Added copy_file, and move_file. (dd9f776)

2.0.0 (2022-03-10)

Bug Fixes

GTDB Tree: Added option to force underscores. (8c87e70)

Features

GUNC: Added GTDB R95 dataset methods. (aff82f6)
Refactored code, added CI for docs. (e891e84)

BREAKING CHANGES

Re-organised folder structure.

1.4.0 (2022-02-18)

Features

gtdb: Added GTDB trees. (08ba91c)

1.3.0 (2022-02-17)

Features

gunc: Updated GUNC dataset for MAXCss (ffaf645)

1.2.0 (2022-02-16)

Features

accession: Add canonical_gid function. (95067ca)

1.1.0 (2022-02-16)

Features

GTDB: Add R202 and Genome. (31e5bc3)

1.0.3 (2022-02-02)

Bug Fixes

datasets: Reduced the gunc dataset to just RefSeq/GenBank genomes. (d432765)

1.0.2 (2022-02-02)

Bug Fixes

datasets: Updated the GTDB R95 bac source. (d74eccf)

1.0.1 (2022-02-02)

Performance Improvements

dataset: Updated GTDB/GUNC to use feather file format. (90fe0fd)

1.0.0 (2022-02-02)

Features

dataset: Added GTDBR95 metadata, and GUNC data. (1755414)

1.0.0 (2021-11-08)

Features

Trigger release (6435c4f)