Releases
v2.6.0
Changes
Added min kmer fraction threshold (#140 )
added --min-kmer-frac
for exclusion of low abundance kmers from subtype calling
detailed report adds columns: kmer_fraction
, total_refposition_kmer_frequency
, is_kmer_fraction_okay
increased default --max-kmer-freq
for amplicon seq data compatibility
Added bump2version config for easy version updating (#141 )
Bump version with $ bump2version major|minor|patch
Codebase clean-up (#143 )
Added Rich for logging and informative tracebacks
refactoring and reformatting; fixed some docstrings; simplified some logic
moved some functions to more appropriate places
replaced string.format
with f-string literals
moved check_total_kmers
call to right after parsing of CLI args
replaced bio_hansel.parsers._parse_fasta
with BioPython 's Bio.SeqIO.FastaIO.SimpleFastaParser
; forcing uppercase of sequence
cleaned up some tests
updated help message to show program name and version as well as nice list of built-in schemes
ignoring/fixed some warnings when pytest
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