biohansel v2.6.1 - Bioconda patch fix

Patch fix for Bioconda (Conda build issue due to pytest-runner and pip conflict; see https://github.com/pytest-dev/pytest-runner/#deprecation-notice)

Also adds biohansel console script entry point so users can run either $ biohansel ... or $ hansel ...

biohansel 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

biohansel v2.5.0

• updated the S. Typhi scheme and metadata table (Issue #131)
• 7 new genotypes were added to the S. Typhi scheme
• Updated S. Typhi metadata table with results from an analysis of ~8,100 public S. Typhi genomes
• updated README with 3 additional citations for the expanded S. Typhi scheme (Issue #124)
• Test file and S. Typhi scheme version were updated. This addresses issue #128
• updated QC message for inconclusive results (Issue #122)

biohansel v2.5.0

• updated the S. Typhi scheme and metadata table (Issue #131)
• 7 new genotypes were added to the S. Typhi scheme
• Updated S. Typhi metadata table with results from an analysis of ~8,100 public S. Typhi genomes
• updated README with 3 additional citations for the expanded S. Typhi scheme (Issue #124)
• Test file and S. Typhi scheme version were updated. This addresses issue #128
• updated QC message for inconclusive results (Issue #122)

biohansel v2.4.0

• added scheme metadata table to Python package data (#109)
• typing scheme name change from tb_speciation to tb_lineage (#110)
• updated README (#111)
• updated default low coverage depth value for SE scheme from 50 to 20, max kmer frequency from 1000 to 10,000 and updated help/usage docs (#114)
• improved reverse complement function performance (#118)
• fixed merging of subtyping results with subtype result metadata table (#120)
• added CI testing for Python 3.7, cleaned up setup.py (#119)

biohansel v2.3.0

Changes:

• Updated TB_Speciation and Typhi subtyping schemes to versions 1.0.5 and 1.2.0, respectively
• Added auto deploy on release tagging via Travis CI (#84)

Fixes:

• Added QC check for mixed subtypes (#98)

biohansel v2.2.0

Changes:

• Adds ‘#N/A’ to the subtype column if no k-mers are found (#69)
• New QC check for missing nested k-mers leading to the final subtype call (#88)
  • ex. all subtypes is 2, 2.2.2, 2.2.2.2, QC will return that you are missing subtype 2.2
• New Feature: Degenerate Base Expansion for scheme k-mers using the IUPAC degenerate bases (#60)
  • ex. DAR = [‘AAA’, ‘AAG’, ‘GAA’, ‘GAG’, ‘TAA’, ‘TAG’]
• New Schemes:
  • Typhi
  • Typhimurium
  • Mycobacterium Tuberculosis
• Fixes:
  • Changed all mentions of ‘tile’ to ‘kmer’
  • Update enteritidis scheme to 1.0.7
  • Match positive k-mers first (#77)

biohansel v2.1.1

• Fix command-line parameter parsing issue #61
• Fix lower-case sequence issue

biohansel v2.1.0

Changes:

• Adds optional subtype metadata table merging into biohansel results
• Name change from bio_hansel to biohansel

Fixes:

• Change Salmonella Enteritidis scheme version to 0.8.0 from 0.7.0
• Shorter more informative QC messages (#47)
• MacOS X gzipped FASTA/FASTQ issue (#40)
• Fix empty output files when no targets are found in inputs (#51)

bio_hansel v2.0.0

Changes:

• bio_hansel now only uses Aho-Corasick string searching for finding kmers in sequences using the pyahocorasick Python library. NCBI BLAST+ and Jellyfish are no longer needed and have been removed as external dependencies.
• Sorting inconsistent subtypes for QC reporting

Testing:

• Travis CI config simplified; no longer need to download and install Conda since it's now using the Python installation available through Travis CI Linux VMs.