Bio-hansel

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 ...`

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](https://rich.readthedocs.io/en/stable/) 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](https://github.com/biopython/biopython/)'s [`Bio.SeqIO.FastaIO.SimpleFastaParser`](https://github.com/biopython/biopython/blob/92c07ce7dce91078edc9b77fb71dbbe5646565bb/Bio/SeqIO/FastaIO.py#L24); 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

* 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)

- 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)

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)

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)