HAMRonization Versions Save

Minor version bump to resychonrize library versioning with tag.

Improve parsing of AMRFinderPlus based on recommendation from development team @evolarjun (https://github.com/evolarjun) to skip entries with "INTERNAL_STOP" in method (representing truncated likely non-functional ORF). Note: PARTIAL and PARTIAL_CONTIG_END (ORF continues past end of contig) still reported in hAMRonized results.

Minor release without any code changes to get zenodo to assign a DOI.

Fix for unresolved empty summary bug (#80)

• Adds support for fARGene retrieve gene file
• Resolves issue with RGI parsing when RGI is run on ORFs
• Addressing running hamronize or summarize on empty output files
• Add additional integration tests
• Add testing for interface outputs (empty parsed reports, empty summarised reports, mixed tsv + json in input)
• Add additional validation tests
• Closes all current external requests/established issues.
• Supersedes and closes #79 and should address #78

What's Changed

• Update installation via conda in README.md by @thanhleviet in https://github.com/pha4ge/hAMRonization/pull/51
• Update README.md by @thanhleviet in https://github.com/pha4ge/hAMRonization/pull/55
• TB-Profiler IO by @jodyphelan in https://github.com/pha4ge/hAMRonization/pull/62
• specify protein or nt variant by @jodyphelan in https://github.com/pha4ge/hAMRonization/pull/63
• add tb tests by @jodyphelan in https://github.com/pha4ge/hAMRonization/pull/64
• Changes to TBProfilerIO by @jodyphelan in https://github.com/pha4ge/hAMRonization/pull/68
• Add draft parser for mykrobe by @pvanheus in https://github.com/pha4ge/hAMRonization/pull/69
• Update parsers with new schema version by @cimendes in https://github.com/pha4ge/hAMRonization/pull/76
• Update parsers by @fmaguire in https://github.com/pha4ge/hAMRonization/pull/77
• Update AMR Gene Detection Scheme by @cimendes in https://github.com/pha4ge/hAMRonization/pull/60

New Contributors

• @thanhleviet made their first contribution in https://github.com/pha4ge/hAMRonization/pull/51
• @jodyphelan made their first contribution in https://github.com/pha4ge/hAMRonization/pull/62
• @pvanheus made their first contribution in https://github.com/pha4ge/hAMRonization/pull/69

Full Changelog: https://github.com/pha4ge/hAMRonization/compare/v1.0.3...v1.0.4

Incoporate bug fixes from @aunderwo and add packaging for pypi

• Release adds support for resfinder v4 courtest of @aunderwo
• Fixes a bug in resfinder v3 strand orientation parsing

Officially 1.0.0 release

• Implements latest version of the AMR detection specification scheme
• Includes automated sanity and functional tests
• Performs various options of summarizing results.

Alpha release pending proper verification of outputs