Staramr

* Updated the Resfinder database to use the 2024-08-06 release.
* Updated the Pointfinder database to use the 2024-08-08 release.
* The Resfinder and Pointfinder databases now use FASTA record IDs with accession numbers (ex: `pmrA` -> `pmrA_1_CP055130.1`). StarAMR has been updated to support this, but database backwards compatibility is unlikely.
* The `genes_to_exclude` is affected by the above change and must now use gene IDs that exactly match the new FASTA record IDs with accession IDs.
* Removed ARG drug key entries with "None" or missing resistance.

* Updated the Plasmidfinder database to use the January 18th 2023 release.
* Fixed an issue where the string "None" in the drug table would be parsed differently by different versions of pandas (175).
* Upgraded to pandas version 2.
* Added the CGE-predicted phenotypes, PMID, Mechanism, and the Required Mutation columns to the Pointfinder output.
* The resfinder.tsv and pointfinder.tsv outputs now contain a Notes column.
* Updated the help description of the --mlst-scheme parameter to include a more useful link for available schemas.
* Switched to only officially supporting Python 3.7+ due to recent incompatibilities with Python 3.6 and some Python packages (numpy, biopython, and others).
* Adds the ability to handle "complex" pbp5 mutations. When appriopriate many pbp5 point mutations will be reported as a single mutation.
* Resfinder CGE-predicted phenotypes are now reported in the summary and detailed summary alongside existing predictions.
* Corrected a typo in the position for acrB in the PointFinder drug key table.
* Removed "enterobacteriaceae" from the list of supported PlasmindFinder databases.
* Changed the word sensitive to susceptible in outputs.

* Fixed a bug that occured when parsing some plasmid FASTA record IDs ([PR 159](https://github.com/phac-nml/staramr/pull/159)).
* Fixed issue where sometimes the extraction of error messages from `makeblastdb` was crashing leading to less useful errors ([PR 160](https://github.com/phac-nml/staramr/pull/160)).

* Updates to PointFinder database handling
* Adds the ability to handle promoters (regions with both promoter nucleotide information and non-promoter codon information)
* Adds handling of insertions and deletions in nucleotide and codon sequence
* Updates list of supported PointFinder species to `salmonella`, `campylobacter`, `enterococcus_faecalis`, `enterococcus_faecium`, `escherichia_coli`, `helicobacter_pylori`.
* Switch name `e.coli` to `escherichia_coli` in PointFinder gene-drug key to match organism name in PointFinder database.

* Fixed issue when using older version of pandas (136) (0.8.0.dev0).
* Fixed up some Python warnings related to pandas (0.8.0.dev0).
* Adjusted `mlst` tests to account for differences in results for newer versions (0.8.0.dev0).
* Drop support for Python 3.5 as it leads to issues with managing dependency versions (0.8.0.dev0).
* Switched from disallowing to generating a warning when the PointFinder organism is not one of the validated organisms (0.8.0.dev1).
* Updated ResFinder and PointFinder gene drug key to `072621` (0.8.0.dev2).
* Updated default database commits to those corresponding to dates used by ResFinder (2022-05-24), PointFinder (2021-02-01), and PlasmidFinder (2021-11-29) (0.8.0.dev2).
* Fixed issue when multiple matches for same amino acid change to try and select the most specific amino acid change (0.8.0.dev2).
* Fixed up PlasmidFinder database handling to account for changes to PlasmidFinder database structure (0.8.0.dev2).

Version 0.7.2.zenodo0

* Identical code to version `0.7.2` but made mainly to upload this version into Zenodo.
* Migrated integration tests from TravisCI to GitHub Actions
* A few small fixes to `README.md`.

* Fixed `KeyError` issue with later versions of pandas (115, thanks javiertognarelli).