Genomad

Added
- Add the `--lenient-taxonomy` and `--full-ictv-lineage` options to the `annotate`, `find-proviruses`, and `end-to-end` modules. The `--lenient-taxonomy` option enables assignment of genomes to taxa below the family rank (subfamily, genus, subgenus, and species). The `--full-ictv-lineage` option enables the output of the full ICTV lineage of each genome, including ranks that are hidden by default (subrealm, subkingdom, subphylum, subclass, suborder, subfamily, and subgenus).

Changed
- Remove the `--conservative-taxonomy` option of the `annotate` and `end-to-end` modules.

Changed
- Add support for the geNomad database v1.8, which introduced an additional column in the metadata table.
- Update `README.md` to the database v1.8.
- Set the minimum Python version to `3.9`.

Changed
- Add installation instructions using Pixi.
- Use raw strings for the regular expression in `utils.natsort`.
- Update the version requirements for `keras` to `>=3` and `tensorflow` to `>=2.16`.

Fixed
- Write the `min_number_genes` value to the parameters JSON file of the `summary` module.
- Set maximum `tensorflow` version to below `2.16`.

Changed
- Set the `break_on_hyphens` parameter of the `textwrap.fill` function to `False` to prevent line breaks at `-` characters. This ensures that sequences with gaps in FASTA files generated using `Sequence.__str__()` maintain consistent line width.
- Compare `Enum` by identity in the `open_file` function.

Added
- Added the `--min-number-genes` parameter to the `summary` module. This parameter allows users to set the minimum number of genes a sequence must encode to be considered for classification as a plasmid or virus. The default value is `1`. When `--conservative` is used, this parameter is set to `1`. When `--relaxed` is used, this parameter is set to `0`. This filter has no effect if the `annotate` module is not executed.

Changed
- Added a hyperlink to the official documentation in the help dialogue.
- The virus taxonomic lineage is presented using a fixed number of fields separated by semicolons (`;`). As a result, for genomes that could not be assigned to the family level (the most specific taxonomic rank), there will be trailing semicolons at the end of the lineage string.
- Do not apply the gene-based post-classification filters when the `annotate` module is not executed.
- Set the default value of `--min-plasmid-marker-enrichment` to `0.1`.

Fixed
- Set maximum `keras` version to below `3.0`. This prevents errors due to incompatibility with `keras >=3.0`, such as the `shape` parameter not accepting an integer as input.