Genomad

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.

Fixed
- Set the `CUDA_VISIBLE_DEVICES` environment variable to `-1` in `nn_classification`. This fixes a bug where the `nn_classification` module would fail to run when a GPU was available and the input had a single sequence.

Fixed
- Fixed the parsing of MMseqs2 integrase output to extract only the gene accession, rather than the entire header. This addresses a bug introduced in version 1.5.2, where the integrase gene accession was not accurately parsed because the entire header was extracted. As a result, the `find-proviruses` module can now properly add integrases to gene tables and extend boundaries using integrase coordinates.

Changed
- Replace ambiguous variable name in `read_fasta`.
- Define name `current_contig` at the beginning of `_append_aragorn_tsv`.

Fixed
- Set minimum `pyrodigal-gv` version to `0.3.1`. This fixes a bug introduced in `0.3.0` that led to the identification of RBS motifs not reported by Prodigal.

Changed
- Remove the `CCGGGG` RBS motif from the list of motifs.

Fixed
- Add the `CCGGGG` RBS motif to the list of motifs.

Changed
- Do not include stop codon (`*`) at the end of protein sequences.
- Set minimum `pyrodigal-gv` version to `0.2.0`.