Pyrodigal

Added
- Support for reading from `stdin` in CLI ([35](https://github.com/althonos/pyrodigal/issues/35)).
- Flag for changing parallel computation to use `Pool` instead of `ThreadPool` ([57](https://github.com/althonos/pyrodigal/issues/57)).
- Better documentation of command line interface ([56](https://github.com/althonos/pyrodigal/issues/56)).
- Allow changing the formatter class in `pyrodigal.cli.argument_parser`.

Changed
- Migrate documentation to `pydata-sphinx-theme`.

Fixed
- Cython warnings with unused `except *` statements in `MetagenomicBins`.
- Signatures of `__init__` methods missing from all Cython types after the `v3.0` update.
- Small typos in documentation.

Changed
- Refactor SIMD code to reduce number of required registers, and improve SSE2 performance.
- Refactor Prodigal initialization functions into sparse initializer code to reduce library size.

Added
- `strict` argument to `Gene.translate` to control translation of ambiguous codons with unambiguous translation ([54](https://github.com/althonos/pyrodigal/issues/54)).
- `strict_translation` argument to `Genes.write_genbank` and `Genes.write_translation`.
- Support for translation tables 26 to 33 in `Gene.translate`.
- Support for translation tables 26, 29, 30, 32 and 33 in `GeneFinder.train`.
- `Genes.score` property to count the total score of all extracted genes.
- `full_id` parameter to `Genes.write_gff`, `Genes.write_translation` and `Genes.write_genes` to control the `ID` field written for each gene ([53](https://github.com/althonos/pyrodigal/issues/53)).

Changed
- `Gene.translate` now raises a warning when called with a translation table incompatible with the training info.

Fixed
- Bug in code for masking trailing nucleotides ([55](https://github.com/althonos/pyrodigal/issues/55)).

Added
- CLI option to disable translation of stop codons ([51](https://github.com/althonos/pyrodigal/pull/51), by [zclaas](https://github.com/zclaas)).

Changed
- `Scorer` internal API to separate connection scoring and overlap disentangling.

Fixed
- Bug with computation of minimum node in connection scoring loop ([hyattpd/Prodigal108](https://github.com/hyattpd/Prodigal/pull/108)).
- Out-of-bounds sequence access in `_shine_dalgarno_exact` and `_shine_dalgarno_mm` methods of `Sequence`.
- Memory leak in `Nodes.__setstate__` caused by incorrect reallocation.

Fixed
- Always mark SSE2 support on x86-64 CPUs independently of `archspec`-detected features ([49](https://github.com/althonos/pyrodigal/issues/49)).

Added
- Option to change argument parser in `pyrodigal.cli.main`.