Gcgc

Development

Fixed

- Broken test due to platform differences in `Path.glob` sorting.

Added

- User can specify to use start or end tokens optionally.

Removed

- Removed one_hot_encoding. The user can do that pretty easily if needed. E.g.
see `scatter` in PyTorch.

Added

- Properties to access the integer encodings of special tokens. (35cae2a)
- `Alphabet.encoded_start`
- `Alphabet.encoded_end`
- `Alphabet.encoded_padding`
- Remove uniprot dataset creation. (e233162)
- Simplify index handling for GenomicDataset. (3213a9e)

Added

- Updated package management so gcgc is easier to use with other version of
torch.

Added

- Ability for kmer size to be passed to an alphabet.

Added

- Add Dockerfile and docker-compose.yml for development.
- `EncodedSeq.shift`, which will shift sequence by an offset integer.
- `EncodedSeq.from_integer_encoded_seq` will take a list of integers and an
alphabet and return an EncodedSeq object.
- Add the ability to apply a function to the rollout_kmers yielded values.

Changed

- Alphabet special characters are now located at the start, rather than the end,
of the letters and token sequence.