Dscript

- Resolve 35 to use `require_dataset` -- can now add multiple .fasta files to the same h5 file
- Update pretrained API and docs to include Topsy-Turvy
- Add retry decorator to get_pretrained if download fails
- Add ability to set a random seed for training
- Update `evaluate` code to also store metrics in a file

- Add biopython to setup.py

- Integrate Topsy-Turvy to allow for top-down supervision
- Use utils.log function across all commands
- Speed up loading embeddings into memory using parallel processing
- Update fasta parse and write to use BioPython SeqIO (better error checking)
- More comprehensive test suite for main commands

- Updated model loading on new version to handle re-named parameters
- Updated cpu-only loading during prediction with map_location

- Resolve 24 by fixing training
- Can now run `dscript train --train data/pairs/human_train.tsv --test data/pairs/human_test.tsv --embedding /afs/csail/u/s/samsl/Work/databases/STRING/homo.sapiens/human_nonRed.h5 --output [output] --save-prefix [prefix] --device 0` to replicate paper results
- Updated code formatting with black and pre-commit