Instanovo

Improved code utility and data validation
- Check labels match precursor
- Check for data leakage
- Verify residue vocabulary
- Added better residue support
- Fine-tuning trainer automatically updates model weights with new sizes
- Added Flash attention, torch.compile(), AMP (fp16)
- Added improved fast greedy search
- Improved test coverage

Added Spectrum Data Handler
- Supports lazy loading with asynchronous prefetching
- Filtering and sampling performed non-destructively (by updating the row filter)
- Two-fold shuffling strategy for training ensures optimal load times

Extended model checkpoint released. Trained on 32M spectra with additional PTMs:
- AC-PT
- Additional PRIDE dataset
- Additional phosphorylation dataset

**Full Changelog**: https://github.com/instadeepai/InstaNovo/compare/0.1.6...0.1.7

- Add data conversion scripts
- Add InstaNovo+ to starter notebook
- Add functionality to return all beams (`return_all_beams=True` argument in `decoder.decode`) 12

- Add code for diffusion model
- Add checkpoint for diffusion model pre-trained on HC-PT fine-tuned on Nine Species excluding yeast.

**Full Changelog**: https://github.com/instadeepai/InstaNovo/compare/0.1.4...0.1.5

What's Changed
* feat: bundle config files with checkpoints
* add checkpoints `instanovo.pt` trained on HC-PT, and `instanovo_yeast.pt` fine-tuned on nine-species excluding yeast.


**Full Changelog**: https://github.com/instadeepai/InstaNovo/compare/0.1.2...0.1.4

What's Changed
* docs: add hyperlinks by BioGeek in https://github.com/instadeepai/InstaNovo/pull/6
* fix: update URLs by BioGeek in https://github.com/instadeepai/InstaNovo/pull/7


**Full Changelog**: https://github.com/instadeepai/InstaNovo/compare/0.1.2...0.1.3