removed local path from uv source in pyproject

Merge pull request #250 from ArcInstitute/remove_preprocess_infer

removed preprocess infer command that was outdated

also added toml files for reproducing preprint splits

Merge pull request #203 from ArcInstitute/aadduri/simulation

Updates code to allow:

data.kwargs.output_space == "embedding" to train on only embeddings without a gene decoder
update predict to clip [0,14]
update model hyperparameters for better preset values

Merge pull request #205 from ArcInstitute/dhruv/pyproject-scipy-downg…

…rade

Update pyproject.toml fixes reversion in uv

Merge pull request #174 from ArcInstitute/aadduri/auto_config

updated gitignore. Closes #140

Merge pull request #142 from ArcInstitute/clean_state

this version updates the help command for state tx and also uses bfloat16 for inference for significantly improved speeds.

future pr's after this will be gated behind review

Merge pull request #139 from ArcInstitute/fix_broken_main

fixes inference

remove double nesting in config

Merge pull request #114 from ArcInstitute/update_example

updated with example files

Merge pull request #113 from ArcInstitute/aadduri/add_barcodes

updated to yield barcodes with data loader