Merge remote-tracking branch 'origin/dev'

.gitignore

@@ -131,3 +131,42 @@ dmypy.json
 # templates
 .github/templates/*
 .DS_Store
+data/temp/*
+.sync-conflict*
+notebooks/tests/mytest2
+notebooks/tests/mytest
+notebooks/tests/wandb
+data/GroundTruth/*
+data/adamson
+data/fasta/*
+data/scGPT_human
+wandb/*
+*/lightning_logs/*
+*.lock
+data/tensorboard/*
+notebooks/tests/*/
+data/logs/*
+.lr_find_*
+step_*_.*
+data/main/embeddings.parquet
+slurm-*.out
+notebooks/tests/step_0_.h5ad
+data/main/gene_embeddings.parquet
+*.h5ad
+data/main/main_scenic+.parquet
+scdataloader.out
+data/main/9606.protein.links.v12.0.txt.gz
+data/main/motifs-v10-nr.hgnc-m0.00001-o0.0.tbl
+data/main/main_scenic+_database.feather
+*.npy
+*.joblib
+notebooks/tests/collator_output.txt
+notebooks/tests/curr_genes_mouse.csv
+notebooks/tests/curr_genes.csv
+notebooks/tests/precision_recall_plot.png
+notebooks/tests/lightning_logs/*
+notebooks/additional/lightning_logs/*
+lightning_logs/
+collator_output.txt
+data/bias_sparse.npz
+todel/

.gitmodules

@@ -0,0 +1,6 @@
+[submodule "scDataLoader"]
+path = scDataLoader
+url = https://github.com/jkobject/scDataLoader
+[submodule "RNABERT"]
+path = RNABERT
+url = https://github.com/jkobject/RNABERT

README.md

@@ -1,47 +1,98 @@
 
-# scprint
+# scprint: Large Cell Model for scRNAseq data
 
-[![codecov](https://codecov.io/gh/jkobject/scPRINT/branch/main/graph/badge.svg?token=scPRINT_token_here)](https://codecov.io/gh/jkobject/scPRINT)
-[![CI](https://github.com/jkobject/scPRINT/actions/workflows/main.yml/badge.svg)](https://github.com/jkobject/scPRINT/actions/workflows/main.yml)
+[![PyPI version](https://badge.fury.io/py/scprint.svg)](https://badge.fury.io/py/scprint)
+[![Documentation Status](https://readthedocs.org/projects/scprint/badge/?version=latest)](https://scprint.readthedocs.io/en/latest/?badge=latest)
+[![Downloads](https://pepy.tech/badge/scprint)](https://pepy.tech/project/scprint)
+[![Downloads](https://pepy.tech/badge/scprint/month)](https://pepy.tech/project/scprint)
+[![Downloads](https://pepy.tech/badge/scprint/week)](https://pepy.tech/project/scprint)
+[![GitHub issues](https://img.shields.io/github/issues/jkobject/scPRINT)](https://img.shields.io/github/issues/jkobject/scPRINT)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![DOI](https://zenodo.org/badge/391909874.svg)](https://zenodo.org/badge/latestdoi/391909874)
 
-Awesome scprint created by Jeremie Kalfon
+![logo](logo.png)
 
-using: 
-[pytorch template](https://github.com/victoresque/pytorch-template)
-[python template](https://github.com/rochacbruno/python-project-template)
+scPRINT is a novel transformer model for the inference of gene regulatory network from scRNAseq data. It uses novel encoding and decoding schemes as well as new pre-training methodologies to learn a model of the cell. But scPRINT can do lots of things: [Read the paper!]()
+
+![figure1](figure1.png)
 
 ## Install it from PyPI
 
+If you want to be using flashattention2, know that it only supports torch==2.0.0 for now.
+
+🚨 **Important Notice:** Only the **development install** currently works (see [dev mode](#in-dev-mode))! 🚨
+
+```bash
+pip install 'lamindb[jupyter,bionty]'
+```
+
+then install scPrint
+
 ```bash
 pip install scprint
 ```
+> if you have a GPU that you want to use, you will benefit from flashattention. and you will have to do some more specific installs:
+
+1. find the version of torch 2.0.0 / torchvision 0.15.0 / torchaudio 2.0.0 that match your nvidia drivers in the torch website.
+2. apply the install command
+3. do `pip install pytorch-fast-transformers torchtext==0.15.1`
+4. do `pip install triton==2.0.0.dev20221202 --no-deps`
+
+You should be good to go. You need those specific versions for everything to work.. 
+not my fault, scream at nvidia, pytorch, Tri Dao and OpenAI :wink:
+
+
+### in dev mode
+
+```python
+conda create ...
+git clone https://github.com/jkobject/scPRINT
+git clone https://github.com/jkobject/GRnnData
+git clone https://github.com/jkobject/benGRN
+cd scPRINT
+git checkout dev
+git submodule init
+git submodule update
+pip install -e scDataloader
+pip install -e ../GRnnData/
+pip install -e ../benGRN/
+tall torch==2.0.0 torchvision==0.15.1 torchaudio==2.0.1
+# install pytorch as mentionned above if you have a GPU
+pip install -e .[dev]
+pip install 'lamindb[jupyter,bionty]'
+pip install triton==2.0.0.dev20221202 --no-deps
+```
 
 ## Usage
 
 ```py
-from scprint import BaseClass
-from scprint import base_function
+from lightning.pytorch import Trainer
+from scprint import scPrint
+from scdataloader import DataModule
 
-BaseClass().base_method()
-base_function()
+datamodule = DataModule(...)
+model = scPrint(...)
+trainer = Trainer(...)
+trainer.fit(model, datamodule=datamodule)
+...
 ```
 
+or
+
 ```bash
-$ python -m scprint
-#or
-$ scprint
+$ scprint fit/train/predict/test --config config/[medium|large|vlarge] ...
 ```
 
+for more information on usage please see the documentation in [https://www.jkobject.com/scPrint/](https://www.jkobject.com/scPrint/)
+
 ## Development
 
 Read the [CONTRIBUTING.md](CONTRIBUTING.md) file.
 
-### What is included?
+acknowledgement:
+[python template](https://github.com/rochacbruno/python-project-template)
+[laminDB](https://lamin.ai/)
+[Lightning](https://lightning.ai/)
+
+Awesome Large Cell Model created by Jeremie Kalfon.
 
-- 📃 Documentation structure using [mkdocs](http://www.mkdocs.org)
-- 🧪 Testing structure using [pytest](https://docs.pytest.org/en/latest/)
-  If you want [codecov](https://about.codecov.io/sign-up/) Reports and Automatic Release to [PyPI](https://pypi.org)  
-  On the new repository `settings->secrets` add your `PYPI_API_TOKEN` and `CODECOV_TOKEN` (get the tokens on respective websites)
-- ✅ Code linting using [flake8](https://flake8.pycqa.org/en/latest/)
-- 📊 Code coverage reports using [codecov](https://about.codecov.io/sign-up/)
-- 🛳️ Automatic release to [PyPI](https://pypi.org) using [twine](https://twine.readthedocs.io/en/latest/) and github actions.