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cleanup further
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jkobject committed Jul 24, 2024
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Expand Up @@ -41,30 +41,36 @@ pip install scprint
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/jkcobject/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 'lamindb[jupyter,bionty]'
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
pip install 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
pip install -e ".[dev]"
pip install -r requirements-dev.txt
pip install triton==2.0.0.dev20221202 --no-deps # only if you have a matching gpu (e.g. not available for apple GPUs for now)
# install triton as mentioned in .toml if you want to
mkdocs serve # to view the dev documentation
```

## Usage

if you want to use the scDataloader's multi dataset mode or some of the functions of the model you might need to use lamin.ai, in that case connect with google or github to [lamin.ai](https://lamin.ai/login), then be sure to connect before running anything (or before starting a notebook): `lamin login <email> --key <API-key>`

If you do not have triton installed

```py
from lightning.pytorch import Trainer
from scprint import scPrint
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