Metadata-Version: 2.4
Name: EveryQuery
Version: 0.2.0
Summary: A framework for training and evaluating foundation models, using the MEDS ecosystem for data processing and PyTorch Lightning for training.
Author-email: Payal Chandak <payal.chandak@gmail.com>, Matthew McDermott <mattmcdermott8@gmail.com>, Gregory Kondas <gregkondas9@gmail.com>
Project-URL: Homepage, https://github.com/payalchandak/EveryQuery
Project-URL: Issues, https://github.com/payalchandak/EveryQuery/issues
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.11
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: polars~=1.30.0
Requires-Dist: pyarrow==21.0.0
Requires-Dist: hydra-core==1.3.2
Requires-Dist: numpy==2.3.3
Requires-Dist: meds==0.4.0
Requires-Dist: filelock==3.19.1
Requires-Dist: pytest==8.4.2
Requires-Dist: meds-transforms==0.5.3
Requires-Dist: meds-torch-data[lightning]~=0.6.3
Requires-Dist: transformers>=4.48.0
Requires-Dist: torch==2.8.0
Requires-Dist: torchmetrics==1.8.2
Requires-Dist: lightning==2.5.5
Requires-Dist: dotenv==0.9.9
Requires-Dist: wandb>=0.22.3
Requires-Dist: ipykernel>=7.2.0
Requires-Dist: scikit-learn>=1.6.0
Dynamic: license-file

# EveryQuery

.env

```
PROJECT_DIR="/home/pac4279/EveryQuery"
DATA_DIR="/n/data1/hms/dbmi/zaklab/payal/mimic"
SAVE_DIR="/n/data1/hms/dbmi/zaklab/payal/EveryQuery/results"
RAW="${DATA_DIR}/raw"
INTERMEDIATE="${DATA_DIR}/intermediate"
PROCESSED="${DATA_DIR}/processed"
```

run for processing data

```
MEICAR_process_data input_dir="$RAW" intermediate_dir="$INTERMEDIATE" output_dir="$PROCESSED"
```

run for training

```
source .env; set -a; . ./.env; set +a; python source/train.py
```
