Metadata-Version: 2.1
Name: gen3_util_plugin_nvidia
Version: 0.0.2rc1
Summary: CEDAR / NVIDIA collaboration
Home-page: https://github.com/ACED-IDP/nvidia-collaboration
Author: compbio
License: UNKNOWN
Project-URL: Bug Reports, https://github.com/ACED-IDP/nvidia_collaboration/issues
Project-URL: Source, https://github.com/ACED-IDP/nvidia_collaboration
Keywords: bioinformatics
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development :: Build Tools
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.9
Requires-Python: >=3.9, <4
Description-Content-Type: text/markdown

# nvidia-collaboration
OHSU CEDAR Cyclic IF and H&amp;E images

## Getting started

### Setup python environment

```commandline
source venv/bin/activate
python3 -m pip install -r requirements.txt
python3 -m pip install -r requirements-dev.txt  
python3 -m pip install -e .
```

## Run the import with `--plugin_path` 

```
gen3_util meta  import dir INPUT_PATH OUTPUT_PATH --project_id aced-nvidia --plugin_path {plugin_path}
```

### expected results

```
data
├── fhir
│   ├── DocumentReference.ndjson
│   ├── Patient.ndjson
│   ├── ResearchStudy.ndjson
│   ├── ResearchSubject.ndjson
│   ├── Specimen.ndjson
│   └── Task.ndjson


```

## Run the tests

```
pytest  tests/
```
## Distribution

- PyPi

```
# update pypi

# pypi credentials - see https://twine.readthedocs.io/en/stable/#environment-variables

export TWINE_USERNAME=  #  the username to use for authentication to the repository.
export TWINE_PASSWORD=  # the password to use for authentication to the repository.

# this could be maintained as so: export $(cat .env | xargs)

rm -r dist/
python3  setup.py sdist bdist_wheel
twine upload dist/*
```


