Metadata-Version: 2.1
Name: gene-normalizer
Version: 0.1.0
Summary: VICC normalization routine for genes
Home-page: https://github.com/cancervariants/gene-normalization
Author: VICC
Author-email: help@cancervariants.org
License: MIT
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Requires-Dist: pysam
Requires-Dist: pyyaml
Requires-Dist: pydantic
Requires-Dist: fastapi
Requires-Dist: uvicorn
Requires-Dist: click
Requires-Dist: civicpy
Requires-Dist: boto3
Requires-Dist: beautifulsoup4
Requires-Dist: gffutils
Requires-Dist: requests
Requires-Dist: biocommons.seqrepo
Requires-Dist: ga4gh.vrs

# Gene Normalization
Services and guidelines for normalizing gene terms

## Developer instructions
Following are sections include instructions specifically for developers.

### Installation
For a development install, we recommend using Pipenv. See the 
[pipenv docs](https://pipenv-fork.readthedocs.io/en/latest/#install-pipenv-today) 
for direction on installing pipenv in your compute environment.

Once installed, from the project root dir, just run:

```shell script
pipenv sync
```

### Data files
For now, data files supporting the normalizers need to be obtained independently.
See issue #7 for progress on updaters.

### Init coding style tests

Code style is managed by [flake8](https://github.com/PyCQA/flake8) and checked prior to commit.

We use [pre-commit](https://pre-commit.com/#usage) to run conformance tests.

This ensures:

* Check code style
* Check for added large files
* Detect AWS Credentials
* Detect Private Key

Before first commit run:

```
pre-commit install
```


### Running unit tests

Running unit tests is as easy as pytest.

```
pipenv run pytest
```

### Starting the gene normalization service

From the project root, run the following:

```shell script
 uvicorn main:app --reload
```

Next, view the OpenAPI docs on your local machine: 

http://127.0.0.1:8000/docs


