Graph Based Imputation
How to develop on the project locally.
- Make sure the following pre-requites are installed.
python >= 3.8
- build tools eg
- Clone the repository locally
git clone email@example.com:pbashyal-nmdp/py-grim cd py-grim
- Make a virtual environment and activate it, run
> make venv python3 -m venv venv --prompt py-grim-venv ===================================================================== To activate the new virtual environment, execute the following from your shell source venv/bin/activate
- Source the virtual environment
- Development workflow is driven through
maketo list show all targets.
> make clean remove all build, test, coverage and Python artifacts clean-build remove build artifacts clean-pyc remove Python file artifacts clean-test remove test and coverage artifacts lint check style with flake8 behave run the behave tests, generate and serve report pytest run tests quickly with the default Python test run all(BDD and unit) tests coverage check code coverage quickly with the default Python dist builds source and wheel package docker-build build a docker image for the service docker build a docker image for the service install install the package to the active Python's site-packages venv creates a Python3 virtualenv environment in venv activate activate a virtual environment. Run `make venv` before activating.
- Install all the development dependencies. Will install packages from all
- The Gherkin Feature files, step files and pytest files go in
tests |-- features | |-- algorithm | | `-- SLUG\ Match.feature | `-- definition | `-- Class\ I\ HLA\ Alleles.feature |-- steps | |-- HLA_alleles.py | `-- SLUG_match.py `-- unit `-- test_grim.py
- Package Module files go in the
grim |-- __init__.py |-- algorithm | `-- match.py |-- model | |-- allele.py | `-- slug.py `-- grim.py
- Run all tests with
make testor different tests with
make behavewill generate report files and open the browser to the report.
python app.pyto run the Flask service app in debug mode. Service will be available at http://localhost:8080/
make docker-buildto build a docker image using the current
make dockerwill build and run the docker image with the service. Service will be available at http://localhost:8080/
- First release on PyPI.
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Hashes for py_grim-0.0.3-py2.py3-none-any.whl