pyopera 0.1.1

The NIH OPERA suite of models with Python specific functionality

pyOPERA

Full python implementation of the NIH OPERA suite of models
docker run -it -v %cd%:/app --rm pyopera_pyopera /bin/bash
docker compose -f docker-compose.yml build
docker run --rm pyopera_pyopera ~/.local/share/pypoetry/venv/bin/poetry run coverage run -m pytest tests
docker build -t cabreratoxy/pyopera:0.0.1 .

poetry run python -m pip install -r requirements.txt  
poetry run black . --exclude="docs/" 
poetry run isort . --skip docs/
poetry run pylint $(find . -name "*.py" | xargs) --ignore-paths docs/ 
poetry run pytest tests    
poetry run coverage run --source pyopera -m pytest  
poetry run coverage report --skip-empty --fail-under=85  
poetry build  
poetry config repositories.testpypi https://test.pypi.org/legacy/  

docker run --rm pyopera_pyopera /bin/bash -c 'poetry run coverage run -m pytest tests'   

TODO: Fully install poetry in the container (maybe use the long name as a variable for now) TODO: Create CI/CD for package in TestPypi and the prod Pypi (CircleCI maybe?)
~~TODO: Documentation using Sphinx (make sure original repo/builders are credited) ~~ TODO: Start adding the wrapper code and files - in progress
TODO: Benchmarking with airspeed velocity
TODO: Don't repeat the library name in the Dockerfile
TODO: Struggling to run commands inside Docker from the host, will run commands from inside container for now
TODO: Test TestPypi package locally
TODO: Add actual documentation in this readme
TODO: Auto semantic versioning with poetry too
TODO: Create a python package around the Matlab package (the base files) using Poetry
TODO: Formatting/Linting/Coverage
TODO: Choose between Pytest an Unittest
TODO: Automate black, isort, pylint, coverage, pytest on build or push. - just have to finish coverage TODO: Auto docstring generating? -- used autodocstring extension for vscode
TODO: How to autobuild the base image the CI/CD will work with - could not be done

Full Documentation can be found here