My Project Template

How to use the template:

1. Click on the top-right green "Use this template" button. Make sure to select all branches This will create a new repository with the given name e.g. urban-potato
2. Clone the repository locally

   git clone git@github.com:pbashyal-nmdp/urban-potato.git
   cd urban-potato

3. Make a virtual environment and activate it, run make venv

    > make venv
        Using CPython 3.13.7
        Creating virtual environment at: .venv
        Activate with: source .venv/bin/activate

4. Source the virtual environment

   source .venv/bin/activate

5. Development workflow is driven through Makefile. Use make to 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 ruff
    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 and run the service
    sync                 install the package to the active Python's site-packages
    install              Sync pyproject.toml to .venv as well as install tools
    venv                 creates a Python3 virtualenv environment in venv
    activate             activate a virtual environment. Run `make venv` before activating.
   

6. Install and sync all the project and development dependencies.

    make install

7. The Gherkin Feature files, step files and pytest files go in tests directory:

   tests
   |-- features
   |   |-- algorithm
   |   |   `-- SLUG\ Match.feature
   |   `-- definition
   |       `-- Class\ I\ HLA\ Alleles.feature
   |-- steps
   |   |-- HLA_alleles.py
   |   `-- SLUG_match.py
   `-- unit
       `-- test_my_project_template.py
   

8. Package Module files go in the src/my_project_template directory.

   my_project_template
   |-- __init__.py
   |-- algorithm
   |   `-- match.py
   |-- model
   |   |-- allele.py
   |   `-- slug.py
   `-- my_project_template.py
   

9. Run all tests with make test or different tests with make behave or make pytest. make behave will generate report files and open the browser to the report.
10. Use uv run app.py to run the Flask service app in debug mode. Service will be available at http://localhost:8080/
11. Use make docker-build to build a docker image using the current Dockerfile.
12. make docker will build and run the docker image with the service. Service will be available at http://localhost:8080/