pyproject.toml-upgrade (#6)

* Created pyproject.toml and removed setup.py

* Remove requirement*.txt files

* Add 'Bump My Version' config

* Update all the versions to the latest

* Make flask work with api-spec

* Docker support

- Use Python 3.13
- Update Dockerfile to use uv
- Update docker targets in Makefile

* Removed HISTORY file

* package in src/ and Docker build

 - Moved package under src/
 - Dockerfile builds image

* Update dockerfile and project

* Update all the versions to the latest
Fix Conflicts

* Make flask work with api-spec

* Use uv in GitHub Action

* Use ruff instead of black in CI

* Update bug_report template

* README and CONTRIBUTING.md updated

* Docker Fix
 - Fix final sync
 - Use script for app start

Author: pbashyal-nmdp

CONTRIBUTING.md

@@ -0,0 +1,127 @@
+# Contributing
+
+Contributions are welcome, and they are greatly appreciated! Every
+little bit helps, and credit will always be given.
+
+You can contribute in many ways:
+
+## Types of Contributions
+
+### Report Bugs
+
+Report bugs at
+<https://github.com/nmdp-bioinformatics/my_project_template/issues>.
+
+If you are reporting a bug, please include:
+
+- Your operating system name and version.
+- Any details about your local setup that might be helpful in
+  troubleshooting.
+- Detailed steps to reproduce the bug.
+
+### Fix Bugs
+
+Look through the GitHub issues for bugs. Anything tagged with "bug"
+and "help wanted" is open to whoever wants to implement it.
+
+### Implement Features
+
+Look through the GitHub issues for features. Anything tagged with
+"enhancement" and "help wanted" is open to whoever wants to
+implement it.
+
+### Write Documentation
+
+My Project Template could always use more documentation, whether as part
+of the official My Project Template docs, in docstrings, or even on the
+web in blog posts, articles, and such.
+
+### Submit Feedback
+
+The best way to send feedback is to file an issue at
+<https://github.com/nmdp-bioinformatics/my_project_template/issues>.
+
+If you are proposing a feature:
+
+- Explain in detail how it would work.
+- Keep the scope as narrow as possible, to make it easier to implement.
+- Remember that this is a volunteer-driven project, and that
+  contributions are welcome :)
+
+## Get Started!
+
+Ready to contribute? Here's how to set up for local development.
+
+1.  Fork the repo on GitHub.
+
+2.  Clone your fork locally:
+
+    ``` shell
+    $ git clone [email protected]:your_name_here/my_project_template.git
+    ```
+
+3.  Install your local copy into a virtual environment. This is how you
+    set up your fork for local development:
+
+    ``` shell
+    $ cd my_project_template/
+    $ make venv
+    $ source .venv/bin/activate
+    $ make install
+    $ make sync
+    ```
+
+4.  Create a branch for local development:
+
+    ``` shell
+    $ git checkout -b name-of-your-bugfix-or-feature
+    ```
+
+    Now you can make your changes locally.
+
+   5.  When done making changes, check that your changes pass
+       flake8 and the tests, including testing other Python versions with
+       tox:
+
+       ``` shell
+       $ pre-commit
+       $ make test
+       ```
+
+6.  Commit your changes and push your branch to GitHub:
+
+    ``` shell
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+    ```
+
+7.  Submit a pull request through the GitHub website.
+
+## Pull Request Guidelines
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1.  The pull request should include tests.
+2.  If the pull request adds functionality, the docs should be updated.
+    Put your new functionality into a function with a docstring, and add
+    the feature to the list in README.rst.
+3.  The pull request should work for Python 3.6 and higher.
+
+## Tips
+
+To run a subset of tests:
+
+``` shell
+$ pytest tests.test_my_project_template
+```
+
+## Release a new version
+
+Make sure all your changes are committed. Then run:
+
+``` shell
+$ bump-my-version bump patch -vv # possible: major / minor / patch
+$ git push
+```
+Maintainer can publish a release, which will submit to PyPi.

CONTRIBUTING.rst

@@ -44,6 +44,6 @@ ENV PYTHONPATH="/app/.venv/lib/python3.13/site-packages/:"
 # Sync the project into a new environment, asserting the lockfile is up to date
 COPY pyproject.toml /app/
 COPY uv.lock /app/
-RUN /bin/uv sync --locked --group deploy
+RUN uv sync --no-build --no-install-project --locked --group deploy
 
-CMD [".venv/bin/gunicorn"  , "--bind", "0.0.0.0:8080", "--worker-tmp-dir", "/dev/shm", "app:app"]
+CMD ["/app/run-app.sh"]

Dockerfile

@@ -4,7 +4,7 @@ My Project Template
 
 How to use the template:
 
-1. Create a template by clicking on the "Use this template" button. Make sure to select all branches
+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
     ```shell
@@ -14,14 +14,13 @@ How to use the template:
 3. Make a virtual environment and activate it, run `make venv`
    ```shell
     > make venv
-      python3 -m venv venv --prompt urban-potato-venv
-      =====================================================================
-    To activate the new virtual environment, execute the following from your shell
-    source venv/bin/activate
-   ```
+        Using CPython 3.13.7
+        Creating virtual environment at: .venv
+        Activate with: source .venv/bin/activate
+    ```
 4. Source the virtual environment
    ```shell
-   source venv/bin/activate
+   source .venv/bin/activate
    ```
 5. Development workflow is driven through `Makefile`. Use `make` to list show all targets.
    ```
@@ -30,21 +29,23 @@ How to use the template:
     clean-build          remove build artifacts
     clean-pyc            remove Python file artifacts
     clean-test           remove test and coverage artifacts
-    lint                 check style with flake8
+    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 for the service
-    install              install the package to the active Python's site-packages
+    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 all the development dependencies. Will install packages from all `requirements-*.txt` files.
+6. Install and sync all the project and development dependencies.
    ```shell
     make install
+    make sync
    ```
 7. The Gherkin Feature files, step files and pytest files go in `tests` directory:
     ```
@@ -60,7 +61,7 @@ How to use the template:
     `-- unit
         `-- test_my_project_template.py
     ```
-8. Package Module files go in the `my_project_template` directory.
+8. Package Module files go in the `src/my_project_template` directory.
     ```
     my_project_template
     |-- __init__.py
@@ -72,6 +73,6 @@ How to use the template:
     `-- 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 `python app.py` to run the Flask service app in debug mode. Service will be available at http://localhost:8080/
+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/