pyproject.toml-upgrade

.bumpversion.toml

@@ -20,9 +20,8 @@ setup_hooks = []
 pre_commit_hooks = []
 post_commit_hooks = []
 
-
 [[tool.bumpversion.files]]
-filename = "my_project_template/__init__.py"
+filename = "src/my_project_template/__init__.py"
 search =  "__version__ = \"{current_version}\""
 replace = "__version__ = \"{new_version}\""
 
@@ -35,3 +34,8 @@ replace = "version = \"{new_version}\""
 filename = "api-spec.yaml"
 search =  "version: {current_version}"
 replace = "version: {new_version}"
+
+[[tool.bumpversion.files]]
+filename = "Makefile"
+search =  "VERSION := {current_version}"
+replace = "VERSION := {new_version}"

.dockerignore

@@ -1,3 +1,4 @@
+.git
 .github
 .eggs/
 build
@@ -6,9 +7,9 @@ dist
 *.egg-info
 tests
 venv
+.venv
 
 __pycache__
-*.pyc
 *.pyo
 *.pyd
 *.output

.github/ISSUE_TEMPLATE/bug_report.md

@@ -12,27 +12,13 @@ A clear and concise description of what the bug is.
 
 **To Reproduce**
 Steps to reproduce the behavior:
-1. Go to '...'
-2. Click on '....'
-3. Scroll down to '....'
-4. See error
+
 
 **Expected behavior**
 A clear and concise description of what you expected to happen.
 
 **Screenshots**
 If applicable, add screenshots to help explain your problem.
 
-**Desktop (please complete the following information):**
- - OS: [e.g. iOS]
- - Browser [e.g. chrome, safari]
- - Version [e.g. 22]
-
-**Smartphone (please complete the following information):**
- - Device: [e.g. iPhone6]
- - OS: [e.g. iOS8.1]
- - Browser [e.g. stock browser, safari]
- - Version [e.g. 22]
-
 **Additional context**
 Add any other context about the problem here.

.github/workflows/python-tests.yml

@@ -1,6 +1,3 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
 name: BDD and Unit Tests
 
 on:
@@ -10,24 +7,29 @@ on:
     branches: [ master ]
 
 jobs:
-  build:
-
+  run-tests:
+    name: python
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.9
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-        if [ -f requirements-tests.txt ]; then pip install -r requirements-tests.txt; fi
-    - name: Test with pytest
-      run: |
-        pytest
-    - name: Run BDD Tests
-      run: |
-        behave
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: ".python-version"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          # Install a specific version of uv.
+          version: "0.8.15"
+
+      - name: Install the project
+        run: uv sync --locked  --group=test
+
+      - name: Run pytests
+        run: uv run pytest
+
+      - name: Run BDD Tests
+        run: uv run behave

.github/workflows/ruff.yml

@@ -0,0 +1,20 @@
+name: CI
+on: push
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: ".python-version"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+
+      # Update output format to enable automatic inline annotations.
+      - name: Run Ruff
+        run: ruff check --output-format=github .

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 git@github.com: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.