chore: migrate to uv, update CI for Python 3.13

.gitattributes

@@ -0,0 +1,3 @@
+
+# Use bd merge for beads JSONL files
+.beads/issues.jsonl merge=beads

.github/workflows/python-publish.yml

@@ -1,31 +1,18 @@
-# This workflows will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
-name: Upload Python Package
+name: Publish to PyPI
 
 on:
   release:
     types: [created]
 
 jobs:
-  deploy:
-
-    runs-on: self-hosted 
-
+  publish:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+      - name: Build package
+        run: uv build
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test.yml

@@ -1,30 +1,26 @@
 name: Run tests
 
-on: [push]
+on:
+  push:
+    branches: [master, main]
+  pull_request:
+    branches: [master, main]
 
 jobs:
-  example-1:
-    name: Testing (${{ matrix.python-version }}, ${{ matrix.os }})
+  test:
+    name: Test (Python ${{ matrix.python-version }}, ${{ matrix.os }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest"]
-        python-version: ["3.10"]
+        os: [ubuntu-latest]
+        python-version: ["3.11", "3.12", "3.13"]
     steps:
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Check repo out
-      uses: actions/checkout@v4
-      with:
-        ref: ${{ github.head_ref }}
-        fetch-depth: 0
-    - name: Install dependencies
-      run: |
-        pip install -r requirements.txt  
-    - name: Run tests
-      shell: bash -l {0}
-      run: |
-        pytest -vv
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: uv sync --extra dev --extra api
+      - name: Run tests
+        run: uv run pytest -vv

.gitignore

@@ -1,11 +1,33 @@
-ORC_VPP_2019.pdf
-sphinx/_build/
-src/__pycache__/
-dev.py
-venv
-.vscode
+# Python
+__pycache__/
 *.pyc
+*.pyo
+*.egg-info/
+dist/
+build/
+
+# Environments
+.venv/
+venv/
+
+# IDE
+.vscode/
+.idea/
+
+# Sphinx
+sphinx/_build/
+
+# pytest
+.pytest_cache/
+
+# Claude Code
+.claude/
+CLAUDE.md
+AGENTS.md
+.beads/
+
+# Project
+ORC_VPP_2019.pdf
 dev.py
-/.pytest_cache
-/__pycache__/
-.pytest_cache
+
+.playwright-cli/

README.md

@@ -64,17 +64,16 @@ Follow the steps below to contribute to this project.
 
 ### Install dependencies
 
-Install the required dependencies from the `requirements.txt` file.
+Install the project using [uv](https://docs.astral.sh/uv/):
 
-If using `pip` then `pip install requirements.txt`.
+```bash
+uv sync --extra dev
+```
 
-If using `conda` then follow these steps to create an environment with the right dependencies:
+If using `pip`:
 
 ```bash
-conda create --name Python-VPP \
-    && conda config --add channels conda-forge \
-    && conda activate Python-VPP \
-    && conda install -y --file requirements.txt
+pip install -e ".[dev]"
 ```
 
 ### Run tests

pyproject.toml

@@ -0,0 +1,51 @@
+[project]
+name = "python-vpp"
+version = "0.0.2"
+description = "OOP Velocity Prediction Program"
+readme = "README.md"
+license = "MIT"
+requires-python = ">=3.11"
+authors = [
+    { name = "Marin Lauber", email = "M.Lauber@soton.ac.uk" },
+    { name = "Otto Villani" },
+    { name = "Thomas Dickson" },
+]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+    "numpy>=2.0",
+    "matplotlib>=3.8",
+    "scipy>=1.12",
+    "tqdm>=4.66",
+    "flask",
+    "streamlit>=1.37",
+    "plotly>=6.6.0",
+]
+
+[project.optional-dependencies]
+api = ["flask"]
+demo = ["streamlit>=1.37"]
+dev = [
+    "pytest",
+    "ruff",
+    "mypy",
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+
+[tool.ruff]
+line-length = 100
+
+[tool.ruff.lint]
+select = ["E", "F", "I", "W"]