Wire up remaining uv migration changes

Second half of the tox/pip -> uv replacement, accidentally left out of
the previous commit: pyproject.toml dependency-group, CI/deploy
workflows, README, and dev docs.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Author: dweindl

.github/workflows/ci_tests.yml

@@ -12,47 +12,32 @@ jobs:
     strategy:
       matrix:
         platform: [windows-latest, macos-latest, ubuntu-latest]
-        python-version: ["3.12", "3.x"]
+        python-version: ["3.12", "3.14"]
     runs-on: ${{ matrix.platform }}
 
     steps:
     - name: Check out repository
       uses: actions/checkout@v7
 
-    - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v7
+    - name: Install uv and python ${{ matrix.python-version }}
+      uses: astral-sh/setup-uv@v9
       with:
+        enable-cache: true
         python-version: ${{ matrix.python-version }}
 
-    - name: Get pip cache directory
-      id: pip_cache_dir
-      run: |
-        echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
-      shell: bash
-
-    - name: Cache
-      uses: actions/cache@v6
-      with:
-        path: ${{ steps.pip_cache_dir.outputs.dir }}
-        key: ${{ runner.os }}-${{ matrix.python-version }}-${{ hashFiles('**/.ci_pip_reqs.txt') }}-${{ hashFiles('**/setup.py') }}
-        restore-keys: |
-          ${{ runner.os }}-${{ matrix.python-version }}-
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip wheel
-        pip install -r requirements-dev.txt
-
     - name: Quality tests
-      run: tox -e quality
+      run: uvx pre-commit run --all-files
       if: matrix.platform == 'ubuntu-latest'
 
     - name: Unit tests
-      run: tox -e unit
+      run: |
+        uv sync --extra tests --extra reports --extra combine --extra vis --group ci
+        uv pip install "sympy>=1.12.1"
+        uv run --no-sync pytest --cov=petab --cov-report=xml --cov-append --durations=10 tests
 
     - name: Coverage
       uses: codecov/codecov-action@v7
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         files: ./coverage.xml
-      if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.x'
+      if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.14'

.github/workflows/deploy.yml

@@ -16,16 +16,11 @@ jobs:
     steps:
     - name: Check out repository
       uses: actions/checkout@v7
-    - name: Set up python
-      uses: actions/setup-python@v7
-      with:
-        python-version: 3.x
+    - name: Install uv
+      uses: astral-sh/setup-uv@v9
 
-    - name: Install dependencies / build sdist
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel build
-        python -m build -s
+    - name: Build sdist
+      run: uv build --sdist
 
     - name: Publish a Python distribution to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1

README.md

@@ -22,7 +22,7 @@ and the easiest way to install it is running
 
     pip3 install petab
 
-`petab` requires Python>=3.11. We are following
+`petab` requires Python>=3.12. We are following
 [NumPy's Python support policy](https://numpy.org/neps/nep-0029-deprecation_policy.html).
 
 Development versions of the PEtab library can be installed using

doc/development.rst

@@ -60,7 +60,7 @@ the pre-commit hooks, run:
 
 .. code-block:: bash
 
-    pip install pre-commit
+    uv tool install pre-commit
     pre-commit install
 
 To run the pre-commit checks manually on all, not just the modified files, run:
@@ -85,6 +85,7 @@ To build the documentation, run:
 
 .. code-block:: bash
 
+    uv sync --extra doc --extra vis
     cd doc
     make html
     # then open `build/html/index.html` in a browser

pyproject.toml

@@ -84,6 +84,12 @@ petab_visualize = "petab.v1.visualize.cli:_petab_visualize_main"
 Repository = "https://github.com/PEtab-dev/libpetab-python"
 Documentation = "https://petab.readthedocs.io/projects/libpetab-python/"
 
+[dependency-groups]
+ci = [
+    "petabtests @ git+https://github.com/PEtab-dev/petab_test_suite@main",
+    "benchmark_models_petab @ git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master#subdirectory=src/python",
+]
+
 [tool.setuptools.packages.find]
 include = ["petab", "petab.*"]
 namespaces = false