Move from Poetry to uv and from black to ruff format

.devcontainer/Dockerfile

@@ -26,7 +26,7 @@ RUN DEBIAN_FRONTEND=noninteractive \
         libffi-dev \
         liblzma-dev
 
-# Python and poetry installation
+# Python and uv installation
 USER $USER
 ARG HOME="/home/$USER"
 ARG PYTHON_VERSION=3.11
@@ -41,6 +41,5 @@ RUN echo "linux installed" \
     && pyenv install ${PYTHON_VERSION} \
     && echo "python installed" \
     && pyenv global ${PYTHON_VERSION} \
-    && curl -sSL https://install.python-poetry.org | python3 - \
-    && echo "poetry installed" \
-    && poetry config virtualenvs.in-project true
+    && curl -LsSf https://astral.sh/uv/install.sh | sh \
+    && echo "uv installed"

.devcontainer/devcontainer-lock.json

@@ -1,9 +1,3 @@
 {
-  "features": {
-    "ghcr.io/devcontainers-extra/features/poetry:2": {
-      "version": "2.0.18",
-      "resolved": "ghcr.io/devcontainers-extra/features/poetry@sha256:7b5f2c66d25d8b3cc5d601af6b81b720c77dd315f24d5e6f84b342cccc3c9228",
-      "integrity": "sha256:7b5f2c66d25d8b3cc5d601af6b81b720c77dd315f24d5e6f84b342cccc3c9228"
-    }
-  }
+  "features": {}
 }

.devcontainer/devcontainer.json

@@ -1,5 +1,5 @@
 {
-	"name": "poetry3-poetry-pyenv-mdopt",
+	"name": "mdopt",
 	"build": {
 		"dockerfile": "Dockerfile"
 	},
@@ -11,7 +11,7 @@
 	// "forwardPorts": [],
 
 	// 👇 Use 'postCreateCommand' to run commands after the container is created.
-	"postCreateCommand": "poetry install --with dev,test,docs",
+	"postCreateCommand": "uv sync --group dev --group test --group docs",
 
 	// 👇 Configure tool-specific properties.
 	"customizations": {
@@ -23,9 +23,7 @@
 				]
             }
 		},
-		"features": {
-			"ghcr.io/devcontainers-extra/features/poetry:2": {}
-		}
+		"features": {}
 
 	// 👇 Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
 	// "remoteUser": "root"

.github/CONTRIBUTING.md

@@ -11,7 +11,7 @@ Additionally, make sure any new code is properly accompanied by working through
   - [ ] All other tests still pass (when running ``pytest`` in the root directory)
   - [ ] Any functions added have [``numpy`` style docstrings](http://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_numpy.html)
   - [ ] If suitable, funtionality is documented in ``docs`` or an example added in ``examples``
-  - [ ] The code is linted with ``black``.
+  - [ ] The code is formatted with ``ruff format``.
 
 
 # Contributor Covenant Code of Conduct

.github/dependabot.yml

@@ -7,8 +7,8 @@ updates:
     schedule:
       interval: "daily"
 
-  # Maintain dependencies for Poetry
-  - package-ecosystem: "pip"
+  # Maintain dependencies in pyproject.toml and uv.lock
+  - package-ecosystem: "uv"
     directory: "/"
     schedule:
       interval: "daily"

.github/workflows/dependency-review.yml

@@ -12,3 +12,10 @@ jobs:
         uses: actions/checkout@v7
       - name: 'Dependency Review'
         uses: actions/dependency-review-action@v5
+        with:
+          # diskcache <= 5.6.3 unpickles cache files, so anyone who can write
+          # to the cache directory can run code (CVE-2025-69872). No fixed
+          # release exists. qldpc imports it at module level (qldpc.cache,
+          # loaded by qldpc.codes), so it cannot be dropped. Remove this entry
+          # once diskcache ships a fix or qldpc stops requiring it.
+          allow-ghsas: GHSA-w8v5-vhqr-4h9v

.github/workflows/lint.yml

@@ -8,16 +8,13 @@ jobs:
       steps:
         - uses: actions/checkout@v7
 
-        - name: Set up Python 3.11
-          uses: actions/setup-python@v7
+        - name: Set up uv and Python 3.11
+          uses: astral-sh/setup-uv@v10.1.0
           with:
-           python-version: '3.11'
-
-        - name: Set up Poetry
-          run: pip install poetry
+            python-version: '3.11'
 
         - name: Install dependencies
-          run: poetry install --with dev
+          run: uv sync --locked --group dev
 
         - name: Run linter
-          run: poetry run pylint mdopt --fail-under=9
+          run: uv run pylint mdopt --fail-under=9

.github/workflows/mypy.yml

@@ -8,16 +8,13 @@ jobs:
       steps:
         - uses: actions/checkout@v7
 
-        - name: Set up Python 3.11
-          uses: actions/setup-python@v7
+        - name: Set up uv and Python 3.11
+          uses: astral-sh/setup-uv@v10.1.0
           with:
-           python-version: '3.11'
-
-        - name: Set up Poetry
-          run: pip install poetry
+            python-version: '3.11'
 
         - name: Install dependencies
-          run: poetry install --with dev
+          run: uv sync --locked --group dev
 
         - name: Run mypy
-          run: poetry run mypy mdopt
+          run: uv run mypy mdopt

.github/workflows/notebooks.yml

@@ -21,15 +21,15 @@ on:
       - "mdopt/**"
       - "scripts/run_notebooks.py"
       - "pyproject.toml"
-      - "poetry.lock"
+      - "uv.lock"
       - ".github/workflows/notebooks.yml"
   pull_request:
     paths:
       - "examples/**/*.ipynb"
       - "mdopt/**"
       - "scripts/run_notebooks.py"
       - "pyproject.toml"
-      - "poetry.lock"
+      - "uv.lock"
       - ".github/workflows/notebooks.yml"
   workflow_dispatch:
 
@@ -51,7 +51,8 @@ jobs:
     steps:
       - uses: actions/checkout@v7
 
-      - uses: actions/setup-python@v7
+      - name: Set up uv and Python 3.11
+        uses: astral-sh/setup-uv@v10.1.0
         with:
           python-version: "3.11"
 
@@ -65,15 +66,12 @@ jobs:
             texlive-latex-base texlive-latex-extra texlive-fonts-recommended \
             cm-super dvipng ghostscript
 
-      - name: Set up Poetry
-        run: pip install poetry
-
       # The dev group carries ipykernel, nbclient, nbformat and matplotlib.
       - name: Install package and notebook dependencies
-        run: poetry install --with dev
+        run: uv sync --locked --group dev
 
       - name: Execute notebooks
         env:
           MDOPT_NB_FAST: "1"
           MPLBACKEND: Agg
-        run: poetry run python scripts/run_notebooks.py
+        run: uv run python scripts/run_notebooks.py

.github/workflows/tests.yml

@@ -12,20 +12,17 @@ jobs:
     steps:
       - uses: actions/checkout@v7
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v7
+      - name: Set up uv and Python 3.11
+        uses: astral-sh/setup-uv@v10.1.0
         with:
           python-version: '3.11'
 
-      - name: Set up Poetry
-        run: pip install poetry
-
       - name: Install dependencies
-        run: poetry install --with test
+        run: uv sync --locked --group test
 
       - name: Generate report
         run: |
-          poetry run pytest --cov=./ --cov-report=xml -W ignore::DeprecationWarning
+          uv run pytest --cov=./ --cov-report=xml -W ignore::DeprecationWarning
 
       - name: Upload Coverage to Codecov
         uses: codecov/codecov-action@v7

.pre-commit-config.yaml

@@ -3,18 +3,19 @@ repos:
     rev: v6.0.0
     hooks:
       - id: check-added-large-files
+        # uv.lock is generated and larger than the 500 KB default.
+        exclude: ^uv\.lock$
       - id: check-docstring-first
       - id: check-merge-conflict
       - id: check-toml
       - id: check-yaml
       - id: detect-private-key
       - id: trailing-whitespace
 
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 26.5.1
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.16.7
     hooks:
-      - id: black
-        entry: black .
+      - id: ruff-format
 
   - repo: local
     hooks:
@@ -38,7 +39,11 @@ repos:
         - id: mypy
           exclude: '(^examples|^docs|^mdopt/examples)/.*'
 
-  - repo: https://github.com/python-poetry/poetry
-    rev: 2.4.1
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    rev: 0.12.13
     hooks:
-      - id: poetry-check
+      # Fails when uv.lock is out of date with pyproject.toml.
+      - id: uv-lock
+      # Keeps requirements.txt (read by readthedocs) in step with uv.lock.
+      - id: uv-export
+        args: ["--frozen", "--no-default-groups", "--no-emit-project", "--output-file=requirements.txt", "--quiet"]

README.md

@@ -26,12 +26,14 @@ To install the current release, use the package manager [pip](https://pip.pypa.i
 pip install mdopt
 ```
 
-Otherwise, you can clone the repository and use [poetry](https://python-poetry.org/).
+Otherwise, you can clone the repository and use [uv](https://docs.astral.sh/uv/).
 
 ```bash
-poetry install
+uv sync
 ```
 
+`uv sync --group dev --group test` also installs the development and test tools.
+
 ### A note on NumPy's BLAS on Apple silicon
 
 On Apple silicon running macOS 14 or later, pip installs the NumPy and
@@ -61,6 +63,16 @@ pip download "scipy==$(python -c 'import scipy; print(scipy.__version__)')" \
 pip install --force-reinstall --no-deps /tmp/openblas-wheels/*.whl
 ```
 
+In a uv checkout, a reinstall like this lasts only until the next `uv run`
+or `uv sync`, which put the locked Accelerate wheels back. Sync against a
+macOS 13 target instead (adding your usual `--group` flags). It selects the
+same OpenBLAS wheels, and later `uv run` and `uv sync` calls keep them. Run
+it again whenever the lock moves NumPy or SciPy to a new version:
+
+```bash
+uv sync --python-platform aarch64-apple-darwin
+```
+
 Set `MDOPT_ALLOW_ACCELERATE=1` to silence the warning if you must keep
 Accelerate. Use `OMP_NUM_THREADS=1` (or `OPENBLAS_NUM_THREADS=1`) for the
 per-process BLAS of worker pools.
@@ -190,11 +202,11 @@ Developers may find the following guidelines useful:
   ```
 
 - **Coding style.**
-  The project follows the [Black](https://black.readthedocs.io/en/stable/) code style.
-  Please run Black before submitting a pull request:
+  The code is formatted with [Ruff](https://docs.astral.sh/ruff/formatter/), whose style matches Black's.
+  Please run the formatter before submitting a pull request:
 
   ```bash
-  black .
+  uv run --group dev ruff format .
   ```
 
 - **Pre-commit hooks.**

docs/source/README.rst

@@ -23,11 +23,13 @@ To install the current release, use the package manager
    pip install mdopt
 
 Otherwise, you can clone the repository and use
-`poetry <https://python-poetry.org/>`__.
+`uv <https://docs.astral.sh/uv/>`__.
 
 .. code:: bash
 
-   poetry install
+   uv sync
+
+``uv sync --group dev --group test`` also installs the development and test tools.
 
 Minimal example
 ---------------
@@ -199,13 +201,13 @@ Developers may find the following guidelines useful:
 
      ./generate_docs.sh
 
-- **Coding style.** The project follows the
-  `Black <https://black.readthedocs.io/en/stable/>`__ code style. Please
-  run Black before submitting a pull request:
+- **Coding style.** The code is formatted with
+  `Ruff <https://docs.astral.sh/ruff/formatter/>`__, whose style matches
+  Black's. Please run the formatter before submitting a pull request:
 
   .. code:: bash
 
-     black .
+     uv run --group dev ruff format .
 
 - **Pre-commit hooks.** `Pre-commit <https://pre-commit.com/>`__ hooks
   are configured to enforce consistent style automatically. To enable

docs/source/contributing.rst

@@ -4,11 +4,11 @@ Contributing
 We welcome contributions of all sizes! Before opening a pull request, please:
 
 1. Run the test suite (see :doc:`testing`).
-2. Follow the **Black** code style:
+2. Format the code with **Ruff**:
 
    .. code-block:: bash
 
-      black .
+      uv run --group dev ruff format .
 
 3. Install pre-commit hooks:
 

docs/source/getting_started.rst

@@ -10,13 +10,13 @@ You can install the package from PyPI:
 
    pip install mdopt
 
-Or, alternatively, from source using Poetry:
+Or, alternatively, from source using uv:
 
 .. code-block:: bash
 
    git clone https://github.com/quicophy/mdopt.git
    cd mdopt
-   poetry install
+   uv sync
 
 Minimal example
 ---------------------

docs/source/testing.rst

@@ -6,8 +6,8 @@ We use ``pytest`` for tests. From the project root:
 .. code-block:: bash
 
    pytest
-   # or, if installed with poetry:
-   poetry run pytest
+   # or, from a uv checkout:
+   uv run --group test pytest
 
 Tips
 ----