Use dependency groups, uv, and local pre-commit hooks

Author: Patrick Kidger Bot

.github/workflows/build_docs.yml

@@ -16,19 +16,18 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v2
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v7
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install '.[docs]'
+          uv run echo done
 
       - name: Build docs
         run: |
-          mkdocs build
+          uv run mkdocs build
 
       - name: Upload docs
         uses: actions/upload-artifact@v4

.github/workflows/release.yml

@@ -13,10 +13,12 @@ jobs:
         uses: patrick-kidger/action_update_python_project@v8
         with:
             python-version: "3.11"
+            # Uninstall and reinstall pytest to work around the fact that it doesn't get put into `bin` otherwise.
             test-script: |
                 cp -r ${{ github.workspace }}/test ./test
                 cp ${{ github.workspace }}/pyproject.toml ./pyproject.toml
-                uv sync --extra tests --no-install-project --inexact
+                uv pip uninstall pytest
+                uv sync --no-install-project --inexact
                 uv run --no-sync python -m test
             pypi-token: ${{ secrets.pypi_token }}
             github-user: patrick-kidger

.github/workflows/run_tests.yml

@@ -15,24 +15,23 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v2
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v7
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install '.[dev,docs,tests]'
+          uv run echo done
 
       - name: Checks with pre-commit
         run: |
-          pre-commit run --all-files
+          uv run prek run --all-files
 
       - name: Test with pytest
         run: |
-          python -m test
+          uv run python -m test
 
       - name: Check that documentation can be built.
         run: |
-          mkdocs build
+          uv run mkdocs build

.pre-commit-config.yaml

@@ -1,22 +1,38 @@
+fail_fast: true
 repos:
-  - repo: local
+  - repo: meta
     hooks:
-      - id: sort_pyproject
-        name: sort_pyproject
-        entry: toml-sort -i --sort-table-keys --sort-inline-tables
-        language: python
-        files: ^pyproject\.toml$
-        additional_dependencies: ["toml-sort==0.23.1"]
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.13.0
+    - id: check-hooks-apply
+    - id: check-useless-excludes
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
     hooks:
-      - id: ruff-format  # formatter
-        types_or: [ python, pyi, jupyter, toml ]
-      - id: ruff  # linter
-        types_or: [ python, pyi, jupyter, toml ]
-        args: [ --fix ]
-  - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.405
+    - id: trailing-whitespace
+      exclude: \.md$
+    - id: check-toml
+    - id: mixed-line-ending
+  - repo: local
     hooks:
-    - id: pyright
-      additional_dependencies: [equinox, jax, jaxtyping, optax, optimistix, lineax, pytest, typeguard==2.13.3, typing_extensions, wadler_lindig]
+      - id: sort-pyproject
+        name: sort pyproject
+        files: ^pyproject\.toml$
+        language: system
+        entry: uv run -- toml-sort -i --sort-table-keys --sort-inline-tables
+      - id: ruff-format
+        name: ruff format
+        types_or: [python, pyi, jupyter, toml]
+        language: system
+        entry: uv run -- ruff format --
+        require_serial: true
+      - id: ruff-lint
+        name: ruff lint
+        types_or: [python, pyi, jupyter, toml]
+        language: system
+        entry: uv run -- ruff check --fix --
+        require_serial: true
+      - id: pyright
+        name: pyright
+        types_or: [python]
+        language: system
+        entry: uv run -- pyright
+        require_serial: true

CONTRIBUTING.md

@@ -4,30 +4,24 @@ Contributions (pull requests) are very welcome! Here's how to get started.
 
 ---
 
-**Getting started**
+### Getting started
 
-First fork the library on GitHub.
-
-Then clone and install the library:
+[We assume that you have `uv` installed.](https://docs.astral.sh/uv/) Now fork the library on GitHub. Then clone and install the library:
 
 ```bash
 git clone https://github.com/your-username-here/diffrax.git
 cd diffrax
-pip install -e '.[dev]'
-pre-commit install  # `pre-commit` is installed by `pip` on the previous line
+uv run prek install  # Creates a local venv + installs dependencies + installs pre-commit hooks.
 ```
 
 ---
 
-**If you're making changes to the code:**
-
-Now make your changes. Make sure to include additional tests if necessary.
+### If you're making changes to the code
 
-Next verify the tests all pass:
+Now make your changes. Make sure to include additional tests if necessary. Next verify the tests all pass:
 
 ```bash
-pip install -e '.[tests]'
-pytest  # `pytest` is installed by `pip` on the previous line.
+uv run pytest
 ```
 
 Then push your changes back to your fork of the repository:
@@ -40,13 +34,12 @@ Finally, open a pull request on GitHub!
 
 ---
 
-**If you're making changes to the documentation:**
+### If you're making changes to the documentation
 
 Make your changes. You can then build the documentation by doing
 
 ```bash
-pip install -e '.[docs]'
-mkdocs serve
+uv run mkdocs serve
 ```
 
 You can then see your local copy of the documentation by navigating to `localhost:8000` in a web browser.

diffrax/_autocitation.py

@@ -222,7 +222,7 @@ def _backsolve_adjoint(adjoint, terms=None):
                 r"""
     % You are backpropagating through an SDE using optimise-then-discretise
     % (`adjoint=BacksolveAdjoint(...)`)
-    % This technique was introduced in 
+    % This technique was introduced in
     """
                 + vbt_ref
                 + r"""
@@ -273,10 +273,10 @@ def _discrete_adjoint(adjoint):
 % If using forward-mode autodifferentiation, then this was studied in:
 @inproceedings{ma2021comparison,
   title={A Comparison of Automatic Differentiation and Continuous Sensitivity Analysis
-         for Derivatives of Differential Equation Solutions}, 
+         for Derivatives of Differential Equation Solutions},
   author={Ma, Yingbo and Dixit, Vaibhav and Innes, Michael J and Guo, Xingjian and
           Rackauckas, Chris},
-  booktitle={2021 IEEE High Performance Extreme Computing Conference (HPEC)}, 
+  booktitle={2021 IEEE High Performance Extreme Computing Conference (HPEC)},
   year={2021},
   pages={1-9},
   doi={10.1109/HPEC49654.2021.9622796}

diffrax/_event.py

@@ -62,7 +62,7 @@ def __init__(
     the exact time of the event. If the triggered condition function returns a real
     number, then the final time will be the time at which that real number equals zero.
     (If the triggered condition function returns a boolean, then the returned time will
-    just be the end of the step on which it becomes `True`.) 
+    just be the end of the step on which it becomes `True`.)
     [`optimistix.Newton`](https://docs.kidger.site/optimistix/api/root_find/#optimistix.Newton)
     would be a typical choice here.
 
@@ -74,12 +74,12 @@ def __init__(
 
 !!! Example
 
-    Consider a bouncing ball dropped from some intial height $x_0$. We can model 
+    Consider a bouncing ball dropped from some intial height $x_0$. We can model
     the ball by a 2-dimensional ODE
 
     $\\frac{dx_t}{dt} = v_t, \\quad \\frac{dv_t}{dt} = -g,$
 
-    where $x_t$ represents the height of the ball, $v_t$ its velocity, 
+    where $x_t$ represents the height of the ball, $v_t$ its velocity,
     and $g$ is the gravitational constant. With $g=8$, this corresponds to the
     vector field:
 
@@ -89,8 +89,8 @@ def vector_field(t, y, args):
         return jnp.array([v, -8.0])
     ```
 
-    Figuring out exactly when the ball hits the ground amounts to 
-    solving the ODE until the event $x_t=0$ is triggered. This can be done by using 
+    Figuring out exactly when the ball hits the ground amounts to
+    solving the ODE until the event $x_t=0$ is triggered. This can be done by using
     the real-valued condition function:
 
     ```python

diffrax/_progress_meter.py

@@ -190,8 +190,8 @@ def __check_init__(self):
             )
 
     @staticmethod
-    def _init_bar() -> "tqdm.tqdm":  # pyright: ignore  # noqa: F821
-        import tqdm  # pyright: ignore
+    def _init_bar() -> "tqdm.tqdm":  # pyright: ignore[reportUndefinedVariable]  # noqa: F821
+        import tqdm
 
         bar_format = (
             "{percentage:.2f}%|{bar}| [{elapsed}<{remaining}, {rate_fmt}{postfix}]"

diffrax/_root_finder/_verychord.py

@@ -189,7 +189,7 @@ def postprocess(
 
 - `rtol`: Relative tolerance for terminating the solve.
 - `atol`: Absolute tolerance for terminating the solve.
-- `norm`: The norm used to determine the difference between two iterates in the 
+- `norm`: The norm used to determine the difference between two iterates in the
     convergence criteria. Should be any function `PyTree -> Scalar`, for example
     `optimistix.max_norm`.
 - `kappa`: A tolerance for the early convergence check.

diffrax/_saveat.py

@@ -53,7 +53,7 @@ def __check_init__(self):
 - `t0`: If `True`, save the initial input `y0`.
 - `t1`: If `True`, save the output at `t1`.
 - `ts`: Some array of times at which to save the output.
-- `steps`: If `n>0`, save the output at every `n`th step of the numerical solver. 
+- `steps`: If `n>0`, save the output at every `n`th step of the numerical solver.
     `0` means no saving.
 - `fn`: A function `fn(t, y, args)` which specifies what to save into `sol.ys` when
     using `t0`, `t1`, `ts` or `steps`. Defaults to `fn(t, y, args) -> y`, so that the
@@ -110,7 +110,7 @@ def __init__(
 - `t0`: If `True`, save the initial input `y0`.
 - `t1`: If `True`, save the output at `t1`.
 - `ts`: Some array of times at which to save the output.
-- `steps`: If `n>0`, save the output at every `n`th step of the numerical solver. 
+- `steps`: If `n>0`, save the output at every `n`th step of the numerical solver.
     `0` means no saving.
 - `dense`: If `True`, save dense output, that can later be evaluated at any part of
     the interval $[t_0, t_1]$ via `sol = diffeqsolve(...); sol.evaluate(...)`.