Test move from pip to uv for tooling

.github/workflows/publish_release.yaml

@@ -9,14 +9,10 @@ jobs:
         env:
             VERSION: ${{ github.ref_name }}
         steps:
-            - uses: actions/checkout@v3
-            - uses: actions/setup-python@v4
+            - uses: actions/checkout@v4
+            - uses: astral-sh/setup-uv@v6
               with:
-                  python-version: "3.10"
-                  cache: "pip"
-            - run: pip install -e '.[dev]'
-            - run: python -m build
-            - run: twine upload
-                  -u __token__
-                  -p ${{ secrets.PYPI_API_TOKEN }}
-                  dist/*
+                  enable-cache: true
+                  python-version-file: "pyproject.toml"
+            - run: uv build
+            - run: uv publish -u __token__ -p ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/tests.yaml

@@ -1,78 +1,83 @@
 name: Tests
 on:
-  push:
-    branches:
-      - main
-  pull_request:
-  workflow_dispatch:
+    push:
+        branches:
+            - main
+    pull_request:
+    workflow_dispatch:
+
 jobs:
-  ruff:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.10", "3.13"]
-    name: ruff on ${{ matrix.python-version }}
-    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: "pip"
-      - run: pip install -e '.[dev]'
-      - run: ruff check .
-  mypy:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.10", "3.13"]
-    name: mypy on ${{ matrix.python-version }}
-    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: "pip"
-      - run: pip install -e '.[dev]'
-      - run: mypy .
-  ruff-format:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.10", "3.13"]
-    name: ruff-format on ${{ matrix.python-version }}
-    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: "pip"
-      - run: pip install -e '.[dev]'
-      - run: ruff format --check .
-  pytest:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.10", "3.13"]
-    name: pytest on ${{ matrix.python-version }}
-    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: "pip"
-      - run: pip install -e '.[dev]'
-      - run: pytest --cov=src --cov-report term-missing
-  doctest:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.10", "3.13"]
-    name: doctest on ${{ matrix.python-version }}
-    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: "pip"
-      - run: pip install -e '.[dev]'
-      - run: make -C docs doctest
+    ruff:
+        runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                python-version: ["3.10", "3.13"]
+        name: ruff on ${{ matrix.python-version }}
+        steps:
+            - uses: actions/checkout@v4
+            - uses: astral-sh/setup-uv@v6
+              with:
+                  enable-cache: true
+                  python-version: ${{ matrix.python-version }}
+            - run: uv sync --all-extras --dev
+            - run: uv run ruff check .
+
+    mypy:
+        runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                python-version: ["3.10", "3.13"]
+        name: mypy on ${{ matrix.python-version }}
+        steps:
+            - uses: actions/checkout@v4
+            - uses: astral-sh/setup-uv@v6
+              with:
+                  enable-cache: true
+                  python-version: ${{ matrix.python-version }}
+            - run: uv sync --all-extras --dev
+            - run: uv run mypy .
+
+    ruff-format:
+        runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                python-version: ["3.10", "3.13"]
+        name: ruff-format on ${{ matrix.python-version }}
+        steps:
+            - uses: actions/checkout@v4
+            - uses: astral-sh/setup-uv@v6
+              with:
+                  enable-cache: true
+                  python-version: ${{ matrix.python-version }}
+            - run: uv sync --all-extras --dev
+            - run: uv run ruff format --check .
+
+    pytest:
+        runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                python-version: ["3.10", "3.13"]
+        name: pytest on ${{ matrix.python-version }}
+        steps:
+            - uses: actions/checkout@v4
+            - uses: astral-sh/setup-uv@v6
+              with:
+                  enable-cache: true
+                  python-version: ${{ matrix.python-version }}
+            - run: uv sync --all-extras --dev
+            - run: uv run pytest
+
+    doctest:
+        runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                python-version: ["3.10", "3.13"]
+        name: doctest on ${{ matrix.python-version }}
+        steps:
+            - uses: actions/checkout@v4
+            - uses: astral-sh/setup-uv@v6
+              with:
+                  enable-cache: true
+                  python-version: ${{ matrix.python-version }}
+            - run: uv sync --all-extras --dev
+            - run: uv run make -C docs doctest

.readthedocs.yaml

@@ -1,16 +1,18 @@
 version: 2
 
-build:
-    os: ubuntu-22.04
-    tools:
-      python: "3.10"
-
 sphinx:
     configuration: docs/source/conf.py
 
-python:
-    install:
-        - method: pip
-          path: .
-          extra_requirements:
-            - dev
+build:
+    os: ubuntu-24.04
+    tools:
+        python: "3.13"
+    jobs:
+        pre_create_environment:
+            - asdf plugin add uv
+            - asdf install uv latest
+            - asdf global uv latest
+        create_environment:
+            - uv venv "${READTHEDOCS_VIRTUALENV_PATH}"
+        install:
+            - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen --extra dev

README.rst

@@ -43,7 +43,7 @@ How to get started
 ------------------
 
 We suggest you give a read to the ``dynsight.trajectory`` module documentation,
-which offers a compact and easy way of using most of the ``dynsight`` tools. 
+which offers a compact and easy way of using most of the ``dynsight`` tools.
 Also, the documentation offers some copiable Recipes and Examples for the most
 common analyses.
 
@@ -60,14 +60,17 @@ Developer Setup
 ---------------
 
 #. Install `just`_.
+#. Install `uv <https://docs.astral.sh>`_
 #. In a new virtual environment run::
 
-    $ just dev
+    $ just setup
+
 
 #. Run code checks::
 
     $ just check
 
+
 .. _`just`: https://github.com/casey/just
 
 Examples

docs/source/_static/recipes/info_gain.py

@@ -63,7 +63,7 @@ def info_gain_with_onion(
             tmp_entr.append(
                 dynsight.analysis.compute_shannon(
                     selected_points,
-                    data_range,
+                    data_range,  # type: ignore[arg-type]
                     n_bins=n_bins,
                 )
             )

docs/source/index.rst

@@ -81,7 +81,7 @@ How to get started
 ------------------
 
 We suggest you give a read to the ``dynsight.trajectory`` module documentation,
-which offers a compact and easy way of using most of the ``dynsight`` tools. 
+which offers a compact and easy way of using most of the ``dynsight`` tools.
 Also, the documentation offers some copiable Recipes and Examples for the most
 common analyses.
 
@@ -98,9 +98,10 @@ Developer Setup
 ---------------
 
 #. Install `just`_.
+#. Install `uv <https://docs.astral.sh>`_
 #. In a new virtual environment run::
 
-    $ just dev
+    $ just setup
 
 
 #. Run code checks::

justfile

@@ -2,15 +2,9 @@
 default:
   @just --list
 
-# Build docs.
-docs:
-  rm -rf docs/build docs/source/_autosummary
-  make -C docs html
-  echo Docs are in $PWD/docs/build/html/index.html
-
 # Do a dev install.
-dev:
-  pip install -e '.[dev]'
+setup:
+  uv sync --all-extras --dev
 
 # Run code checks.
 check:
@@ -20,27 +14,33 @@ check:
   trap error=1 ERR
 
   echo
-  (set -x; ruff check . )
+  ( set -x; uv run ruff check . )
 
   echo
-  ( set -x; ruff format --check . )
+  ( set -x; uv run ruff format --check . )
 
   echo
-  ( set -x; mypy . )
+  ( set -x; uv run mypy . )
 
   echo
-  ( set -x; pytest --cov=src --cov-report term-missing )
+  ( set -x; uv run pytest --cov=src --cov-report term-missing )
 
   echo
-  ( set -x; make -C docs doctest )
+  ( set -x; uv run make -C docs doctest )
 
   test $error = 0
 
 # Auto-fix code issues.
 fix:
-  ruff format .
-  ruff check --fix .
+  uv run ruff format .
+  uv run ruff check --fix .
 
 # Build a release.
 build:
-  python -m build
+  uv build
+
+# Build docs.
+docs:
+  rm -rf docs/source/_autosummary
+  uv run make -C docs html
+  echo Docs are in $PWD/docs/build/html/index.html

pyproject.toml

@@ -11,7 +11,7 @@ maintainers = [
 ]
 
 dependencies = [
-    "numpy",
+    "numpy<2",
     "dscribe",
     "tropea-clustering",
     "MDAnalysis",
@@ -22,7 +22,7 @@ dependencies = [
 ]
 
 # Set by cpctools.
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 dynamic = ["version"]
 readme = "README.rst"
 description = "Simplifies analysis of simulation and experimental trajectories."

src/dynsight/_internal/utilities/utilities.py

@@ -1,7 +1,12 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from collections.abc import Mapping, Sequence
+
 from pathlib import Path
-from typing import Callable, Literal, Mapping, Sequence
+from typing import Callable, Literal
 
 import numpy as np
 import numpy.typing as npt