chore(tox): faster with uv and caches

.github/workflows/architecture-tests.yml

@@ -25,14 +25,23 @@ jobs:
     steps:
     - uses: actions/checkout@v5
 
-    - name: Set up Python
-      uses: actions/setup-python@v6
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
       with:
+        version: "0.9.0"
         python-version: "3.13"
-    - run: pip install tox
+        enable-cache: true
+        activate-environment: true
+
+    - name: Set up Python and install tox
+      run: |
+        uv python install
+        uv tool install tox --with tox-uv
 
     - name: run architecture tests
       run: tox -e ${{ matrix.architecture-name }}-tests
       env:
         # Use the CPU only version of torch when building/running the code
         PIP_EXTRA_INDEX_URL: https://download.pytorch.org/whl/cpu
+        # For tox to use uv..
+        ENV_INSTALLER: "uv pip"

.github/workflows/build.yml

@@ -11,14 +11,24 @@ jobs:
 
     steps:
     - uses: actions/checkout@v5
-    - name: Set up Python
-      uses: actions/setup-python@v6
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
       with:
+        version: "0.9.0"
         python-version: "3.13"
-    - run: pip install tox
+        enable-cache: true
+        activate-environment: true
+
+    - name: Set up Python and install tox
+      run: |
+        uv python install
+        uv tool install tox --with tox-uv
 
     - name: Test build integrity
       run: tox -e build
       env:
         # Use the CPU only version of torch when building/running the code
         PIP_EXTRA_INDEX_URL: https://download.pytorch.org/whl/cpu
+        # For tox to use uv..
+        ENV_INSTALLER: "uv pip"

.github/workflows/docs.yml

@@ -14,17 +14,26 @@ jobs:
     runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v5
-      - name: setup Python
-        uses: actions/setup-python@v6
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
         with:
+          version: "0.9.0"
           python-version: "3.13"
-      - name: install dependencies
-        run: python -m pip install tox
+          enable-cache: true
+          activate-environment: true
+
+      - name: Set up Python and install tox
+        run: |
+          uv python install
+          uv tool install tox --with tox-uv
+
       - name: build documentation
         run: tox -e docs
         env:
           # Use the CPU-only version of torch
           PIP_EXTRA_INDEX_URL: https://download.pytorch.org/whl/cpu
+          # For tox to use uv..
+          ENV_INSTALLER: "uv pip"
 
       - name: put documentation in the website
         run: |

.github/workflows/lint.yml

@@ -11,11 +11,21 @@ jobs:
     steps:
     - uses: actions/checkout@v5
 
-    - name: Set up Python
-      uses: actions/setup-python@v6
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
       with:
+        version: "0.9.0"
         python-version: "3.13"
-    - run: pip install tox
+        enable-cache: true
+        activate-environment: true
+
+    - name: Set up Python and install tox
+      run: |
+        uv python install
+        uv tool install tox --with tox-uv
 
     - name: Lint the code
       run: tox -e lint
+      env:
+        # For tox to use uv..
+        ENV_INSTALLER: "uv pip"

.github/workflows/release.yml

@@ -19,13 +19,24 @@ jobs:
     - uses: actions/checkout@v5
       with:
         fetch-depth: 0
-    - name: setup Python
-      uses: actions/setup-python@v6
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
       with:
+        version: "0.9.0"
         python-version: "3.13"
-    - run: python -m pip install tox
+        enable-cache: true
+        activate-environment: true
+
+    - name: Set up Python and install tox
+      run: |
+        uv python install
+        uv tool install tox --with tox-uv
+
     - name: Build package
       run: tox -e build
+      env:
+        # For tox to use uv..
+        ENV_INSTALLER: "uv pip"
     - name: Publish distribution to PyPI
       if: startsWith(github.ref, 'refs/tags/v')
       uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/tests.yml

@@ -36,8 +36,21 @@ jobs:
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v6
       with:
+        python-version:
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+      with:
+        version: "0.9.0"
         python-version: ${{ matrix.python-version }}
-    - run: pip install tox coverage[toml]
+        enable-cache: true
+        activate-environment: true
+
+    - name: Set up Python and install tox
+      run: |
+        uv python install
+        uv pip install coverage[toml]
+        uv tool install tox --with tox-uv
 
     - name: run Python tests and collect coverage
       run: |
@@ -47,6 +60,8 @@ jobs:
         # Use the CPU only version of torch when building/running the code
         PIP_EXTRA_INDEX_URL: https://download.pytorch.org/whl/cpu
         HUGGINGFACE_TOKEN_METATRAIN: ${{ secrets.HUGGINGFACE_TOKEN }}
+        # For tox to use uv..
+        ENV_INSTALLER: "uv pip"
 
     - name: upload to codecov.io
       uses: codecov/codecov-action@v5

ci/containers/Containerfile.base

@@ -2,10 +2,18 @@ FROM docker://nvidia/cuda:12.9.1-cudnn-devel-ubuntu24.04
 
 # FFTW library required by spinfast: https://github.com/moble/spinsfast?tab=readme-ov-file#pip
 RUN apt update && \
-	apt install -y libfftw3-dev python3 python3-pip python3-venv git && \
+	apt install -y libfftw3-dev \
+    python3 python3-pip python3-venv \
+    git curl && \
 	apt clean
 
 RUN python3 -m pip install --break-system-packages tox
 
+# Install uv, using the recommended script
+RUN curl -LsSf https://astral.sh/uv/install.sh | sh
+ENV PATH="/root/.local/bin:$PATH"
+# Setup tox for uv usage
+ENV ENV_INSTALLER="uv pip"
+
 ENV PIP_EXTRA_INDEX_URL=https://download.pytorch.org/whl/cu129
 ENV CUDA_HOME="/usr/local/cuda"

ci/containers/Containerfile.mtt

@@ -5,8 +5,8 @@ FROM $BASE_IMAGE
 # The repo is cloned by CI (GIT_STRATEGY: clone)
 COPY . /metatrain/
 
-RUN python3 -m venv /mtt-venv && \
+RUN uv venv /mtt-venv && \
 	. /mtt-venv/bin/activate && \
-	python -m pip install torch==2.8.0+cu129 setuptools wheel cmake>=3.30 && \
-	python -m pip install --no-build-isolation sphericart-torch && \ 
-	python -m pip install /metatrain[soap-bpnn]
+	uv pip install --no-cache-dir torch==2.8.0+cu129 setuptools wheel cmake>=3.30 && \
+	uv pip install --no-cache-dir --no-build-isolation sphericart-torch && \
+	uv pip install --no-cache-dir /metatrain[soap-bpnn]

pyproject.toml

@@ -101,6 +101,9 @@ source = [
     ".tox/*/lib/python*/site-packages/metatrain"
 ]
 
+[tool.coverage.run]
+patch = ["subprocess"]
+
 [tool.ruff]
 exclude = ["docs/src/examples/**", "src/metatrain/_version.py"]
 line-length = 88

tox.ini

@@ -1,5 +1,8 @@
 [tox]
 min_version = 4.0
+requires =
+    tox>=4.31 
+    tox-uv>=1.23 
 # these are the default environments, i.e. the list of tests running when you
 # execute `tox` in the command-line without anything else
 envlist =
@@ -12,7 +15,8 @@ envlist =
     nanopet-tests
 
 [testenv]
-package = editable
+package = wheel
+wheel_build_env = .pkg
 passenv = *
 lint_folders =
     "{toxinidir}/developer/" \
@@ -103,9 +107,11 @@ extras =  # architectures used in the package tests
     pet
 setenv =
     COVERAGE_RUN = 1
-allowlist_externals = bash
+allowlist_externals =
+    uv
+    bash
 commands_pre =
-    python -m pip install --no-build-isolation sphericart torch-spex>=0.1,<0.2 wigners
+    {env:ENV_INSTALLER:python -m pip} install --no-build-isolation sphericart torch-spex>=0.1,<0.2 wigners
     bash {toxinidir}/tests/resources/generate-outputs.sh
 commands =
     pytest \
@@ -123,7 +129,9 @@ deps =
     build
     check-manifest
     twine
-allowlist_externals = bash
+allowlist_externals =
+    uv
+    bash
 commands_pre =
     bash -c "rm -f dist/*.whl"
     bash -c "rm -f dist/*.tar.gz"
@@ -143,7 +151,7 @@ deps =
     cmake
 changedir = src/metatrain/soap_bpnn/tests/
 commands =
-    python -m pip install --no-build-isolation sphericart torch-spex>=0.1,<0.2 wigners cmake
+    {env:ENV_INSTALLER:python -m pip} install --no-build-isolation sphericart torch-spex>=0.1,<0.2 wigners cmake
     pytest {posargs}
 
 
@@ -203,11 +211,13 @@ description = builds the documentation with sphinx
 deps =
     -r docs/requirements.txt
     cmake
-allowlist_externals = bash
+allowlist_externals =
+    uv
+    bash
 extras = # these models are used in the documentation
     gap
 commands =
-    python -m pip install --no-build-isolation sphericart torch-spex>=0.1,<0.2 wigners
+    {env:ENV_INSTALLER:python -m pip} install --no-build-isolation sphericart torch-spex>=0.1,<0.2 wigners
     # Run example and usage scripts.
     bash -c "set -e && cd {toxinidir}/examples/basic_usage && bash usage.sh"
     bash -c "set -e && cd {toxinidir}/examples/ase && bash train.sh"