Change poetry to uv (#358)

* Change poetry to uv * Update docs * Update tox to use uv * Update publish workflow * Tidy and remove unnecessary dependencies * Update uv version
stfc · Dec 13, 2024 · 6d3310f · 6d3310f
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -12,34 +12,30 @@ jobs:
         python-version: ['3.9','3.10','3.11','3.12']
 
     steps:
-    - uses: actions/checkout@v4
-
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install poetry
-      run: pipx install poetry
-
-    - name: Install python dependencies
-      run: |
-        poetry env use ${{ matrix.python-version }}
-        poetry install --with dev --extras all
-
-    - name: Run test suite
-      env:
-        # show timings of tests
-        PYTEST_ADDOPTS: "--durations=0"
-      run: poetry run pytest --run-extra-mlips --cov janus_core --cov-append .
-
-    - name: Report coverage to Coveralls
-      uses: coverallsapp/github-action@v2
-      with:
-        parallel: true
-        flag-name: run-${{ matrix.python-version }}
-        file: coverage.xml
-        base-path: janus_core
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          version: "0.5.7"
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --all-extras
+
+      - name: Run test suite
+        env:
+          # show timings of tests
+          PYTEST_ADDOPTS: "--durations=0"
+        run: uv run pytest --run-extra-mlips --cov janus_core --cov-append .
+
+      - name: Report coverage to Coveralls
+        uses: coverallsapp/github-action@v2
+        with:
+          parallel: true
+          flag-name: run-${{ matrix.python-version }}
+          file: coverage.xml
+          base-path: janus_core
 
   coverage:
     needs: tests
@@ -54,50 +50,42 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 15
     steps:
-    - uses: actions/checkout@v4
-
-    - name: Check all sources documented
-      run: |
-        diff -y --suppress-common-lines \
-             <(git ls-files janus_core/** | sed '/.py$/!d; s/\/__init__.py//; s#/#.#g; s/.py$//' | sort) \
-             <(sed -nr '/automodule/{s/.*::\s*//;p}' docs/source/apidoc/* | sort)
+      - uses: actions/checkout@v4
 
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.11'
+      - name: Check all sources documented
+        run: |
+          diff -y --suppress-common-lines \
+               <(git ls-files janus_core/** | sed '/.py$/!d; s/\/__init__.py//; s#/#.#g; s/.py$//' | sort) \
+               <(sed -nr '/automodule/{s/.*::\s*//;p}' docs/source/apidoc/* | sort)
 
-    - name: Install poetry
-      run: pipx install poetry
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          version: "0.5.7"
+          python-version: "3.12"
 
-    - name: Install python dependencies
-      run: |
-        poetry env use 3.11
-        poetry install --with docs
+      - name: Install dependencies
+        run: uv sync
 
-    - name: Build docs
-      run: cd docs && poetry run make
+      - name: Build docs
+        run: cd docs && uv run make html
 
   pre-commit:
     runs-on: ubuntu-latest
     timeout-minutes: 15
     steps:
-    - uses: actions/checkout@v4
+      - uses: actions/checkout@v4
 
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.11'
-
-    - name: Install poetry
-      run: pipx install poetry
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          version: "0.5.7"
+          python-version: "3.12"
 
-    - name: Install python dependencies
-      run: |
-        poetry env use 3.11
-        poetry install --with pre-commit,docs,dev --extras "chgnet m3gnet"
+      - name: Install dependencies
+        run: uv sync
 
-    - name: Run pre-commit
-      run: |
-        poetry run pre-commit install
-        poetry run pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
+      - name: Run pre-commit
+        run: |
+          uv run pre-commit install
+          uv run pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -22,35 +22,28 @@ jobs:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}
     runs-on: ubuntu-latest
-    container: sphinxdoc/sphinx
 
     steps:
-    - uses: actions/checkout@v4
-
-    - name: Install poetry
-      run: |
-        apt update
-        apt upgrade -y
-        apt install -y pipx
-        pipx install poetry
-
-    - name: add deps
-      run: |
-        apt install -y python3-dev build-essential
-
-    - name: sphinx
-      run: |
-        export PATH="$HOME/.local/bin:$PATH"
-        poetry install --with docs
-        cd docs
-        poetry run make html
-
-    - name: upload
-      uses: actions/upload-pages-artifact@v3
-      with:
-        # Upload entire repository
-        path: './docs/build/html/.'
-
-    - name: Deploy to GitHub Pages
-      id: deployment
-      uses: actions/deploy-pages@v4
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          version: "0.5.7"
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: uv sync
+
+      - name: Build docs
+        run: cd docs && uv run make html
+
+      - name: upload
+        uses: actions/upload-pages-artifact@v3
+        with:
+          # Upload entire repository
+          path: './docs/build/html/.'
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
diff --git a/.github/workflows/publish-on-pypi.yml b/.github/workflows/publish-on-pypi.yml
@@ -10,50 +10,42 @@ jobs:
   publish:
     runs-on: ubuntu-latest
     if: github.repository == 'stfc/janus-core' && startsWith(github.ref, 'refs/tags/v')
+    environment:
+      name: release
 
     steps:
-    - name: Checkout repository
-      uses: actions/checkout@v4
-
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.11'
-
-    - name: Install poetry
-      run: pipx install poetry
-
-    - name: Build project for distribution
-      run: |
-        poetry env use 3.11
-        poetry build
-
-    - name: Check prerelease
-      id: check-prerelease
-      run: |
-        [[ "$(poetry version --short)" =~ ^[0-9]+\.[0-9]+\.[0-9]+$ ]] || echo prerelease=true >> $GITHUB_OUTPUT
-
-    - name: Get version from pyproject.toml
-      run: |
-        export PYTHONPATH=$(pwd)
-        echo "VERSION=$(poetry version --short)" >> $GITHUB_ENV
-
-    - name: Check version matches tag
-      if: ${{ ! contains(github.ref, env.VERSION) }}
-      run: |
-        echo "Git tag does not match version in pyproject.toml"
-        exit 1
-
-    - name: Create Release
-      uses: ncipollo/release-action@v1
-      with:
-        artifacts: "dist/*"
-        token: ${{ secrets.GITHUB_TOKEN }}
-        draft: false
-        prerelease: steps.check-prerelease.outputs.prerelease == 'true'
-        skipIfReleaseExists: true
-
-    - name: Publish to PyPI
-      env:
-        POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
-      run: poetry publish
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          version: "0.5.7"
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: uv sync
+
+      - name: Build
+        run: uv build
+
+      - name: Get version from pyproject.toml
+        run: echo "VERSION=$(uvx --from=toml-cli toml get --toml-path=pyproject.toml project.version)" >> $GITHUB_ENV
+
+      - name: Check version matches tag
+        if: ${{ ! contains(github.ref, env.VERSION) }}
+        run: |
+          echo "Git tag does not match version in pyproject.toml"
+          exit 1
+
+      - name: Create Release
+        uses: ncipollo/release-action@v1
+        with:
+          artifacts: "dist/*"
+          token: ${{ secrets.GITHUB_TOKEN }}
+          draft: false
+          prerelease: steps.check-prerelease.outputs.prerelease == 'true'
+          skipIfReleaseExists: true
+
+      - name: Publish to PyPI
+        run: uv publish
diff --git a/README.md b/README.md
@@ -60,7 +60,7 @@ or to install all supported MLIPs:
 python3 -m pip install janus-core[all]
 ```
 
-Individual `extras` are listed in [Getting Started](https://stfc.github.io/janus-core/getting_started/getting_started.html#installation), as well as in [pyproject.toml](pyproject.toml) under `[tool.poetry.extras]`.
+Individual `extras` are listed in [Getting Started](https://stfc.github.io/janus-core/getting_started/getting_started.html#installation), as well as in [pyproject.toml](pyproject.toml) under `[project.optional-dependencies]`.
 
 
 ### Further help
@@ -282,19 +282,18 @@ This is also the case the calculations performed using the CLI, with the same in
 
 ## Development
 
-We recommend installing poetry for dependency management when developing for `janus-core`:
+We recommend installing uv for dependency management when developing for `janus-core`:
 
-1. Install [poetry](https://python-poetry.org/docs/#installation)
-2. (Optional) Create a virtual environment
-3. Install `janus-core` with dependencies:
+1. Install [uv](https://docs.astral.sh/uv/getting-started/installation)
+2. Install `janus-core` with dependencies in a virtual environment:
 
 ```shell
 git clone https://github.com/stfc/janus-core
 cd janus-core
-python3 -m pip install --upgrade pip
-poetry install --with pre-commit,dev,docs  # install with useful dev dependencies
-pre-commit install  # install pre-commit hooks
-pytest -v  # discover and run all tests
+uv sync --all-extras # Create a virtual environment and install all dependencies
+source .venv/bin/activate
+pre-commit install  # Install pre-commit hooks
+pytest -v  # Discover and run all tests
 ```
 
 

diff --git a/docs/source/developer_guide/get_started.rst b/docs/source/developer_guide/get_started.rst
@@ -2,27 +2,36 @@
 Getting started
 ===============
 
-We recommend `installing poetry <https://python-poetry.org/docs/#installation>`_ for dependency management when developing for ``janus-core``.
+We recommend `installing uv <https://docs.astral.sh/uv/getting-started/installation/>`_ for dependency management when developing for ``janus-core``.
 
 This provides a number of useful features, including:
 
-- Dependency management (``poetry [add,update,remove]`` etc.) and organization (groups)
-- Storing the versions of all installations in a ``poetry.lock`` file, for reproducible builds
-- Improved dependency resolution
-- Virtual environment management (optional)
-- Building and publishing tools
+- `Dependency management <https://docs.astral.sh/uv/concepts/projects/dependencies/>`_ (``uv [add,remove]`` etc.) and organization (`groups <https://docs.astral.sh/uv/concepts/projects/dependencies/#dependency-groups>`_)
+
+- Storing the versions of all installations in a `uv.lock <https://docs.astral.sh/uv/concepts/projects/sync/>`_ file, for reproducible builds
+
+- Improved `dependency resolution <https://docs.astral.sh/uv/concepts/resolution/>`_
+
+- Virtual environment management
+
+- `Building and publishing <https://docs.astral.sh/uv/guides/publish/>`_ tools
+
+  * Currently, an external build backend, such as `pdm <https://pypi.org/project/pdm-backend>`_, is required
+
 
 Dependencies useful for development can then be installed by running::
 
-    poetry install --with pre-commit,dev,docs
+    uv sync
+    source .venv/bin/activate
+
 
 Extras, such as optional MLIPs, can also be installed by running::
 
-    poetry install --with pre-commit,dev,docs --extras "alignn sevennet"
+    uv sync --extra alignn --extra sevennet
 
 or to install all supported MLIPs::
 
-    poetry install --with pre-commit,dev,docs --extras all
+    uv sync --all-extras
 
 
 Running unit tests