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ElliottKasoarElliottKasoar
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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
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‎.github/workflows/ci.yml‎

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@@ -12,34 +12,30 @@ jobs:
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python-version: ['3.9','3.10','3.11','3.12']
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install poetry
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run: pipx install poetry
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- name: Install python dependencies
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run: |
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poetry env use ${{ matrix.python-version }}
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poetry install --with dev --extras all
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- name: Run test suite
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env:
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# show timings of tests
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PYTEST_ADDOPTS: "--durations=0"
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run: poetry run pytest --run-extra-mlips --cov janus_core --cov-append .
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- name: Report coverage to Coveralls
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uses: coverallsapp/github-action@v2
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with:
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parallel: true
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flag-name: run-${{ matrix.python-version }}
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file: coverage.xml
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base-path: janus_core
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- uses: actions/checkout@v4
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- name: Install uv
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uses: astral-sh/setup-uv@v4
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with:
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version: "0.5.7"
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: uv sync --all-extras
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- name: Run test suite
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env:
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# show timings of tests
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PYTEST_ADDOPTS: "--durations=0"
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run: uv run pytest --run-extra-mlips --cov janus_core --cov-append .
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- name: Report coverage to Coveralls
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uses: coverallsapp/github-action@v2
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with:
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parallel: true
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flag-name: run-${{ matrix.python-version }}
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file: coverage.xml
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base-path: janus_core
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coverage:
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needs: tests
@@ -54,50 +50,42 @@ jobs:
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runs-on: ubuntu-latest
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timeout-minutes: 15
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steps:
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- uses: actions/checkout@v4
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- name: Check all sources documented
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run: |
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diff -y --suppress-common-lines \
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<(git ls-files janus_core/** | sed '/.py$/!d; s/\/__init__.py//; s#/#.#g; s/.py$//' | sort) \
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<(sed -nr '/automodule/{s/.*::\s*//;p}' docs/source/apidoc/* | sort)
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- uses: actions/checkout@v4
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- name: Set up Python 3.11
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Check all sources documented
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run: |
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diff -y --suppress-common-lines \
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<(git ls-files janus_core/** | sed '/.py$/!d; s/\/__init__.py//; s#/#.#g; s/.py$//' | sort) \
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<(sed -nr '/automodule/{s/.*::\s*//;p}' docs/source/apidoc/* | sort)
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- name: Install poetry
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run: pipx install poetry
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- name: Install uv
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uses: astral-sh/setup-uv@v4
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with:
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version: "0.5.7"
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python-version: "3.12"
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- name: Install python dependencies
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run: |
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poetry env use 3.11
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poetry install --with docs
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- name: Install dependencies
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run: uv sync
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- name: Build docs
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run: cd docs && poetry run make
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- name: Build docs
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run: cd docs && uv run make html
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pre-commit:
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runs-on: ubuntu-latest
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timeout-minutes: 15
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steps:
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- uses: actions/checkout@v4
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- uses: actions/checkout@v4
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- name: Set up Python 3.11
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Install poetry
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run: pipx install poetry
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- name: Install uv
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uses: astral-sh/setup-uv@v4
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with:
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version: "0.5.7"
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python-version: "3.12"
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- name: Install python dependencies
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run: |
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poetry env use 3.11
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poetry install --with pre-commit,docs,dev --extras "chgnet m3gnet"
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- name: Install dependencies
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run: uv sync
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- name: Run pre-commit
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run: |
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poetry run pre-commit install
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poetry run pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
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- name: Run pre-commit
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run: |
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uv run pre-commit install
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uv run pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )

‎.github/workflows/docs.yml‎

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@@ -22,35 +22,28 @@ jobs:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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runs-on: ubuntu-latest
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container: sphinxdoc/sphinx
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steps:
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- uses: actions/checkout@v4
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- name: Install poetry
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run: |
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apt update
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apt upgrade -y
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apt install -y pipx
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pipx install poetry
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- name: add deps
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run: |
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apt install -y python3-dev build-essential
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- name: sphinx
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run: |
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export PATH="$HOME/.local/bin:$PATH"
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poetry install --with docs
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cd docs
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poetry run make html
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- name: upload
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uses: actions/upload-pages-artifact@v3
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with:
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# Upload entire repository
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path: './docs/build/html/.'
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v4
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- uses: actions/checkout@v4
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- name: Install uv
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uses: astral-sh/setup-uv@v4
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with:
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version: "0.5.7"
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python-version: "3.12"
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- name: Install dependencies
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run: uv sync
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- name: Build docs
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run: cd docs && uv run make html
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- name: upload
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uses: actions/upload-pages-artifact@v3
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with:
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# Upload entire repository
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path: './docs/build/html/.'
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v4

‎.github/workflows/publish-on-pypi.yml‎

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publish:
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runs-on: ubuntu-latest
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if: github.repository == 'stfc/janus-core' && startsWith(github.ref, 'refs/tags/v')
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environment:
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name: release
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Set up Python 3.11
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Install poetry
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run: pipx install poetry
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- name: Build project for distribution
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run: |
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poetry env use 3.11
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poetry build
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- name: Check prerelease
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id: check-prerelease
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run: |
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[[ "$(poetry version --short)" =~ ^[0-9]+\.[0-9]+\.[0-9]+$ ]] || echo prerelease=true >> $GITHUB_OUTPUT
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- name: Get version from pyproject.toml
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run: |
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export PYTHONPATH=$(pwd)
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echo "VERSION=$(poetry version --short)" >> $GITHUB_ENV
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- name: Check version matches tag
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if: ${{ ! contains(github.ref, env.VERSION) }}
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run: |
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echo "Git tag does not match version in pyproject.toml"
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exit 1
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- name: Create Release
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uses: ncipollo/release-action@v1
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with:
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artifacts: "dist/*"
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token: ${{ secrets.GITHUB_TOKEN }}
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draft: false
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prerelease: steps.check-prerelease.outputs.prerelease == 'true'
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skipIfReleaseExists: true
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- name: Publish to PyPI
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env:
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POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
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run: poetry publish
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Install uv
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uses: astral-sh/setup-uv@v4
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with:
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version: "0.5.7"
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python-version: "3.12"
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- name: Install dependencies
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run: uv sync
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- name: Build
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run: uv build
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- name: Get version from pyproject.toml
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run: echo "VERSION=$(uvx --from=toml-cli toml get --toml-path=pyproject.toml project.version)" >> $GITHUB_ENV
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- name: Check version matches tag
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if: ${{ ! contains(github.ref, env.VERSION) }}
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run: |
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echo "Git tag does not match version in pyproject.toml"
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exit 1
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- name: Create Release
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uses: ncipollo/release-action@v1
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with:
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artifacts: "dist/*"
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token: ${{ secrets.GITHUB_TOKEN }}
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draft: false
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prerelease: steps.check-prerelease.outputs.prerelease == 'true'
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skipIfReleaseExists: true
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- name: Publish to PyPI
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run: uv publish

‎README.md‎

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python3 -m pip install janus-core[all]
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```
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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]`.
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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]`.
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### Further help
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## Development
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We recommend installing poetry for dependency management when developing for `janus-core`:
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We recommend installing uv for dependency management when developing for `janus-core`:
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1. Install [poetry](https://python-poetry.org/docs/#installation)
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2. (Optional) Create a virtual environment
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3. Install `janus-core` with dependencies:
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1. Install [uv](https://docs.astral.sh/uv/getting-started/installation)
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2. Install `janus-core` with dependencies in a virtual environment:
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```shell
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git clone https://github.com/stfc/janus-core
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cd janus-core
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python3 -m pip install --upgrade pip
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poetry install --with pre-commit,dev,docs # install with useful dev dependencies
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pre-commit install # install pre-commit hooks
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pytest -v # discover and run all tests
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uv sync --all-extras # Create a virtual environment and install all dependencies
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source .venv/bin/activate
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pre-commit install # Install pre-commit hooks
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pytest -v # Discover and run all tests
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```
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‎docs/source/developer_guide/get_started.rst‎

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

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