Merge pull request #447 from linkml/migrate-to-uv-clean

Migrate to uv clean

Author: sierra-moxon

.github/dependabot.yml

@@ -8,19 +8,17 @@ updates:
     schedule:
       interval: monthly
 
-  # Activate after migration to uv as package manager
-  # - package-ecosystem: "uv"
-  #   directories:
-  #     - "/"
-  #   schedule:
-  #     interval: "weekly"
-  #     day: "sunday"
-  #   groups:
-  #     # Individual pull requests for major/minor updates and grouped for patch updates
-  #     angular:
-  #       applies-to: version-updates
-  #       patterns:
-  #         - "*"
-  #       update-types:
-  #         - "patch"
-  #   open-pull-requests-limit: 10
+  - package-ecosystem: "uv"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "sunday"
+    groups:
+      # Individual pull requests for major/minor updates and grouped for patch updates
+      dependencies:
+        applies-to: version-updates
+        patterns:
+          - "*"
+        update-types:
+          - "patch"
+    open-pull-requests-limit: 10

.github/workflows/check-dependencies.yaml

@@ -1,5 +1,6 @@
 name: Build and test linkml-runtime with latest dependency versions
-
+env:
+  UV_VERSION: "0.7.13"
 on:
   schedule:
     - cron: '0 5 * * 1'  # once per week on Monday at 05:00 UTC
@@ -12,15 +13,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@4.2.2
-      - name: Install Poetry
-        run: |
-          pipx install poetry
-          pipx inject poetry poetry-dynamic-versioning
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          version: ${{ env.UV_VERSION }}
+          enable-cache: true
       - uses: actions/setup-python@v5.6.0
         with:
           python-version: 3.13
-      - name: Check pyproject.toml and poetry.lock
-        run: poetry check
       - name: Install tox
         run: python -m pip install tox
       - name: Run codespell
@@ -47,10 +47,13 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-      - name: Install Poetry
-        run: |
-          pipx install poetry
-          pipx inject poetry poetry-dynamic-versioning
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+          version: ${{ env.UV_VERSION }}
+          python-version: ${{ matrix.python-version }}
+
 
       - name: Check out repository
         uses: actions/checkout@v4.2.2
@@ -59,21 +62,13 @@ jobs:
           # The tags are required for dynamic versioning.
           fetch-depth: 0
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5.6.0
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: 'poetry'
-
-      - name: Install library
-        run: poetry install --no-interaction
+      - name: Regenerate lock file with latest dependencies
+        run: uv lock --upgrade
 
-      - name: Regenerating poetry.lock file & install (sync) dependencies
-        run: |
-          poetry lock --regenerate
-          poetry sync
+      - name: Install dependencies
+        run: uv sync --group dev
 
       - name: Run tests
         # Set bash shell to fail correctly on Windows https://github.com/actions/runner-images/issues/6668
         shell: bash
-        run: poetry run python -m pytest --with-slow
+        run: uv run -m pytest --with-slow

.github/workflows/main.yaml

@@ -4,7 +4,8 @@
 # https://github.com/codecov/codecov-action
 
 name: Build and test linkml-runtime
-
+env:
+  UV_VERSION: "0.7.13"
 on:
   push:
     branches:
@@ -17,15 +18,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@4.2.2
-      - name: Install Poetry
-        run: |
-          pipx install poetry
-          pipx inject poetry poetry-dynamic-versioning
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          version: ${{ env.UV_VERSION }}
+          enable-cache: true
       - uses: actions/setup-python@v5.6.0
         with:
           python-version: 3.13
-      - name: Check pyproject.toml and poetry.lock
-        run: poetry check
       - name: Install tox
         run: python -m pip install tox
       - name: Run codespell
@@ -62,28 +62,41 @@ jobs:
         with:
           fetch-depth: 0
 
-
-      - name: Install Poetry
-        run: |
-          pipx install poetry
-          pipx inject poetry poetry-dynamic-versioning
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5.6.0
+      #----------------------------------------------
+      #          install uv
+      #----------------------------------------------
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
         with:
+          version: ${{ env.UV_VERSION }}
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
           python-version: ${{ matrix.python-version }}
-          cache: 'poetry'
 
-      - name: Install library
+      #----------------------------------------------
+      #    install your root project, if required 
+      #----------------------------------------------      
+      - name: Install dependencies
         run: |
-          poetry install --no-interaction
+          uv sync --group dev 
+
+      - name: Verify uv.lock is up-to-date
+        run: uv lock --check
+
+      #----------------------------------------------
+      #              coverage report   
+      #----------------------------------------------
       - name: Generate coverage results
         # Set bash shell to fail correctly on Windows https://github.com/actions/runner-images/issues/6668
         shell: bash
         run: |
-          poetry run coverage run -m pytest
-          poetry run coverage xml
-          poetry run coverage report -m
+          uv run coverage run -m pytest
+          uv run coverage xml
+          uv run coverage report -m
+
+      #----------------------------------------------
+      #           upload coverage results
+      #----------------------------------------------
       - name: Upload coverage report
         uses: codecov/codecov-action@v5
         with:

.github/workflows/pypi-publish.yaml

@@ -1,6 +1,7 @@
 name: Publish Python Package
 # Upload to PyPI is triggered by creating & publishing a release in GitHub UI
-
+env:
+  UV_VERSION: "0.7.13"
 on:
   release:
     # Trigger the workflow only for real releases but not for draft releases
@@ -21,14 +22,15 @@ jobs:
       with:
         python-version: 3.13
 
-    - name: Install Poetry
-      run: |
-        pipx install poetry
-        pipx inject poetry poetry-dynamic-versioning
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+      with:
+        enable-cache: true
+        version: ${{ env.UV_VERSION }}
 
     - name: Build source and wheel archives
       run: |
-        poetry build
+        uv build
 
     - name: Store built distribution
       uses: actions/upload-artifact@v4.6.2

.github/workflows/test-upstream.yaml

@@ -1,5 +1,7 @@
 # Test linkml-runtime with upstream linkml and run linkml tests
 name: Test with upstream linkml
+env:
+  UV_VERSION: "0.7.13"
 on:
   pull_request:
   workflow_dispatch:
@@ -28,8 +30,6 @@ jobs:
           - os: windows-latest
             python-version: "3.12"
     runs-on: ${{ matrix.os }}
-    env:
-      POETRY_VIRTUALENVS_IN_PROJECT: true
 
     steps:
       - name: Get upstream branch and repo from first lines of PR Body
@@ -109,43 +109,33 @@ jobs:
           git remote add upstream https://github.com/linkml/linkml-runtime
           git fetch upstream --tags
 
-      - name: set up python
-        uses: actions/setup-python@v5.6.0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
         with:
+          enable-cache: true
+          version: ${{ env.UV_VERSION }}
           python-version: ${{ matrix.python-version }}
 
-      - name: Install poetry
-        run: |
-          pipx install poetry
-          pipx inject poetry poetry-dynamic-versioning
-
-      - name: Load cached venv
-        id: cached-poetry-dependencies
-        uses: actions/cache@v4.2.3
-        with:
-          path: linkml/.venv
-          key: venv-${{ matrix.python-version }}-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
-
       # we are not using linkml-runtime's lockfile, but simulating what will happen
       # when we merge this and update linkml's lockfile
       - name: add linkml-runtime to lockfile
         working-directory: linkml
-        run: poetry add ../linkml-runtime
+        run: uv add ../linkml-runtime
 
       # note that we run the installation step always, even if we restore a venv,
       # the cache will restore the old version of linkml-runtime, but the lockfile
       # will only store the directory dependency (and thus will reinstall it)
       # the cache will still speedup the rest of the installation
       - name: install linkml
         working-directory: linkml
-        run: poetry sync --no-interaction --all-extras
+        run: uv sync --all-groups
 
       - name: print linkml-runtime version
         working-directory: linkml
-        run: poetry run python -c 'import linkml_runtime; from importlib.metadata import version; print(linkml_runtime.__file__); print(version("linkml_runtime"))'
+        run: uv run python -c 'import linkml_runtime; from importlib.metadata import version; print(linkml_runtime.__file__); print(version("linkml_runtime"))'
 
       - name: run linkml tests
         # Set bash shell to fail correctly on Windows https://github.com/actions/runner-images/issues/6668
         shell: bash
         working-directory: linkml
-        run: poetry run python -m pytest --with-slow
+        run: uv run -m pytest --with-slow

CONTRIBUTING.md

@@ -68,22 +68,22 @@ are correct and expected given the context of the PR.
 
 ## Development environment setup
 
-1. Install [poetry](https://python-poetry.org/docs/#installation).
-2. Install all the dependencies from your project, which are typically specified in a `poetry.lock` file.
+1. Install [uv](https://docs.astral.sh/uv/getting-started/installation/).
+2. Install all the dependencies from your project, which are typically specified in a `uv.lock` file.
 
 ```
-poetry install
+uv sync --all-extras --dev  
 ```
 
-3. Run any python scripts or CLI commands by prefixing with `poetry run`.
+3. Run any python scripts or CLI commands by prefixing with `uv run`.
 
 ```
-poetry run python your_script.py  # ex of how to run standalone python script
-poetry run pytest # ex of how to invoke CLI tools
+uv run python your_script.py  # ex of how to run standalone python script
+uv run pytest # ex of how to invoke CLI tools
 ```
 
-4. Refer to the poetry docs for details on how to use the [add](https://python-poetry.org/docs/cli/#add), [update](https://python-poetry.org/docs/cli/#update) and [remove](https://python-poetry.org/docs/cli/#remove) commands.
-
+4. Refer to the uv docs for details on how to use the [add](https://docs.astral.sh/uv/concepts/dependencies/), [update](https://docs.astral.sh/uv/concepts/dependencies/#updating-dependencies) and
+[remove](https://docs.astral.sh/uv/concepts/dependencies/#removing-dependencies) commands.
 ## Release process
 
 Once the code has been merged into the `main` branch on this repo, there are a few steps that need to be completed to ensure a release is complete.
@@ -105,21 +105,21 @@ All code added to the linkml-runtime source must have tests. The repo uses the n
 You can run the test suite in the following way:
 
 ```
-poetry run python -m pytest
+uv run python -m pytest
 ```
 
 ### Upstream Testing
 
 To run the upstream `linkml` tests against your branch,
-install `linkml` locally with poetry, and then manually install your
+install `linkml` locally with uv, and then manually install your
 local copy of `linkml-runtime`
 
 ```shell
 git clone https://github.com/linkml/linkml
 cd linkml
-poetry install --all-extras --with tests
-poetry run pip install -e ~/location/of/linkml-runtime
-poetry run pytest
+uv sync --all-extras
+uv add ~/location/of/linkml-runtime
+uv run pytest
 ```
 
 ## Code style

Makefile

@@ -10,7 +10,7 @@ update_model:
 	cp -pr $(MODEL_DIR)/* linkml_runtime/linkml_model
 
 test:
-	poetry run pytest
+	uv run pytest
 
 
 # temporary measure until linkml-model is synced