Migrate project and CI to standard uv workflow

Author: cmungall

.github/workflows/deploy_documentation.yml

@@ -4,7 +4,7 @@ name: Deploy Documentation
 on:
   workflow_dispatch:
   push:
-    branches: [ main ]
+    branches: [main]
 
     paths:
     - 'src/docs/*'
@@ -22,38 +22,26 @@ jobs:
     #       check-out repo and set-up python
     #----------------------------------------------
     - name: Check out repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         # persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal token
         fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
 
-    - name: Set up Python3
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.11'
-
     #----------------------------------------------
     #                 install uv
     #----------------------------------------------
     - name: Install uv
-      uses: astral-sh/setup-uv@v5
+      uses: astral-sh/setup-uv@v6
       with:
+        python-version: "3.11"
         enable-cache: true
+        cache-dependency-glob: "uv.lock"
 
     #----------------------------------------------
-    #          create env and install deps
+    #          install project dependencies
     #----------------------------------------------
     - name: Install dependencies
-      run: |
-        uv venv
-        uv pip install . \
-          mkdocs \
-          "linkml>=1.7.4" \
-          mkdocs-mermaid2-plugin \
-          jupyter \
-          ipython-sql \
-          tox \
-          black
+      run: uv sync --dev --locked --no-progress
 
     #----------------------------------------------
     #  Create documentation and deploy.
@@ -63,5 +51,5 @@ jobs:
         mkdir docs
         touch docs/.nojekyll
         cp -r src/docs/* docs/
-        make RUN="uv run" gendoc
-        make RUN="uv run" mkd-gh-deploy
+        make gendoc
+        make mkd-gh-deploy

.github/workflows/main.yaml

@@ -2,38 +2,34 @@ name: Build and test
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
-    branches: [ main ]
+    branches: [main]
 
 jobs:
   lint:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.11' ]
+        python-version: ["3.11"]
     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 uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v6
         with:
+          python-version: ${{ matrix.python-version }}
           enable-cache: true
-      - name: Create virtual environment
-        run: uv venv
-      - name: Install lint dependencies
-        run: uv pip install tox
+          cache-dependency-glob: "uv.lock"
+      - name: Install dependencies
+        run: uv sync --dev --locked
       - name: Check code quality with flake8
         run: uv run tox -e flake8
 
   test:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.11' ]
+        python-version: ["3.11"]
 
     steps:
 
@@ -43,30 +39,21 @@ jobs:
       - name: Check out repository
         uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-
       #----------------------------------------------
       #                 install uv
       #----------------------------------------------
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v6
         with:
+          python-version: ${{ matrix.python-version }}
           enable-cache: true
-
-      #----------------------------------------------
-      #             create virtualenv
-      #----------------------------------------------
-      - name: Create virtual environment
-        run: uv venv
+          cache-dependency-glob: "uv.lock"
 
       #----------------------------------------------
       #             install dependencies
       #----------------------------------------------
       - name: Install dependencies
-        run: uv pip install .
+        run: uv sync --dev --locked
 
       #----------------------------------------------
       #              run test suite   

.github/workflows/pypi-publish.yaml

@@ -12,22 +12,16 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.11'
-
     - name: Install uv
-      uses: astral-sh/setup-uv@v5
+      uses: astral-sh/setup-uv@v6
       with:
+        python-version: "3.12"
         enable-cache: true
-
-    - name: Create virtual environment
-      run: uv venv
+        cache-dependency-glob: "uv.lock"
 
     - name: Build source and wheel archives
       run: |
-        uv pip install build
+        uv sync --locked --no-dev
         VERSION="$(git describe --tags --abbrev=0)"
         VERSION="${VERSION#v}"
         export VERSION
@@ -49,7 +43,7 @@ jobs:
         path.write_text(updated)
         print(f"Set project version to {version}")
         PY
-        uv run python -m build
+        uv build
 
     - name: Publish distribution 📦 to PyPI
       uses: pypa/gh-action-pypi-publish@v1.2.2

AGENTS.md

@@ -11,8 +11,8 @@ Semantic-SQL transforms OWL/RDF ontologies into SQLite databases with standardiz
 ```bash
 # Build/test
 make test                     # Run unit tests
-poetry run pytest tests/      # Run specific tests
-poetry run pytest tests/test_orm/test_basic_sqla.py -k "test_name"  # Single test
+uv run pytest tests/          # Run specific tests
+uv run pytest tests/test_orm/test_basic_sqla.py -k "test_name"  # Single test
 
 # Schema development (after editing src/semsql/linkml/*.yaml)
 make gen-ddl                  # Generate SQL DDL from LinkML
@@ -103,8 +103,8 @@ runoak -i db/NAME.db terms
 Tests use pytest, not unittest. Integration tests require rdftab/relation-graph and are marked `@pytest.mark.integration`.
 
 ```bash
-poetry run pytest tests/test_orm/      # ORM tests use tests/inputs/go-nucleus.db
-poetry run pytest tests/test_builder/  # Builder tests
+uv run pytest tests/test_orm/      # ORM tests use tests/inputs/go-nucleus.db
+uv run pytest tests/test_builder/  # Builder tests
 ```
 
 ## Best Practices from User

Makefile

@@ -1,5 +1,5 @@
 OBO = http://purl.obolibrary.org/obo
-RUN = poetry run
+RUN ?= uv run
 VERSION = $(shell git tag | tail -1)
 SRC_DIR = src/semsql/linkml
 BUILDER_DIR = src/semsql/builder
@@ -228,7 +228,7 @@ $(SQLA_DIR)/%.py: $(YAML_DIR)/%.yaml
 # can be added to your $PATH that will execute the
 # version of semsql used in github
 bin/%:
-	echo `poetry run which $*` '$$*' > $@ && chmod +x $@
+	echo `uv run which $*` '$$*' > $@ && chmod +x $@
 
 ### DEPLOY
 

README.md

@@ -208,7 +208,7 @@ Even if using OAK, it can be useful to access SQL tables directly to do complex
 ## Optimization
 
 ```bash
-poetry run semsql view2table edge --full-index | sqlite3 $db/mydb.db
+uv run semsql view2table edge --full-index | sqlite3 $db/mydb.db
 ```
 
 See [indexes](indexes) for some ready-made indexes

pyproject.toml

@@ -1,29 +1,56 @@
-[tool.poetry]
+[build-system]
+requires = ["hatchling>=1.26.3"]
+build-backend = "hatchling.build"
+
+[project]
 name = "semsql"
 version = "0.2.1"
-description = ""
-authors = ["cmungall <cjm@berkeleybop.org>"]
+description = "Transform OWL/RDF ontologies into SQLite databases with standardized SQL views."
+authors = [{ name = "cmungall", email = "cjm@berkeleybop.org" }]
 readme = "README.md"
+requires-python = ">=3.10,<4.0"
+dependencies = [
+  "click>=8.1.3,<9",
+  "linkml-runtime>=1.2.15",
+  "requests>=2.31.0",
+  "SQLAlchemy>=1.4,<3",
+  "SQLAlchemy-Utils>=0.38.2",
+  "PyYAML>=6.0.1",
+  "ruamel.yaml>=0.17.0",
+  "rdflib>=6.3.2",
+]
 
-[tool.poetry.dependencies]
-python = "^3.8.1"
-linkml-runtime = "^1.2.15"
-SQLAlchemy-Utils = "^0.38.2"
-click = "^8.1.3"
-
-[tool.poetry.dev-dependencies]
-mkdocs = "^1.3.0"
-linkml = ">=1.7.4"
-mkdocs-mermaid2-plugin = "^0.6.0"
-jupyter = "^1.0.0"
-ipython-sql = "^0.4.1"
-tox = "*"
-black = "*"
+[dependency-groups]
+dev = [
+  "black",
+  "tox",
+  "pytest",
+  "mkdocs>=1.3.0",
+  "linkml>=1.7.4",
+  "mkdocs-mermaid2-plugin>=0.6.0",
+  "jupyter>=1.0.0",
+  "ipython-sql>=0.4.1",
+]
 
-[tool.poetry.scripts]
+[project.scripts]
 semsql = "semsql.builder.cli:main"
 gen-semsql-views = "semsql.sqlutils.viewgen:cli"
 
-[build-system]
-requires = ["poetry-core>=1.0.0"]
-build-backend = "poetry.core.masonry.api"
+[tool.hatch.build]
+exclude = [
+  "**/.#*",
+  "**/#*#",
+  "**/__pycache__/**",
+  "**/*.pyc",
+]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/semsql"]
+
+[tool.hatch.build.targets.sdist]
+include = [
+  "src/semsql",
+  "README.md",
+  "LICENSE",
+  "pyproject.toml",
+]

tests/integration/Makefile

@@ -1,4 +1,4 @@
-RUN = poetry run
+RUN ?= uv run
 
 input/%.owl:
 	robot merge -I http://purl.obolibrary.org/obo/$*.owl -o $@

tests/test_builder/test_cli.py

@@ -17,7 +17,7 @@
 
 class TestCommandLineInterface(unittest.TestCase):
     def setUp(self) -> None:
-        runner = CliRunner(mix_stderr=False)
+        runner = CliRunner()
         self.runner = runner
 
     def test_main_help(self):