From 2eb544638bf9907f8a0219ad82b38a73a2ce4481 Mon Sep 17 00:00:00 2001 From: Mehmet Can Ay Date: Fri, 21 Nov 2025 15:21:56 +0100 Subject: [PATCH 1/4] build: migrate pyproject.toml to PEP 621 metadata format --- pyproject.toml | 103 ++++++++++++++++++++++++------------------------- 1 file changed, 50 insertions(+), 53 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index eda73b6..61f4620 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,72 +1,69 @@ [build-system] -requires = [ - "poetry-core>=1.0.0", - "setuptools>=65.0", - "wheel", -] -build-backend = "poetry.core.masonry.api" +requires = ["uv_build>=0.9.10,<0.10.0"] +build-backend = "uv_build" + +[tool.uv.build-backend] +module-name = "datastew" +module-root = "" -[tool.poetry] +[project] name = "datastew" version = "0.1.0" description = "Datastew is a python library for intelligent data harmonization using Large Language Model (LLM) vector embeddings." -authors = ["Tim Adams ", "Mehmet Can Ay "] -license = "Apache-2.0" readme = "README.md" -homepage = "https://github.com/SCAI-BIO/datastew" -repository = "https://github.com/SCAI-BIO/datastew" -documentation = "https://github.com/SCAI-BIO/datastew#readme" +license = { file = "LICENSE" } +requires-python = ">=3.10,<3.14" +authors = [ + { name = "Tim Adams", email = "tim.adams@scai.fraunhofer.de" }, + { name = "Mehmet Can Ay", email = "mehmet.ay@scai.fraunhofer.de" }, +] keywords = ["data-harmonization", "LLM", "embeddings", "data-steward"] classifiers = [ "Development Status :: 3 - Alpha", "Intended Audience :: Developers", - "License :: OSI Approved :: Apache Software License", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", "Programming Language :: Python :: 3.13", ] -[tool.poetry.urls] -homepage = "https://github.com/SCAI-BIO/datastew" -repository = "https://github.com/SCAI-BIO/datastew" -documentation = "https://github.com/SCAI-BIO/datastew#readme" -tracker = "https://github.com/SCAI-BIO/datastew/issues" +dependencies = [ + "matplotlib>=3.10.7,<4.0.0", + "numpy>=2.2.6,<3.0.0", + "openai>=2.7.1,<3.0.0", + "openpyxl>=3.1.5,<4.0.0", + "pandas>=2.3.3,<3.0.0", + "plotly>=6.4.0,<7.0.0", + "python-dateutil>=2.9.0.post0,<3.0.0", + "python-dotenv>=1.2.1,<2.0.0", + "pytz>=2025.2,<2026.0", + "seaborn>=0.13.2,<1.0.0", + "sentence-transformers>=5.1.2,<6.0.0", + "scikit-learn>=1.7.2,<2.0.0", + "six>=1.17.0,<2.0.0", + "thefuzz>=0.22.1,<1.0.0", + "tzdata>=2025.2,<2026.0", + "wheel>=0.45.1,<1.0.0", + "aiofiles>=25.1.0,<26.0.0", + "SQLAlchemy>=2.0.44,<3.0.0", + "scipy>=1.15.3,<2.0.0", + "pydantic>=2.12.4,<3.0.0", + "requests>=2.32.5,<3.0.0", + "uuid>=1.30,<2.0.0", + "weaviate-client>=4.17.0,<5.0.0", + "cachetools>=6.2.1,<7.0.0", + "ollama>=0.6.0,<1.0.0", + "pgvector>=0.4.1,<1.0.0", + "psycopg2-binary>=2.9.11,<3.0.0", + "torch>=2.9.0,<3.0.0", +] -[[tool.poetry.packages]] -include = "datastew" +[project.optional-dependencies] +dev = ["flake8>=7.3.0,<8.0.0", "pytest>=9.0.0,<10.0.0"] -[tool.poetry.dependencies] -python = ">=3.10,<3.14" -matplotlib = "^3.10.7" -numpy = "^2.2.6" -openai = "^2.7.1" -openpyxl = "^3.1.5" -pandas = "^2.3.3" -plotly = "^6.4.0" -python-dateutil = "^2.9.0.post0" -python-dotenv = "^1.2.1" -pytz = "^2025.2" -seaborn = "^0.13.2" -sentence-transformers = "^5.1.2" -scikit-learn = "^1.7.2" -six = "^1.17.0" -thefuzz = "^0.22.1" -tzdata = "^2025.2" -wheel = "^0.45.1" -aiofiles = "^25.1.0" -SQLAlchemy = "^2.0.44" -scipy = "^1.15.3" -pydantic = "^2.12.4" -requests = "^2.32.5" -uuid = "^1.30" -weaviate-client = "^4.17.0" -cachetools = "^6.2.1" -ollama = "^0.6.0" -pgvector = "^0.4.1" -psycopg2-binary = "^2.9.11" -torch = "^2.9.0" -[tool.poetry.group.dev.dependencies] -flake8 = "^7.3.0" -pytest = "^9.0.0" +[project.urls] +Homepage = "https://github.com/SCAI-BIO/datastew" +Repository = "https://github.com/SCAI-BIO/datastew" +Documentation = "https://github.com/SCAI-BIO/datastew#readme" +Tracker = "https://github.com/SCAI-BIO/datastew/issues" From 04bc33e06e5bc4fa3b63bd2567580060874c0c23 Mon Sep 17 00:00:00 2001 From: Mehmet Can Ay Date: Fri, 21 Nov 2025 15:22:41 +0100 Subject: [PATCH 2/4] build: migrate lockfile from Poetry to UV --- poetry.lock | 3779 --------------------------------------------------- uv.lock | 2653 ++++++++++++++++++++++++++++++++++++ 2 files changed, 2653 insertions(+), 3779 deletions(-) delete mode 100644 poetry.lock create mode 100644 uv.lock diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index d91e078..0000000 --- a/poetry.lock +++ /dev/null @@ -1,3779 +0,0 @@ -# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand. - 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72494, upload-time = "2024-11-23T00:18:21.207Z" }, +] From 374ac4109219f16f812898d40aa3b43c939e09a1 Mon Sep 17 00:00:00 2001 From: Mehmet Can Ay Date: Fri, 21 Nov 2025 15:23:23 +0100 Subject: [PATCH 3/4] test: add smoke tests for built distribution --- tests/smoke_test.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 tests/smoke_test.py diff --git a/tests/smoke_test.py b/tests/smoke_test.py new file mode 100644 index 0000000..b255adb --- /dev/null +++ b/tests/smoke_test.py @@ -0,0 +1,17 @@ +def test_package_imports(): + """ + Basic check that the installed wheel can be imported. + """ + import datastew + + assert datastew is not None + + +def test_version_exists(): + """ + Ensure version metadata is accessible. + """ + from datastew import __version__ + + assert isinstance(__version__, str) + assert len(__version__) > 0 From 5515ab4a5187de21df3884b9de096b2a0d64137e Mon Sep 17 00:00:00 2001 From: Mehmet Can Ay Date: Fri, 21 Nov 2025 15:25:18 +0100 Subject: [PATCH 4/4] ci: migrate GitHub Actions workflows from Poetry to UV --- .github/dependabot.yml | 2 +- .github/workflows/python-publish.yaml | 60 +++++++++++---------------- .github/workflows/tests.yml | 17 ++++---- 3 files changed, 33 insertions(+), 46 deletions(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index ed9dbd4..5b9cf5e 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -5,7 +5,7 @@ version: 2 updates: - - package-ecosystem: "pip" # See documentation for possible values + - package-ecosystem: "uv" # See documentation for possible values directory: "/" # Location of package manifests schedule: interval: "weekly" diff --git a/.github/workflows/python-publish.yaml b/.github/workflows/python-publish.yaml index 4f3c393..d6a0175 100644 --- a/.github/workflows/python-publish.yaml +++ b/.github/workflows/python-publish.yaml @@ -12,41 +12,31 @@ on: release: types: [published] -permissions: - contents: read - jobs: - deploy: - + run: runs-on: ubuntu-latest - + environment: + name: pypi + permissions: + id-token: write + contents: read steps: - - uses: actions/checkout@v4 - - name: Set up Python - uses: actions/setup-python@v5 - with: - python-version: '3.12' - - - name: Install Poetry - run: | - curl -sSL https://install.python-poetry.org | python3 - - - - name: Update package version - run: | - VERSION=${{ github.event.release.tag_name }} - sed -i 's/__version__ = ".*"/__version__ = "'${VERSION}'"/' datastew/_version.py - sed -i "s/^version = \".*\"/version = \"${VERSION}\"/" pyproject.toml - - - name: Install dependencies - run: | - poetry install - - - name: Build package - run: | - poetry build - - - name: Publish package - env: - POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_API_TOKEN }} - run: | - poetry publish --username __token__ --password $POETRY_PYPI_TOKEN_PYPI + - name: Checkout + uses: actions/checkout@v5 + - name: Install uv + uses: astral-sh/setup-uv@v7 + - name: Install Python 3.13 + run: uv python install 3.13 + - name: Update package version + run: | + VERSION=${{ github.event.release.tag_name }} + sed -i 's/__version__ = ".*"/__version__ = "'${VERSION}'"/' datastew/_version.py + uv version "$VERSION" + - name: Build + run: uv build + - name: Smoke test (wheel) + run: uv run --isolated --no-project --with dist/*.whl tests/smoke_test.py + - name: Smoke test (source distribution) + run: uv run --isolated --no-project --with dist/*.tar.gz tests/smoke_test.py + - name: Publish + run: uv publish diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index cc78d01..da02c73 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -37,27 +37,24 @@ jobs: TEST_POSTGRES_URI: postgresql://testuser:testpass@localhost:5432/testdb steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - - name: Install Poetry - run: curl -sSL https://install.python-poetry.org | python3 - - - - name: Configure Poetry environment - run: | - poetry config virtualenvs.create true - poetry env use python${{ matrix.python-version }} + - name: Install the latest version of uv + uses: astral-sh/setup-uv@v7 + with: + python-version: ${{ matrix.python-version }} - name: Install dependencies - run: poetry install + run: uv sync --locked --all-extras --dev - name: Wait for PostgreSQL to become ready run: | until pg_isready -h localhost -U testuser -d testdb; do sleep 1; done - name: Run tests - run: poetry run pytest + run: uv run pytest tests