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Merge pull request #165 from SCAI-BIO/refactor/migrate-poetry-to-uv
Refactor/migrate poetry to uv
2 parents 1567ec7 + 5515ab4 commit ff24616

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‎.github/dependabot.yml‎

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version: 2
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updates:
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- package-ecosystem: "pip" # See documentation for possible values
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- package-ecosystem: "uv" # See documentation for possible values
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directory: "/" # Location of package manifests
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schedule:
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interval: "weekly"

‎.github/workflows/python-publish.yaml‎

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release:
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types: [published]
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permissions:
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contents: read
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jobs:
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deploy:
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run:
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runs-on: ubuntu-latest
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environment:
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name: pypi
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permissions:
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id-token: write
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contents: read
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.12'
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- name: Install Poetry
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run: |
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curl -sSL https://install.python-poetry.org | python3 -
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- name: Update package version
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run: |
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VERSION=${{ github.event.release.tag_name }}
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sed -i 's/__version__ = ".*"/__version__ = "'${VERSION}'"/' datastew/_version.py
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sed -i "s/^version = \".*\"/version = \"${VERSION}\"/" pyproject.toml
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- name: Install dependencies
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run: |
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poetry install
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- name: Build package
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run: |
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poetry build
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- name: Publish package
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env:
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POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_API_TOKEN }}
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run: |
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poetry publish --username __token__ --password $POETRY_PYPI_TOKEN_PYPI
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- name: Checkout
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uses: actions/checkout@v5
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- name: Install uv
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uses: astral-sh/setup-uv@v7
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- name: Install Python 3.13
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run: uv python install 3.13
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- name: Update package version
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run: |
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VERSION=${{ github.event.release.tag_name }}
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sed -i 's/__version__ = ".*"/__version__ = "'${VERSION}'"/' datastew/_version.py
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uv version "$VERSION"
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- name: Build
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run: uv build
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- name: Smoke test (wheel)
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run: uv run --isolated --no-project --with dist/*.whl tests/smoke_test.py
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- name: Smoke test (source distribution)
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run: uv run --isolated --no-project --with dist/*.tar.gz tests/smoke_test.py
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- name: Publish
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run: uv publish

‎.github/workflows/tests.yml‎

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TEST_POSTGRES_URI: postgresql://testuser:testpass@localhost:5432/testdb
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steps:
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- uses: actions/checkout@v4
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- uses: actions/checkout@v5
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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: ${{ matrix.python-version }}
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- name: Install Poetry
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run: curl -sSL https://install.python-poetry.org | python3 -
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- name: Configure Poetry environment
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run: |
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poetry config virtualenvs.create true
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poetry env use python${{ matrix.python-version }}
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- name: Install the latest version of uv
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uses: astral-sh/setup-uv@v7
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: poetry install
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run: uv sync --locked --all-extras --dev
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- name: Wait for PostgreSQL to become ready
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run: |
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until pg_isready -h localhost -U testuser -d testdb; do sleep 1; done
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- name: Run tests
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run: poetry run pytest
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run: uv run pytest tests

‎poetry.lock‎

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This file was deleted.

‎pyproject.toml‎

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[build-system]
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requires = [
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"poetry-core>=1.0.0",
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"setuptools>=65.0",
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"wheel",
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]
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build-backend = "poetry.core.masonry.api"
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requires = ["uv_build>=0.9.10,<0.10.0"]
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build-backend = "uv_build"
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[tool.uv.build-backend]
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module-name = "datastew"
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module-root = ""
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[tool.poetry]
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[project]
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name = "datastew"
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version = "0.1.0"
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description = "Datastew is a python library for intelligent data harmonization using Large Language Model (LLM) vector embeddings."
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authors = ["Tim Adams <tim.adams@scai.fraunhofer.de>", "Mehmet Can Ay <mehmet.ay@scai.fraunhofer.de>"]
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license = "Apache-2.0"
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readme = "README.md"
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homepage = "https://github.com/SCAI-BIO/datastew"
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repository = "https://github.com/SCAI-BIO/datastew"
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documentation = "https://github.com/SCAI-BIO/datastew#readme"
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license = { file = "LICENSE" }
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requires-python = ">=3.10,<3.14"
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authors = [
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{ name = "Tim Adams", email = "tim.adams@scai.fraunhofer.de" },
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{ name = "Mehmet Can Ay", email = "mehmet.ay@scai.fraunhofer.de" },
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]
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keywords = ["data-harmonization", "LLM", "embeddings", "data-steward"]
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classifiers = [
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"Development Status :: 3 - Alpha",
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"Intended Audience :: Developers",
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"License :: OSI Approved :: Apache Software License",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Programming Language :: Python :: 3.13",
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]
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[tool.poetry.urls]
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homepage = "https://github.com/SCAI-BIO/datastew"
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repository = "https://github.com/SCAI-BIO/datastew"
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documentation = "https://github.com/SCAI-BIO/datastew#readme"
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tracker = "https://github.com/SCAI-BIO/datastew/issues"
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dependencies = [
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"matplotlib>=3.10.7,<4.0.0",
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"numpy>=2.2.6,<3.0.0",
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"openai>=2.7.1,<3.0.0",
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"openpyxl>=3.1.5,<4.0.0",
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"pandas>=2.3.3,<3.0.0",
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"plotly>=6.4.0,<7.0.0",
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"python-dateutil>=2.9.0.post0,<3.0.0",
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"python-dotenv>=1.2.1,<2.0.0",
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"pytz>=2025.2,<2026.0",
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"seaborn>=0.13.2,<1.0.0",
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"sentence-transformers>=5.1.2,<6.0.0",
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"scikit-learn>=1.7.2,<2.0.0",
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"six>=1.17.0,<2.0.0",
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"thefuzz>=0.22.1,<1.0.0",
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"tzdata>=2025.2,<2026.0",
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"wheel>=0.45.1,<1.0.0",
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"aiofiles>=25.1.0,<26.0.0",
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"SQLAlchemy>=2.0.44,<3.0.0",
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"scipy>=1.15.3,<2.0.0",
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"pydantic>=2.12.4,<3.0.0",
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"requests>=2.32.5,<3.0.0",
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"uuid>=1.30,<2.0.0",
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"weaviate-client>=4.17.0,<5.0.0",
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"cachetools>=6.2.1,<7.0.0",
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"ollama>=0.6.0,<1.0.0",
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"pgvector>=0.4.1,<1.0.0",
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"psycopg2-binary>=2.9.11,<3.0.0",
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"torch>=2.9.0,<3.0.0",
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]
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[[tool.poetry.packages]]
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include = "datastew"
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[project.optional-dependencies]
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dev = ["flake8>=7.3.0,<8.0.0", "pytest>=9.0.0,<10.0.0"]
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[tool.poetry.dependencies]
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python = ">=3.10,<3.14"
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matplotlib = "^3.10.7"
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numpy = "^2.2.6"
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openai = "^2.7.1"
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openpyxl = "^3.1.5"
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pandas = "^2.3.3"
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plotly = "^6.4.0"
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python-dateutil = "^2.9.0.post0"
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python-dotenv = "^1.2.1"
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pytz = "^2025.2"
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seaborn = "^0.13.2"
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sentence-transformers = "^5.1.2"
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scikit-learn = "^1.7.2"
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six = "^1.17.0"
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thefuzz = "^0.22.1"
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tzdata = "^2025.2"
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wheel = "^0.45.1"
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aiofiles = "^25.1.0"
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SQLAlchemy = "^2.0.44"
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scipy = "^1.15.3"
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pydantic = "^2.12.4"
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requests = "^2.32.5"
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uuid = "^1.30"
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weaviate-client = "^4.17.0"
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cachetools = "^6.2.1"
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ollama = "^0.6.0"
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pgvector = "^0.4.1"
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psycopg2-binary = "^2.9.11"
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torch = "^2.9.0"
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[tool.poetry.group.dev.dependencies]
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flake8 = "^7.3.0"
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pytest = "^9.0.0"
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[project.urls]
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Homepage = "https://github.com/SCAI-BIO/datastew"
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Repository = "https://github.com/SCAI-BIO/datastew"
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Documentation = "https://github.com/SCAI-BIO/datastew#readme"
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Tracker = "https://github.com/SCAI-BIO/datastew/issues"

‎tests/smoke_test.py‎

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def test_package_imports():
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"""
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Basic check that the installed wheel can be imported.
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"""
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import datastew
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assert datastew is not None
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def test_version_exists():
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"""
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Ensure version metadata is accessible.
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"""
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from datastew import __version__
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assert isinstance(__version__, str)
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assert len(__version__) > 0

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