Migrate quilt3 package to UV for dependency management (#4507)

Co-authored-by: Sergey Fedoseev <[email protected]>

Author: nl0

.flake8

@@ -6,82 +6,66 @@ on:
       - "*"
   pull_request:
   merge_group:
+env:
+  UV_LOCKED: 1
 jobs:
-  linter:
+  # Lint the entire Python codebase (except catalog/ and api/python/)
+  lint-root:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v5
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.11'
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip setuptools
-          python -m pip install 'pylint==3.2.7' 'pycodestyle>=2.6.1'
-      - name: Run pylint
-        run: |
-          pylint .
-      - name: Run pycodestyle
-        run: |
-          pycodestyle $(find -name '*.py' -not -path './venv/*')
+      - uses: astral-sh/setup-uv@v6
+      - name: Run Ruff linter on entire codebase
+        run: uvx [email protected] check . --exclude catalog/ --exclude api/python/
 
-  isort:
+  lint:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: api/python
     steps:
       - uses: actions/checkout@v5
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.11'
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip setuptools
-          python -m pip install isort
-      - name: Run isort
-        run: |
-          isort --check --diff .
+      - uses: astral-sh/setup-uv@v6
+      - name: Lint
+        run: uv run poe lint
+
+  # Formatting check disabled until codebase is reformatted
+  # format:
+  #   runs-on: ubuntu-latest
+  #   defaults:
+  #     run:
+  #       working-directory: api/python
+  #   steps:
+  #     - uses: actions/checkout@v5
+  #     - uses: astral-sh/setup-uv@v6
+  #     - name: Check formatting
+  #       run: uv run poe fmt --check
 
   test-gendocs:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: api/python
     env:
       QUILT_DISABLE_USAGE_METRICS: true
     steps:
       - uses: actions/checkout@v5
-      - uses: actions/setup-python@v5
-        with:
-          # on newer versions it crashes with
-          # TypeError: <classmethod(<function Package.install at 0x105219f30>)> is not a callable object
-          python-version: '3.9'
-      - name: install deps
-        run: |
-          python -m pip install --upgrade pip setuptools
-          python -m pip install api/python nbconvert git+https://github.com/quiltdata/[email protected]+quilt3.2
-      - name: generate docs
-        run: cd gendocs && python build.py
-      - name: show invisible changes via cat
-        run: git diff | cat -A
-      - name: check there are no changes
-        run: git diff --exit-code
+      - uses: astral-sh/setup-uv@v6
+      - name: Check generated docs are up-to-date
+        run: uv run poe gendocs-check
 
   test-testdocs:
     runs-on: ubuntu-latest
     env:
       QUILT_DISABLE_USAGE_METRICS: true
     defaults:
       run:
-        working-directory: testdocs
+        working-directory: api/python
     steps:
       - uses: actions/checkout@v5
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.11'
-      - name: install poetry
-        run: python -m pip install poetry
-      - name: install deps
-        run: poetry install
-      - name: install current version of quilt
-        run: poetry run pip install ../api/python
-      - name: test codeblocks
-        run: poetry run pytest --codeblocks ../docs
+      - uses: astral-sh/setup-uv@v6
+      - name: Test codeblocks
+        run: uv run poe testdocs
 
   test-client:
     strategy:
@@ -91,18 +75,14 @@ jobs:
     runs-on: ${{ matrix.os }}
     env:
       QUILT_DISABLE_USAGE_METRICS: true
+    defaults:
+      run:
+        working-directory: api/python
     steps:
       - uses: actions/checkout@v5
-      - uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip setuptools
-          python -m pip install -e api/python[tests]
+      - uses: astral-sh/setup-uv@v6
       - name: Run Pytest
-        run: |
-          pytest --cov=api/python api/python
+        run: uv run --python ${{ matrix.python-version }} poe test-cov --cov-report xml
       - uses: codecov/codecov-action@v5
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
@@ -136,24 +116,16 @@ jobs:
         working-directory: api/python
     steps:
       - uses: actions/checkout@v5
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.12'
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip setuptools
-          python -m pip install build==1.3.0 twine==6.1.0
+      - uses: astral-sh/setup-uv@v6
       - name: verify git tag vs. version
-        env:
-          CIRCLE_TAG: ${{ github.ref_name }}
-        run: python setup.py verify
+        run: uv run poe verify-release-tag "${{ github.ref_name }}"
       - name: build
-        run: python -m build
+        run: uv build
       - name: upload to PyPI
         env:
-          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-        run: twine upload dist/*
+          UV_PUBLISH_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          UV_PUBLISH_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: uv publish
 
   test-lambda:
     strategy:

.github/workflows/py-ci.yml

@@ -21,16 +21,9 @@ jobs:
     runs-on: ubuntu-latest
     defaults:
       run:
-        working-directory: ./api/python/quilt3-admin
+        working-directory: ./api/python
     steps:
       - uses: actions/checkout@v5
-      - uses: actions/setup-python@v5
-        with:
-          python-version-file: 'api/python/quilt3-admin/.python-version'
-          cache: 'pip'
-          cache-dependency-path: 'api/python/quilt3-admin/requirements.txt'
-      - run: pip install -r requirements.txt
-      - run: rm -r ../quilt3/admin/_graphql_client
-      - run: ariadne-codegen
-      - name: Check for changes
-        run: git diff --exit-code
+      - uses: astral-sh/setup-uv@v6
+      - name: Check GraphQL client is up-to-date
+        run: uv run poe gql-check

.github/workflows/test-quilt3-admin-codegen.yaml

@@ -14,14 +14,14 @@ metastore_db
 derby.log
 
 # let users have their own local ignores
-**/*.gitignore
 
 # Visual Studio Code
 .vscode
 .imdone
 
 # Test coverage
-.coverage
+.coverage*
+coverage.xml
 cov_html/*
 
 # Pytest cache
@@ -40,13 +40,7 @@ registry/dpmd
 
 # Doc Build
 _build
-testdocs/*.json*
-testdocs/test_workflow
-testdocs/references
-testdocs/notebooks
-testdocs/scripts
 
 .env
 
-.venv
 .aider*

.gitignore

@@ -0,0 +1,7 @@
+Quilt manages data like code (with packages, repositories, browsing and
+revision history) so that teams can experiment faster in machine learning,
+biotech, and other data-driven domains.
+
+The `quilt3` PyPI package allows you to build, push, and install data packages.
+Visit the `documentation quickstart <https://docs.quilt.bio/quickstart>`_
+to learn more.