Migrate to uv and upgrade min Python to 3.10

Closes #1.

Author: rycwo

.github/workflows/python-docs.yml

@@ -13,14 +13,13 @@ jobs:
     if: ${{ github.event.workflow_run.conclusion == 'success' }}
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - name: Set up Python and uv
+        uses: astral-sh/setup-uv@v7
         with:
-          python-version: "3.x"
+          version: "0.9.26"
+          python-version: "3.12"
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install -r requirements.txt
-          python -m pip install sphinx sphinx_rtd_theme typing_extensions
+        run: uv sync --locked
       - name: Build docs
         run: |
           cd docs

.github/workflows/python-package.yml

@@ -9,25 +9,20 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+      - name: Set up Python ${{ matrix.python-version }} and uv
+        uses: astral-sh/setup-uv@v7
         with:
+          version: "0.9.26"
           python-version: ${{ matrix.python-version }}
-          cache: "pip"
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install -r requirements-test.txt
-      - name: Lint with Ruff
-        run: ruff check --output-format=github .
-      - run: |
-          mypy metafold
-          mypy --check-untyped-defs tests/test_func.py
+        run: uv sync --locked
+      - run: uvx ruff check --output-format=github .
+      - run: uv run mypy ./metafold
       - name: Test with pytest
-        run: pytest --junitxml=junit/test-results-${{ matrix.python-version }}.xml
+        run: uv run pytest --junitxml=junit/test-results-${{ matrix.python-version }}.xml ./tests
       - name: Upload pytest test results
         uses: actions/upload-artifact@v4
         with:

.github/workflows/python-publish.yml

@@ -10,14 +10,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - name: Set up Python and uv
+        uses: astral-sh/setup-uv@v7
         with:
-          # Use latest stable version
-          python-version: "3.x"
-      - name: Install build dependencies
-        run: python -m pip install --upgrade pip build
+          version: "0.9.26"
+          python-version: "3.12"
       - name: Build package
-        run: python -m build
+        run: uv build
       - uses: actions/upload-artifact@v4
         with:
           name: python-dist

.gitlab-ci.yml

@@ -0,0 +1,31 @@
+---
+stages:
+- test
+
+default:
+  image: ghcr.io/astral-sh/uv:python3.12-alpine
+
+lint:
+  stage: test
+  script:
+  - uvx ruff check --output-format gitlab . > gl-code-quality-report.json
+  artifacts:
+    reports:
+      codequality: gl-code-quality-report.json
+
+type check:
+  stage: test
+  script:
+  - uv run --locked mypy ./metafold
+
+test:
+  stage: test
+  script:
+  - uv run --locked pytest --junitxml=pytest.xml ./tests
+  artifacts:
+    when: always
+    paths:
+    - pytest.xml
+    reports:
+      junit: pytest.xml
+...

docs/Makefile

@@ -4,7 +4,7 @@
 # You can set these variables from the command line, and also
 # from the environment for the first two.
 SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
+SPHINXBUILD   ?= uv run sphinx-build
 SOURCEDIR     = .
 BUILDDIR      = _build
 

docs/make.bat

@@ -1,35 +1,35 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=.
-set BUILDDIR=_build
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.https://www.sphinx-doc.org/
-	exit /b 1
-)
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set "SPHINXBUILD=uv run sphinx-build"
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/metafold.rst

@@ -33,7 +33,7 @@ metafold.jobs module
    :show-inheritance:
 
 metafold.workflows module
---------------------
+-------------------------
 
 .. automodule:: metafold.workflows
    :members:

examples/lattice_infill.py

@@ -14,7 +14,7 @@
 import os
 import sys
 
-Vec3: TypeAlias = [float, float, float]
+Vec3: TypeAlias = list[float]
 
 
 class Patch(TypedDict):

examples/run_workflow.py

@@ -4,7 +4,6 @@
 from multiprocessing import Pool
 from pathlib import Path
 from pprint import pprint
-from typing import Optional
 import json
 import os
 import sys
@@ -13,8 +12,8 @@
 def run_workflow(
         m: MetafoldClient,
         definition: str,
-        assets: Optional[dict[str, str]] = None,
-        params: Optional[dict[str, str]] = None,
+        assets: dict[str, str] | None = None,
+        params: dict[str, str] | None = None,
         timeout: int = 5 * 60):
     print("Running workflow…")
     w = m.workflows.run(definition, assets=assets, parameters=params, timeout=timeout)

metafold/__init__.py

@@ -4,7 +4,6 @@
 from metafold.jobs import JobsEndpoint
 from metafold.workflows import WorkflowsEndpoint
 from metafold.auth import AuthProvider
-from typing import Optional
 
 
 class MetafoldClient(Client):
@@ -22,10 +21,10 @@ class MetafoldClient(Client):
 
     def __init__(
         self,
-        access_token: Optional[str] = None,
-        project_id: Optional[str] = None,
-        client_id: Optional[str] = None,
-        client_secret: Optional[str] = None,
+        access_token: str | None = None,
+        project_id: str | None = None,
+        client_id: str | None = None,
+        client_secret: str | None = None,
         auth_domain: str = "metafold3d.us.auth0.com",
         base_url: str = "https://api.metafold3d.com/",
     ) -> None: