Corrected typo, set up UV, ensured tests pass

.github/actions/setup/action.yaml

@@ -0,0 +1,28 @@
+name: Setup Package
+description: This workflow sets up the package for other workflows.
+inputs:
+  python-version:
+    description: The Python version to use for the setup.
+    required: true
+    default: "3.11"
+  group:
+    description: The dependency group to install (benchmarks, dev, docs)
+    required: false
+    default: "dev"
+runs:
+  using: "composite"
+  steps:
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "${{ inputs.python-version }}"
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+      with:
+        enable-cache: true
+        cache-suffix: "py${{ inputs.python-version }}"
+
+    - name: Install packages
+      shell: bash
+      run: |
+        uv sync --locked --group ${{ inputs.group }}

.github/workflows/code-quality-main.yaml

@@ -12,17 +12,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
+      - uses: actions/checkout@v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+      - name: Setup package
+        uses: ./.github/actions/setup
         with:
-          python-version: "3.11"
-
-      - name: Install packages
-        run: |
-          pip install .[dev]
+          python-version: "3.12"
 
       - name: Run pre-commits
-        uses: pre-commit/action@v3.0.1
+        run: uv run pre-commit run --all-files --show-diff-on-failure

.github/workflows/code-quality-pr.yaml

@@ -14,28 +14,21 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
+      - uses: actions/checkout@v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+      - name: Setup package
+        uses: ./.github/actions/setup
         with:
-          python-version: "3.11"
-
-      - name: Install packages
-        run: |
-          pip install .[dev]
+          python-version: "3.12"
 
       - name: Find modified files
         id: file_changes
-        uses: trilom/file-changes-action@v1.2.4
-        with:
-          output: " "
+        uses: tj-actions/changed-files@v46.0.5
 
-      - name: List modified files
-        run: echo '${{ steps.file_changes.outputs.files}}'
+      - name: List all changed files
+        run: echo '${{ steps.file_changes.outputs.all_changed_files }}'
 
       - name: Run pre-commits
-        uses: pre-commit/action@v3.0.1
-        with:
-          extra_args: --all-files
+        run: >
+          uv run pre-commit run --show-diff-on-failure
+          --files ${{ steps.file_changes.outputs.all_changed_files}}

.github/workflows/python-build.yaml

@@ -9,34 +9,35 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: "3.x"
-      - name: Install pypa/build
-        run: >-
-          python3 -m
-          pip install
-          build
-          --user
-      - name: Build a binary wheel and a source tarball
-        run: python3 -m build
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+
+      - name: Build
+        run: uv build
+
       - name: Store the distribution packages
         uses: actions/upload-artifact@v4
         with:
           name: python-package-distributions
           path: dist/
 
   publish-to-pypi:
-    name: >-
-      Publish Python 🐍 distribution 📦 to PyPI
+    name: Publish Python 🐍 distribution 📦 to PyPI
     if: startsWith(github.ref, 'refs/tags/') # only publish to PyPI on tag pushes
     needs:
       - build
     runs-on: ubuntu-latest
     environment:
       name: pypi
-      url: https://pypi.org/p/flexible_schema # Replace <package-name> with your PyPI project name
+      url: https://pypi.org/p/flexible_schema
     permissions:
       id-token: write # IMPORTANT: mandatory for trusted publishing
 

.github/workflows/tests.yaml

@@ -1,35 +1,33 @@
-name: Run tests
+name: Tests
 
 on:
   push:
-    branches: ["main"]
+    branches: [main]
   pull_request:
-    branches: ["main", "dev"]
 
 jobs:
-  build:
+  run_tests_ubuntu:
     runs-on: ubuntu-latest
 
     strategy:
+      fail-fast: false
       matrix:
         python-version: ["3.10", "3.11", "3.12"]
 
+    timeout-minutes: 30
+
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
+      - uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+      - name: Setup package @ python ${{ matrix.python-version }}
+        uses: ./.github/actions/setup
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install dependencies
-        run: |
-          pip install -e .[tests]
-
       - name: Run tests
-        run: |
-          pytest -v --cov=src
+        run: >
+          uv run pytest -v --cov=src -m "not parallelized and not lightning"
+          --ignore="benchmark" --ignore="src/meds_torchdata/extensions"
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4.0.1

README.md

@@ -4,7 +4,7 @@
 [![Documentation Status](https://readthedocs.org/projects/flexible-schema/badge/?version=latest)](https://flexible-schema.readthedocs.io/en/latest/?badge=latest)
 ![python](https://img.shields.io/badge/-Python_3.10-blue?logo=python&logoColor=white)
 [![codecov](https://codecov.io/gh/Medical-Event-Data-Standard/flexible_schema/graph/badge.svg?token=89SKXPKVRA)](https://codecov.io/gh/Medical-Event-Data-Standard/flexible_schema)
-[![tests](https://github.com/Medical-Event-Data-Standard/flexible_schema/actions/workflows/tests.yaml/badge.svg)](https://github.com/Medical-Event-Data-Standard/flexible_schema/actions/workflows/tests.yml)
+[![tests](https://github.com/Medical-Event-Data-Standard/flexible_schema/actions/workflows/tests.yaml/badge.svg)](https://github.com/Medical-Event-Data-Standard/flexible_schema/actions/workflows/tests.yaml)
 [![code-quality](https://github.com/Medical-Event-Data-Standard/flexible_schema/actions/workflows/code-quality-main.yaml/badge.svg)](https://github.com/Medical-Event-Data-Standard/flexible_schema/actions/workflows/code-quality-main.yaml)
 [![license](https://img.shields.io/badge/License-MIT-green.svg?labelColor=gray)](https://github.com/Medical-Event-Data-Standard/flexible_schema#license)
 [![PRs](https://img.shields.io/badge/PRs-welcome-brightgreen.svg)](https://github.com/Medical-Event-Data-Standard/flexible_schema/pulls)

pyproject.toml

@@ -22,17 +22,16 @@ dependencies = [
     "typing_extensions >= 4.0",
 ]
 
-[tool.setuptools_scm]
-
-[project.optional-dependencies]
-dev = ["pre-commit<4", "ruff"]
-tests = ["pytest", "pytest-cov[toml]"]
+[dependency-groups]
+dev = ["pre-commit<4", "ruff", "pytest", "pytest-cov[toml]"]
 docs = [
   "mkdocs==1.6.1", "mkdocs-material==9.6.7", "mkdocstrings[python,shell]==0.28.2", "mkdocs-gen-files==0.5.0",
   "mkdocs-literate-nav==0.6.1", "mkdocs-section-index==0.3.9", "mkdocs-git-authors-plugin==0.9.2",
   "mkdocs-git-revision-date-localized-plugin==1.3.0", "markdown-callouts",
 ]
 
+[tool.setuptools_scm]
+
 [project.urls]
 Homepage = "https://github.com/mmcdermott/flexible_schema"
 Issues = "https://github.com/mmcdermott/flexible_schema/issues"