Merge pull request #39 from Medical-Event-Data-Standard/dev

Added uv, updated pre-commit

Author: mmcdermott

.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
-        uses: actions/setup-python@v5
+      - name: Setup package
+        uses: ./.github/actions/setup
         with:
           python-version: "3.11"
 
-      - name: Install packages
-        run: |
-          pip install .[dev]
-
       - 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

@@ -8,35 +8,27 @@ name: Code Quality PR
 
 on:
   pull_request:
-    branches: [main, "release/*", "dev"]
 
 jobs:
   code-quality:
     runs-on: ubuntu-latest
 
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
+      - uses: actions/checkout@v4
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Setup package
+        uses: ./.github/actions/setup
         with:
           python-version: "3.11"
 
-      - name: Install packages
-        run: |
-          pip install .[dev]
-
       - 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: --files ${{ steps.file_changes.outputs.files}}
+        run: >
+          uv run pre-commit run --show-diff-on-failure
+          --files ${{ steps.file_changes.outputs.all_changed_files}}

.github/workflows/python-build.yaml

@@ -13,27 +13,28 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - 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

.github/workflows/tests.yaml

@@ -4,7 +4,6 @@ on:
   push:
     branches: [main]
   pull_request:
-    branches: [main, "release/*", "dev"]
 
 jobs:
   run_tests_ubuntu:
@@ -16,25 +15,18 @@ jobs:
       fail-fast: false
 
     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
+        uses: ./.github/actions/setup
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install packages
-        run: |
-          pip install -e .[tests]
-
-      #----------------------------------------------
-      #              run test suite
-      #----------------------------------------------
       - name: Run tests
-        run: |
-          pytest -v --doctest-modules --cov=src --junitxml=junit.xml -s --ignore=docs
+        run: >
+          uv run pytest -v --cov=src
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4.0.1
@@ -46,7 +38,3 @@ jobs:
         uses: codecov/test-results-action@v1
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-
-      - name: Check README code snippets
-        run: |
-          python -m doctest README.md

.pre-commit-config.yaml

@@ -5,7 +5,7 @@ exclude: "docs/index.md"
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       # list of supported hooks: https://pre-commit.com/hooks.html
       - id: trailing-whitespace
@@ -22,7 +22,7 @@ repos:
 
   # python code formatting, linting, and import sorting using ruff
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.5
+    rev: v0.14.5
     hooks:
       # Run the formatter
       - id: ruff-format
@@ -32,7 +32,7 @@ repos:
 
   # python docstring formatting
   - repo: https://github.com/myint/docformatter
-    rev: v1.7.5
+    rev: v1.7.7
     hooks:
       - id: docformatter
         args: [--in-place, --wrap-summaries=110, --wrap-descriptions=110]
@@ -47,7 +47,7 @@ repos:
 
   # shell scripts linter
   - repo: https://github.com/shellcheck-py/shellcheck-py
-    rev: v0.10.0.1
+    rev: v0.11.0.1
     hooks:
       - id: shellcheck
 
@@ -62,7 +62,7 @@ repos:
           - mdformat-gfm-alerts
           - mdformat-tables
           - mdformat_frontmatter
-          - mdformat-black
+          - mdformat-ruff
           - mdformat-config
           - mdformat-shfmt
           - mdformat-mkdocs
@@ -79,7 +79,7 @@ repos:
 
   # jupyter notebook cell output clearing
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.8.1
+    rev: 0.8.2
     hooks:
       - id: nbstripout
 

pyproject.toml

@@ -28,9 +28,11 @@ dependencies = [
   "pytimeparse"
 ]
 
+[dependency-groups]
+dev = ["pre-commit<4", "ruff", "pytest-cov"]
+
 [project.optional-dependencies]
-dev = ["pre-commit<4", "ruff"]
-tests = ["pytest-cov"]
+
 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",
@@ -53,6 +55,8 @@ addopts = [
   "--doctest-modules",
   "--ignore=docs",
   "--ignore=AGENTS.md",
+  "--ignore=CONTRIBUTORS.md",
+  "--doctest-glob=*.md",
 ]
 doctest_optionflags = ["NORMALIZE_WHITESPACE", "ELLIPSIS"]
 

src/meds_testing_helpers/dataset_generator.py

@@ -470,7 +470,7 @@ class MEDSDatasetGenerator:
         dataset_version: 0.0.1
         etl_name: meds_testing_helpers
         etl_version: ...
-        meds_version: 0.4.0
+        meds_version: 0.4.1
         created_at: ...
         extension_columns: []
         >>> dataset._pl_code_metadata # This is always empty for now as these codes are meaningless.