Sync changes from crfm helm into medhelm main

.github/dependabot.yml

@@ -3,7 +3,7 @@ updates:
   - package-ecosystem: "uv"
     directory: "/"
     schedule:
-      interval: "weekly"
+      interval: "monthly"
     ignore:
       - dependency-name: "*"
         update-types: ["version-update:semver-major"]
@@ -14,7 +14,7 @@ updates:
   - package-ecosystem: "npm"
     directory: "/helm-frontend/"
     schedule:
-      interval: "weekly"
+      interval: "monthly"
     ignore:
       - dependency-name: "*"
         update-types: ["version-update:semver-major"]

.github/workflows/frontend.yml → .github/workflows/deploy-frontend.yaml

@@ -1,47 +1,13 @@
-name: Frontend
+name: Deploy Frontend
 
-on:
-  push:
-    branches:
-      - '*'
-    paths:
-      - 'helm-frontend/**'
-  pull_request:
-    branches:
-      - '*'
-    paths:
-      - 'helm-frontend/**'
+on: workflow_dispatch
 
 jobs:
-  test:
-    runs-on: ubuntu-latest
-    steps:
-    - name: Checkout code
-      uses: actions/checkout@v4
-    - name: Use Node.js
-      uses: actions/setup-node@v4
-      with:
-        node-version: '18'
-    - name: Install Yarn
-      run: npm install --global yarn
-    - name: Install dependencies
-      working-directory: ./helm-frontend
-      run: yarn install
-    - name: Run pre-commit
-      run: ./pre-commit-frontend.sh
-    - name: Build
-      working-directory: ./helm-frontend
-      run: yarn build
-    - name: Run tests
-      working-directory: ./helm-frontend
-      run: yarn test
-
   build:
     runs-on: ubuntu-latest
     # Deploy to only run on pushes to master
     # if: github.event_name == 'push' && github.ref == 'refs/heads/main'
     if: github.event_name == 'push' && github.ref == 'refs/heads/react_frontend'
-    needs: test
     environment:
       name: github-pages
     env:

.github/workflows/publish-pypi.yml

@@ -0,0 +1,48 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+name: Publish Python package to PyPI
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  pypi-publish:
+    name: Publish Python package to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/crfm-helm
+    permissions:
+      id-token: write
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+      with:
+        version: "0.9.4"
+    - name: Build
+      run: uv build
+    - name: helm-run (wheel)
+      run: uv run --isolated --no-project --with dist/*.whl helm-run --run-entries simple1:model=simple/model1 --max-eval-instances 10 --suite test
+    - name: helm-summarize (wheel)
+      run: uv run --isolated --no-project --with dist/*.whl helm-summarize --suite test
+    - name: helm-server (wheel)
+      run: uv run --isolated --no-project --with dist/*.whl helm-server --help
+    - name: helm-run (source distribution)
+      run: uv run --isolated --no-project --with dist/*.tar.gz helm-run --run-entries simple1:model=simple/model1 --max-eval-instances 10 --suite test
+    - name: helm-summarize (source distribution)
+      run: uv run --isolated --no-project --with dist/*.tar.gz helm-summarize --suite test
+    - name: helm-server (source distribution)
+      run: uv run --isolated --no-project --with dist/*.tar.gz helm-server --help
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test-frontend.yml

@@ -0,0 +1,37 @@
+name: Test Frontend
+
+on:
+  push:
+    branches:
+      - '*'
+    paths:
+      - 'helm-frontend/**'
+  pull_request:
+    branches:
+      - '*'
+    paths:
+      - 'helm-frontend/**'
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+    - name: Use Node.js
+      uses: actions/setup-node@v4
+      with:
+        node-version: '18'
+    - name: Install Yarn
+      run: npm install --global yarn
+    - name: Install dependencies
+      working-directory: ./helm-frontend
+      run: yarn install
+    - name: Run pre-commit
+      run: ./pre-commit-frontend.sh
+    - name: Build
+      working-directory: ./helm-frontend
+      run: yarn build
+    - name: Run tests
+      working-directory: ./helm-frontend
+      run: yarn test

.github/workflows/test.yml → .github/workflows/test-python.yml

@@ -1,4 +1,4 @@
-name: Test
+name: Test Python
 on:
   push:
     branches: [ main ]

.github/workflows/test_scenarios.yml → .github/workflows/test-scenarios.yml

@@ -1,4 +1,4 @@
-name: Scenario tests
+name: Test Scenarios
 on:
   push:
     branches: [ main ]

.github/workflows/update-requirements.yml → .github/workflows/update-dependencies.yml

@@ -2,11 +2,7 @@
 # for all Python dependencies (including transitive dependencies)
 # whenever pyproject.toml is modified or the workflow is manually triggered.
 
-name: Update requirements
-
-permissions:
-  contents: write
-  pull-requests: write
+name: Update dependencies
 
 on:
   push:
@@ -15,16 +11,13 @@ on:
     paths:
       - "pyproject.toml"
       - "constraints.txt"
-      - '.github/workflows/update-requirements.yml'
+      - '.github/workflows/update-dependencies.yml'
   workflow_dispatch:
 
 jobs:
-  update-requirements:
-    name: Update requirements
+  update-dependencies:
+    name: Update dependencies
     runs-on: ubuntu-latest
-    permissions:
-      contents: write
-      pull-requests: write
     strategy:
       matrix:
         python-version: ["3.10"]
@@ -39,17 +32,10 @@ jobs:
         uses: astral-sh/setup-uv@v6
         with:
           version: "0.9.4"
-          enable-cache: true
-      - name: Create build env with setuptools (for openai-whisper)
-        run: |
-          python -m venv .build-venv
-          .build-venv/bin/pip install setuptools wheel --quiet
       - name: Lock dependencies
-        run: UV_PYTHON=".build-venv/bin/python" uv lock --no-build-isolation-package openai-whisper
+        run: uv lock
       - name: Install dependencies
-        run: UV_PYTHON=".build-venv/bin/python" uv sync --extra ci --no-build-isolation-package openai-whisper
-      - name: Write requirements.txt
-        run: uv pip freeze --exclude-editable > requirements.txt
+        run: uv sync --extra ci
         # Need to manually run tests here because the pull request opened later will not
         # run the test workflow.
         #
@@ -66,14 +52,11 @@ jobs:
         run: uv run pytest
       - name: Run helm-run
         run: uv run helm-run --suite test --run-entries simple1:model=simple/model1 --max-eval-instances 10 --exit-on-error
-      - name: Remove build venv before PR (do not commit)
-        run: rm -rf .build-venv
       - name: Create pull request
         uses: peter-evans/create-pull-request@v6
         with:
-          token: ${{ secrets.REPO_TOKEN || secrets.GITHUB_TOKEN }}
-          commit-message: Update requirements
-          title: "Update requirements"
-          branch: actions/update-requirements
+          commit-message: Update dependencies
+          title: "Update dependencies"
+          branch: actions/update-dependencies
           delete-branch: true
           body: Auto-generated from GitHub Actions.

.github/workflows/upgrade-requirements.yml → .github/workflows/upgrade-dependencies.yml

@@ -2,16 +2,16 @@
 # for all Python dependencies (including transitive dependencies)
 # every Monday or whenever the workflow is manually triggered.
 
-name: Upgrade requirements
+name: Upgrade dependencies
 
 on:
   # schedule:
   #   - cron: "30 15 * * 1"
   workflow_dispatch:
 
 jobs:
-  upgrade-requirements:
-    name: Upgrade requirements
+  upgrade-dependencies:
+    name: Upgrade dependencies
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -27,17 +27,10 @@ jobs:
         uses: astral-sh/setup-uv@v6
         with:
           version: "0.9.4"
-          enable-cache: true
-      - name: Create build env with setuptools (for openai-whisper)
-        run: |
-          python -m venv .build-venv
-          .build-venv/bin/pip install setuptools wheel --quiet
       - name: Upgrade dependencies
-        run: UV_PYTHON=".build-venv/bin/python" uv lock --upgrade --no-build-isolation-package openai-whisper
+        run: uv lock --upgrade
       - name: Install dependencies
-        run: UV_PYTHON=".build-venv/bin/python" uv sync --extra ci --no-build-isolation-package openai-whisper
-      - name: Write requirements.txt
-        run: uv pip freeze --exclude-editable > requirements.txt
+        run: uv sync --extra ci
         # Need to manually run tests here because the pull request opened later will not
         # run the test workflow.
         #
@@ -57,8 +50,8 @@ jobs:
       - name: Create pull request
         uses: peter-evans/create-pull-request@v6
         with:
-          commit-message: Upgrade requirements
-          title: "Upgrade requirements"
-          branch: actions/upgrade-requirements
+          commit-message: Upgrade dependencies
+          title: "Upgrade dependencies"
+          branch: actions/upgrade-dependencies
           delete-branch: true
           body: Auto-generated from GitHub Actions.

.readthedocs.yaml

@@ -6,9 +6,12 @@ build:
   os: "ubuntu-20.04"
   tools:
     python: "3.10"
-
-python:
-  install:
-  - requirements: docs/requirements.txt
-  - method: pip
-    path: .
+  jobs:
+    pre_create_environment:
+        - asdf plugin add uv
+        - asdf install uv latest
+        - asdf global uv latest
+    create_environment:
+        - uv venv "${READTHEDOCS_VIRTUALENV_PATH}"
+    install:
+        - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen --group docs