Migrate from poetry to uv, sphinx to mkdocs

.github/workflows/docs.yml

@@ -0,0 +1,102 @@
+name: docs
+permissions:
+  contents: write
+  pull-requests: write
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/docs.yml
+      - '**.py'
+      - '**.ipynb'
+      - '**.html'
+      - '**.js'
+      - '**.md'
+      - '**.rst'
+      - uv.lock
+      - pyproject.toml
+      - mkdocs.yml
+      - '**.png'
+      - '**.svg'
+  pull_request:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/docs.yml
+      - '**.py'
+      - '**.ipynb'
+      - '**.js'
+      - '**.html'
+      - uv.lock
+      - pyproject.toml
+      - '**.md'
+      - '**.rst'
+      - mkdocs.yml
+      - '**.png'
+      - '**.svg'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7.1.5
+        with:
+          version: "0.9.11"
+          enable-cache: true
+
+      - name: Set up Python
+        uses: actions/setup-python@v6.1.0
+        with:
+          python-version-file: ".python-version"
+
+      - name: Install the project
+        run: uv sync --group docs --group test
+
+      - name: Build docs
+        run: uv run mkdocs build
+
+      - name: Create .nojekyll file
+        run: touch site/.nojekyll
+
+      - name: Upload artifact
+        uses: actions/upload-artifact@v5
+        with:
+          name: docs-site
+          path: site/
+          retention-days: 1
+
+  deploy:
+    needs: build
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6
+
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+
+      - name: Download artifact
+        uses: actions/download-artifact@v6
+        with:
+          name: docs-site
+          path: site
+
+      - name: Ensure .nojekyll exists
+        run: touch site/.nojekyll
+
+      - name: Deploy to Github pages
+        uses: JamesIves/github-pages-deploy-action@v4.7.6
+        with:
+          branch: github_pages
+          folder: site

.github/workflows/publish_and_release.yml

@@ -14,14 +14,24 @@ jobs:
       - name: Install apt dependencies
         run: |
           sudo apt-get update
-      - uses: actions/checkout@v6
-      - name: Install poetry
-        run: pipx install poetry
-      - uses: actions/setup-python@v6
+
+      - name: Checkout code
+        uses: actions/checkout@v6
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7.1.5
+        with:
+          version: "0.9.11"
+          enable-cache: true
+
+      - name: Set up Python
+        uses: actions/setup-python@v6.1.0
         with:
-          python-version: "3.10"
+          python-version-file: ".python-version"
+
       - name: Build package
-        run: poetry build
+        run: uv build
+
       - name: Publish package
         uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e
         with:

.github/workflows/smoke_tests.yaml

@@ -11,7 +11,7 @@ on:
 
 jobs:
   test:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     permissions:
       contents: read
       actions: write
@@ -22,39 +22,35 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v6
 
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v6
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7.1.5
         with:
-          python-version: "3.10"
+          version: "0.9.11"
+          enable-cache: true
+
+      - name: Set up Python
+        uses: actions/setup-python@v6.1.0
+        with:
+          python-version-file: ".python-version"
 
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
 
-      - name: Set up file descriptor limit
-        run: ulimit -n 4096
-
-      - name: Install and configure Poetry
-        uses: snok/install-poetry@v1
-        with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-
       - name: Set up cache
         uses: actions/cache@v5
-        id: cached-poetry-dependencies
+        id: cached-uv-dependencies
         with:
           path: .venv
-          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+          key: venv-${{ runner.os }}-${{ hashFiles('**/uv.lock') }}
+
+      - name: Set up file descriptor limit
+        run: ulimit -n 4096
 
       - name: Install dependencies
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-        run: |
-          poetry install --with "dev, test"
+        run: uv sync --group dev --group test
 
       - name: Run Script
-        run: |
-          source .venv/bin/activate
-          pytest --test-group-count=4 --test-group=${{ matrix.group }} -v --cov fl4health --cov-report=xml tests/smoke_tests/test_smoke_tests.py
+        run: uv run pytest --test-group-count=4 --test-group=${{ matrix.group }} -v --cov fl4health --cov-report=xml tests/smoke_tests/test_smoke_tests.py
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v5
@@ -64,14 +60,14 @@ jobs:
           fail_ci_if_error: true
           verbose: true
 
-      # Deleting some temporary files and useless folders to free up space in order to have space for
-      # the cache file, and printing the disk space info at the beggining and end.
-      # Deleting poetry cache should clear ~4GB of space.
+      # Deleting some temporary files and useless folders to free up space
       # Deleting /usr/share/dotnet should clear ~4GB of space.
       # Deleting /usr/local/lib/android should clear ~12GB of space.
       - name: Cleanup space (before cache save)
         run: |
           df -h /dev/root
-          poetry cache clear --all . --no-interaction
           sudo rm -rf /usr/share/dotnet /usr/local/lib/android
           df -h /dev/root
+
+      - name: Minimize uv cache
+        run: uv cache prune --ci

.github/workflows/static_code_checks.yaml

@@ -18,52 +18,60 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v6
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v6
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7.1.5
         with:
-          python-version: "3.10"
-      - name: Install and configure Poetry
-        uses: snok/install-poetry@v1
+          version: "0.9.11"
+          enable-cache: true
+
+      - name: Set up Python
+        uses: actions/setup-python@v6.1.0
         with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
+          python-version-file: ".python-version"
+
       - name: Set up cache
         uses: actions/cache@v5
-        id: cached-poetry-dependencies
+        id: cached-uv-dependencies
         with:
           path: .venv
-          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+          key: venv-${{ runner.os }}-${{ hashFiles('**/uv.lock') }}
+
       - name: Install dependencies
-        run: poetry install --with "dev, test, codestyle"
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: uv sync --group dev --group test --group codestyle
+
       - name: Pre-commit Checks
-        run: |
-          source .venv/bin/activate
-          pre-commit run --all-files
+        run: uv run pre-commit run --all-files
+
       - name: pip-audit (gh-action-pip-audit)
         uses: pypa/gh-action-pip-audit@v1.1.0
         with:
           virtual-environment: .venv/
           # GHSA-3749-ghw9-m3mg and GHSA-887c-mr87-cxwp are pytorch vulnerabilities that require 2.7 and 2.8 but we're
           # pinning to 2.6.0 for now.
-          # GHSA-wf7f-8fxf-xfxc ML Flow vulnerability in deserialization that hasn't been patched yet.
           # CVE-2025-53000 NBConvert issue, no fix yet.
           # CVE-2026-21851 is a MonAI issue with no fix at the moment.
+          # CVE-2024-55459, CVE-2025-9906, CVE-2025-12058, CVE-2025-12060 are keras vulnerabilities that require
+          # keras>=3.12.0 which needs tensorflow>=2.16, but we're pinning to tensorflow 2.15 due to tensorflow-io
+          # compatibility constraints.
           ignore-vulns: |
             GHSA-3749-ghw9-m3mg
             GHSA-887c-mr87-cxwp
-            GHSA-wf7f-8fxf-xfxc
             CVE-2025-53000
             CVE-2026-21851
+            CVE-2024-55459
+            CVE-2025-9906
+            CVE-2025-12058
+            CVE-2025-12060
 
-      # Deleting some temporary files and useless folders to free up space in order to have space for
-      # the cache file, and printing the disk space info at the beggining and end.
-      # Deleting poetry cache should clear ~4GB of space.
+      # Deleting some temporary files and useless folders to free up space
       # Deleting /usr/share/dotnet should clear ~4GB of space.
       # Deleting /usr/local/lib/android should clear ~12GB of space.
       - name: Cleanup space (before cache save)
         run: |
           df -h /dev/root
-          poetry cache clear --all . --no-interaction
           sudo rm -rf /usr/share/dotnet /usr/local/lib/android
           df -h /dev/root
+
+      - name: Minimize uv cache
+        run: uv cache prune --ci