Merge pull request #61 from Annotation-Garden/copilot/migrate-from-pip-to-uv

Migrate from pip to uv for faster CI and Docker builds

Author: neuromechanist

.github/workflows/publish-testpypi.yml

@@ -62,10 +62,12 @@ jobs:
         with:
           python-version: '3.12'
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
       - name: Install build dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install build twine
+          uv pip install --system build twine
 
       - name: Build package
         run: python -m build

.github/workflows/publish.yml

@@ -26,10 +26,12 @@ jobs:
         with:
           python-version: '3.12'
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
       - name: Install build dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install build twine
+          uv pip install --system build twine
 
       - name: Build package
         run: python -m build

.github/workflows/test.yml

@@ -19,9 +19,12 @@ jobs:
         with:
           python-version: '3.12'
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
       - name: Install linting tools
         run: |
-          pip install ruff
+          uv pip install --system ruff
 
       - name: Lint with Ruff
         run: ruff check src tests
@@ -44,9 +47,12 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
       - name: Install dependencies
         run: |
-          pip install -e ".[dev]"
+          uv pip install --system -e ".[dev]"
 
       - name: Run unit tests (excluding integration)
         run: |
@@ -124,10 +130,13 @@ jobs:
         with:
           python-version: '3.12'
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
       - name: Install dependencies
         run: |
-          pip install -e ".[dev]"
-          pip install pytest-timeout
+          uv pip install --system -e ".[dev]"
+          uv pip install --system pytest-timeout
 
       - name: Run integration tests only
         env:

Dockerfile

@@ -61,7 +61,8 @@ COPY src/ ./src/
 COPY scripts/ ./scripts/
 
 # Install Python dependencies with API extras (includes uvicorn, FastAPI, etc.)
-RUN pip install --no-cache-dir ".[api]"
+RUN pip install uv && \
+    uv pip install --system --no-cache ".[api]"
 
 # Set environment variables for HED resources (internal paths)
 ENV HED_SCHEMA_DIR=/app/hed-schemas/schemas_latest_json \

deploy/Dockerfile

@@ -40,8 +40,8 @@ ENV GIT_COMMIT=${GIT_COMMIT}
 
 # Copy requirements and install Python dependencies with API extras
 COPY pyproject.toml README.md /app/
-RUN pip install --no-cache-dir --upgrade pip && \
-    pip install --no-cache-dir ".[api]"
+RUN pip install uv && \
+    uv pip install --system --no-cache ".[api]"
 
 # Copy the application code
 COPY src /app/src

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "hedit"
-version = "0.6.3a2"
+version = "0.6.3a3"
 description = "Multi-agent system for HED annotation generation and validation"
 readme = "PKG_README.md"
 requires-python = ">=3.12"

src/version.py

@@ -1,6 +1,6 @@
 """Version information for HEDit."""
 
-__version__ = "0.6.3a2"
+__version__ = "0.6.3a3"
 __version_info__ = (0, 6, 3, "alpha")