chore: migrate first OC Python projects to uv (SMR-2)

.gitignore

@@ -85,6 +85,7 @@ var/
 *.egg-info/
 .installed.cfg
 *.egg
+.pdm-build
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

apps/openchallenges/data-lambda/Dockerfile

@@ -1,18 +1,34 @@
-FROM python:3.13.0-slim-bullseye AS builder
+FROM ghcr.io/astral-sh/uv:0.5.14 AS uv
 
-# Install the same version of Poetry as inside the dev container
-RUN pip install --no-cache-dir poetry==1.8.3
+# First, bundle the dependencies into the task root.
+FROM public.ecr.aws/lambda/python:3.13 AS builder
 
+# Enable bytecode compilation, to improve cold-start performance.
+ENV UV_COMPILE_BYTECODE=1
+
+# Disable installer metadata, to create a deterministic layer.
+ENV UV_NO_INSTALLER_METADATA=1
+
+# Enable copy mode to support bind mount caching.
+ENV UV_LINK_MODE=copy
+
+# Copy uv binary
+COPY --from=uv /uv /bin/uv
+
+# Copy dependency files
 WORKDIR /app
-COPY pyproject.toml poetry.lock ./
-RUN poetry export --without-hashes --format=requirements.txt > requirements.txt
+COPY pyproject.toml uv.lock ./
+
+# Generate requirements.txt and install dependencies
+RUN uv export --frozen --no-emit-workspace --no-dev --no-editable -o requirements.txt && \
+    uv pip install -r requirements.txt --target "${LAMBDA_TASK_ROOT}"
 
 FROM public.ecr.aws/lambda/python:3.13
 
-COPY --from=builder /app/requirements.txt ${LAMBDA_TASK_ROOT}/
-COPY openchallenges_data_lambda/app.py ${LAMBDA_TASK_ROOT}/
+# Copy the runtime dependencies from the builder stage.
+COPY --from=builder ${LAMBDA_TASK_ROOT} ${LAMBDA_TASK_ROOT}
 
-RUN python3.13 -m pip install --no-cache-dir -r requirements.txt -t .
+# Copy the application code.
+COPY ./openchallenges_data_lambda ${LAMBDA_TASK_ROOT}/app
 
-# Command can be overwritten by providing a different command in the template directly.
-CMD ["app.lambda_handler"]
+CMD ["app.app.lambda_handler"]

apps/openchallenges/data-lambda/project.json

@@ -13,7 +13,7 @@
     "prepare": {
       "executor": "nx:run-commands",
       "options": {
-        "command": "./install.sh",
+        "command": "uv sync",
         "cwd": "{projectRoot}"
       }
     },

apps/openchallenges/data-lambda/pyproject.toml

@@ -1,17 +1,27 @@
-[tool.poetry]
+[build-system]
+requires = ["pdm-backend"]
+build-backend = "pdm.backend"
+
+[project]
+authors = [
+    {name = "Verena Chung", email = "verena.chung@sagebase.org"},
+]
+requires-python = "==3.13.1"
+dependencies = [
+    "requests==2.32.3",
+    "gspread==6.1.4",
+    "pandas==2.2.3",
+    "numpy==2.1.0",
+]
 name = "openchallenges-data-lambda"
 version = "0.1.0"
 description = "A containerized AWS Lambda to import challenge data into the OC database"
-authors = ["Verena Chung <verena.chung@sagebase.org>"]
 readme = "README.md"
 
-[tool.poetry.dependencies]
-python = "3.11.10"
-requests = "2.32.3"
-gspread = "6.1.4"
-pandas = "2.2.3"
-numpy = "2.1.0"
+[dependency-groups]
+dev = []
+prod = []
+test = []
 
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
+[tool.uv]
+default-groups = []

apps/openchallenges/edam-etl/Dockerfile

@@ -1,4 +1,29 @@
-FROM python:3.12.0-slim
+FROM ghcr.io/astral-sh/uv:0.5.14 AS uv
+
+# First, bundle the dependencies into the task root.
+FROM python:3.12.8-slim AS builder
+
+# Enable bytecode compilation, to improve cold-start performance.
+ENV UV_COMPILE_BYTECODE=1
+
+# Disable installer metadata, to create a deterministic layer.
+ENV UV_NO_INSTALLER_METADATA=1
+
+# Enable copy mode to support bind mount caching.
+ENV UV_LINK_MODE=copy
+
+# Copy uv binary
+COPY --from=uv /uv /bin/uv
+
+# Copy dependency files
+WORKDIR /app
+COPY pyproject.toml uv.lock ./
+
+# Generate requirements.txt and install dependencies
+RUN uv export --frozen --no-emit-workspace --no-dev --no-editable -o requirements.txt && \
+    uv pip install -r requirements.txt --target "/app"
+
+FROM python:3.12.8-slim
 
 ARG USERNAME=app
 ARG USER_UID=1000
@@ -16,16 +41,22 @@ RUN groupadd --gid "$USER_GID" "$USERNAME" \
   && apt-get -y autoremove \
   && rm -rf /var/lib/apt/lists/*
 
-WORKDIR ${APP_DIR}
-COPY src src/
-COPY pyproject.toml poetry.lock ./
+# WORKDIR ${APP_DIR}
+# COPY src src/
+# COPY pyproject.toml uv.lock ./
 
 # Use the version of Poetry installed in the dev container.
 # See /workspaces/sage-monorepo/tools/devcontainers/sage/.devcontainer/Dockerfile
-RUN pip install --no-cache-dir poetry==1.6.1 \
-  && poetry config --local virtualenvs.create false \
-  && poetry install --with prod --no-root --no-interaction --no-ansi \
-  && pip cache purge
+# RUN pip install --no-cache-dir uv==0.5.14 \
+#   && poetry config --local virtualenvs.create false \
+#   && poetry install --with prod --no-root --no-interaction --no-ansi \
+#   && pip cache purge
+
+# Copy the runtime dependencies from the builder stage.
+COPY --from=builder /app /app
+
+# Copy the application code.
+COPY ./src /app/src
 
 WORKDIR /
 COPY docker-entrypoint.sh ./