Convert Poetry to UV

.dockerignore

@@ -1,5 +1,115 @@
-assetstore
-db
-logs
-**/node_modules
-.env
+# Git
+.gitignore
+.gitattributes
+dive-dsa-slicer/
+scripts/
+testutils/
+# Documentation
+docs/
+*.md
+README*
+
+# Development files
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# Virtual environments
+.env
+.venv
+env/
+venv/
+server/.venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+.tox/
+.nox/
+coverage.xml
+*.cover
+.hypothesis/
+
+# Node.js
+node_modules/
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+
+# Build artifacts
+client/dist/
+client/node_modules/
+*.log
+
+# OS
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# Temporary files
+*.tmp
+*.temp
+/tmp/
+/var/tmp/
+
+# Docker
+Dockerfile*
+docker-compose*.yml
+.dockerignore
+
+# CI/CD
+.github/
+.gitlab-ci.yml
+.travis.yml
+.circleci/
+
+# IDE
+.vscode/
+.idea/
+*.sublime-*
+
+# Large data files
+*.zip
+*.tar.gz
+*.tar.bz2
+*.7z
+*.rar
+
+# Test data
+testutils/
+tests/
+*_test.py
+test_*.py

docker/entrypoint_server.sh

@@ -21,5 +21,5 @@ chmod 777 /var/run/docker.sock 2>/dev/null || true
 
 
 set -e
-python /server_setup.py
-exec girder serve --host 0.0.0.0 $@
+uv run python /server_setup.py
+exec uv run girder serve --host 0.0.0.0 $@

docker/entrypoint_worker.sh

@@ -35,7 +35,7 @@ if [ -n "$WORKER_CONCURRENCY" ]; then
     CONCURRENCY_ARGUMENT="--concurrency $WORKER_CONCURRENCY"
 fi
 
-su $(id -nu ${DSA_USER%%:*}) -c "GW_DIRECT_PATHS=true python -m dive_tasks -l info --without-gossip --without-mingle $QUEUE_ARGUMENT $CONCURRENCY_ARGUMENT -Ofair --prefetch-multiplier=1"
+su $(id -nu ${DSA_USER%%:*}) -c "GW_DIRECT_PATHS=true uv run python -m dive_tasks -l info --without-gossip --without-mingle $QUEUE_ARGUMENT $CONCURRENCY_ARGUMENT -Ofair --prefetch-multiplier=1"
 
 # su $(id -nu ${DSA_USER%%:*}) -c "GW_DIRECT_PATHS=true python -m girder_worker $CONCURRENCY_ARGUMENT -Ofair --prefetch-multiplier=1"
 # exec python \

docker/entrypoint_worker_gpu.sh

@@ -1,23 +1,55 @@
-#!/bin/sh
+#!/bin/bash
+set -euo pipefail
 
-# Environment variables that may be supplied
-# WORKER_CONCURRENCY: The number of concurrent jobs to run at once. If not supplied, the celery default is used.
-# WORKER_WATCHING_QUEUES: The comma separated list of queues to take tasks from. If not supplied, the celery default of 'celery' is used.
-export PATH="/opt/dive/local/ffmpeg:$PATH"
+# Environment variables that may be supplied:
+# WORKER_CONCURRENCY: The number of concurrent jobs to run at once. If not supplied, celery default is used.
+# WORKER_WATCHING_QUEUES: The comma-separated list of queues to take tasks from. If not supplied, default 'celery' is used.
 
-QUEUE_ARGUMENT=
-CONCURRENCY_ARGUMENT=
+QUEUE_ARGUMENT=""
+CONCURRENCY_ARGUMENT=""
 
-if [ -n "$WORKER_WATCHING_QUEUES" ]; then
+if [[ -z "${DSA_USER:-}" ]]; then
+  echo "Set the DSA_USER before starting (e.g., DSA_USER=\$$(id -u):\$$(id -g) <up command>)"
+  exit 1
+fi
+
+USER_ID=${DSA_USER%%:*}
+GROUP_ID=${DSA_USER#*:}
+
+# Ensure group exists
+if ! getent group "${GROUP_ID}" >/dev/null 2>&1; then
+  groupadd -g "${GROUP_ID}" dsa_group
+fi
+
+# Ensure user exists
+if ! id -u "${USER_ID}" >/dev/null 2>&1; then
+  useradd -m -u "${USER_ID}" -g "${GROUP_ID}" -s /bin/bash ubuntu2 || true
+fi
+
+# Handle docker.sock if present
+if [[ -S /var/run/docker.sock ]]; then
+  DOCKER_GID=$(stat -c "%g" /var/run/docker.sock)
+  if ! getent group "${DOCKER_GID}" >/dev/null 2>&1; then
+    groupadd -g "${DOCKER_GID}" docker
+  fi
+  usermod -aG "${DOCKER_GID}" "$(id -nu ${USER_ID})" || true
+  chmod 777 /var/run/docker.sock || true
+fi
+
+# Ensure tmp is writable
+chmod 1777 "${TMPDIR:-/tmp}" || true
+
+# Worker arguments
+if [[ -n "${WORKER_WATCHING_QUEUES:-}" ]]; then
     QUEUE_ARGUMENT="--queues $WORKER_WATCHING_QUEUES"
 fi
 
-if [ -n "$WORKER_CONCURRENCY" ]; then
+if [[ -n "${WORKER_CONCURRENCY:-}" ]]; then
     CONCURRENCY_ARGUMENT="--concurrency $WORKER_CONCURRENCY"
 fi
 
-exec poetry run python \
-    -m dive_tasks \
-    -l info \
-    --without-gossip --without-mingle \
-    $QUEUE_ARGUMENT $CONCURRENCY_ARGUMENT
+# Sanity checks for required tools
+command -v uv >/dev/null 2>&1 || { echo "Error: 'uv' not found in PATH"; exit 1; }
+command -v python >/dev/null 2>&1 || { echo "Error: 'python' not found in PATH"; exit 1; }
+
+su $(id -nu ${DSA_USER%%:*}) -c "GW_DIRECT_PATHS=true uv run python -m dive_tasks -l info --without-gossip --without-mingle $QUEUE_ARGUMENT $CONCURRENCY_ARGUMENT -Ofair --prefetch-multiplier=1"

docker/girder.Dockerfile

@@ -3,6 +3,7 @@
 # ========================
 FROM node:20 AS client-builder
 WORKDIR /app
+SHELL ["/bin/bash", "-c"]
 
 # Install dependencies
 COPY client/package.json client/yarn.lock /app/
@@ -15,34 +16,43 @@ RUN yarn build:web
 # ========================
 # == SERVER BUILD STAGE ==
 # ========================
-# Note: server-builder stage will be the same in both dockerfiles
-FROM python:3.11-bookworm AS server-builder
+FROM ghcr.io/astral-sh/uv:python3.11-bookworm-slim AS server-builder
+SHELL ["/bin/bash", "-c"]
 
 WORKDIR /opt/dive/src
 
-# https://cryptography.io/en/latest/installation/#debian-ubuntu
-RUN apt-get update
-RUN apt-get install -y build-essential libssl-dev libffi-dev python3-dev cargo npm libgl1
-# Recommended poetry install https://python-poetry.org/docs/master/#installation
-RUN curl -sSL https://install.python-poetry.org | POETRY_VERSION=2.1.2 POETRY_HOME=/opt/dive/poetry python -
-ENV PATH="/opt/dive/poetry/bin:$PATH"
-# Create a virtual environment for the installation
-RUN python -m venv /opt/dive/local/venv
-# Poetry needs this set to recognize it as ane existing environment
+# Install only essential build dependencies
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+        build-essential \
+        curl \
+        git \
+        pkg-config \
+        libgomp1 && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+ENV UV_COMPILE_BYTECODE=1 UV_LINK_MODE=copy
 ENV VIRTUAL_ENV="/opt/dive/local/venv"
+ENV UV_PROJECT_ENVIRONMENT=/opt/dive/local/venv
 ENV PATH="/opt/dive/local/venv/bin:$PATH"
 
-# Copy only the lock and project files to optimize cache
+# Create virtual environment
+RUN uv venv /opt/dive/local/venv
+
+# Copy dependency files first for better caching
 COPY server/pyproject.toml /opt/dive/src/
+COPY server/uv.lock /opt/dive/src/
 COPY .git/ /opt/dive/src/.git/
-RUN poetry env use system
-RUN poetry config virtualenvs.create false
-# Install dependencies only
-RUN poetry install --no-root
-# Build girder client, including plugins like worker/jobs
-# Copy full source code and install
+
+# Install dependencies without SAM2 (web server doesn't need it)
+RUN uv sync --frozen --no-install-project --no-dev
+
+# Copy source and install project
 COPY server/ /opt/dive/src/
-RUN poetry install --only main
+RUN uv sync --frozen --no-dev --extra cpu
+
+# Install Node.js for Girder build
 RUN curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.5/install.sh | bash
 RUN . ~/.bashrc && \
     nvm install 14 && \
@@ -51,28 +61,42 @@ RUN . ~/.bashrc && \
     ln -s $(dirname `which npm`) /usr/local/node
 
 ENV PATH="/usr/local/node:$PATH"
-
 RUN girder build
 
+# Clean up build artifacts and cache
+RUN rm -rf /root/.cache /tmp/* /var/tmp/* && \
+    find /opt/dive/local/venv -name "*.pyc" -delete && \
+    find /opt/dive/local/venv -name "__pycache__" -type d -exec rm -rf {} + 2>/dev/null || true
+
 # =================
 # == DIST SERVER ==
 # =================
-FROM python:3.11-slim-bookworm AS server
+FROM ghcr.io/astral-sh/uv:python3.11-bookworm-slim AS server
 
-RUN apt-get update
-RUN apt-get install -y libgl1 libglib2.0-0
+# Install only runtime dependencies
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+        libgomp1 \
+        ca-certificates && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 # Hack: Tell GitPython to be quiet, we aren't using git
 ENV GIT_PYTHON_REFRESH="quiet"
-ENV PATH="/opt/dive/local/venv/bin:$PATH"
+ENV PATH="/opt/dive/local/venv/bin:/usr/local/bin:$PATH"
 
-# Copy site packages and executables
+# Copy only the essential parts from builder
 COPY --from=server-builder /opt/dive/local/venv /opt/dive/local/venv
-# Copy the source code of the editable module
 COPY --from=server-builder /opt/dive/src /opt/dive/src
-# Copy the client code into the static source location
 COPY --from=client-builder /app/dist/ /opt/dive/local/venv/share/girder/static/dive/
+
+# Copy uv binary for runtime use
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /usr/local/bin/uv
+
 # Install startup scripts
 COPY docker/entrypoint_server.sh docker/server_setup.py /
 
+# Create non-root user for security
+RUN useradd --create-home --uid 1000 --shell=/bin/bash dive && \
+    chown -R dive:dive /opt/dive
 ENTRYPOINT [ "/entrypoint_server.sh" ]