diff --git a/.dockerignore b/.dockerignore index 46e7a757..24ad7d4c 100644 --- a/.dockerignore +++ b/.dockerignore @@ -1,5 +1,115 @@ -assetstore -db -logs -**/node_modules -.env \ No newline at end of file +# 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 \ No newline at end of file diff --git a/docker/entrypoint_server.sh b/docker/entrypoint_server.sh index 493c9bb9..2f1c61af 100755 --- a/docker/entrypoint_server.sh +++ b/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 $@ diff --git a/docker/entrypoint_worker.sh b/docker/entrypoint_worker.sh index fb5b3400..9a56ac5e 100755 --- a/docker/entrypoint_worker.sh +++ b/docker/entrypoint_worker.sh @@ -35,7 +35,7 @@ if [ -n "$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 $CONCURRENCY_ARGUMENT -Ofair --prefetch-multiplier=1" # exec python \ diff --git a/docker/entrypoint_worker_gpu.sh b/docker/entrypoint_worker_gpu.sh index 3c38798a..7e14318e 100755 --- a/docker/entrypoint_worker_gpu.sh +++ b/docker/entrypoint_worker_gpu.sh @@ -1,23 +1,57 @@ -#!/bin/sh +#!/bin/bash +set -euo pipefail -# Environment variables that may be supplied -# WORKER_CONCURRENCY: The number of concurrent jobs to run at once. If not supplied, the celery default is used. -# WORKER_WATCHING_QUEUES: The comma separated list of queues to take tasks from. If not supplied, the celery default of 'celery' is used. -export PATH="/opt/dive/local/ffmpeg:$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) )" + 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 ${USER_ID})" || true + usermod -aG dive "$(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 +chown -R ${USER_ID}:${GROUP_ID} /opt/dive/local/venv + +# Sanity checks for required tools +command -v uv >/dev/null 2>&1 || { echo "Error: 'uv' not found in PATH"; exit 1; } +command -v uv run python >/dev/null 2>&1 || { echo "Error: 'python' not found in PATH"; exit 1; } -exec poetry run python \ - -m dive_tasks \ - -l info \ - --without-gossip --without-mingle \ - $QUEUE_ARGUMENT $CONCURRENCY_ARGUMENT +su $(id -nu ${DSA_USER%%:*}) -c "GW_DIRECT_PATHS=true uv run python -m dive_tasks -l info --without-gossip --without-mingle $QUEUE_ARGUMENT $CONCURRENCY_ARGUMENT -Ofair --prefetch-multiplier=1" diff --git a/docker/girder.Dockerfile b/docker/girder.Dockerfile index 2c743296..c4777353 100644 --- a/docker/girder.Dockerfile +++ b/docker/girder.Dockerfile @@ -3,6 +3,7 @@ # ======================== FROM node:20 AS client-builder WORKDIR /app +SHELL ["/bin/bash", "-c"] # Install dependencies COPY client/package.json client/yarn.lock /app/ @@ -15,34 +16,43 @@ RUN yarn build:web # ======================== # == SERVER BUILD STAGE == # ======================== -# Note: server-builder stage will be the same in both dockerfiles -FROM python:3.11-bookworm AS server-builder +FROM ghcr.io/astral-sh/uv:python3.11-bookworm-slim AS server-builder +SHELL ["/bin/bash", "-c"] WORKDIR /opt/dive/src -# https://cryptography.io/en/latest/installation/#debian-ubuntu -RUN apt-get update -RUN apt-get install -y build-essential libssl-dev libffi-dev python3-dev cargo npm libgl1 -# Recommended poetry install https://python-poetry.org/docs/master/#installation -RUN curl -sSL https://install.python-poetry.org | POETRY_VERSION=2.1.2 POETRY_HOME=/opt/dive/poetry python - -ENV PATH="/opt/dive/poetry/bin:$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" ] diff --git a/docker/girder_worker.Dockerfile b/docker/girder_worker.Dockerfile index 3f3d9c39..a6b6bfc5 100644 --- a/docker/girder_worker.Dockerfile +++ b/docker/girder_worker.Dockerfile @@ -1,41 +1,45 @@ # ======================== # == 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:$PATH" -# Create a virtual environment for the installation -RUN python -m venv --copies /opt/dive/local/venv -# Poetry needs this set to recognize it as ane existing environment +# Install build dependencies +RUN apt-get update && \ + apt-get install -y --no-install-recommends \ + build-essential \ + curl \ + git \ + pkg-config \ + libgomp1 && \ + apt-get clean && \ + rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* + +ENV UV_COMPILE_BYTECODE=1 UV_LINK_MODE=copy ENV VIRTUAL_ENV="/opt/dive/local/venv" +ENV UV_PROJECT_ENVIRONMENT=/opt/dive/local/venv ENV PATH="/opt/dive/local/venv/bin:$PATH" -# Copy only the lock and project files to optimize cache + +# Copy dependency files first for better caching COPY server/pyproject.toml /opt/dive/src/ -COPY .git/ /opt/dive/src/.git/ -# Use the system installation -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 -# RUN girder build - -# Copy full source code and install +COPY server/uv.lock /opt/dive/src/ + +# Install dependencies with CPU-only PyTorch for smaller size +RUN uv sync --frozen --no-install-project --no-dev --extra cpu + +# Copy source and install project COPY server/ /opt/dive/src/ -RUN poetry install --only main +RUN uv sync --frozen --no-dev --extra cpu + # ==================== # == FFMPEG FETCHER == # ==================== -FROM python:3.11-bookworm AS ffmpeg-builder +FROM ghcr.io/astral-sh/uv:python3.11-bookworm-slim AS ffmpeg-builder +RUN apt-get update +RUN apt-get install -y wget tar xz-utils RUN wget -O ffmpeg.tar.xz https://johnvansickle.com/ffmpeg/releases/ffmpeg-release-amd64-static.tar.xz RUN mkdir /tmp/ffextracted RUN tar -xvf ffmpeg.tar.xz -C /tmp/ffextracted --strip-components 1 @@ -43,30 +47,39 @@ RUN tar -xvf ffmpeg.tar.xz -C /tmp/ffextracted --strip-components 1 # ================= # == DIST WORKER == # ================= -FROM python:3.11-bookworm AS worker -# VIAME install at /opt/noaa/viame/ -# VIAME pipelines at /opt/noaa/viame/configs/pipelines/ +FROM ghcr.io/astral-sh/uv:python3.11-bookworm-slim AS server -RUN apt-get update -RUN apt-get install -y build-essential libssl-dev libffi-dev python3-dev cargo npm libgl1 +# 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/* -# install tini init system +# Install tini init system ENV TINI_VERSION=v0.19.0 ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /tini RUN chmod +x /tini -RUN useradd --create-home --uid 1099 --shell=/bin/bash dive -RUN install -g dive -o dive -d /tmp/SAM2 -# Setup the path of the incoming python installation +# Create user and directories +RUN useradd --create-home --uid 1099 --shell=/bin/bash dive && \ + install -g dive -o dive -d /tmp/SAM2 + +# Setup environment ENV PATH="/opt/dive/local/venv/bin:$PATH" -# Copy the built python installation +# Copy the built python installation and source COPY --chown=dive:dive --from=server-builder /opt/dive/local/venv/ /opt/dive/local/venv/ -# Copy the source code of the editable module COPY --chown=dive:dive --from=server-builder /opt/dive/src /opt/dive/src -# Copy ffmpeg + +# Copy ffmpeg binaries COPY --from=ffmpeg-builder /tmp/ffextracted/ffmpeg /tmp/ffextracted/ffprobe /opt/dive/local/venv/bin/ -# Copy provision scripts + +# Copy uv binary for runtime use +COPY --from=ghcr.io/astral-sh/uv:latest /uv /usr/local/bin/uv + +# Copy startup script COPY --chown=dive:dive docker/entrypoint_worker.sh / ENTRYPOINT ["/tini", "--"] diff --git a/docker/girder_worker_gpu.Dockerfile b/docker/girder_worker_gpu.Dockerfile index 4cc8f87b..efc5ea1f 100644 --- a/docker/girder_worker_gpu.Dockerfile +++ b/docker/girder_worker_gpu.Dockerfile @@ -1,101 +1,78 @@ -# ======================== -# == SERVER BUILD STAGE == -# ======================== - -FROM nvidia/cuda:12.6.0-devel-ubuntu20.04 AS server-builder - -# ---------------------------- -# Environment Configuration -# ---------------------------- -ENV NVIDIA_VISIBLE_DEVICES=${NVIDIA_VISIBLE_DEVICES:-all} -ENV NVIDIA_DRIVER_CAPABILITIES=${NVIDIA_DRIVER_CAPABILITIES:+$NVIDIA_DRIVER_CAPABILITIES,}graphics -ENV PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:$PATH -ENV CUDA_HOME="/usr/local/cuda" -ENV TORCH_CUDA_ARCH_LIST="6.0 6.1 7.0 7.5 8.0 8.6+PTX 8.9" -ENV DEBIAN_FRONTEND=noninteractive -ENV TZ=Etc/UTC + +# ==================== +# == FFMPEG FETCHER == +# ==================== +FROM ubuntu:22.04 AS ffmpeg-builder +RUN apt-get update && \ + apt-get install -y wget tar xz-utils && \ + rm -rf /var/lib/apt/lists/* +RUN wget -O ffmpeg.tar.xz https://johnvansickle.com/ffmpeg/releases/ffmpeg-release-amd64-static.tar.xz +RUN mkdir /tmp/ffextracted +RUN tar -xvf ffmpeg.tar.xz -C /tmp/ffextracted --strip-components 1 + + +# ================= +# == DIST WORKER == +# ================= +FROM nvidia/cuda:12.8.1-cudnn-runtime-ubuntu24.04 AS server + +# Install only runtime dependencies +RUN apt-get update && \ + apt-get install -y --no-install-recommends \ + adduser \ + passwd \ + gosu \ + libgomp1 \ + ca-certificates && \ + rm -rf /var/lib/apt/lists/* + +# Install tini init system ENV TINI_VERSION=v0.19.0 +ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /tini +RUN chmod +x /tini -# ---------------------------- -# System Dependencies & Python 3.11 -# ---------------------------- -RUN apt-get update && apt-get install -y \ - software-properties-common \ - build-essential \ - libssl-dev \ - libffi-dev \ - libsm6 \ - libxext6 \ - libgl1 \ - curl \ - wget \ - git && \ - wget -O ffmpeg.tar.xz https://johnvansickle.com/ffmpeg/releases/ffmpeg-release-amd64-static.tar.xz && \ - mkdir /tmp/ffextracted && \ - tar -xvf ffmpeg.tar.xz -C /tmp/ffextracted --strip-components=1 && \ - add-apt-repository ppa:deadsnakes/ppa && \ - apt-get update && apt-get install -y \ - python3.11 \ - python3.11-venv \ - python3.11-dev \ - python3.11-tk && \ - update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.11 1 && \ - curl -sS https://bootstrap.pypa.io/get-pip.py | python3.11 - && \ - ln -s /usr/bin/python3.11 /usr/bin/python && \ - apt-get clean && rm -rf /var/lib/apt/lists/* ffmpeg.tar.xz - -# ---------------------------- -# Working Directory & Entrypoint -# ---------------------------- +# Create user and directories +RUN useradd --create-home --uid 1099 --shell=/bin/bash dive && \ + install -g dive -o dive -d /tmp/SAM2 +# Setup environment WORKDIR /opt/dive/src -ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /tini -COPY docker/entrypoint_worker_gpu.sh /entrypoint_worker_gpu.sh -RUN chmod +x /tini /entrypoint_worker_gpu.sh -# ---------------------------- -# Poetry Installation & Python venv -# ---------------------------- -RUN curl -sSL https://install.python-poetry.org | POETRY_VERSION=2.1.2 POETRY_HOME=/opt/dive/poetry python3.11 - -ENV PATH="/opt/dive/poetry/bin:$PATH" +COPY --from=ghcr.io/astral-sh/uv:latest /uv /usr/local/bin/uv +RUN PATH="/usr/local/bin:$PATH" +# Copy the built python installation and source + +# Copy ffmpeg binaries +COPY --from=ffmpeg-builder /tmp/ffextracted/ffmpeg /tmp/ffextracted/ffprobe /opt/dive/local/venv/bin/ -RUN python3.11 -m venv --copies /opt/dive/local/venv +ENV UV_COMPILE_BYTECODE=1 UV_LINK_MODE=copy ENV VIRTUAL_ENV="/opt/dive/local/venv" -ENV PATH="$VIRTUAL_ENV/bin:$PATH" +ENV UV_PROJECT_ENVIRONMENT=/opt/dive/local/venv +ENV UV_VENV_CLEAR=1 +ENV PATH="/opt/dive/local/venv/bin:$PATH" -# ---------------------------- -# Dependency Installation -# ---------------------------- -COPY server/pyproject.toml /opt/dive/src/ -COPY .git/ /opt/dive/src/.git/ -RUN poetry env use system && \ - poetry config virtualenvs.create false && \ - poetry install --no-root -# ---------------------------- -# Application Source Code -# ---------------------------- -COPY server/ /opt/dive/src/ -# Create user & assign permissions +# Copy startup script +RUN uv python install 3.11 +RUN uv python pin 3.11 +COPY server/pyproject.toml /opt/dive/src/ +COPY server/uv.lock /opt/dive/src/ +# Create virtual environment +RUN uv venv /opt/dive/local/venv +# Install dependencies with CUDA-enabled PyTorch +RUN uv sync --frozen --no-install-project --no-dev --extra cu128 -# Final install in user context -RUN poetry install --only main -# ---------------------------- -# FFmpeg Binary into venv -# ---------------------------- -RUN cp /tmp/ffextracted/ffmpeg /opt/dive/local/venv/bin/ffmpeg && \ - cp /tmp/ffextracted/ffprobe /opt/dive/local/venv/bin/ffprobe +# Copy source and install project +COPY server/ /opt/dive/src/ +# Install dependencies with CUDA-enabled PyTorch +RUN uv sync --frozen --no-dev --extra cu128 +RUN chmod -R a+rX /opt/dive/local/venv -RUN useradd --create-home --uid 1099 --shell=/bin/bash dive && \ - chown -R dive /opt/dive -RUN install -g dive -o dive -d /tmp/SAM2 -USER dive +COPY --chown=dive:dive docker/entrypoint_worker_gpu.sh / +RUN chmod -R a+rX /entrypoint_worker_gpu.sh -# ---------------------------- -# Entrypoint & CMD -# ---------------------------- ENTRYPOINT ["/tini", "--"] CMD ["/entrypoint_worker_gpu.sh"] diff --git a/server/README.md b/server/README.md index e3e29823..2137739a 100644 --- a/server/README.md +++ b/server/README.md @@ -15,11 +15,11 @@ Set up your system as described in the [Basic Deployment](https://kitware.github In development, the server and client are run in separate processes. In production, the client is built and bundled as static files into the server image. -This python project uses [Poetry](https://python-poetry.org/). +This python project uses [uv](https://astral.sh/uv) for dependency management. ```bash # Optional, for intellisense or whatever. Not required for docker-compose -poetry install +uv sync ``` ### Running in development with docker @@ -54,45 +54,45 @@ To work on the Vue client, see development instructions in `../client`. ## Unit Testing and Static Checks -Automation is done with [Tox](https://pypi.org/project/tox/), installed by poetry above. +Automation is done with [Tox](https://pypi.org/project/tox/) with tox-uv plugin. ```bash # run only lint checks -poetry run tox -e check +tox -e lint # run only type checks -poetry run tox -e type +tox -e type # run only unit tests -poetry run tox -e testunit +tox -e testunit # run only a particular test -poetry run tox -e testunit -- -k test_image_sort +tox -e testunit -- -k test_image_sort -# run all three tests above -poetry run tox +# run all tests +tox # automatically format all code to comply to linting checks -poetry run tox -e format +tox -e format # run mkdocs and serve the documentation page -poetry run tox -e docs +tox -e docs # creates docs in the /site folder for eventual deployment -poetry run tox -e builddocs +tox -e builddocs ``` ## Debug utils and command line tools ``` bash -# Requires a local poetry installation -poetry install +# Requires a local uv installation +uv sync # show options -poetry run dive --help +uv run dive --help # build the standalone executable into ./dist -poetry run tox -e buildcli +tox -e buildcli ``` ## Metadata properties diff --git a/server/dive_server/sam_model_downloader.py b/server/dive_server/sam_model_downloader.py new file mode 100644 index 00000000..4b0b1193 --- /dev/null +++ b/server/dive_server/sam_model_downloader.py @@ -0,0 +1,103 @@ +""" +SAM2 Model Downloader - Web Server Component + +This module handles downloading SAM2 models without requiring SAM2 to be installed. +It only downloads the model files and updates configuration - no SAM2 inference. +""" + +import math +import os +from pathlib import Path +from urllib import request +from urllib.parse import urlparse + +from girder_client import GirderClient +from girder_worker.app import app +from girder_worker.task import Task +from girder_worker.utils import JobManager, JobStatus + +from dive_utils import constants + + +def get_filename_from_url(url): + """Extracts the filename from a URL.""" + parsed_url = urlparse(url) + return os.path.basename(parsed_url.path) + + +@app.task(bind=True, acks_late=True, ignore_result=True) +def download_sam_models_web( + self: Task, + sam2_config=constants.DEFAULT_SAM2_FILES, + force: bool = False, +): + """Download and organize SAM models - Web Server Version""" + manager: JobManager = self.job_manager + if self.check_canceled(): + manager.updateStatus(JobStatus.CANCELED) + return + + gc: GirderClient = self.girder_client + Path(constants.SAM2_MODEL_PATH).mkdir(parents=True, exist_ok=True) + + def progress_report_hook_factory(filename): + last_percent = {'value': -1} + + def reporthook(block_num, block_size, total_size): + downloaded = block_num * block_size + if total_size > 0: + percent = math.floor(downloaded * 100 / total_size) + if percent != last_percent['value']: + last_percent['value'] = percent + manager.write(f"{filename}: {percent}% downloaded\n") + else: + manager.write(f"{filename}: downloading... {downloaded} bytes so far\n") + + return reporthook + + models = [] + for model_name, files in sam2_config.items(): + model_dir = Path(constants.SAM2_MODEL_PATH) / model_name + models.append(model_name) + model_dir.mkdir(parents=True, exist_ok=True) + + if self.check_canceled(): + manager.updateStatus(JobStatus.CANCELED) + return + + # Download the checkpoint + checkpoint_url = files['checkpoint'] + checkpoint_dest = model_dir / Path(checkpoint_url).name + if not checkpoint_dest.exists() or force: + manager.write(f"Downloading checkpoint for {model_name} - {checkpoint_url}\n") + request.urlretrieve( + checkpoint_url, + checkpoint_dest, + reporthook=progress_report_hook_factory(checkpoint_dest.name), + ) + + # Download the config + config_url = files['config'] + config_dest = model_dir / Path(config_url).name + if not config_dest.exists() or force: + manager.write(f"Downloading config for {model_name} - {config_url}.\n") + request.urlretrieve( + config_url, config_dest, reporthook=progress_report_hook_factory(config_dest.name) + ) + + if self.check_canceled(): + manager.updateStatus(JobStatus.CANCELED) + return + + # Update configuration + base_dive_config = gc.get('dive_configuration/dive_config') + manager.write(f'{base_dive_config}\n') + sam2_base_config = base_dive_config.get('SAM2Config', {'queues': ['celery'], 'models': []}) + dive_config_queue = base_dive_config.get('celeryQueue', False) + if dive_config_queue and dive_config_queue not in sam2_base_config.get('queues', []): + sam2_base_config['queues'].insert(0, dive_config_queue) + + sam2_base_config['models'] = models + base_dive_config["SAM2Config"] = sam2_base_config + manager.write(f'{base_dive_config}\n') + gc.put('dive_configuration/dive_config', json=base_dive_config) diff --git a/server/dive_server/views_configuration.py b/server/dive_server/views_configuration.py index 95a23c02..fec132e7 100644 --- a/server/dive_server/views_configuration.py +++ b/server/dive_server/views_configuration.py @@ -7,6 +7,7 @@ from girder_jobs.models.job import Job from dive_server import crud +# Import Celery app for task scheduling from dive_tasks.sam_tasks import download_sam_models from dive_utils import constants, models @@ -100,6 +101,7 @@ def update_sam2_configs(self, data, force): } base_config['celeryQueue'] = base_queue Setting().set(constants.DIVE_CONFIG, base_config) + newjob = download_sam_models.apply_async( queue=base_queue, kwargs=dict( diff --git a/server/dive_server/views_rpc.py b/server/dive_server/views_rpc.py index e4154ffc..7bdb3da2 100644 --- a/server/dive_server/views_rpc.py +++ b/server/dive_server/views_rpc.py @@ -10,6 +10,7 @@ from girder.models.token import Token from girder_jobs.models.job import Job +# Import Celery app for task scheduling from dive_tasks.sam_tasks import run_sam2_inference from dive_utils import asbool, fromMeta from dive_utils.constants import ( @@ -340,6 +341,8 @@ def sam2_mask_track( self, datasetId, queue, trackId, frameId, frameCount, SAMModel, batchSize, notifyPercent ): token = Token().createToken(user=self.getCurrentUser(), days=1) + + # Schedule SAM2 task using module path - no import needed newjob = run_sam2_inference.apply_async( queue=queue, kwargs=dict( diff --git a/server/dive_tasks/__main__.py b/server/dive_tasks/__main__.py index 5bc7f499..91f0bcad 100644 --- a/server/dive_tasks/__main__.py +++ b/server/dive_tasks/__main__.py @@ -2,6 +2,8 @@ from girder_worker.app import app +# Import tasks to ensure they are registered +from dive_tasks import tasks # noqa: F401 def main(): """ @@ -9,7 +11,8 @@ def main(): is initialized, we have to override the module entrypoint and force our config to run last """ - app.worker_main(argv=['worker'] + sys.argv[1:] if 'worker' not in sys.argv else sys.argv) + argv = ['worker'] + sys.argv[1:] if 'worker' not in sys.argv else sys.argv + app.worker_main(argv=argv) if __name__ == '__main__': diff --git a/server/dive_tasks/sam_tasks.py b/server/dive_tasks/sam_tasks.py index f7fa8ed3..e3d61dce 100644 --- a/server/dive_tasks/sam_tasks.py +++ b/server/dive_tasks/sam_tasks.py @@ -9,7 +9,6 @@ from urllib.parse import urlparse from PIL import Image -import cv2 from girder_client import GirderClient from girder_worker.app import app from girder_worker.task import Task @@ -331,7 +330,10 @@ def save_and_record_mask( rgba = np.zeros((h, w, 4), dtype=np.uint8) rgba[..., 0:3] = 255 rgba[..., 3] = alpha - 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"] -license = "Apache 2.0" -include = ["**/*.mako"] +authors = [{name = "Kitware, Inc.", email = "viame-web@kitware.com"}] +license = {text = "Apache 2.0"} readme = "README.md" keywords = ["DIVE", "VIAME", "Annotation", "Computer Vision", "Marine"] +default-optional-dependency-keys = [ + "cpu", +] classifiers = [ "License :: OSI Approved :: Apache Software License", "Natural Language :: English", @@ -39,63 +41,97 @@ classifiers = [ "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.11", ] +requires-python = ">=3.10.0,<=3.12" packages = [ { include = "dive_server" }, { include = "dive_tasks" }, - { include = "dive_utils" }, ] +dependencies = [ + "cheroot>=8.4.5", + "click>=8.1.3", + "girder>=3.2.8", + "girder_jobs>=3.2.8", + "girder_client>=3.2.8", + "girder_worker>=0.10.3", + "girder_worker_utils>=0.9.1", + "girder_large_image>=1.30.2", + "pydantic==1.10.13", + "pyrabbit2==1.0.7", + "typing-extensions>=4.2.0", + "GPUtil>=1.4.0", + "requests<2.33.0", + "urllib3<2.6", + "girder-slicer-cli-web>=1.3.5", + "pycocotools>=2.0.8", + "pillow>=11.3.0", + "numpy>=1.21.4", + "pandas>=2.3.2", +] + +[project.optional-dependencies] +dev = [ + "tox>=3.25.0", +] +cpu = [ + "torch>=2.7.1", + "triton>=3.4.0", + "sam2>=1.1.0", +] +cu128 = [ + "torch>=2.7.1", + "sam2>=1.1.0", +] + -[tool.poetry.dependencies] -python = ">=3.11.0,<=3.12" -cheroot = ">=8.4.5" -click = "^8.1.3" -girder = ">=3.2.11" -girder_jobs = ">=3.2.11" -girder_client = ">=3.2.11" -girder_worker = ">=0.10.3" -girder_worker_utils = ">=0.9.1" -girder_large_image = ">=1.30.2" -pydantic = "1.10.13" -pyrabbit2 = "1.0.7" -typing-extensions = "^4.2.0" -GPUtil = "^1.4.0" -requests = "<2.33.0" -urllib3 = "<2.6" -poetry-dynamic-versioning = {extras = ["plugin"], version = "^0.21.4"} -girder-slicer-cli-web = "^1.3.5" -pycocotools = "^2.0.8" -pillow = "^11.3.0" -numpy = "^2.3.0" -torch = "^2.8.0" -sam2 = "^1.1.0" -opencv-python-headless = "^4.11.0.86" -pandas = "^2.3.2" - - -[tool.poetry.group.dev.dependencies] -numpy = "^2.3.0" -opencv-python = "^4.5.5" -tox = "^3.25.0" - -[tool.poetry.scripts] +[project.scripts] diveutils = "scripts.entrypoint_dev:cli" dive = "scripts.entrypoint_main:cli" -[tool.poetry.plugins."girder.plugin"] +[project.entry-points."girder.plugin"] dive_server = "dive_server:GirderPlugin" - -[tool.poetry.plugins."girder_worker_plugins"] +[project.entry-points."girder_worker_plugins"] dive_tasks = "dive_tasks:DIVEPlugin" [build-system] -requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning>=1.0.0,<2.0.0"] -build-backend = "poetry_dynamic_versioning.backend" +requires = ["hatchling", "uv-dynamic-versioning"] +build-backend = "hatchling.build" + +[tool.hatch.build.targets.wheel] +packages = ["dive_server", "dive_tasks", "dive_utils"] +include = ["**/*.mako"] + +[tool.hatch.build.targets.sdist] +include = ["dive_server/", "dive_tasks/", "dive_utils/", "**/*.mako", "README.md"] + +[tool.hatch.version] +source = "uv-dynamic-versioning" + + +[tool.uv] +conflicts = [ + [ + { extra = "cpu" }, + { extra = "cu128" }, + ], +] + + +[tool.uv.sources] +torch = [ + { index = "pytorch-cpu", extra = "cpu" }, + { index = "pytorch-cu128", extra = "cu128" }, +] + +[[tool.uv.index]] +name = "pytorch-cpu" +url = "https://download.pytorch.org/whl/cpu" +explicit = true -[tool.poetry-dynamic-versioning] -enable = true -vcs = "any" -metadata = true +[[tool.uv.index]] +name = "pytorch-cu128" +url = "https://download.pytorch.org/whl/cu128" +explicit = true -[tool.poetry-dynamic-versioning.substitution] -files = ["dive_server/__init__.py", "dive_tasks/__init__.py"] +[tool.uv-dynamic-versioning] +fallback-version = "0.0.0" diff --git a/server/tox.ini b/server/tox.ini index 1799d496..64da1b94 100644 --- a/server/tox.ini +++ b/server/tox.ini @@ -1,9 +1,11 @@ [tox] -envlist = +envlist = lint type testunit isolated_build = True +requires = + tox-uv>=1.0.0 [testenv:lint] skipsdist = true @@ -48,13 +50,13 @@ commands = mypy 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