Merge pull request #337 from girder/deepssm

Deepssm
MedVIC-Lab · Apr 9, 2024 · 7fcf40c · 7fcf40c
2 parents 4313760 + b71902a
commit 7fcf40c
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -16,13 +16,13 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: "3.8"
-      - name: Install tox
-        run: |
-          pip install --upgrade pip
-          pip install tox
 
       - name: Build images
         run: docker-compose -f "docker-compose.yml" build
+      - name: Install Tox
+        run: |
+          docker-compose run --rm django pip install --upgrade pip
+          docker-compose run --rm django pip install tox
       - name: Start services
         run: docker-compose -f "docker-compose.yml" up -d
 
@@ -32,7 +32,7 @@ jobs:
           verbose: true
 
       - name: Run tox
-        run: tox
+        run: docker-compose run --rm django tox
         env:
           DJANGO_DATABASE_URL: postgres://postgres:postgres@localhost:5432/django
           DJANGO_MINIO_STORAGE_ENDPOINT: localhost:9000

diff --git a/dev/django.Dockerfile b/dev/django.Dockerfile
@@ -3,34 +3,56 @@ FROM python:3.8-slim
 # * psycopg2
 RUN apt-get update && \
     apt-get install --no-install-recommends --yes \
-    libpq-dev gcc libc6-dev curl unzip \
+    git-all libpq-dev gcc libc6-dev curl unzip \
     libgl1-mesa-glx libxt6 libglib2.0-0 \
     libqt5core5a \
+    libxrender1 \
     && \
     rm -rf /var/lib/apt/lists/*
 
 ENV PYTHONDONTWRITEBYTECODE 1
 ENV PYTHONUNBUFFERED 1
 
+# install_shapeworks.sh for DeepSSM python api. This must be run from within a conda environment
+# install conda
+ENV PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ENV LDFLAGS=-L/opt/conda/lib
+RUN curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o /tmp/Miniconda3-latest-Linux-x86_64.sh \
+    && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \
+    && ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
+    && conda update -n base -c defaults conda \
+    && conda install pip \
+    && echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc
+
 # Only copy the setup.py, it will still force all install_requires to be installed,
 # but find_packages() will find nothing (which is fine). When Docker Compose mounts the real source
 # over top of this directory, the .egg-link in site-packages resolves to the mounted directory
 # and all package modules are importable.
-COPY ./setup.py /opt/django-project/setup.py
-COPY ./swcc/setup.py /opt/django-project/swcc/setup.py
-RUN pip install -U pip && \
-    pip install --editable /opt/django-project[dev] && \
-    pip install --editable /opt/django-project/swcc
 
 RUN export url=$(curl -s https://api.github.com/repos/SCIInstitute/ShapeWorks/releases | grep -o "http.*dev-linux.*.gz"); \
     curl -L -o /tmp/shapeworks.tgz $url
 RUN mkdir /opt/shapeworks && \
     tar -zxvf /tmp/shapeworks.tgz -C /opt/shapeworks --strip-components 1 && \
     rm /tmp/shapeworks.tgz
+
+COPY ./setup.py /opt/django-project/setup.py
+COPY ./swcc/setup.py /opt/django-project/swcc/setup.py
+
+# Run install_shapeworks.sh
+SHELL ["conda", "run", "/bin/bash", "-c"]
+RUN cd /opt/shapeworks ; ls ; source install_shapeworks.sh ; conda clean -t -y
+SHELL ["conda", "run", "-n", "shapeworks", "bin/bash", "-c"]
+RUN echo "conda activate shapeworks" >> ~/.bashrc
+
+RUN pip install -U pip && \
+    pip install --editable /opt/django-project[dev] && \
+    pip install --editable /opt/django-project/swcc
+
 ENV PATH $PATH:/opt/shapeworks/bin
 ENV LD_LIBRARY_PATH $LD_LIBRARY_PATH:/opt/shapeworks/lib
 
 RUN pip install awscli
 
 # Use a directory name which will never be an import name, as isort considers this as first-party.
 WORKDIR /opt/django-project
+ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "shapeworks"]
diff --git a/docker-compose.override.yml b/docker-compose.override.yml
@@ -4,7 +4,11 @@ services:
     build:
       context: .
       dockerfile: ./dev/django.Dockerfile
-    command: [ "./manage.py", "runserver", "0.0.0.0:8000" ]
+    command: [
+      "./manage.py", 
+      "runserver", 
+      "0.0.0.0:8000"
+    ]
     # Log printing via Rich is enhanced by a TTY
     tty: true
     env_file: ./dev/.env.docker-compose
@@ -45,22 +49,45 @@ services:
       - rabbitmq
       - minio
 
-  celery-beat:
+  celery-gpu:
     build:
       context: .
       dockerfile: ./dev/django.Dockerfile
-    command: [ "celery", "--app", "shapeworks_cloud.celery", "beat" ]
+    command:
+      [
+        "celery",
+        "--app",
+        "shapeworks_cloud.celery",
+        "worker",
+        "-Q",
+        "gpu",
+        "-n=gpu",
+        "-P",
+        "threads",
+        "--loglevel",
+        "INFO",
+        "--without-heartbeat"
+      ]
+    # Docker Compose does not set the TTY width, which causes Celery errors
     tty: false
     env_file: ./dev/.env.celery.docker-compose
     volumes:
       - .:/opt/django-project
+    # Use host mode so that celery can use the localhost:8000 API in dev deployments
     network_mode: host
+    shm_size: 8gb
     depends_on:
-      - celery
+      - postgres
+      - rabbitmq
+      - minio
 
   yarn:
     image: node:17
-    command: [ "/bin/bash", "-c", "yarn install && yarn serve" ]
+    command: [ 
+      "/bin/bash",
+      "-c",
+      "yarn install && yarn serve"
+    ]
     env_file: ./dev/yarn.env
     environment:
       - NODE_OPTIONS=--openssl-legacy-provider