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Merge pull request #19 from kushalbakshi/codespace
Add DevContainer and tutorial + fix `Segmentation` make + update docs
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| Original file line number | Diff line number | Diff line change |
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| FROM python:3.9-slim@sha256:5f0192a4f58a6ce99f732fe05e3b3d00f12ae62e183886bca3ebe3d202686c7f | ||
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| ENV PATH /usr/local/bin:$PATH | ||
| ENV PYTHON_VERSION 3.9.17 | ||
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| RUN \ | ||
| adduser --system --disabled-password --shell /bin/bash vscode && \ | ||
| # install docker | ||
| apt-get update && \ | ||
| apt-get install ca-certificates curl gnupg lsb-release -y && \ | ||
| mkdir -m 0755 -p /etc/apt/keyrings && \ | ||
| curl -fsSL https://download.docker.com/linux/debian/gpg | gpg --dearmor -o /etc/apt/keyrings/docker.gpg && \ | ||
| echo "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/debian $(lsb_release -cs) stable" | tee /etc/apt/sources.list.d/docker.list > /dev/null && \ | ||
| apt-get update && \ | ||
| apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin -y && \ | ||
| usermod -aG docker vscode && \ | ||
| apt-get clean | ||
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| RUN \ | ||
| # dev setup | ||
| apt update && \ | ||
| apt-get install sudo git bash-completion graphviz default-mysql-client s3fs procps -y && \ | ||
| usermod -aG sudo vscode && \ | ||
| echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers && \ | ||
| pip install --no-cache-dir --upgrade black pip nbconvert && \ | ||
| echo '. /etc/bash_completion' >> /home/vscode/.bashrc && \ | ||
| echo 'export PS1="\[\e[32;1m\]\u\[\e[m\]@\[\e[34;1m\]\H\[\e[m\]:\[\e[33;1m\]\w\[\e[m\]$ "' >> /home/vscode/.bashrc && \ | ||
| apt-get clean | ||
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| COPY ./ /tmp/element-zstack/ | ||
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| RUN \ | ||
| # pipeline dependencies | ||
| apt-get install gcc g++ ffmpeg libsm6 libxext6 -y && \ | ||
| pip install --no-cache-dir -e /tmp/element-zstack[elements,tests] && \ | ||
| # clean up | ||
| rm -rf /tmp/element-zstack && \ | ||
| apt-get clean | ||
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| ENV DJ_HOST fakeservices.datajoint.io | ||
| ENV DJ_USER root | ||
| ENV DJ_PASS simple | ||
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| ENV VOLUME_ROOT_DATA_DIR /workspaces/element-zstack/example_data | ||
| ENV DATABASE_PREFIX neuro_ | ||
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| USER vscode | ||
| CMD bash -c "sudo rm /var/run/docker.pid; sudo dockerd" |
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| { | ||
| "name": "Environment + Data", | ||
| "dockerComposeFile": "docker-compose.yaml", | ||
| "service": "app", | ||
| "workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}", | ||
| "remoteEnv": { | ||
| "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}" | ||
| }, | ||
| "onCreateCommand": "mkdir -p ${VOLUME_ROOT_DATA_DIR} && pip install -e .", | ||
| "postStartCommand": "docker volume prune -f && s3fs ${DJ_PUBLIC_S3_LOCATION} ${VOLUME_ROOT_DATA_DIR} -o nonempty,multipart_size=530,endpoint=us-east-1,url=http://s3.amazonaws.com,public_bucket=1", | ||
| "hostRequirements": { | ||
| "cpus": 4, | ||
| "memory": "8gb", | ||
| "storage": "32gb" | ||
| }, | ||
| "forwardPorts": [ | ||
| 3306 | ||
| ], | ||
| "customizations": { | ||
| "settings": { | ||
| "python.pythonPath": "/usr/local/bin/python" | ||
| }, | ||
| "vscode": { | ||
| "extensions": [ | ||
| "[email protected]", | ||
| "[email protected]" | ||
| ] | ||
| } | ||
| } | ||
| } |
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| version: "3" | ||
| services: | ||
| app: | ||
| cpus: 4 | ||
| mem_limit: 8g | ||
| build: | ||
| context: .. | ||
| dockerfile: ./.devcontainer/Dockerfile | ||
| # image: datajoint/element_array_ephys:latest | ||
| extra_hosts: | ||
| - fakeservices.datajoint.io:127.0.0.1 | ||
| environment: | ||
| - DJ_PUBLIC_S3_LOCATION=djhub.vathes.datapub.elements:/workflow-zstack-v1 | ||
| devices: | ||
| - /dev/fuse | ||
| cap_add: | ||
| - SYS_ADMIN | ||
| security_opt: | ||
| - apparmor:unconfined | ||
| volumes: | ||
| - ..:/workspaces/element-zstack:cached | ||
| - docker_data:/var/lib/docker # persist docker images | ||
| privileged: true # only because of dind | ||
| volumes: | ||
| docker_data: |
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