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Merge pull request #91 from datajoint/dev
Update tutorial and codespace
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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-deeplabcut/ | ||
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| RUN \ | ||
| # pipeline dependencies | ||
| apt-get update && \ | ||
| apt-get install -y gcc ffmpeg graphviz && \ | ||
| pip install --no-cache-dir -e /tmp/element-deeplabcut[elements,dlc_default] && \ | ||
| # clean up | ||
| rm -rf /tmp/element-deeplabcut/ && \ | ||
| 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 DATA_MOUNTPOINT /workspaces/element-deeplabcut/example_data | ||
| ENV DLC_ROOT_DATA_DIR $DATA_MOUNTPOINT/inbox | ||
| ENV DLC_PROCESSED_DATA_DIR $DATA_MOUNTPOINT/outbox | ||
| ENV DATABASE_PREFIX neuro_ | ||
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| USER vscode | ||
| CMD bash -c "sudo rm /var/run/docker.pid; sudo dockerd" | ||
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| ENV LD_LIBRARY_PATH="/lib:/opt/conda/lib" |
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| { | ||
| "name": "Environment + Data", | ||
| "dockerComposeFile": "docker-compose.yaml", | ||
| "service": "app", | ||
| "workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}", | ||
| "remoteEnv": { | ||
| "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}" | ||
| }, | ||
| "onCreateCommand": "mkdir -p ${DATA_MOUNTPOINT} && pip install -e .", | ||
| "postStartCommand": "docker volume prune -f && s3fs ${DJ_PUBLIC_S3_LOCATION} ${DATA_MOUNTPOINT} -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_deeplabcut:latest | ||
| extra_hosts: | ||
| - fakeservices.datajoint.io:127.0.0.1 | ||
| environment: | ||
| - DJ_PUBLIC_S3_LOCATION=djhub.vathes.datapub.elements:/workflow-dlc-data/v2 | ||
| devices: | ||
| - /dev/fuse | ||
| cap_add: | ||
| - SYS_ADMIN | ||
| security_opt: | ||
| - apparmor:unconfined | ||
| volumes: | ||
| - ..:/workspaces/element-deeplabcut:cached | ||
| - docker_data:/var/lib/docker # persist docker images | ||
| privileged: true # only because of dind | ||
| volumes: | ||
| docker_data: |
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| blank_issues_enabled: false | ||
| contact_links: | ||
| - name: DataJoint Contribution Guideline | ||
| url: https://docs.datajoint.org/python/community/02-Contribute.html | ||
| url: https://datajoint.com/docs/about/contribute/ | ||
| about: Please make sure to review the DataJoint Contribution Guidelines |
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| default_stages: [commit, push] | ||
| exclude: (^.github/|^docs/|^images/|^notebooks/|^tests/) | ||
| # Current tests/__init__ violates many flake8. Excluding pending change to conftest | ||
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| repos: | ||
| - repo: https://github.com/pre-commit/pre-commit-hooks | ||
| rev: v4.4.0 | ||
| hooks: | ||
| - id: trailing-whitespace | ||
| - id: end-of-file-fixer | ||
| - id: check-yaml | ||
| - id: check-added-large-files # prevent giant files from being committed | ||
| - id: requirements-txt-fixer | ||
| - id: mixed-line-ending | ||
| args: ["--fix=lf"] | ||
| description: Forces to replace line ending by the UNIX 'lf' character. | ||
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| # black | ||
| - repo: https://github.com/psf/black | ||
| rev: 22.12.0 | ||
| hooks: | ||
| - id: black | ||
| - id: black-jupyter | ||
| args: | ||
| - --line-length=88 | ||
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| # isort | ||
| - repo: https://github.com/pycqa/isort | ||
| rev: 5.12.0 | ||
| hooks: | ||
| - id: isort | ||
| args: ["--profile", "black"] | ||
| description: Sorts imports in an alphabetical order | ||
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| # flake8 | ||
| - repo: https://github.com/pycqa/flake8 | ||
| rev: 4.0.1 | ||
| hooks: | ||
| - id: flake8 | ||
| args: # arguments to configure flake8 | ||
| # making isort line length compatible with black | ||
| - "--max-line-length=88" | ||
| - "--max-complexity=18" | ||
| - "--select=B,C,E,F,W,T4,B9" | ||
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| # these are errors that will be ignored by flake8 | ||
| # https://www.flake8rules.com/rules/{code}.html | ||
| - "--ignore=E203,E501,W503,W605,E402" | ||
| # E203 - Colons should not have any space before them. | ||
| # Needed for list indexing | ||
| # E501 - Line lengths are recommended to be no greater than 79 characters. | ||
| # Needed as we conform to 88 | ||
| # W503 - Line breaks should occur after the binary operator. | ||
| # Needed because not compatible with black | ||
| # W605 - a backslash-character pair that is not a valid escape sequence now | ||
| # generates a DeprecationWarning. This will eventually become a SyntaxError. | ||
| # Needed because we use \d as an escape sequence | ||
| # E402 - Place module level import at the top. | ||
| # Needed to prevent circular import error |
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