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kushalbakshikushalbakshi
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First commit for codespace compatability
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‎.devcontainer/Dockerfile‎

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FROM python:3.9-slim@sha256:5f0192a4f58a6ce99f732fe05e3b3d00f12ae62e183886bca3ebe3d202686c7f
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ENV PATH /usr/local/bin:$PATH
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ENV PYTHON_VERSION 3.9.17
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RUN \
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adduser --system --disabled-password --shell /bin/bash vscode && \
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# install docker
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apt-get update && \
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apt-get install ca-certificates curl gnupg lsb-release -y && \
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mkdir -m 0755 -p /etc/apt/keyrings && \
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curl -fsSL https://download.docker.com/linux/debian/gpg | gpg --dearmor -o /etc/apt/keyrings/docker.gpg && \
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echo "deb [arch=$(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 && \
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apt-get update && \
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apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin -y && \
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usermod -aG docker vscode && \
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apt-get clean
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RUN \
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# dev setup
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apt update && \
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apt-get install sudo git bash-completion graphviz default-mysql-client s3fs procps -y && \
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usermod -aG sudo vscode && \
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echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers && \
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pip install --no-cache-dir --upgrade black pip nbconvert && \
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echo '. /etc/bash_completion' >> /home/vscode/.bashrc && \
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echo 'export PS1="\[\e[32;1m\]\u\[\e[m\]@\[\e[34;1m\]\H\[\e[m\]:\[\e[33;1m\]\w\[\e[m\]$ "' >> /home/vscode/.bashrc && \
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apt-get clean
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COPY ./ /tmp/element-array-ephys/
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RUN \
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# pipeline dependencies
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apt-get install gcc g++ ffmpeg libsm6 libxext6 -y && \
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pip install --no-cache-dir -e /tmp/element-array-ephys[elements,tests] && \
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# clean up
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rm -rf /tmp/element-array-ephys && \
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apt-get clean
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ENV DJ_HOST fakeservices.datajoint.io
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ENV DJ_USER root
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ENV DJ_PASS simple
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ENV IMAGING_ROOT_DATA_DIR /workspaces/element-array-ephys/example_data
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ENV DATABASE_PREFIX neuro_
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USER vscode
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CMD bash -c "sudo rm /var/run/docker.pid; sudo dockerd"

‎.devcontainer/devcontainer.json‎

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{
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"name": "Environment + Data",
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"dockerComposeFile": "docker-compose.yaml",
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"service": "app",
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"workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}",
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"remoteEnv": {
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"LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
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},
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"onCreateCommand": "mkdir -p ${EPHYS_ROOT_DATA_DIR} && pip install -e .",
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"postStartCommand": "docker volume prune -f && s3fs ${DJ_PUBLIC_S3_LOCATION} ${EPHYS_ROOT_DATA_DIR} -o nonempty,multipart_size=530,endpoint=us-east-1,url=http://s3.amazonaws.com,public_bucket=1",
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"hostRequirements": {
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"cpus": 4,
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"memory": "8gb",
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"storage": "32gb"
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},
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"forwardPorts": [
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3306
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],
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"customizations": {
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"settings": {
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"python.pythonPath": "/usr/local/bin/python"
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},
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"vscode": {
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"extensions": [
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"[email protected]",
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"[email protected]"
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]
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}
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}
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}

‎.devcontainer/docker-compose.yaml‎

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version: "3"
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services:
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app:
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cpus: 4
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mem_limit: 8g
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# build:
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# context: ..
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# dockerfile: ./.devcontainer/Dockerfile
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image: datajoint/element_array_ephys:latest
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extra_hosts:
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- fakeservices.datajoint.io:127.0.0.1
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environment:
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- DJ_PUBLIC_S3_LOCATION=djhub.vathes.datapub.elements:/workflow-array-ephys-benchmark/v2
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devices:
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- /dev/fuse
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cap_add:
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- SYS_ADMIN
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security_opt:
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- apparmor:unconfined
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volumes:
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- ..:/workspaces/element-array-ephys:cached
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- docker_data:/var/lib/docker # persist docker images
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privileged: true # only because of dind
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volumes:
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docker_data:

‎.gitignore‎

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**/#*#
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**/.#*
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docker-compose.y*ml
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# include
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!docs/docker-compose.yaml
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# vscode settings
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.vscode
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*.code-workspace
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# exports/notes

‎.markdownlint.yaml‎

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MD033: # HTML elements allowed
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allowed_elements:
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- "br"
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- "figure"
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- "figcaption"
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MD034: false # Permit bare URLs
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MD031: false # Spacing w/code blocks. Conflicts with `??? Note` and code tab styling
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MD046: false # Spacing w/code blocks. Conflicts with `??? Note` and code tab styling

‎.vscode/launch.json‎

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{
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// Use IntelliSense to learn about possible attributes.
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// Hover to view descriptions of existing attributes.
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// For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
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"version": "0.2.0",
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"configurations": [
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{
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"name": "Python: Current File",
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"type": "python",
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"request": "launch",
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"program": "${file}",
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"console": "integratedTerminal",
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"justMyCode": false
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}
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]
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}

‎.vscode/settings.json‎

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{
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"editor.formatOnPaste": false,
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"editor.formatOnSave": true,
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"editor.rulers": [
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88
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],
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"python.formatting.provider": "black",
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"[python]": {
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"editor.defaultFormatter": null
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},
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"[markdown]": {
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"editor.defaultFormatter": "disable"
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},
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"files.autoSave": "off"
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}

‎CHANGELOG.md‎

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Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
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[Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
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## [0.3.0] - 2023-10-25
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+ Add - DevContainer for codespaces
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+ Add - `tutorial_pipeline.py`
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+ Add - 60 min tutorial using Jupyter Notebooks, short demo notebook
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+ Update - General improvements to increase consistency with other DataJoint Elements
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## [0.2.11] - 2023-06-29
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+ Update - Improve kilosort triggering routine - better logging, remove temporary files, robust resumable processing
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+ Add - Probe table supporting: Neuropixels probes 1.0 - 3A, 1.0 - 3B, 2.0 - SS,
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2.0 - MS
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[0.3.0]: https://github.com/datajoint/element-array-ephys/releases/tag/0.3.0
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[0.2.11]: https://github.com/datajoint/element-array-ephys/releases/tag/0.2.11
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[0.2.10]: https://github.com/datajoint/element-array-ephys/releases/tag/0.2.10
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[0.2.9]: https://github.com/datajoint/element-array-ephys/releases/tag/0.2.9
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[0.2.8]: https://github.com/datajoint/element-array-ephys/releases/tag/0.2.8

‎CONTRIBUTING.md‎

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# Contribution Guidelines
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This project follows the
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[DataJoint Contribution Guidelines](https://datajoint.com/docs/community/contribute/).
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[DataJoint Contribution Guidelines](https://datajoint.com/docs/about/contribute/).
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Please reference the link for more full details.

‎Dockerfile‎

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