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Merge pull request #2 from eywalker/main
Add dev container setup
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‎.devcontainer/devcontainer.json

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// For format details, see https://aka.ms/devcontainer.json. For config options, see the
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// README at: https://github.com/devcontainers/templates/tree/main/src/docker-existing-docker-compose
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{
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"name": "Docker compose dev",
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// Update the 'dockerComposeFile' list if you have more compose files or use different names.
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// The .devcontainer/docker-compose.yml file contains any overrides you need/want to make.
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"dockerComposeFile": [
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"../docker-compose.yml",
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"docker-compose.yml"
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],
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// The 'service' property is the name of the service for the container that VS Code should
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// use. Update this value and .devcontainer/docker-compose.yml to the real service name.
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"service": "notebook",
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// The optional 'workspaceFolder' property is the path VS Code should open by default when
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// connected. This is typically a file mount in .devcontainer/docker-compose.yml
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"workspaceFolder": "/src",
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// Features to add to the dev container. More info: https://containers.dev/features.
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// "features": {},
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// Use 'forwardPorts' to make a list of ports inside the container available locally.
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// "forwardPorts": [],
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// Uncomment the next line if you want start specific services in your Docker Compose config.
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// "runServices": [],
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// Uncomment the next line if you want to keep your containers running after VS Code shuts down.
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// "shutdownAction": "none",
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// Uncomment the next line to run commands after the container is created.
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// "postCreateCommand": "cat /etc/os-release",
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// Configure tool-specific properties.
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// "customizations": {},
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// Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root.
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// "remoteUser": "devcontainer"
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}

‎.devcontainer/docker-compose.yml

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version: '3'
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services:
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# Update this to the name of the service you want to work with in your docker-compose.yml file
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notebook:
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# Uncomment if you want to override the service's Dockerfile to one in the .devcontainer
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# folder. Note that the path of the Dockerfile and context is relative to the *primary*
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# docker-compose.yml file (the first in the devcontainer.json "dockerComposeFile"
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# array). The sample below assumes your primary file is in the root of your project.
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#
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# build:
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# context: .
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# dockerfile: .devcontainer/Dockerfile
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volumes:
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# Update this to wherever you want VS Code to mount the folder of your project
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- .:/src/project
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# Uncomment the next four lines if you will use a ptrace-based debugger like C++, Go, and Rust.
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# cap_add:
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# - SYS_PTRACE
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# security_opt:
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# - seccomp:unconfined
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# Overrides default command so things don't shut down after the process ends.
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command: /bin/sh -c "while sleep 1000; do :; done"

‎.gitignore

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# Mac files
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.DS_Stores
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# temp files
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~*
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*~
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# computed
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computed/
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# just for testing
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rough/
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# image models
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trained_models
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# wandb
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wandb/
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artifacts/
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# pytorch and pickle files
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*.pt
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*.pickle
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# custom temp files
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temp/
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# matlab data files
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*.mat
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# ignore singularity images
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*.sif
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# vscode specifics
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.vscode/
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# data
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data/
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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pip-wheel-metadata/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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.python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/

‎Dockerfile

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# FROM walkerlab/pytorch:python3.8-torch1.11.0-cuda11.2.1
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FROM walkerlab/pytorch-jupyter:cuda-11.3.1-pytorch-1.12.0-torchvision-0.12.0-torchaudio-0.11.0-ubuntu-20.04
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FROM ghcr.io/walkerlab/pytorch-jupyter:cuda-11.8.0-pytorch-1.13.0-torchvision-0.14.0-torchaudio-0.13.0-ubuntu-22.04
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RUN git clone https://github.com/learning-2-learn/lfp_tools /src/lfp_tools &&\
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pip3 install -e /src/lfp_tools

‎README.md

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# wcst_encode
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# wcst_encode

‎docker-compose.yml

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notebook:
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build: .
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ports:
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- "${JUPYTER_IP:-127.0.0.1}:${JUPYTER_PORT:-8888}:8888"
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- "${JUPYTER_IP:-127.0.0.1}:${JUPYTER_PORT:-8888}:8888"
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environment:
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- "JUPYTER_PASSWORD=${JUPYTER_PASSWORD:-simple}"
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runtime: nvidia
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volumes:
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- .:/src/wcst_encode
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- $HOME/.aws/credentials:/root/.aws/credentials:ro
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- $HOME/.ssh/id_rsa:/root/.ssh/id_rsa
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- /mnt/U19_NAS/hackathon:/data
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‎setup.py

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#!/usr/bin/env python
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from setuptools import setup, find_packages
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from os import path
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here = path.abspath(path.dirname(__file__))
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setup(
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name='wcst_encode',
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version='0.0.0',
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name="wcst_encode",
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version="0.0.0",
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description='Tools and analysis for encoding behavioral/experimental variables from neural data',
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author='Patrick Zhang',
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author_email='[email protected]',
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packages=find_packages(exclude=[]),
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packages=find_packages(),
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)

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