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Remi-GauRemi-Gau
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Merge pull request #10 from Remi-Gau/lint
[ENH] package and container
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‎.dockerignore

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# ignoring this might speed up build
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# by preventing passing extra content to the docker daemon
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# General
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.DS_Store
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.github
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.vscode
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**/data
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**/docs
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**/tests
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**/*.zip
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**/*.asc
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**/*.edf
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**/*.EDF
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**/build
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.pytest_cache
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.mypy_cache
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coverage_html
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.coverage

‎.flake8

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max-line-length = 90
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max_complexity = 15
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max_function_length = 100
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per-file-ignores =
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**/__init__.py: D104
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# for compatibility with black
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# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#flake8
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extend-ignore = E203

‎.github/workflows/docker.yml

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---
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name: docker
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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on:
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push:
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branches: [main]
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pull_request:
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branches: [main]
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- name: Clone
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uses: actions/checkout@v3
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with:
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fetch-depth: 0
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- name: Build docker image
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run: docker build -t eye2bids:latest .

‎.gitignore

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**/*.asc
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**/*.edf
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**/*.EDF
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eye2bids/_version.py
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# General
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.DS_Store
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# Byte-compiled / optimized / DLL files
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__pycache__/

‎Dockerfile

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# Generated by Neurodocker and Reproenv.
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FROM ubuntu:22.04
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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ca-certificates \
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curl \
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gcc \
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gnupg2 \
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pip \
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python3 \
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software-properties-common \
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&& rm -rf /var/lib/apt/lists/*
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RUN apt-key adv --fetch-keys https://apt.sr-research.com/SRResearch_key && add-apt-repository 'deb [arch=amd64] https://apt.sr-research.com SRResearch main'
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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eyelink-display-software \
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&& rm -rf /var/lib/apt/lists/*
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RUN mkdir /eye2bids
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COPY [".", \
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"/eye2bids"]
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WORKDIR /eye2bids
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RUN pip install .[dev]
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# Save specification to JSON.
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RUN printf '{ \
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"pkg_manager": "apt", \
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"existing_users": [ \
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"root" \
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], \
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"instructions": [ \
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{ \
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"name": "from_", \
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"kwds": { \
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"base_image": "ubuntu:22.04" \
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} \
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}, \
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{ \
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"name": "install", \
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"kwds": { \
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"pkgs": [ \
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"gnupg2", \
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"curl", \
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"gcc", \
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"ca-certificates", \
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"software-properties-common", \
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"python3", \
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"pip" \
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], \
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"opts": null \
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} \
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}, \
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{ \
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"name": "run", \
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"kwds": { \
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"command": "apt-get update -qq \\\\\\n && apt-get install -y -q --no-install-recommends \\\\\\n ca-certificates \\\\\\n curl \\\\\\n gcc \\\\\\n gnupg2 \\\\\\n pip \\\\\\n python3 \\\\\\n software-properties-common \\\\\\n && rm -rf /var/lib/apt/lists/*" \
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} \
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}, \
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{ \
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"name": "run", \
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"kwds": { \
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"command": "apt-key adv --fetch-keys https://apt.sr-research.com/SRResearch_key && add-apt-repository '"'"'deb [arch=amd64] https://apt.sr-research.com SRResearch main'"'"'" \
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} \
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}, \
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{ \
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"name": "install", \
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"kwds": { \
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"pkgs": [ \
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"eyelink-display-software" \
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], \
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"opts": null \
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} \
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}, \
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{ \
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"name": "run", \
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"kwds": { \
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"command": "apt-get update -qq \\\\\\n && apt-get install -y -q --no-install-recommends \\\\\\n eyelink-display-software \\\\\\n && rm -rf /var/lib/apt/lists/*" \
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} \
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}, \
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{ \
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"name": "run", \
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"kwds": { \
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"command": "mkdir /eye2bids" \
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} \
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}, \
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{ \
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"name": "copy", \
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"kwds": { \
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"source": [ \
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".", \
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"/eye2bids" \
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], \
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"destination": "/eye2bids" \
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} \
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}, \
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{ \
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"name": "workdir", \
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"kwds": { \
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"path": "/eye2bids" \
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} \
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}, \
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{ \
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"name": "run", \
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"kwds": { \
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"command": "pip install .[dev]" \
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} \
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} \
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] \
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}' > /.reproenv.json
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# End saving to specification to JSON.

‎Makefile

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.PHONY: Dockerfile
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Dockerfile:
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docker run --rm repronim/neurodocker:0.9.5 generate docker \
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--pkg-manager apt \
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--base-image ubuntu:22.04 \
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--install gnupg2 curl gcc ca-certificates software-properties-common python3 pip \
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--run "apt-key adv --fetch-keys https://apt.sr-research.com/SRResearch_key && add-apt-repository 'deb [arch=amd64] https://apt.sr-research.com SRResearch main'" \
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--install eyelink-display-software \
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--run "mkdir /eye2bids" \
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--copy "." "/eye2bids" \
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--workdir "/eye2bids" \
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--run "pip install .[dev]" \
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> Dockerfile
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docker_build:
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docker build -t eye2bids .
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test_data:
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python tools/download_test_data.py

‎README.md

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# eye2bids
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## Instructions for testing conversion_json
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## Installation
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### Requirements
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- edf file by EyeLink Eye Tracker
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- Python3
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- EyeLink Developers Kit. Download from [SR-Research support forum] (forum registration required)
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- Python >= 3.8
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If you want to use eye2bids to convert EyeLink data,
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you will need to install the EyeLink Developers Kit.
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It can be downloaded from SR-Research support forum (forum registration required).
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The installation on Ubuntu can also be done with the following commands:
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Taken from: https://www.sr-research.com/support/docs.php?topic=linuxsoftware
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```bash
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sudo add-apt-repository universe
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sudo apt update
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sudo apt install ca-certificates
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sudo apt-key adv --fetch-keys https://apt.sr-research.com/SRResearch_key
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sudo add-apt-repository 'deb [arch=amd64] https://apt.sr-research.com SRResearch main'
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sudo apt update
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sudo apt install eyelink-display-software
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```
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### Install eye2bids
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- Clone the repository
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```bash
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git clone https://github.com/bids-standard/eye2bids.git
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```
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- Install the package in editatble mode
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```bash
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cd eye2bids
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pip install .
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```
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## Using eye2bids
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- Supporeted Input data:
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- edf file by EyeLink Eye Tracker
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To try it, you can install our test data from OSF by running the following command:
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```bash
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python tools/download_test_data.py
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```
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- manual_metadata.yml file (find template and an example in conversion_json folder)
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### Run code
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```
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python3 edf2bids_json.py
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```bash
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python edf2bids_json.py
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```
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[SR-Research support forum]: https://www.sr-research.com/support/forum-9.html
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## Docker
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You can build the docker image with the following command:
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```bash
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docker build -t eye2bids:latest .
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```
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## Contributing
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Make sure you install eye2bids in editable mode (see above) and install the development dependencies:
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```bash
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pip install --editable .[dev]
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```
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## Related projects

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