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‎.gitignore

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stimuli/*
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data/*
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*.pyc
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docs/build/*

‎.readthedocs.yaml

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# .readthedocs.yaml
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# Read the Docs configuration file
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# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
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# Required
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version: 2
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# Set the version of Python and other tools you might need
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build:
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os: ubuntu-20.04
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tools:
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python: "3.9"
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# Build documentation in the docs/ directory with Sphinx
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sphinx:
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configuration: docs/conf.py
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# Optionally build your docs in additional formats such as PDF
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formats:
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- pdf
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# Optionally declare the Python requirements required to build your docs
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python:
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install:
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- requirements: docs/requirements-build-docs.txt

‎.vscode/settings.json

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{
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"esbonio.sphinx.confDir": ""
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}

‎README.md

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The tasks are Visual Search, Action Observation, N Back,
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Social Prediction, and Semantic Prediction
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#### Authors: Maedbh King, Ladan Shahshahani, Suzanne Witt
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#### Authors: Diedrichsenlab (Maedbh King, Ladan Shahshahani, Suzanne Witt, Bassel Arafat, Ince Hussain)
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## Installation
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### Installing the Required Python Version
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This project requires **python version 3.7.0**. Please ensure it is installed globally on your local machine.
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This project requires **python version >3.7.0**. Please ensure it is installed globally on your local machine.
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If you are running Mac OS X or Linux, it is recommended to use [`pyenv`](https://github.com/pyenv/pyenv)
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for python version management. The full installation instructions can be found [here](https://github.com/pyenv/pyenv#installation).

‎docs/Makefile

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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line, and also
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# from the environment for the first two.
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SPHINXOPTS ?=
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SPHINXBUILD ?= sphinx-build
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SOURCEDIR = .
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BUILDDIR = build
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: help Makefile
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

‎docs/building_experiment.rst

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‎docs/conf.py

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# Configuration file for the Sphinx documentation builder.
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#
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# This file only contains a selection of the most common options. For a full
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# list see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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# -- Path setup --------------------------------------------------------------
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# If extensions (or modules to document with autodoc) are in another directory,
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# add these directories to sys.path here. If the directory is relative to the
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# documentation root, use os.path.abspath to make it absolute, like shown here.
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#
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import os
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import sys
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sys.path.insert(0, os.path.abspath('../experiment_code'))
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# -- Project information -----------------------------------------------------
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project = 'MDTB_experiment'
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copyright = '2023, Diedrichsenlab'
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author = 'Diedrichsenlab'
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# The full version, including alpha/beta/rc tags
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release = 'v.0.1a'
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# -- General configuration ---------------------------------------------------
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = ['sphinx.ext.napoleon',
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'sphinx.ext.autodoc',
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'sphinx.ext.autosectionlabel',
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'sphinx.ext.mathjax',
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'sphinx.ext.intersphinx',
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'sphinx.ext.doctest',
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'nbsphinx']
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napoleon_custom_sections = [('Returns', 'params_style')]
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ['_templates']
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This pattern also affects html_static_path and html_extra_path.
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exclude_patterns = ['build']
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# Make sure that class constructors are documented
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autoclass_content = 'both'
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# -- Options for HTML output -------------------------------------------------
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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#
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html_theme = 'sphinx_rtd_theme'
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# so a file named "default.css" will overwrite the builtin "default.css".
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html_static_path = ['_static']

‎docs/index.rst

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.. MDTB_experiment index
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Multi-domain task Battery (MDTB) experiments
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============================================
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Licence and Acknowledgements
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----------------------------
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Documentation
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-------------
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.. toctree::
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:maxdepth: 2
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:caption: Contents:
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installation.rst
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running_experiment.rst
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building_experiment.rst
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reference.rst
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Indices and tables
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------------------
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* :ref:`genindex`
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* :ref:`modindex`
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* :ref:`search`

‎docs/installation.rst

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Installation
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============
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Cloning this Repository
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=======================
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1. Copy the git repo URL. Click the "Clone or Download" button and copy the link (`https://github.com/maedbhk/mdtb_reduced.git`).
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2. Go to your terminal and navigate (using `cd` and `ls` commands) to the directory where you want to clone the repository.
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3. Use `git clone` to download the entire folder to your computer:
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```
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git clone https://github.com/maedbhk/mdtb_reduced.git
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```
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> NOTE: If you want to learn more about git, check out this tutorial [here](https://rogerdudler.github.io/git-guide/).
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### Installing the Required Python Version
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This project requires **python version >3.7.0**. Please ensure it is installed globally on your local machine.
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If you are running Mac OS X or Linux, it is recommended to use [`pyenv`](https://github.com/pyenv/pyenv)
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for python version management. The full installation instructions can be found [here](https://github.com/pyenv/pyenv#installation).
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Below is an abridged version of the `pyenv` install procedure for Max OS X:
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Install `pyenv` using Homebrew:
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$ brew update
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$ brew install pyenv
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Add `pyenv init` to your shell:
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$ echo -e 'if command -v pyenv 1>/dev/null 2>&1; then\n eval "$(pyenv init -)"\nfi' >> ~/.bash_profile
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$ source ~/.bash_profile
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Install the required version of python:
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$ pyenv install 3.7.0
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Installing the Required Python Packages
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=======================================
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This project uses [`pipenv`](https://github.com/pypa/pipenv) for virtual environment and python package management.
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Ensure pipenv is installed globally:
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$ brew install pipenv
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Navigate to the top-level directory in `mdtb_reduced` and install the packages from the `Pipfile.lock`.
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This will automatically create a new virtual environment for you and install all requirements using the correct version of python.
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$ pipenv install

‎docs/reference.rst

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‎docs/requirements-build-docs.txt

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numpy
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sphinx>=1.4
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sphinxcontrib-bibtex
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sphinx-copybutton
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pandas
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matplotlib
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ipykernel
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nbsphinx
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scipy
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seaborn

‎docs/running_experiment.rst

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‎psychopy-env.yml

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name: psychopy
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channels:
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- conda-forge
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dependencies:
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- python=3.8
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- psychopy
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- pip
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- pip:
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- psychtoolbox
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- pygame
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- pyo
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- pyparallel; platform_system != "Windows"
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- SoundFile; platform_system == "Windows"
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- websocket_client

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