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_config.yml
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_config.yml
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# Book settings
# Learn more at https://jupyterbook.org/customize/config.html
title: Training Manual For Reproducibility Verification
author: Lars Vilhuber, Michael Darisse, Sofia Encarnación, Ilanith Nizard, Leonel Borja Plaza, Takshil Sachdev, Hyuk Son, Linda Wang, David Wasser, Meredith Welch
logo: logo.jpg
copyright: 2018-2024
exclude_patterns : ["*venv*",".git*",".devcontainer"]
# Force re-execution of notebooks on each build.
# See https://jupyterbook.org/content/execute.html
execute:
execute_notebooks: force
# Define the name of the latex output file for PDF builds
latex:
latex_documents:
targetname: book.tex
# Add a bibtex file so that we can create citations
bibtex_bibfiles:
# - packages.bib
- paper.bib
# Information about where the book exists on the web
repository:
url: https://github.com/labordynamicsinstitute/ldilab-manual # Online location of your book
#path_to_book: # Optional path to your book, relative to the repository root
branch: main # Which branch of the repository should be used when creating links (optional)
#######################################################################################
# Parse and render settings
parse:
myst_enable_extensions: # default extensions to enable in the myst parser. See https://myst-parser.readthedocs.io/en/latest/using/syntax-optional.html
# - amsmath
- colon_fence
# - deflist
- dollarmath
# - html_admonition
# - html_image
- linkify
# - replacements
# - smartquotes
- substitution
- tasklist
myst_url_schemes: [mailto, http, https] # URI schemes that will be recognised as external URLs in Markdown links
myst_dmath_double_inline: true # Allow display math ($$) within an inline context
#######################################################################################
# HTML-specific settings
html:
favicon : "" # A path to a favicon image
use_edit_page_button : true # Whether to add an "edit this page" button to pages. If `true`, repository information in repository: must be filled in
use_repository_button : true # Whether to add a link to your repository button
use_issues_button : true # Whether to add an "open an issue" button
use_multitoc_numbering : true # Continuous numbering across parts/chapters
extra_navbar : <a href="https://labordynamicsinstitute.github.io/replicability-training-curriculum/">Link to old documentation</a> # Will be displayed underneath the left navbar.
extra_footer : "" # Will be displayed underneath the footer.
google_analytics_id : "" # A GA id that can be used to track book views.
home_page_in_navbar : true # Whether to include your home page in the left Navigation Bar
baseurl : "https://labordynamicsinstitute.github.io/ldilab-manual/" # The base URL where your book will be hosted. Used for creating image previews and social links. e.g.: https://mypage.com/mybook/
comments:
hypothesis : false
utterances : false
announcement : "This is not yet fully debugged - report any issues!" # A banner announcement at the top of the site.
# Advanced and power-user settings
sphinx:
extra_extensions : # A list of extra extensions to load by Sphinx.
config : # key-value pairs to directly over-ride the Sphinx configuration
bibtex_reference_style: author_year
# Custom data
data:
pandp:
# For instructions to set up, see Lab Assistant Setup document
# This is the URL of the Google Folder
- googlefolderurl: "https://drive.google.com/drive/u/1/folders/1BhqECqYdBQJecRcDaJf_Jl2NoyiyrYzl"
# This is the google Form URL that the replicator/ assessor accesses.
- googleformurl: "https://docs.google.com/forms/d/e/1FAIpQLSdUUZiGw3Rsv7RDimEhmQT4G1T7ZBWUR0Td_lNmAdKs5UGB0w/viewform?usp=sf_link"
# This will need to be integrated using GLUE, see https://jupyterbook.org/en/stable/content/executable/output-insert.html
# - at setup, read in _config.yml, make glue variables
# - able to reference anywhere in the document.
url:
acre: https://bitss.github.io/ACRE/
replraw: https://github.com/labordynamicsinstitute/replicability-training/raw/master/
replmd: https://github.com/labordynamicsinstitute/replicability-training-curriculum/blob/master/
reploldmd: https://github.com/labordynamicsinstitute/replicability-training/blob/master/
templmd: https://github.com/AEADataEditor/replication-template/blob/master/
pandp:
# For instructions to set up, see Lab Assistant Setup document
# This is the URL of the Google Folder
- googlefolderurl: "https://drive.google.com/drive/u/1/folders/1BhqECqYdBQJecRcDaJf_Jl2NoyiyrYzl"
# This is the google Form URL that the replicator/ assessor accesses.
- googleformurl: "https://docs.google.com/forms/d/e/1FAIpQLSdUUZiGw3Rsv7RDimEhmQT4G1T7ZBWUR0Td_lNmAdKs5UGB0w/viewform?usp=sf_link"