/
_config.yml
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/
_config.yml
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# Book settings
# Learn more at https://jupyterbook.org/customize/config.html
title: Practice and theory of brain imaging
author: The nipraxis team
logo: images/reggie.png
# >- starts a multiline string, where newlines replaced by spaces, and final
# newlines are stripped.
description: >-
Textbook for Practice and Theory of Brain Imaging course.
https://nipraxis.org for more information on the course.
# Force re-execution of notebooks on each build.
# See https://jupyterbook.org/content/execute.html
execute:
# 'cache' attempts to cache the results.
# 'auto' appears to be safer.
execute_notebooks: auto
timeout: 120
exclude_patterns:
# Remove pages from this list as they are fixed.
# When removing, if the pages aren't in the toctree,
# add orphan: true to YaML frontmatter, e.g. syllabus.md.
# https://myst-parser.readthedocs.io/en/latest/sphinx/use.html#sphinx-specific-page-front-matter
# Notebooks need this key/value to be in the `jupyter` YaML section, e.g
# string_formatting.Rmd.
# https://github.com/executablebooks/meta/discussions/105
# https://myst-nb.readthedocs.io/en/latest/use/orphaned_nb.html#orphaned-nb
# OE: I have sorted the pages with a tentative sectioning
#
# Python and Numpy
- array_reductions.md
- comparing_arrays.Rmd
- comparing_floats.md
- diag_inverse.md
- dot_and_outer.md
- floating_in_text.md
- index_reshape.Rmd
- keyword_arguments.Rmd
- nans.md
- numpy_diag.Rmd
- numpy_meshgrid.Rmd
- numpy_squeeze.Rmd
- numpy_transpose.Rmd
- on_loops.Rmd
- packages_namespaces.Rmd
- printing_floating.Rmd
- subtract_mean_math.md
- two_dunders.md
# Images and code and images
- saving_images.Rmd
# Coordinate systems and spatial transforms
# [all transferred already]
# Into the fourth dimension
- tr_and_headers.Rmd
# Statistics
- pearson_functions.md
- validate_against_scipy.Rmd
# Hemodynamic response modeling
- introducing_nipype.Rmd
# Code organization and collaboration
- full_scripting.md
- git_videos.md
- git_walk_through.Rmd
- git_workflow_exercises.md
- github_dummies_homework.md
- github_glm_homework.md
- github_pca_homework.md
# Meta-course
- README.md
- data/README.md
- _todo.md
- _scripts
- bibliography.md
- classes.md
- classes_and_labs.md
- diagnostics_project.md
- ds114_sub009_highres.nii
- example_data.md
- exercises.md
- glossary.md
- index.md
- logistics.md
- mentors.md
- multi_model_homework.md
- participate.md
- participate_grading.md
- preparation.md
- project_grading.md
- projects.md
- topics.md
# Drop?
- using_pythonpath.Rmd
# Define the name of the latex output file for PDF builds
latex:
latex_documents:
targetname: nipraxis.tex
# Add a bibtex file so that we can create citations
bibtex_bibfiles:
- references.bib
html:
# favicon: images/dsfe_favicon.ico
home_page_in_navbar: false
use_edit_page_button: true
use_repository_button: true
use_issues_button: true
baseurl: https://textbook.nipraxis.org
repository:
url: https://github.com/nipraxis/textbook
branch: main
launch_buttons:
# The interface interactive links will activate ["classic", "jupyterlab"]
notebook_interface: "classic"
# The URL of the JupyterHub (e.g., https://datahub.berkeley.edu)
jupyterhub_url: "https://hub.nipraxis.org"
# The URL of the BinderHub (e.g., https://mybinder.org)
binderhub_url: "https://mybinder.org"
# The URL of Google Colab (e.g., https://colab.research.google.com)
colab_url: "https://colab.research.google.com"
# Deepnote
deepnote_url: "https://deepnote.com"
thebe: true
sphinx:
config:
nb_custom_formats:
.Rmd:
- jupytext.reads
- fmt: Rmd
# Add GitHub buttons to your book
# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
html:
use_issues_button: true
use_repository_button: true
# HTML redirection
# Pages linked, but then renamed.
redirection:
builddir : _build/html
# redirects:
# data-types/Ranges: ../arrays/Ranges
#
bibtex_bibfiles:
- _references.bib