ENH start setting up jupyter-book

Author: mvdoc

.gitignore

@@ -12,3 +12,4 @@ dist/
 # Documentation build
 doc/_build/
 doc/_auto_examples/
+tutorials/_build

tutorials/_config.yml

@@ -0,0 +1,47 @@
+# Book settings
+# Learn more at https://jupyterbook.org/customize/config.html
+
+title: Voxelwise Encoding Model tutorials
+author: Tom Dupré la Tour, Matteo Visconti di Oleggio Castello, Jack L. Gallant
+logo: book_assets/static/flatmap.png
+
+# Force re-execution of notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: cache
+  timeout: -1 # do not timeout
+  exclude_patterns:
+    - notebooks/shortclips/00_setup_colab.ipynb
+    - notebooks/shortclips/07_extract_motion_energy.ipynb
+    - notebooks/shortclips/07_extract_motion_energy.ipynb
+    - notebooks/vim2/00_download_vim2.ipynb
+    - notebooks/vim2/01_extract_motion_energy.ipynb
+    - notebooks/vim2/02_plot_ridge_model.ipynb
+
+# 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:
+  - references.bib
+
+# Information about where the book exists on the web
+repository:
+  url: https://github.com/gallantlab/voxelwise_tutorials  # Online location of your book
+  path_to_book: docs  # Optional path to your book, relative to the repository root
+  branch: main  # Which branch of the repository should be used when creating links (optional)
+
+# 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
+
+parse:
+  myst_enable_extensions:
+    - amsmath
+    - dollarmath
+
+  

tutorials/_toc.yml

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+# Table of contents
+# Learn more at https://jupyterbook.org/customize/toc.html
+
+format: jb-article
+root: index
+sections:
+- file: voxelwise_modeling
+  title: Voxelwise modeling framework
+- file: voxelwise_package
+  title: Helper Python package
+- file: notebooks/shortclips/README
+  title: Shortclips tutorial
+  sections:
+  - file: notebooks/shortclips/00_download_shortclips
+    title: Download the data set
+  - file: notebooks/shortclips/00_setup_colab
+    title: Setup Google Colab
+  - file: notebooks/shortclips/01_plot_explainable_variance
+    title: Compute the explainable variance
+  - file: notebooks/shortclips/02_plot_ridge_regression
+    title: Understand ridge regression and cross-validation
+  - file: notebooks/shortclips/03_plot_wordnet_model
+    title: Fit a ridge model with wordnet features
+  - file: notebooks/shortclips/04_plot_hemodynamic_response
+    title: Visualize the hemodynamic response
+  - file: notebooks/shortclips/05_plot_motion_energy_model
+    title: Fit a ridge model with motion energy features
+  - file: notebooks/shortclips/06_plot_banded_ridge_model
+    title: Fit a banded ridge model with both wordnet and motion energy features
+  - file: notebooks/shortclips/07_extract_motion_energy
+    title: Extract motion energy features from the stimuli
+- file: notebooks/vim2/README
+  title: Vim-2 tutorial
+  sections:
+  - file: notebooks/vim2/00_download_vim2
+    title: Download the data set from CRCNS
+  - file: notebooks/vim2/01_extract_motion_energy
+    title: Extract motion energy features from the stimuli
+  - file: notebooks/vim2/02_plot_ridge_model
+    title: Fit a ridge model with motion energy features
+- file: references
+  title: References