updated jbook

docs/_config.yml

@@ -11,6 +11,43 @@ exclude_patterns: [ README.md, _build, Thumbs.db, .DS_Store, "**.ipynb_checkpoin
 execute:
   execute_notebooks: off
 
+#######################################################################################
+# 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      : false  # 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         : false  # Whether to add an "open an issue" button
+  use_multitoc_numbering    : true   # Continuous numbering across parts/chapters
+  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                   : ""  # 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              : "" # A banner announcement at the top of the site.
+
+
 # Define the name of the latex output file for PDF builds
 latex:
   latex_documents:
@@ -22,12 +59,14 @@ bibtex_bibfiles:
 
 # Information about where the book exists on the web
 repository:
-  url: git push --set-upstream origin gh-pages  # Online location of your book
+  url: https://github.com/cosanlab/kernel  # 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
+#######################################################################################
+# Advanced and power-user settings
+sphinx:
+  extra_extensions          :   ['sphinx.ext.autodoc', 'sphinx.ext.napoleon'] # A list of extra extensions to load by Sphinx (added to those already used by JB).
+  local_extensions          :   # A list of local extensions to load by sphinx specified by "name: path" items
+  recursive_update          : false # A boolean indicating whether to overwrite the Sphinx config (true) or recursively update (false)
+  config                    :   # key-value pairs to directly over-ride the Sphinx configuration

docs/_toc.yml

@@ -4,10 +4,14 @@
 format: jb-book
 root: intro
 parts:
-- chapters: 
-  - acquiring_data
-- chapters:
-  - file: analyzing_data
-  - file: FingerTapping
-- chapters:
-  - file: faq
+  - caption: Acquiring Data
+    numbered: False
+    chapters: 
+      - file: acquiring_data
+  - caption: Analyzing Data
+    chapters:
+      - file: analyzing_data
+      - file: FingerTapping
+  - caption: FAQ
+    chapters:
+      - file: faq

docs/intro.md

@@ -16,12 +16,12 @@ TD fNIRS uses time gating to discriminate the photons arriving to the detector a
 
 A common way to summarize information from time-of-flight histograms is to compute the first three moments of the histogram corresponding to the total counts (sum), mean time-of-flight (first moment), and variance of the times of flight (second central moment). Moments have a convenient property: the moments of the DTOF can be obtained from calculating the moments of the TPSF and of the IRF straightforwardly. Accordingly, with Flow2, system drift in the DTOF moments can be corrected for, using the internal IRF detector. However, the instrument response function (IRF) can complicate data interpretation in TD-fNIRS. To address this, moment analysis of the distribution of times of flight (DTOF) has been proposed as an alternative to time gates analysis. Higher statistical moments of the DTOF show increased sensitivity to deeper tissue layers.
 
-{image} images/flow2.png
+![flow2](images/flow2.png)
 
 
 ## Flow 2
 
-{image} images/DTOF.png
+![dtof](images/DTOF.png)
 
 ## Resources