update

binder/environment.yml

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+../conda/environment.yml

book/_config.yml

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+# Book settings
+# Learn more at https://jupyterbook.org/customize/config.html
+
+title: "Use Case Template"
+author: eScience Institute, University of Washington
+logo: img/GeoSMART_logo.svg
+only_build_toc_files: true
+
+# Add GitHub buttons to your book
+# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
+html:
+  use_edit_page_button: true
+  use_issues_button: true
+  use_repository_button: true
+  home_page_in_navbar: false
+  # google_analytics_id: G-XXXXXXXXX
+
+parse:
+  # https://jupyterbook.org/content/content-blocks.html?highlight=myst%20substitution#define-substitutions-for-your-whole-book
+  # https://jupyterbook.org/content/content-blocks.html#using-substitutions-in-links
+  myst_substitutions:
+    website_url: "https://geo-smart.github.io/use_case_template"
+  myst_enable_extensions:
+    # Defaults
+    - dollarmath
+    - linkify
+    - substitution
+    - colon_fence
+    # Extras
+    - html_image
+
+# Force re-execution of notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  # NOTE: 'cache' to use jupyter-cache, or 'force' to run all
+  execute_notebooks: 'cache'
+  exclude_patterns: ["*rendered*", "*skip*"]
+  allow_errors: false
+  # Per-cell notebook execution limit (seconds)
+  timeout: 300
+
+# Define the name of the latex output file for PDF builds
+latex:
+  latex_documents:
+    targetname: book.tex
+
+# Configure your Binder links, such as the URL of the BinderHub.
+launch_buttons:
+  notebook_interface: jupyterlab
+  binderhub_url: "https://mybinder.org"
+
+# Information about where the book exists on the web
+repository:
+  url: https://github.com/geo-smart/use_case_template # Online location of your book
+  path_to_book: 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)
+
+# Bibliography
+bibtex_bibfiles:
+  - references.bib
+sphinx:
+  config:
+    html_js_files:
+    - https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js
+    bibtex_reference_style: author_year  # or label, super, \supercite
+    nb_custom_formats:
+        .py:
+            - jupytext.reads
+            - fmt: py:percent

book/_toc.yml

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+# Table of contents
+# Learn more at https://jupyterbook.org/customize/toc.html
+root: intro
+format: jb-book
+parts:
+- caption: About
+  chapters:
+    - title: Geosmart Website
+      url: https://geo-smart.github.io/index.html
+    - title: Project Pythia Foundations
+      url: https://foundations.projectpythia.org/landing-page.html
+    - title: About Use Case Library
+      file: chapters/about
+
+- caption: Chapter One
+  chapters:
+    - file: chapters/motivation_EC
+
+- caption: Chapter Two
+  chapters:
+    - file: chapters/methods_EC
+
+- caption: Chapter Three
+  chapters:
+    - file: chapters/data_EC
+
+- caption: Chapter Four
+  chapters:
+    - file: chapters/development_EC
+
+- caption: Chapter Five
+  chapters:
+    - file: chapters/training_EC
+
+- caption: Chapter Six
+  chapters:
+    - file: chapters/evaluation_EC
+
+- caption: Chapter Seven
+  chapters:
+    - file: chapters/workflow
+
+- caption: Chapter Eight
+  chapters:
+    - file: chapters/reproducibility
+
+- caption: Chapter Nine
+  chapters:
+    - file: chapters/conclusion_EC
+
+- caption: Chapter Ten (optional)
+  chapters:
+    - file: chapters/todo
+
+- caption: Chapter Eleven (optional)
+  chapters:
+    - file: chapters/questions
+
+- caption: Chapter Twelve (optional)
+  chapters:
+    - file: chapters/troubleshooting
+
+- caption: Chapter Thirteen
+  chapters:
+    - file: chapters/example
+
+- caption: Reference
+  chapters:
+    - file: reference/glossary
+    - file: reference/bibliography