_config.yml

###################################################
# Bucheinstellungen
title: 'BioLabSim:<br> Data Analysis for Biotechnology'
author: Ulf Liebal and BioLabSim Consortium
logo: Figures/Logos/BLS_Icon-medium.png
# exclude_patterns: ["files/_build", "files/**.ipynb_checkpoints","files/teach/ms1","files/teach/ms2", "files/teach/pr"]
only_build_toc_files: true

###################################################
# Ausführungseinstellungen
execute:
  execute_notebooks         : auto  # Whether to execute notebooks at build time. Must be one of ("auto", "force", "cache", "off")
  cache                     : ""    # A path to the jupyter cache that will be used to store execution artifacts. Defaults to `_build/.jupyter_cache/`
  exclude_patterns          : []    # A list of patterns to *skip* in execution (e.g. a notebook that takes a really long time)
  timeout                   : 120    # The maximum time (in seconds) each notebook cell is allowed to run.
  run_in_temp               : false # If `True`, then a temporary directory will be created and used as the command working directory (cwd),
                                    # otherwise the notebook's parent directory will be the cwd.
  allow_errors              : false # If `False`, when a code cell raises an error the execution is stopped, otherwise all cells are always run.
  stderr_output             : show  # One of 'show', 'remove', 'remove-warn', 'warn', 'error', 'severe'

###################################################
# Formateinstellungen
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

###################################################
# HTML 
html:
  html_theme: sphinx_book_theme
  favicon: "" # a path to a favicon image
  use_repository_button: false #true  # Whether to add a link to your repository button
  use_issues_button: false #true
  use_edit_page_button: false # true
  use_fullscreen_button: true
  extra_navbar: Powered by <a href="https://jupyterbook.org">Jupyter Book</a>  # Will be displayed underneath the left navbar.
  # extra_footer: | 
  #   <p>
  #   <a href="https://www.iamb.rwth-aachen.de"><img src="https://git.rwth-aachen.de/ulf.liebal/biolabsim/-/raw/master/Figures/Logos/BLS_ProjectFooter.png" alt="BioLabSim Lizenzhinweis und Danksagung" width='250'></a>
  #   </p>
  # <img src='Figures/Logos/Footer_FundingLicence.png' alt='BioLabSim Lizenzhinweis und Danksagung'  width='50'/><br>
  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

###################################################
# LaTeX
latex: 
  latex_engine: xelatex # one of 'pdflatex', 'xelatex' (recommended for unicode), 'luatex', 'platex', 'uplatex'  
  use_jupyterbook_latex: true # use jupyterbook-latex for pdf builds as default  
  latex_logo: ["Figures/Logos/BLS_ProjectFooter.png"]
  latex_show_urls: 'inline'
  latex_use_xindy: true

  latex_documents:
    targetname: BioLabSim.tex

extensions: ["sphinxcontrib.bibtex"]
bibtex_bibfiles:
  - Notebooks/Bibliography.bib
bibtex_encoding: latin
bibtex_reference_style: ieee


###################################################
# Knöpfe
launch_buttons:
  notebook_interface        : classic  # The interface interactive links will activate ["classic", "jupyterlab"]
#  binderhub_url             : https://mybinder.org  # The URL of the BinderHub (e.g., https://mybinder.org)
  jupyterhub_url            : "https://jupyter.rwth-aachen.de/hub/home"  # 
#  thebe                     : false  # Add a thebe button to pages (requires the repository to run on Binder)

# repository:
#   url: https://git.rwth-aachen.de/ulf.liebal/biolabsim # 
#   path_to_book: ""  # An optional path to your book, defaults to repo root
#   branch: master  # An optional branch, defaults to `master`

###################################################
# Fortgeschrittene Einstellungen
sphinx:
  extra_extensions          :   # 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
  config                    :   # key-value pairs to directly over-ride the Sphinx configuration
    html_js_files:              # plotly anzeigbar machen
    - https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js
    mathjax_path: https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js # Mathjax Version 3
    html_show_copyright: false
    latex_elements:
      # Note this line cheats the table parameter into the documentclass[] parameter
      papersize: a4paper,table
      # These lines add the desired packages to the latex build
      preamble: |+
        \usepackage{xcolor}
        \usepackage{booktabs}
        \usepackage{multirow}