mkdocs.yml

site_name: CCP4-ED
site_author: Tarik Ronan Drevon

docs_dir: 'docs'
site_dir: 'site'

theme: readthedocs
markdown_extensions:
    - wikilinks
    - toc:
        title: Table of Contents
    - attr_list
    #- fenced_code
    - pymdownx.highlight
    - pymdownx.critic
    - pymdownx.tasklist
    - mdx_math:
        enable_dollar_delimiter: True

extra_javascript:
 # - 'MathJax.js'
 - 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS_HTML'
 - 'mathjaxhelper.js'

plugins:
  - macros


nav:
 - Index: 'index.md'
 - ED simulations :
     #- 'Overview' : 'projects/index.md'
     # - 'old' : 'projects/simulations/old_simus.md'
     - 'glycine' : 'projects/simulations/glycine.md'
     # - 'ireloh' : 'projects/simulations/ireloh.md'
 - Programs :
     - 'Multislice 3D TEMSIM' : 'projects/multislice/temsim.md'
     - 'Multislice 2D' : 'projects/multislice/multi2D.md'
     - 'Bloch' : 'projects/bloch/bloch.md'
     - 'Felix' : 'projects/felix.md'
     - 'Dyngo' : 'projects/dyngo.md'
     - 'Edly'  : 'projects/edly.md'
     # - 'NearBragg' : 'projects/nearBragg/index.md'
     #- 'Wallpapers' : 'projects/wallpapers/index.md'
 - Theory:
     - 'Scattering' : 'projects/scattering.md'
     - 'Dynamical diffraction' : 'projects/dynamical_diffraction.md'
     - 'Multislice' : 'projects/multislice/index.md'
 - Books:
     - 'Electron Crystallography, Zou, 2011' : 'readings/zou2011.md'
     # - 'Advanced TEM, Zuo, Spence, 2017' : 'readings/Spence2017.md'
     - 'chronology' : 'readings/chrono.md'
     - 'Advanced computing in EM, Kirkland, 2010' : 'readings/Kirkland2010.md'
 - Literature:
     - 'ED Papers' : 'readings/papers.md'
     - 'Multislice Literature' : 'readings/multislice.md'
     - 'Inelastic scattering' : 'readings/inelastic_scattering.md'
     - 'Quantum computing' : 'readings/qc.md'
     # - 'Misc' : 'readings/misc_papers.md'
     # - 'CowleyMoodie1957' : 'readings/CowleyMoodie1957.md'
     - 'inverse scattering problem' : 'readings/inverse_scattering.md'
 - Planning:
     - 'Week progress' : 'planning/week_progress.md'
     - 'Previous weeks' : 'planning/previous_weeks.md'
     #- 'Meetings' : 'planning/meetings.md'
     - 'TODO' : 'planning/TODO.md'
 - Crystallography:
     - 'Tables and useful links' : 'misc/tables.md'
     - 'Compounds' : 'misc/compounds.md'
     #- 'Instruments' : 'misc/instruments.md'
 - Misc:
     - 'Commands' : 'misc/useful.md'
     - 'Python' : 'misc/python.md'
     - 'Scattering particles' : 'misc/particle_scattering.md'