fix so all md format

Author: jimboid

.gitignore

@@ -0,0 +1 @@
+pages/build/

pages/source/conf.py

@@ -32,26 +32,14 @@
     else f"{copyright_first_year}-{current_year}"
 )
 copyright = f"{copyright_year_string}, {copyright_owners}. All rights reserved"
-
-# The short X.Y version
 version = ""
-# The full version, including alpha/beta/rc tags
 release = ""
 
-
 # -- General configuration ---------------------------------------------------
 
-# If your documentation needs a minimal Sphinx version, state it here.
-#
-# needs_sphinx = '1.0'
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
 extensions = [
     "sphinx.ext.autosummary",
     "sphinx.ext.autodoc",
-    "sphinx.ext.mathjax",
     "sphinx.ext.viewcode",
     "sphinx.ext.napoleon",
     "sphinx.ext.intersphinx",
@@ -65,94 +53,31 @@
 napoleon_use_param = False
 napoleon_use_ivar = True
 
-# Add any paths that contain templates here, relative to this directory.
-# templates_path = ["_templates"]
-
-# The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-#
-source_suffix = ['.rst', '.md']
-#source_suffix = ".md"
-
-# The master toctree document.
+source_suffix = [".rst", ".md"]
 master_doc = "index"
 
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
 language = "en"
 
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This pattern also affects html_static_path and html_extra_path .
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = "default"
 
-
 # -- Options for HTML output -------------------------------------------------
 
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-#
 html_theme = "furo"
-# html_logo = "images/blaah"
-
-# Theme options are theme-specific and customize the look and feel of a theme
-# further.  For a list of options available for each theme, see the
-# documentation.
-#
-# html_theme_options = {}
 html_theme_options = {
 "light_logo": "ccpbiosim-dark-sq.png",  # Your light mode logo file
 "dark_logo": "ccpbiosim-light-sq.png",   # Your dark mode logo file
 }
 
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
 
-# Custom sidebar templates, must be a dictionary that maps document names
-# to template names.
-#
-# The default sidebars (for documents that don't match any pattern) are
-# defined by theme itself.  Builtin themes are using these templates by
-# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
-# 'searchbox.html']``.
-#
-# html_sidebars = {}
-
-
-# -- Options for HTMLHelp output ---------------------------------------------
-
 # Output file base name for HTML help builder.
 htmlhelp_basename = "ccpbiosim_doc"
 
-
 # -- Options for LaTeX output ------------------------------------------------
-
-latex_elements = {
-    # The paper size ('letterpaper' or 'a4paper').
-    #
-    # 'papersize': 'letterpaper',
-    # The font size ('10pt', '11pt' or '12pt').
-    #
-    # 'pointsize': '10pt',
-    # Additional stuff for the LaTeX preamble.
-    #
-    # 'preamble': '',
-    # Latex figure (float) alignment
-    #
-    # 'figure_align': 'htbp',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title,
-#  author, documentclass [howto, manual, or own class]).
+latex_elements = {}
 latex_documents = [
     (
         master_doc,
@@ -163,19 +88,10 @@
     ),
 ]
 
-
 # -- Options for manual page output ------------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
 man_pages = [(master_doc, "CCPBioSim", "CCPBioSim Developers Documentation", [author], 1)]
 
-
 # -- Options for Texinfo output ----------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-#  dir menu entry, description, category)
 texinfo_documents = [
     (
         master_doc,
@@ -187,7 +103,6 @@
     ),
 ]
 
-
 # -- Extension configuration -------------------------------------------------
 def setup(app):
     app.add_css_file("custom.css")

pages/source/index.rst pages/source/index.mdpages/source/index.rst renamed to pages/source/index.md

@@ -1,19 +1,18 @@
-Welcome to CCPBioSim Developer Organisation
-===========================================
+# Welcome to CCPBioSim Developer Organisation
 
 This GitHub organisation contains software, workshop material and many other types of repositories. These pages are aimed at developers, not users. They contain information about our development practices as well as details of which repositories are actively maintained and which are not.
 
 This is currently a work in progress. Over time we wish to add things like roadmaps, dashboards, docs about coding etc etc.
 
-.. toctree::
-   :maxdepth: 2
-   :caption: Contents:
+```{toctree}
+---
+maxdepth: 2
+caption: Contents:
+---
+workshops-dash.md
+```
 
-   workshops-dash
+## Indices and tables
 
-Indices and tables
-------------------
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+- {ref}`genindex`
+- {ref}`search`