Merge pull request #2 from CCPBioSim/docs

put docs in sphinx

Author: jimboid

.github/workflows/sphinx.yaml

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+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -n -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+
+.PHONY: all help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest coverage gettext customdefault
+
+## Runs nit-picky and converting warnings into errors to
+## make sure the documentation is properly written
+customdefault:
+	$(SPHINXBUILD) -b html -nW $(ALLSPHINXOPTS) $(BUILDDIR)/html
+
+all: html
+
+clean:
+	rm -r $(BUILDDIR)
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+
+view:
+	xdg-open $(BUILDDIR)/html/index.html

pages/Makefile

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+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/stable/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+
+# Incase the project was not installed
+import os
+import sys
+import time
+
+sys.path.insert(0, os.path.abspath(".."))
+
+# -- Project information -----------------------------------------------------
+
+project = "ccpbiosim dev"
+copyright_first_year = "2025"
+copyright_owners = "CCPBioSim"
+author = "James Gebbie-Rayet"
+current_year = str(time.localtime().tm_year)
+copyright_year_string = (
+    current_year
+    if current_year == copyright_first_year
+    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",
+    "sphinx.ext.extlinks",
+    "sphinx_copybutton",
+    "myst_parser",
+]
+
+autosummary_generate = True
+napoleon_google_docstring = False
+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.
+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_documents = [
+    (
+        master_doc,
+        "ccpbiosim.tex",
+        "CCPBioSim Developers Documentation",
+        "CCPBioSim",
+        "manual",
+    ),
+]
+
+
+# -- 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,
+        "CCPBioSim",
+        "CCPBioSim Developers Documentation",
+        author,
+        "CCPBioSim",
+        "CCPBioSim developer pages for its GitHub organisation.",
+    ),
+]
+
+
+# -- Extension configuration -------------------------------------------------
+def setup(app):
+    app.add_css_file("custom.css")

pages/source/_static/ccpbiosim-dark-sq.png

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+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:
+
+   workshops-dash
+
+Indices and tables
+------------------
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`