From 4b745fcb75e012dd43943058213826039b07888c Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Mon, 17 Jul 2023 05:08:35 +0200 Subject: [PATCH] chore: update readthedocs config --- .readthedocs.yml | 14 ++ Makefile | 32 ++++ doc/python/Dockerfile | 86 +++++++++++ doc/python/Makefile | 157 ++----------------- doc/python/README.md | 53 +++++++ doc/python/environment.yml | 25 +++ doc/python/source/conf.py | 304 +++++++++++-------------------------- 7 files changed, 313 insertions(+), 358 deletions(-) create mode 100644 .readthedocs.yml create mode 100644 doc/python/Dockerfile create mode 100644 doc/python/README.md create mode 100644 doc/python/environment.yml diff --git a/.readthedocs.yml b/.readthedocs.yml new file mode 100644 index 0000000..2e9af22 --- /dev/null +++ b/.readthedocs.yml @@ -0,0 +1,14 @@ +--- +version: 2 + +conda: + environment: doc/python/environment.yml + +sphinx: + configuration: doc/python/source/conf.py + +build: + os: ubuntu-22.04 + jobs: + pre_build: + - make clean swig python diff --git a/Makefile b/Makefile index abeb339..fd34a89 100644 --- a/Makefile +++ b/Makefile @@ -361,3 +361,35 @@ $(PROFILE_OBJECT:%=$(PFLDIR)/%): $(PROFILE_SOURCE:%=$(PFLDIR)/%) $(CXX) $(PROFILE_CXXFLAGS) -c $(@:.o=.cpp) -o $@ ############################################################################# + + +export UID=$(shell id -u) +export GID=$(shell id -g) + +docs: + @$(MAKE) --no-print-directory -C doc/python html + +docs-clean: + rm -rf doc/python/build + +SHELL := /bin/bash +.ONESHELL: +docker-docs: + set -euxo pipefail + + docker build -t ffpopsim-docs-builder \ + --network=host \ + --build-arg UID=$(shell id -u) \ + --build-arg GID=$(shell id -g) \ + doc/python + + docker run -it --rm \ + --network=host \ + --name=ffpopsim-docs-builder-$(shell date +%s) \ + --init \ + --user=$(shell id -u):$(shell id -g) \ + --volume=$(shell pwd):/home/user/src \ + --publish=8000:8000 \ + --workdir=/home/user/src \ + --env 'TERM=xterm-256colors' \ + ffpopsim-docs-builder diff --git a/doc/python/Dockerfile b/doc/python/Dockerfile new file mode 100644 index 0000000..ea1da62 --- /dev/null +++ b/doc/python/Dockerfile @@ -0,0 +1,86 @@ +FROM continuumio/miniconda3:23.3.1-0 + +SHELL ["bash", "-euxo", "pipefail", "-c"] + +ARG DEBIAN_FRONTEND=noninteractive +ARG USER=user +ARG GROUP=user +ARG UID +ARG GID + +ENV TERM="xterm-256color" +ENV HOME="/home/user" + +# Install required packages if running Debian or Ubuntu +RUN set -euxo pipefail >/dev/null \ +&& export DEBIAN_FRONTEND=noninteractive \ +&& apt-get update -qq --yes \ +&& apt-get install -qq --no-install-recommends --yes \ + apt-transport-https \ + bash \ + bash-completion \ + ca-certificates \ + curl \ + git \ + gnupg \ + make \ + sudo \ +>/dev/null \ +&& apt-get clean autoclean >/dev/null \ +&& apt-get autoremove --yes >/dev/null \ +&& rm -rf /var/lib/apt/lists/* + +# Make a user and group +RUN set -euxo pipefail >/dev/null \ +&& \ + if [ -z "$(getent group ${GID})" ]; then \ + addgroup --system --gid ${GID} ${GROUP}; \ + else \ + groupmod -n ${GROUP} $(getent group ${GID} | cut -d: -f1); \ + fi \ +&& \ + if [ -z "$(getent passwd ${UID})" ]; then \ + useradd \ + --system \ + --create-home --home-dir ${HOME} \ + --shell /bin/bash \ + --gid ${GROUP} \ + --groups sudo \ + --uid ${UID} \ + ${USER}; \ + fi \ +&& sed -i /etc/sudoers -re 's/^%sudo.*/%sudo ALL=(ALL:ALL) NOPASSWD:ALL/g' \ +&& sed -i /etc/sudoers -re 's/^root.*/root ALL=(ALL:ALL) NOPASSWD:ALL/g' \ +&& sed -i /etc/sudoers -re 's/^#includedir.*/## **Removed the include directive** ##"/g' \ +&& echo "%sudo ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers \ +&& echo "${USER} ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers \ +&& touch ${HOME}/.hushlogin \ +&& chown -R ${UID}:${GID} "${HOME}" + +RUN set -euxo pipefail >/dev/null \ + && chown -R ${USER}:${GROUP} ${HOME} + +COPY environment.yml ${HOME}/src/ + +WORKDIR ${HOME}/src + +RUN set -euxo pipefail >/dev/null \ + && cd ${HOME}/src \ + && conda install anaconda-client -n base \ + && conda env create -f environment.yml --name org.neherlab.ffpopsim.docs + +USER ${USER} + +RUN set -euxo pipefail >/dev/null \ + && conda init bash \ + && echo "conda activate org.neherlab.ffpopsim.docs" >> ${HOME}/.bashrc + +ENV PATH="/opt/conda/envs/org.neherlab.ffpopsim.docs/bin:${PATH}" + +CMD bash -c "set -euxo pipefail \ + && source ${HOME}/.bashrc \ + && make -j8 swig python \ + && cd doc/python \ + && rm -rf build \ + && make autobuild \ + " diff --git a/doc/python/Makefile b/doc/python/Makefile index 273fdbc..adfa48a 100644 --- a/doc/python/Makefile +++ b/doc/python/Makefile @@ -1,152 +1,27 @@ -# Makefile for Sphinx documentation +# Minimal makefile for Sphinx documentation # -# You can set these variables from the command line. -SPHINXOPTS = -PAPER = +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = source BUILDDIR = build -# Internal variables. -PAPEROPT_a4 = -D latex_paper_size=a4 -PAPEROPT_letter = -D latex_paper_size=letter -ALLSPHINXOPTS = -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: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext - +# Put it first so that "make" without argument is like "make help". help: - @echo "Please use \`make ' where is one of" - @echo " html to make standalone HTML files" - @echo " dirhtml to make HTML files named index.html in directories" - @echo " singlehtml to make a single large HTML file" - @echo " pickle to make pickle files" - @echo " json to make JSON files" - @echo " htmlhelp to make HTML files and a HTML help project" - @echo " qthelp to make HTML files and a qthelp project" - @echo " devhelp to make HTML files and a Devhelp project" - @echo " epub to make an epub" - @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" - @echo " latexpdf to make LaTeX files and run them through pdflatex" - @echo " text to make text files" - @echo " man to make manual pages" - @echo " texinfo to make Texinfo files" - @echo " info to make Texinfo files and run them through makeinfo" - @echo " gettext to make PO message catalogs" - @echo " changes to make an overview of all changed/added/deprecated items" - @echo " linkcheck to check all external links for integrity" - @echo " doctest to run all doctests embedded in the documentation (if enabled)" - -clean: - -rm -rf $(BUILDDIR)/* - -html: - $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." - -dirhtml: - $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." - -singlehtml: - $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml - @echo - @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." - -pickle: - $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle - @echo - @echo "Build finished; now you can process the pickle files." - -json: - $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json - @echo - @echo "Build finished; now you can process the JSON files." - -htmlhelp: - $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp - @echo - @echo "Build finished; now you can run HTML Help Workshop with the" \ - ".hhp project file in $(BUILDDIR)/htmlhelp." - -qthelp: - $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp - @echo - @echo "Build finished; now you can run "qcollectiongenerator" with the" \ - ".qhcp project file in $(BUILDDIR)/qthelp, like this:" - @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/FFPopSim.qhcp" - @echo "To view the help file:" - @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/FFPopSim.qhc" - -devhelp: - $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp - @echo - @echo "Build finished." - @echo "To view the help file:" - @echo "# mkdir -p $$HOME/.local/share/devhelp/FFPopSim" - @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/FFPopSim" - @echo "# devhelp" - -epub: - $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub - @echo - @echo "Build finished. The epub file is in $(BUILDDIR)/epub." - -latex: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo - @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." - @echo "Run \`make' in that directory to run these through (pdf)latex" \ - "(use \`make latexpdf' here to do that automatically)." - -latexpdf: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo "Running LaTeX files through pdflatex..." - $(MAKE) -C $(BUILDDIR)/latex all-pdf - @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." - -text: - $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text - @echo - @echo "Build finished. The text files are in $(BUILDDIR)/text." - -man: - $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man - @echo - @echo "Build finished. The manual pages are in $(BUILDDIR)/man." - -texinfo: - $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo - @echo - @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." - @echo "Run \`make' in that directory to run these through makeinfo" \ - "(use \`make info' here to do that automatically)." + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) -info: - $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo - @echo "Running Texinfo files through makeinfo..." - make -C $(BUILDDIR)/texinfo info - @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." +.PHONY: help Makefile -gettext: - $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale - @echo - @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) -changes: - $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes - @echo - @echo "The overview file is in $(BUILDDIR)/changes." +autobuild: + cd source && sphinx-autobuild --host=0.0.0.0 --port=8000 . ../build/html linkcheck: - $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck - @echo - @echo "Link check complete; look for any errors in the above output " \ - "or in $(BUILDDIR)/linkcheck/output.txt." + sphinx-build -b linkcheck $(SOURCEDIR) $(BUILDDIR)/linkcheck $(SPHINXOPTS) $(O) -doctest: - $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest - @echo "Testing of doctests in the sources finished, look at the " \ - "results in $(BUILDDIR)/doctest/output.txt." diff --git a/doc/python/README.md b/doc/python/README.md new file mode 100644 index 0000000..b7c219f --- /dev/null +++ b/doc/python/README.md @@ -0,0 +1,53 @@ +# FFPopSim Python documentation + +Readthedocs project for FFPopSim + +## Building the docs with Docker (recommended) + +Once you have [Docker](https://docs.docker.com/get-docker/) installed, run from the root of the project: + + make docker-docs + +The HTML files will appear in `docs/build/html/` (for manual inspection) and served on `http://localhost:8000`. The package `sphinx-autobuild` will watch the files, rebuild the HTML and reload the page in the browser on changes. + + +## Building the docs locally + +Build dependencies are managed with [Conda](https://conda.io). + +Enter the docs directory: + + cd doc/python + +Install them into an isolated environment named `org.neherlab.ffpopsim.docs` with: + + conda env create + +Enter the environment with: + + conda activate org.neherlab.ffpopsim.docs + +You can now build the documentation with: + + make html + +which invokes Sphinx to build static HTML pages in `doc/python/build/html/`. + +On some platforms you can view them in the default browser by running: + + open build/html/index.html + +or + + xdg-open build/html/index.html + + +Alternatively, you can run + + make autobuild + +The HTML files will also appear in `doc/python/build/html/` (for manual inspection) and served on `http://localhost:8000`. The `sphinx-autobuild` will watch the files, rebuild the HTML and reload the page in the browser on changes. + +Leave the environment with: + + conda deactivate diff --git a/doc/python/environment.yml b/doc/python/environment.yml new file mode 100644 index 0000000..003298f --- /dev/null +++ b/doc/python/environment.yml @@ -0,0 +1,25 @@ +name: org.neherlab.ffpopsim.docs +channels: + - conda-forge + - defaults +dependencies: + - anaconda-client + - boost-cpp==1.82.0 + - gcc + - gcc_linux-64 + - gsl==2.7 + - gxx + - gxx_linux-64 + - make==4.3 + - numpy + - pip + - recommonmark + - requests + - sphinx + - swig==4.0.2 + - pip: + - sphinx-argparse + - sphinx-autobuild + - sphinx-markdown-tables + - sphinx-rtd-theme + - sphinx-tabs diff --git a/doc/python/source/conf.py b/doc/python/source/conf.py index 7e0029d..b3ed485 100644 --- a/doc/python/source/conf.py +++ b/doc/python/source/conf.py @@ -1,251 +1,121 @@ -# -*- coding: utf-8 -*- +# Configuration file for the Sphinx documentation builder. # -# FFPopSim documentation build configuration file, created by -# sphinx-quickstart2 on Wed Aug 22 09:37:23 2012. -# -# This file is execfile()d with the current directory set to its containing dir. -# -# Note that not all possible configuration values are present in this -# autogenerated file. -# -# All configuration values have a default; values that are commented out -# serve to show the default. +# This file only contains a selection of the most common options. For a full +# list see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html -import sys, os +# -- 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. -sys.path.insert(0, os.path.abspath('../../../pkg/python')) -sys.path.append(os.path.abspath('../sphinxext')) - -# -- 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.autodoc', - 'sphinx.ext.autosummary', - 'sphinx.ext.todo', - 'sphinx.ext.mathjax', - 'sphinx.ext.ifconfig', - 'ipython_console_highlighting', - ] - -# Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] - -# The suffix of source filenames. -source_suffix = '.rst' - -# The encoding of source files. -#source_encoding = 'utf-8-sig' - -# The master toctree document. -master_doc = 'index' - -# General information about the project. -project = u'FFPopSim' -copyright = u'2012-2013, Fabio Zanini, Richard Neher' - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. # -# The short X.Y version. -version = '2.0' -# The full version, including alpha/beta/rc tags. -release = '2.0' - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -#language = None +import os +import sys +from datetime import datetime +sys.path.insert(0, os.path.abspath('')) +sys.path.insert(0, os.path.abspath('sphinxext')) +sys.path.insert(0, os.path.abspath('../pkg/python')) +sys.path.insert(0, os.path.abspath('../../pkg/python')) +sys.path.insert(0, os.path.abspath('../../pkg/python')) + +sys.path.append('pkg/python') +sys.path.append('../pkg/python') +sys.path.append('../../pkg/python') +sys.path.append('../../../pkg/python') +sys.path.append('../../../../pkg/python') + +sys.path.append('src/python') +sys.path.append('../src/python') +sys.path.append('../../src/python') +sys.path.append('../../../src/python') +sys.path.append('../../../../src/python') + +sys.path.append('..') +sys.path.append('../..') +sys.path.append('../../..') + +# At top on conf.py (with other import statements) +import recommonmark +from recommonmark.transform import AutoStructify + +# -- Project information ----------------------------------------------------- + +project = 'FFPopSim' +copyright = f'2015-{datetime.now().year}, Fabio Zanini and Richard Neher' +author = 'FFPopSim team' + +# -- General configuration --------------------------------------------------- + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [ + 'recommonmark', + 'sphinx.ext.autodoc', + 'sphinx.ext.autosummary', + 'sphinx.ext.ifconfig', + 'sphinx.ext.intersphinx', + 'sphinx.ext.mathjax', + 'sphinx.ext.todo', + 'sphinx_markdown_tables', + 'sphinx_tabs.tabs', + 'sphinxarg.ext', +] -# There are two options for replacing |today|: either, you set today to some -# non-false value, then it is used: -#today = '' -# Else, today_fmt is used as the format for a strftime call. -#today_fmt = '%B %d, %Y' +# Add any paths that contain templates here, relative to this directory. +# templates_path = ['templates'] # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. -exclude_patterns = [] - -# The reST default role (used for this markup: `text`) to use for all documents. -#default_role = None - -# If true, '()' will be appended to :func: etc. cross-reference text. -#add_function_parentheses = True - -# If true, the current module name will be prepended to all description -# unit titles (such as .. function::). -add_module_names = False - -# If true, sectionauthor and moduleauthor directives will be shown in the -# output. They are ignored by default. -#show_authors = False +# This pattern also affects html_static_path and html_extra_path. +exclude_patterns = [ + "README.md" +] # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' -# A list of ignored prefixes for module index sorting. -#modindex_common_prefix = [] +add_module_names = False autodoc_member_order = 'groupwise' -#autosummary_generate = True -# -- Options for HTML output --------------------------------------------------- +# -- 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 = 'default' - -# 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 = {} - -# Add any paths that contain custom themes here, relative to this directory. -#html_theme_path = [] - -# The name for this set of Sphinx documents. If None, it defaults to -# " v documentation". -#html_title = None - -# A shorter title for the navigation bar. Default is the same as html_title. -#html_short_title = None - -# The name of an image file (relative to this directory) to place at the top -# of the sidebar. -#html_logo = None - -# The name of an image file (within the static path) to use as favicon of the -# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 -# pixels large. -#html_favicon = None +html_theme = 'sphinx_rtd_theme' # 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'] - -# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, -# using the given strftime format. -#html_last_updated_fmt = '%b %d, %Y' +# html_static_path = ['_static'] -# If true, SmartyPants will be used to convert quotes and dashes to -# typographically correct entities. -#html_use_smartypants = True +# html_css_files = [ +# 'css/custom.css', +# ] -# Custom sidebar templates, maps document names to template names. -#html_sidebars = {} +# html_favicon = '_static/favicon.ico' -# Additional templates that should be rendered to pages, maps page names to -# template names. -#html_additional_pages = {} - -# If false, no module index is generated. -#html_domain_indices = True - -# If false, no index is generated. -#html_use_index = True - -# If true, the index is split into individual pages for each letter. -#html_split_index = False - -# If true, links to the reST sources are added to the pages. -#html_show_sourcelink = True - -# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. -#html_show_sphinx = True - -# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. -#html_show_copyright = True - -# If true, an OpenSearch description file will be output, and all pages will -# contain a tag referring to it. The value of this option must be the -# base URL from which the finished HTML is served. -#html_use_opensearch = '' - -# This is the file name suffix for HTML files (e.g. ".xhtml"). -#html_file_suffix = None - -# Output file base name for HTML help builder. -htmlhelp_basename = 'FFPopSimdoc' - - -# -- 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': '', +html_theme_options = { + 'logo_only': False, + 'collapse_navigation': False, + 'titles_only': True, } -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, author, documentclass [howto/manual]). -latex_documents = [ - ('index', 'FFPopSim.tex', u'FFPopSim Documentation', - u'Fabio Zanini, Richard Neher', 'manual'), -] - -# The name of an image file (relative to this directory) to place at the top of -# the title page. -#latex_logo = None - -# For "manual" documents, if this is true, then toplevel headings are parts, -# not chapters. -#latex_use_parts = False - -# If true, show page references after internal links. -#latex_show_pagerefs = False - -# If true, show URL addresses after external links. -#latex_show_urls = False -# Documents to append as an appendix to all manuals. -#latex_appendices = [] +# -- Cross-project references ------------------------------------------------ -# If false, no module index is generated. -#latex_domain_indices = True - - -# -- Options for manual page output -------------------------------------------- - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - ('index', 'ffpopsim', u'FFPopSim Documentation', - [u'Fabio Zanini, Richard Neher'], 1) -] - -# If true, show URL addresses after external links. -#man_show_urls = False - - -# -- 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 = [ - ('index', 'FFPopSim', u'FFPopSim Documentation', - u'Fabio Zanini, Richard Neher', 'FFPopSim', 'One line description of project.', - 'Miscellaneous'), -] - -# Documents to append as an appendix to all manuals. -#texinfo_appendices = [] +intersphinx_mapping = { +} -# If false, no module index is generated. -#texinfo_domain_indices = True -# How to display URL addresses: 'footnote', 'no', or 'inline'. -#texinfo_show_urls = 'footnote' +# At the bottom of conf.py +def setup(app): + app.add_config_value('recommonmark_config', { + # 'url_resolver': lambda url: github_doc_root + url, + 'auto_toc_tree_section': 'Contents', + 'enable_math': True, + 'enable_inline_math': True, + }, True) + app.add_transform(AutoStructify)