Skip to content

Commit

Permalink
Add doc generated from code and docstrings
Browse files Browse the repository at this point in the history 
GitHub: fix mxcube#1099
  • Loading branch information
@fabcor-maxiv
fabcor-maxiv committed Oct 16, 2023
1 parent 6cc4c55 commit bfcfba4
Show file tree
Hide file tree
Showing 6 changed files with 54 additions and 250 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/pages.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ jobs:
environment-file: "conda-environment.yml"

- name: "Install dependencies with Poetry"
run: "${MAMBA_EXE} run --name mxcubeweb poetry install"
run: "${MAMBA_EXE} run --name mxcubeweb poetry install --only=docs,main"

- name: "Build documentation with Sphinx"
run: "${MAMBA_EXE} run --name mxcubeweb make --directory=./docs/ html"
Expand Down
7 changes: 3 additions & 4 deletions .readthedocs.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,17 +13,16 @@
version: 2

build:

os: "ubuntu-22.04"

tools:
python: "mambaforge-22.9"

commands:
- "mamba env create --file conda-environment.yml"
- "mamba run --name mxcubeweb poetry install"
- "mamba run --name mxcubeweb poetry install --only=docs,main"
- "(mamba run --name mxcubeweb redis-server &) && mamba run --name mxcubeweb python -m sphinx -T -E -b html -d _build/doctrees -c docs docs/source ${READTHEDOCS_OUTPUT}/html && mamba run --name mxcubeweb redis-cli shutdown"

sphinx:
configuration: "docs/conf.py"


... # EOF
269 changes: 25 additions & 244 deletions docs/conf.py
View file
Original file line number Diff line number Diff line change
@@ -1,16 +1,5 @@
# -*- coding: utf-8 -*-
#
# MXCuBE3 documentation build configuration file, created by
# sphinx-quickstart on Tue Nov 10 16:07:35 2015.
#
# 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.


import datetime
import importlib.metadata
Expand All @@ -29,45 +18,21 @@
server.flask.testing = True


# -- Sphinx configuration -------------------------------------------------


# 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('.'))

# -- 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.doctest', 'sphinx.ext.intersphinx', 'sphinx.ext.todo']
extensions = [
"myst_parser",
"sphinxcontrib.autohttp.flask",
]

# 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": "restructuredtext",
".md": "markdown",
}

# The encoding of source files.
# source_encoding = 'utf-8-sig'

# The master toctree document.
root_doc = "contents"

# General information about the project.
project = "MXCuBE-Web"
author = PROJECT_PACKAGE_METADATA["Author"]
copyright = f"{datetime.datetime.today().year}, {author}"
Expand All @@ -77,70 +42,18 @@
# 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 = PROJECT_PACKAGE_METADATA["Version"]
# The full version, including alpha/beta/rc tags.
release = version

# 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"

# 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'

# 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 = True

# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
# show_authors = False

# 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 = []

# If true, keep warnings as "system message" paragraphs in the built documents.
# keep_warnings = False

# If true, `todo` and `todoList` produce output, else they produce nothing.
# todo_include_todos = False

rst_prolog = f"""
.. |project| replace:: {project}
"""


# -- 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 = "alabaster"

# 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 = {
"description": DOCUMENT_DESCRIPTION,
"github_banner": "true",
Expand All @@ -149,44 +62,6 @@
"github_user": "mxcube",
}

# 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
# "<project> v<release> 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

# 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"]

# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
# html_extra_path = []

# 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'

# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
# html_use_smartypants = True

# Custom sidebar templates, maps document names to template names.
html_sidebars = {
"**": [
"about.html",
Expand All @@ -195,143 +70,49 @@
],
}

# 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
# -- Extensions ---------------------------------------------------------------

# If false, no index is generated.
# html_use_index = True
# -- sphinx.ext.autodoc
# https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html

# If true, the index is split into individual pages for each letter.
# html_split_index = False
extensions.append("sphinx.ext.autodoc")

# 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
autodoc_default_options = {
"members": True,
}

# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
# html_show_copyright = True
autodoc_typehints = "both"

# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> 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
# -- sphinx.ext.autosummary
# https://www.sphinx-doc.org/en/master/usage/extensions/autosummary.html

# Language to be used for generating the HTML full-text search index.
# Sphinx supports the following languages:
# 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
# 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
# html_search_language = 'en'
extensions.append("sphinx.ext.autosummary")

# A dictionary with options for the search language support, empty by default.
# Now only 'ja' uses this config value
# html_search_options = {'type': 'default'}
autosummary_generate = True

# The name of a javascript file (relative to the configuration directory) that
# implements a search results scorer. If empty, the default will be used.
# html_search_scorer = 'scorer.js'

# Output file base name for HTML help builder.
htmlhelp_basename = f"{PROJECT_SLUG_NAME}-doc"
# -- sphinx.ext.intersphinx
# https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html

# -- Options for LaTeX output ---------------------------------------------
extensions.append("sphinx.ext.intersphinx")

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',
intersphinx_mapping = {
"python": ("https://docs.python.org/3/", None),
}

# 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 = [
(
root_doc,
"{PROJECT_SLUG_NAME}.tex",
DOCUMENT_DESCRIPTION,
author,
"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 = []
# -- sphinx.ext.viewcode
# https://www.sphinx-doc.org/en/master/usage/extensions/viewcode.html

# If false, no module index is generated.
# latex_domain_indices = True
extensions.append("sphinx.ext.viewcode")


# -- Options for manual page output ---------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
(
root_doc,
PROJECT_SLUG_NAME,
DOCUMENT_DESCRIPTION,
[author],
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 = [
(
root_doc,
PROJECT_SLUG_NAME,
project,
author,
project,
DOCUMENT_DESCRIPTION,
"Miscellaneous",
),
]

# Documents to append as an appendix to all manuals.
# texinfo_appendices = []
# -- sphinxcontrib.autohttp.flask
# https://sphinxcontrib-httpdomain.readthedocs.io

# If false, no module index is generated.
# texinfo_domain_indices = True
extensions.append("sphinxcontrib.autohttp.flask")

# How to display URL addresses: 'footnote', 'no', or 'inline'.
# texinfo_show_urls = 'footnote'

# If true, do not generate a @detailmenu in the "Top" node's menu.
# texinfo_no_detailmenu = False
# EOF
15 changes: 15 additions & 0 deletions docs/source/dev/api.rst
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
..

***
API
***

.. autosummary::
:toctree: autosummary
:recursive:

mxcube3


.. EOF
Loading

0 comments on commit bfcfba4

Please sign in to comment.