From bfcfba4fdd239fb7b0603f86d6363c8d5fecc55f Mon Sep 17 00:00:00 2001 From: fabcor Date: Mon, 16 Oct 2023 14:46:22 +0200 Subject: [PATCH] Add doc generated from code and docstrings GitHub: fix https://github.com/mxcube/mxcubeweb/issues/1099 --- .github/workflows/pages.yaml | 2 +- .readthedocs.yaml | 7 +- docs/conf.py | 269 +++---------------------- docs/source/dev/api.rst | 15 ++ docs/source/dev/autosummary/.gitignore | 7 + pyproject.toml | 4 +- 6 files changed, 54 insertions(+), 250 deletions(-) create mode 100644 docs/source/dev/api.rst create mode 100644 docs/source/dev/autosummary/.gitignore diff --git a/.github/workflows/pages.yaml b/.github/workflows/pages.yaml index 0c46d9b6a..1712c1f62 100644 --- a/.github/workflows/pages.yaml +++ b/.github/workflows/pages.yaml @@ -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" diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 45d4d23ea..fe2a5fd2d 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -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 diff --git a/docs/conf.py b/docs/conf.py index 11e2c3510..65796e50e 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -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 @@ -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}" @@ -77,56 +42,9 @@ # 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} """ @@ -134,13 +52,8 @@ # -- 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", @@ -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 -# " 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 - -# 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", @@ -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 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 diff --git a/docs/source/dev/api.rst b/docs/source/dev/api.rst new file mode 100644 index 000000000..d5a8db160 --- /dev/null +++ b/docs/source/dev/api.rst @@ -0,0 +1,15 @@ +.. + + +*** +API +*** + +.. autosummary:: + :toctree: autosummary + :recursive: + + mxcube3 + + +.. EOF diff --git a/docs/source/dev/autosummary/.gitignore b/docs/source/dev/autosummary/.gitignore new file mode 100644 index 000000000..6976c6bf7 --- /dev/null +++ b/docs/source/dev/autosummary/.gitignore @@ -0,0 +1,7 @@ +# + + +* + + +# EOF diff --git a/pyproject.toml b/pyproject.toml index 2490a39ff..5ac9d328e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -46,10 +46,12 @@ mxcube_video_streamer = "1.0.0" bcrypt = "^4.0.1" [tool.poetry.dev-dependencies] -myst-parser = "^2.0.0" pre-commit = "2.20.0" pytest = "7.1.3" pytest-cov = "4.0.0" + +[tool.poetry.group.docs.dependencies] +myst-parser = "^2.0.0" sphinx = "<7.2" sphinxcontrib-httpdomain = "^1.8.1"