From e8832e4cc6ce55dc1935db0aaed1f99b39a5e322 Mon Sep 17 00:00:00 2001 From: dcherian Date: Sun, 14 Jun 2020 10:50:38 -0600 Subject: [PATCH] docs. --- ci/doc.yml | 17 ++ doc/Makefile | 20 +++ doc/conf.py | 296 ++++++++++++++++++++++++++++++++ doc/examples/index.rst | 7 + doc/examples/introduction.ipynb | 37 ++-- doc/index.rst | 22 +++ doc/make.bat | 35 ++++ 7 files changed, 407 insertions(+), 27 deletions(-) create mode 100644 ci/doc.yml create mode 100644 doc/Makefile create mode 100644 doc/conf.py create mode 100644 doc/examples/index.rst create mode 100644 doc/index.rst create mode 100644 doc/make.bat diff --git a/ci/doc.yml b/ci/doc.yml new file mode 100644 index 00000000..d6c02a30 --- /dev/null +++ b/ci/doc.yml @@ -0,0 +1,17 @@ +name: cf-xarray-doc +channels: + - conda-forge +dependencies: + - pip + - python=3.8 + - matplotlib + - netcdf4 + - xarray + - sphinx + - nbsphinx + - numpydoc + - ipython + - ipykernel + - pip: + - cf_xarray + - sphinx-book-theme diff --git a/doc/Makefile b/doc/Makefile new file mode 100644 index 00000000..d4bb2cbb --- /dev/null +++ b/doc/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = . +BUILDDIR = _build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# 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) diff --git a/doc/conf.py b/doc/conf.py new file mode 100644 index 00000000..2ee931f9 --- /dev/null +++ b/doc/conf.py @@ -0,0 +1,296 @@ +# -*- coding: utf-8 -*- +# +# complexity documentation build configuration file, created by +# sphinx-quickstart on Tue Jul 9 22:26:36 2013. +# +# 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 os +import sys + +import cf_xarray # noqa + +# 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('.')) + +cwd = os.getcwd() +parent = os.path.dirname(cwd) +sys.path.insert(0, parent) + + +# -- 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.viewcode", + "sphinx.ext.autosummary", + "sphinx.ext.doctest", + "sphinx.ext.intersphinx", + "sphinx.ext.extlinks", + "numpydoc", + "IPython.sphinxext.ipython_console_highlighting", + "IPython.sphinxext.ipython_directive", + "nbsphinx", +] + +extlinks = { + "issue": ("https://github.com/xarray-contrib/cf-xarray/issues/%s", "GH#"), + "pr": ("https://github.com/xarray-contrib/cf-xarray/pull/%s", "GH#"), +} + +# Add any paths that contain templates here, relative to this directory. +templates_path = ["_templates"] + +# The suffix of source filenames. +source_suffix = ".rst" + +# Enable notebook execution +# https://nbsphinx.readthedocs.io/en/0.4.2/never-execute.html +# nbsphinx_execute = 'auto' +# Allow errors in all notebooks by +nbsphinx_allow_errors = True + +# Disable cell timeout +nbsphinx_timeout = -1 + + +# The encoding of source files. +# source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = "index" + +# General information about the project. +project = "cf_xarray" +current_year = datetime.datetime.now().year +copyright = f"2020-{current_year}, cf_xarray Developers" +author = "cf_xarray Developers" +# 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 = cf_xarray.__version__.split("+")[0] +# The full version, including alpha/beta/rc tags. +# release = cf_xarray.__version__ + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# language = None + +# 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 = ["_build"] + +# 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 + + +# -- 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 = "sphinx_book_theme" + +# 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 = { + "github_url": "https://github.com/xarray-contrib/cf-xarray", + "use_edit_page_button": True, +} + +html_context = { + "github_user": "xarray-contrib", + "github_repo": "cf-xarray", + "github_version": "master", + "doc_path": "doc", +} + +# 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"] + +# 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 = {} + +# 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 = "cf_xarraydoc" + + +# -- 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': '', +# } + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, author, documentclass [howto/manual]). +# latex_documents = [ +# ('index', 'cf_xarray.tex', u'cf_xarray Documentation', +# u'Deepak Cherian', '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 = [] + +# 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", "cf_xarray", "cf_xarray Documentation", [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 = [ +# ('index', 'cf_xarray', u'cf_xarray Documentation', +# author, 'cf_xarray', 'One line description of project.', +# 'Miscellaneous'), +# ] + +# Documents to append as an appendix to all manuals. +# texinfo_appendices = [] + +# If false, no module index is generated. +# texinfo_domain_indices = True + +# 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 + +intersphinx_mapping = { + "python": ("https://docs.python.org/3/", None), + "xarray": ("http://xarray.pydata.org/en/stable/", None), +} diff --git a/doc/examples/index.rst b/doc/examples/index.rst new file mode 100644 index 00000000..8aab5625 --- /dev/null +++ b/doc/examples/index.rst @@ -0,0 +1,7 @@ +Examples +======== + +.. toctree:: + :maxdepth: 2 + + introduction diff --git a/doc/examples/introduction.ipynb b/doc/examples/introduction.ipynb index 8b33f250..52d4e683 100644 --- a/doc/examples/introduction.ipynb +++ b/doc/examples/introduction.ipynb @@ -1,20 +1,12 @@ { "cells": [ - { - "cell_type": "markdown", - "metadata": { - "toc": true - }, - "source": [ - "

Table of Contents

\n", - "
" - ] - }, { "cell_type": "markdown", "metadata": {}, "source": [ - "This is a brief introduction to `cf_xarray`'s capabilities." + "# Introduction to `cf_xarray`\n", + "\n", + "This notebook is a brief introduction to `cf_xarray`'s current capabilities." ] }, { @@ -95,7 +87,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# What attributes have been discovered?" + "## What attributes have been discovered?" ] }, { @@ -160,14 +152,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Features" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Accessing coordinate variables\n", + "## Feature: Accessing coordinate variables\n", "\n", "`.cf` implements `__getitem__` to allow easy access to coordinate and axis variables." ] @@ -232,7 +217,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Rewriting arguments\n", + "## Feature: Rewriting arguments\n", "\n", "`cf_xarray` can rewrite arguments for a large number of xarray functions. By this I mean that instead of specifing say `dim=\"lon\"`, you can pass `dim=\"X\"` or `dim=\"longitude\"` and `cf_xarray` will rewrite that to `dim=\"lon\"` based on the attributes present in the dataset. \n", "\n", @@ -381,16 +366,16 @@ } }, "source": [ - "coarsen works but eberything later will break because of xarray bug https://github.com/pydata/xarray/issues/4120\n", + "``coarsen`` works but everything later will break because of xarray bug https://github.com/pydata/xarray/issues/4120\n", "\n", - "ds.isel(lon=slice(50)).cf.coarsen(Y=5, X=10).mean()" + "``ds.isel(lon=slice(50)).cf.coarsen(Y=5, X=10).mean()``" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "### miscellaneous features\n", + "#### miscellaneous features\n", "\n", "You can mix \"special names\" and variable names" ] @@ -413,9 +398,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Augmented functionality\n", - "\n", - "### Cell Measures\n", + "## Feature: Weight by Cell Measures\n", "\n", "`cf_xarray` can weight by cell measure variables `\"area\"` and `\"volume\"` if the appropriate attribute is set" ] diff --git a/doc/index.rst b/doc/index.rst new file mode 100644 index 00000000..8fa889aa --- /dev/null +++ b/doc/index.rst @@ -0,0 +1,22 @@ +.. cf_xarray documentation master file, created by + sphinx-quickstart on Mon Jun 1 06:30:20 2020. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to cf_xarray's documentation! +===================================== + +``cf_xarray`` is a lightweight accessor that allows you to interpret CF attributes present +on xarray objects. + +.. toctree:: + :maxdepth: 2 + + examples/index + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/doc/make.bat b/doc/make.bat new file mode 100644 index 00000000..2119f510 --- /dev/null +++ b/doc/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=. +set BUILDDIR=_build + +if "%1" == "" goto help + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.http://sphinx-doc.org/ + exit /b 1 +) + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd