From 3f153d170f47207840b8fb9b36244c1a1612a4e6 Mon Sep 17 00:00:00 2001 From: Antonio Jimenez Pastor Date: Wed, 10 Jul 2019 22:14:47 +0200 Subject: [PATCH] Added all the documentation files Updated the Makefile: fixed small error in the name of the package Small change in ddFunction.py --- Makefile | 4 +- ajpastor/dd_functions/ddFunction.py | 3 +- docs/Makefile | 177 ++++++++++++++++++ docs/source/conf.py | 351 ++++++++++++++++++++++++++++++++++++ docs/source/ddExamples.rst | 9 + docs/source/ddFunction.rst | 9 + docs/source/index.rst | 35 ++++ docs/source/toDiffAlgebraic.rst | 9 + setup.py | 7 +- 9 files changed, 600 insertions(+), 4 deletions(-) create mode 100644 docs/Makefile create mode 100644 docs/source/conf.py create mode 100644 docs/source/ddExamples.rst create mode 100644 docs/source/ddFunction.rst create mode 100644 docs/source/index.rst create mode 100644 docs/source/toDiffAlgebraic.rst diff --git a/Makefile b/Makefile index 08fca30..a352546 100644 --- a/Makefile +++ b/Makefile @@ -6,7 +6,7 @@ VERSION=$(shell cat ./VERSION) SAGE = sage # Package folder -PACKAGE = sage_sample +PACKAGE = ajpastor all: install test @@ -66,5 +66,5 @@ clean_pyc: @echo "Cleaning the Python precompiled files (.pyc)" @find . -name "*.pyc" -exec rm {} + -.PHONY: all install develop test coverage clean clean-doc doc doc-pdf +.PHONY: all install develop test coverage clean clean_doc doc doc-pdf diff --git a/ajpastor/dd_functions/ddFunction.py b/ajpastor/dd_functions/ddFunction.py index 3e10024..00e8dd9 100644 --- a/ajpastor/dd_functions/ddFunction.py +++ b/ajpastor/dd_functions/ddFunction.py @@ -16,7 +16,6 @@ from sage.categories.pushout import ConstructionFunctor; #ajpastor imports from ajpastor.operator.operator import Operator; -from ajpastor.operator.oreOperator import w_OreOperator; from ajpastor.operator.directStepOperator import DirectStepOperator; from ajpastor.operator.fullLazyOperator import FullLazyOperator; @@ -2935,6 +2934,8 @@ def _command_list(elements): # Some global pre-defined DD-Rings DFinite = None; try: + from ore_algebra import *; + from ajpastor.operator.oreOperator import w_OreOperator; DFinite = DDRing(PolynomialRing(QQ,x), default_operator=w_OreOperator); except ImportError: ## No ore_algebra package found diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..e949e5c --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,177 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = build + +# User-friendly check for sphinx-build +ifeq ($(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 = -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 + +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 " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" + @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 " xml to make Docutils-native XML files" + @echo " pseudoxml to make pseudoxml-XML files for display purposes" + @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. 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The pseudo-XML files are in $(BUILDDIR)/pseudoxml." diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 0000000..767f625 --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,351 @@ +# -*- coding: utf-8 -*- +# +# sample documentation build configuration file, +# inspried by slabbe configuration file created sphinx-quickstart +# +# 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. + +# General information about the project. +project = u"DD-finite functions in Sage" +copyright = u'2019' +package_name = 'ajpastor' +package_folder = "../../ajpastor" +authors = u"Antonio Jimenez-Pastor" + +import sys +import os + +from sage.env import SAGE_DOC_SRC, SAGE_DOC, SAGE_SRC + +try: + import sage.all +except ImportError: + raise RuntimeError("to build the documentation you need to be inside a Sage shell (run first the command 'sage -sh' in a shell") + + + +# 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.append(os.path.abspath(package_folder)) +sys.path.append(os.path.join(SAGE_SRC, "sage_setup", "docbuild", "ext")) + +# -- 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', + 'sage_autodoc', + 'sage_package.sphinx', + 'sphinx.ext.doctest', + 'sphinx.ext.coverage', +] + +# Add any paths that contain templates here, relative to this directory. +# templates_path = ['_templates'] +templates_path = [os.path.join(SAGE_DOC_SRC, 'common', 'templates'), '_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' + + + +# 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 = open("../../VERSION").read().strip() +# 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. +#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 = [] + +# The reST default role (used for this markup: `text`) to use for all +# documents. +default_role = 'math' + +# 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 + +pythonversion = sys.version.split(' ')[0] +# Python and Sage trac ticket shortcuts. For example, :trac:`7549` . +extlinks = { + 'python': ('https://docs.python.org/release/'+pythonversion+'/%s', ''), + 'trac': ('http://trac.sagemath.org/%s', 'trac ticket #'), + 'wikipedia': ('https://en.wikipedia.org/wiki/%s', 'Wikipedia article '), + 'arxiv': ('http://arxiv.org/abs/%s', 'Arxiv '), + 'oeis': ('https://oeis.org/%s', 'OEIS sequence '), + 'doi': ('https://dx.doi.org/%s', 'doi:'), + 'mathscinet': ('http://www.ams.org/mathscinet-getitem?mr=%s', 'MathSciNet ') + } + +# -- 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 = [] +#html_theme_path = [os.path.join(SAGE_DOC_SRC, 'common', 'themes')] +html_theme_path = [os.path.join(SAGE_DOC_SRC, 'common', 'themes', 'sage')] + +# The name for this set of Sphinx documents. If None, it defaults to +# " v documentation". + +# 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'] +html_static_path = [] + +# 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 = {} + +# 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 = package_name + "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': '', +} + +# 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 = [ + ('index', package_name + '.tex', u'Documentation of ' + unicode(package_name), + authors, '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', package_name, unicode(package_name) + u" documentation", + [authors], 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', package_name, unicode(package_name) + u" documentation", + authors, package_name, 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 + +# -- Options copied from Sagemath conf.py file ------------------------------- + +# We use MathJax to build the documentation unless the environment +# variable SAGE_DOC_MATHJAX is set to "no" or "False". (Note that if +# the user does not set this variable, then the script sage-env sets +# it to "True".) + +if (os.environ.get('SAGE_DOC_MATHJAX', 'no') != 'no' + and os.environ.get('SAGE_DOC_MATHJAX', 'no') != 'False'): + + extensions.append('sphinx.ext.mathjax') + mathjax_path = 'MathJax.js?config=TeX-AMS_HTML-full,../mathjax_sage.js' + + from sage.misc.latex_macros import sage_mathjax_macros + # this is broken for now + # html_theme_options['mathjax_macros'] = sage_mathjax_macros() + + from pkg_resources import Requirement, working_set + sagenb_path = working_set.find(Requirement.parse('sagenb')).location + mathjax_relative = os.path.join('sagenb','data','mathjax') + + # It would be really nice if sphinx would copy the entire mathjax directory, + # (so we could have a _static/mathjax directory), rather than the contents of the directory + + mathjax_static = os.path.join(sagenb_path, mathjax_relative) + html_static_path.append(mathjax_static) + exclude_patterns=['**/'+os.path.join(mathjax_relative, i) for i in ('docs', 'README*', 'test', + 'unpacked', 'LICENSE')] +else: + extensions.append('sphinx.ext.pngmath') + +# This is to make the verbatim font smaller; +# Verbatim environment is not breaking long lines +from sphinx.highlighting import PygmentsBridge +from pygments.formatters.latex import LatexFormatter + +class CustomLatexFormatter(LatexFormatter): + def __init__(self, **options): + super(CustomLatexFormatter, self).__init__(**options) + self.verboptions = r"formatcom=\footnotesize" + +PygmentsBridge.latex_formatter = CustomLatexFormatter + +latex_elements['preamble'] += r''' +% One-column index +\makeatletter +\renewenvironment{theindex}{ + \chapter*{\indexname} + \markboth{\MakeUppercase\indexname}{\MakeUppercase\indexname} + \setlength{\parskip}{0.1em} + \relax + \let\item\@idxitem +}{} +\makeatother +\renewcommand{\ttdefault}{txtt} +''' diff --git a/docs/source/ddExamples.rst b/docs/source/ddExamples.rst new file mode 100644 index 0000000..f2e8e37 --- /dev/null +++ b/docs/source/ddExamples.rst @@ -0,0 +1,9 @@ +.. nodoctest + +DDExamples: built-in functions +============================== + +.. automodule:: ajpastor.dd_functions.ddExamples + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/ddFunction.rst b/docs/source/ddFunction.rst new file mode 100644 index 0000000..e229d4e --- /dev/null +++ b/docs/source/ddFunction.rst @@ -0,0 +1,9 @@ +.. nodoctest + +DDFunctions and DDRings +============================== + +.. automodule:: ajpastor.dd_functions.ddFunction + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 0000000..5b38127 --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,35 @@ +============================= +DD-finite functions on Sage +============================= + +This is a sample reference manual for a SageMath package. + +To use this module, you need to import it:: + + from sage_sample import * + +This reference shows a minimal example of documentation of the +Sage sample package following SageMath guidelines. + +This work is licensed under a `Creative Commons Attribution-Share Alike +3.0 License`__. + +__ https://creativecommons.org/licenses/by-sa/3.0/ + +Sage Sample +=========== + +.. toctree:: + :maxdepth: 1 + + ddFunction + ddExamples + toDiffAlgebraic + + +Indices and Tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/docs/source/toDiffAlgebraic.rst b/docs/source/toDiffAlgebraic.rst new file mode 100644 index 0000000..13577f9 --- /dev/null +++ b/docs/source/toDiffAlgebraic.rst @@ -0,0 +1,9 @@ +.. nodoctest + +DDFunction to DA +============================== + +.. automodule:: ajpastor.dd_functions.toDiffAlgebraic + :members: + :undoc-members: + :show-inheritance: diff --git a/setup.py b/setup.py index 4ea1785..90d0eba 100644 --- a/setup.py +++ b/setup.py @@ -42,7 +42,12 @@ setup( 'Programming Language :: Python :: 2.7', ], # classifiers list: https://pypi.python.org/pypi?%3Aaction=list_classifiers keywords = "holonomic SageMath dfinite", - packages = ["ajpastor"], + packages = ["ajpastor", + "ajpastor.dd_functions", + "ajpastor.operator", + "ajpastor.lazy", + "ajpastor.misc", + "ajpastor.tests"], cmdclass = {'test': SageTest}, # adding a special setup command for tests setup_requires = ['sage-package'], install_requires = ['sage-package', 'sphinx'], -- 2.1.4