diff --git a/docs/.nojekyll b/docs/.nojekyll new file mode 100644 index 0000000..e69de29 diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..ed2201d --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,192 @@ +# 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. 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The XML files are in $(BUILDDIR)/xml." + +pseudoxml: + $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml + @echo + @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." diff --git a/docs/index.html b/docs/index.html new file mode 100644 index 0000000..ebe8f9c --- /dev/null +++ b/docs/index.html @@ -0,0 +1,6 @@ + + + + + + diff --git a/docs/source/LICENSE.rst b/docs/source/LICENSE.rst new file mode 100644 index 0000000..12090de --- /dev/null +++ b/docs/source/LICENSE.rst @@ -0,0 +1,5 @@ +License +============== + +.. include:: ../../LICENSE.rst + diff --git a/docs/source/_rst/contributing.rst b/docs/source/_rst/contributing.rst new file mode 100644 index 0000000..d527a0e --- /dev/null +++ b/docs/source/_rst/contributing.rst @@ -0,0 +1,37 @@ +How to contribute +================= + +We'd love to accept your patches and contributions to this project. There are just a few small guidelines you need to follow. + +Submitting a patch +------------------ + + 1. It's generally best to start by opening a new issue describing the bug or + feature you're intending to fix. Even if you think it's relatively minor, + it's helpful to know what people are working on. Mention in the initial + issue that you are planning to work on that bug or feature so that it can + be assigned to you. + + 2. Follow the normal process of forking the project, and setup a new + branch to work in. It's important that each group of changes be done in + separate branches in order to ensure that a pull request only includes the + commits related to that bug or feature. + + 3. To ensure properly formatted code, please make sure to use 4 + spaces to indent the code. The easy way is to run on your bash the provided + script: ./code_formatter.sh. You should also run pylint over your code. + It's not strictly necessary that your code be completely "lint-free", + but this will help you find common style issues. + + 4. Any significant changes should almost always be accompanied by tests. The + project already has good test coverage, so look at some of the existing + tests if you're unsure how to go about it. We're using coveralls that + is an invaluable tools for seeing which parts of your code aren't being + exercised by your tests. + + 5. Do your best to have well-formed commit messages for each change. + This provides consistency throughout the project, and ensures that commit + messages are able to be formatted properly by various git tools. + + 6. Finally, push the commits to your fork and submit a pull request. Please, + remember to rebase properly in order to maintain a clean, linear git history. diff --git a/docs/source/_rst/installation.rst b/docs/source/_rst/installation.rst new file mode 100644 index 0000000..0f6fdb9 --- /dev/null +++ b/docs/source/_rst/installation.rst @@ -0,0 +1,34 @@ +Installation +============ + +**PINA** requires requires `numpy`, `scipy`, `matplotlib`, `future`, `torch`, `sphinx` (for the documentation) and `pytest` (for local test). The code is tested for Python 3, while compatibility of Python 2 is not guaranteed anymore. It can be installed using `pip` or directly from the source code. + +Installing via PIP +__________________ + +Mac and Linux users can install pre-built binary packages using pip. +To install the package just type: + +.. code-block:: bash + + $ pip install git+https://github.com/mathLab/PINA.git + +To uninstall the package: + +.. code-block:: bash + + $ pip uninstall pina + +Installing from source +______________________ +The official distribution is on GitHub, and you can clone the repository using + +.. code-block:: bash + + $ git clone https://github.com/mathLab/PINA + +To install the package just type: + +.. code-block:: bash + + $ pip install -e . diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 0000000..0ca6208 --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,320 @@ +# -*- coding: utf-8 -*- +# +# pydmd documentation build configuration file, created by +# sphinx-quickstart on Mon Jun 22 16:09:40 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 sys +import os +import sphinx_rtd_theme + +# 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('../..')) +import pina + +# -- General configuration ------------------------------------------------ + +# If your documentation needs a minimal Sphinx version, state it here. +# needs_sphinx = '1.4' +# if needs_sphinx > sphinx.__display_version__: +# message = 'This project needs at least Sphinx +# v{0!s}'.format(needs_sphinx) +# raise VersionRequirementError(message) + +# 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.coverage', + 'sphinx.ext.graphviz', + 'sphinx.ext.doctest', + 'sphinx.ext.intersphinx', + 'sphinx.ext.todo', + 'sphinx.ext.coverage', + 'sphinx.ext.viewcode', + 'sphinx.ext.ifconfig', + 'sphinx.ext.mathjax', +] + +intersphinx_mapping = { + 'python': ('http://docs.python.org/2', None), 'numpy': + ('http://docs.scipy.org/doc/numpy/', None), 'scipy': + ('http://docs.scipy.org/doc/scipy/reference/', None), 'matplotlib': + ('http://matplotlib.sourceforge.net/', None) +} + +# 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', '.md'] +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 = pina.__project__ +copyright = pina.__copyright__ +author = pina.__author__ + +# autoclass +autoclass_content = 'both' + +# 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 = pina.__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 = 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 = 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 + +# 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 = True + + +# -- Options for viewcode extension --------------------------------------- + +# Follow alias objects that are imported from another module such as functions, +# classes and attributes. As side effects, this option ... ??? +# If false, ... ???. +# The default is True. +viewcode_import = True + + +# -- 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_rtd_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 = {} + +# Add any paths that contain custom themes here, relative to this directory. +html_theme_path = [sphinx_rtd_theme.get_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 = ['_tutorials'] + +# 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 + +# 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' + +# A dictionary with options for the search language support, empty by default. +# Now only 'ja' uses this config value +# html_search_options = {'type': 'default'} + +# 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 = 'pinadoc' + +# -- Options for LaTeX output --------------------------------------------- + +latex_elements = { + # The paper size ('letterpaper' or 'a4paper'). + 'papersize': 'a4paper', + + # The font size ('10pt', '11pt' or '12pt'). + 'pointsize': '10pt', + + # Additional stuff for the LaTeX preamble. + 'preamble': '', + + # Latex figure (float) alignment + 'figure_align': 'htbp', +} + +# 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 = [ + (master_doc, 'pina.tex', u'PINA Documentation', + u'PINA contributors', '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 = [ + (master_doc, 'pina', u'PINA 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 = [ + (master_doc, 'pina', u'PINA Documentation', + author, 'pina', '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 diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 0000000..9674b80 --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,44 @@ +Welcome to PINA's documentation! +=================================================== + +PINA is a Python package providing an easy interface to deal with +physics-informed neural networks (PINN) for the approximation of (differential, +nonlinear, ...) functions. Based on Pytorch, PINA offers a simple and intuitive +way to formalize a specific problem and solve it using PINN. + +Physics-informed neural network +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +PINN is a novel approach that involves neural networks to solve supervised +learning tasks while respecting any given law of physics described by general +nonlinear differential equations. Proposed in "Physics-informed neural +networks: A deep learning framework for solving forward and inverse problems +involving nonlinear partial differential equations", such framework aims to +solve problems in a continuous and nonlinear settings. + + +.. toctree:: + :maxdepth: 1 + :caption: Package Documentation: + + Installation <_rst/installation> + Contributing <_rst/contributing> + License + +.. the following is demo content intended to showcase some of the features you can invoke in reStructuredText +.. this can be safely deleted or commented out +.. ........................................................................................ + +.. toctree:: + :maxdepth: 2 + :numbered: + :caption: Tutorials + +.. ........................................................................................ + +.. toctree:: + :maxdepth: 2 + :numbered: + :caption: Download + +.. ........................................................................................ diff --git a/pina/__init__.py b/pina/__init__.py index 001036c..c1ce52a 100644 --- a/pina/__init__.py +++ b/pina/__init__.py @@ -7,6 +7,7 @@ __all__ = [ 'Span' ] +from .meta import * from .label_tensor import LabelTensor from .pinn import PINN #from .ppinn import ParametricPINN