Merge pull request #4 from jkglasbrenner/develop

Proof-of-concept prototype for neighbormodels application

The following is a proof-of-concept prototype of the `neighbormodels` application. Using the primary functions within each module, a user is able to build a lattice model with pairwise neighbor interactions.

The API **will** change significantly from the current form. While you can already compute some useful things with this code, if you use this release for anything meaningful, pin the version tag in your project, otherwise an update will most likely break your code.

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+max-line-length=88
+ignore=E121,E123,E126,E226,E24,E704,W503,W504

.gitignore

@@ -349,6 +349,7 @@ local_settings.py
 nosetests.xml
 pip-log.txt
 pip-delete-this-directory.txt
+*.egg-info/
 __pycache__/
 develop-eggs/
 docs/_build/
@@ -377,10 +378,12 @@ vignettes/*.pdf
 
 # track these files, if they exist
 !.editorconfig
+!.env.example
+!.flake8
 !.gitattributes
 !.gitignore
 !.github/
 !.gitlab/
+!.readthedocs.yml
 !.style.yapf
 !.travis.yml
-!.env.example

.readthedocs.yml

@@ -0,0 +1,12 @@
+---
+build:
+  image: latest
+
+python:
+  version: 3.6
+  setup_py_install: true
+  extra_requirements:
+    - docs
+
+formats: []
+...

.style.yapf

@@ -1,7 +1,13 @@
 [style]
-based_on_style = pep8
-align_closing_bracket_with_visual_indent = false
-blank_line_before_nested_class_or_def = true
-indent_width = 4
-join_multiple_lines = false
-split_before_named_assigns = false
+based_on_style=pep8
+align_closing_bracket_with_visual_indent=False
+blank_line_before_nested_class_or_def=True
+coalesce_brackets=True
+column_limit=88
+dedent_closing_brackets=True
+indent_width=4
+join_multiple_lines=False
+spaces_around_default_or_named_assign=False
+split_arguments_when_comma_terminated=True
+split_before_named_assigns=False
+split_complex_comprehension=True

MANIFEST.in

@@ -0,0 +1,8 @@
+include README.rst LICENSE
+
+graft docs
+
+global-exclude *.py[co]
+
+prune docs/_build
+prune docs/_themes

Makefile

@@ -1,33 +1,51 @@
 SHELL				=	/bin/sh
 
+PROJNAME			=	neighbormodels
+
 RM					=	rm
 ECHO				=	echo
 COPY				=	cp
+FIND				=	find
 
 CONDA				=	conda
 CONDA_ENV_FILE		=	environment.yaml
-CONDA_ENV_NAME		=	crystal-structures
-CONDA_ENV_ACTIVATE	=	$(CONDA) activate
+
+PYTHON				=	/usr/bin/env python
+PYTHON_SETUP		=	setup.py
+PYTHON_SETUP_DOCS	=	build_sphinx
 
 ALL_FILES			=
 
-CLEAN_FILES			=	*_cache/
+CLEAN_FILES			=	*_cache/												\
+						docs/_build/*
 
 define cleanup
 	-$(RM) -rf $(CLEAN_FILES)
 endef
 
+define pycache_cleanup
+	$(FIND) -name "__pycache__" -type d -exec $(RM) -rf {} +
+endef
+
 define setup_environment
 	bash -lc "$(CONDA) env update --file $(CONDA_ENV_FILE)"
 endef
 
-.SILENT	:
-.PHONY	:	all clean environment
+define make_docs
+	$(PYTHON) ./$(PYTHON_SETUP) $(PYTHON_SETUP_DOCS)
+endef
+
+.SILENT		:
+.PHONY		:	all clean docs environment
+
+all			:	$(ALL_FILES)
 
-all	: $(ALL_FILES)
+docs		:
+	$(call make_docs)
 
-clean	:
+clean		:
 	$(call cleanup)
+	$(call pycache_cleanup)
 
 environment	:
 	$(ECHO) Setting up conda environment

README.rst

@@ -0,0 +1,17 @@
+DataMaterials — neighbormodels
+==============================
+
+.. image:: https://readthedocs.org/projects/neighbormodels/badge/?version=latest
+   :target: https://neighbormodels.readthedocs.io/en/latest/?badge=latest
+   :alt: Documentation Status
+
+A tool for building crystal lattice models with distance-dependent neighbor interactions.
+
+
+License
+-------
+
+MIT_
+
+.. _MIT: https://opensource.org/licenses/MIT
+

docs/Makefile

@@ -0,0 +1,13 @@
+SPHINXOPTS			=
+SPHINXBUILD			=	sphinx-build
+SPHINXPROJ			=	datamaterials_neighbors
+SOURCEDIR			=	.
+BUILDDIR			=	_build
+
+help	:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY	: help Makefile
+
+%	:	Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_static/theme_overrides.css

@@ -0,0 +1,11 @@
+/* override table width restrictions */
+@media screen and (min-width: 767px) {
+  .wy-table-responsive table td {
+    /* !important prevents the common CSS stylesheets from overriding
+     this as on RTD they are loaded after this stylesheet */
+    white-space: normal !important;
+  }
+  .wy-table-responsive {
+    overflow: visible !important;
+  }
+}

docs/conf.py

@@ -0,0 +1,187 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# 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.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../'))
+
+# -- Project information -----------------------------------------------------
+
+project = 'neighbormodels'
+copyright = '2018, James K. Glasbrenner'
+author = 'James K. Glasbrenner'
+
+# The short X.Y version
+version = '0.1'
+# The full version, including alpha/beta/rc tags
+release = '0.1.0'
+
+# -- 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.autosummary',
+    'sphinx.ext.todo',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.githubpages',
+]
+
+# 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 master toctree document.
+master_doc = 'index'
+
+# 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"
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path .
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+# pygments_style = 'sphinx'
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+add_module_names = False
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+on_rtd = os.environ.get('READTHEDOCS') == 'True'
+if on_rtd:
+    html_theme = 'default'
+else:
+    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 = {}
+
+html_use_index = False
+
+# 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_context = {
+    'css_files': [
+        '_static/theme_overrides.css',  # override wide tables in RTD theme
+    ],
+}
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'neighbormodels'
+
+# -- 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': '',
+
+    # 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, 'neighbormodels.tex', 'neighbormodels Documentation',
+        'James K. Glasbrenner', 'manual'
+    ),
+]
+
+# -- 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, 'neighbormodels', 'neighbormodels Documentation',
+     [author], 1)
+]
+
+# -- 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, 'neighbormodels', 'neighbormodels Documentation', author,
+        'neighbormodels',
+        'A tool for building crystal lattice models with distance-dependent '
+        'neighbor interactions.', 'Miscellaneous'
+    ),
+]
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for autodoc extension -------------------------------------------
+
+autodoc_member_order = "bysource"
+autosummary_generate = True
+
+# -- Options for todo extension ----------------------------------------------
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True

docs/index.rst

@@ -0,0 +1,14 @@
+neighbormodels documentation
+============================
+
+.. include:: ../README.rst
+   :start-line: 6
+
+
+API
+===
+
+.. toctree::
+   :maxdepth: 2
+
+   modules