Merge pull request #37 from dgasmith/schema

Formalizing the Schema

.gitignore

@@ -45,6 +45,7 @@ nosetests.xml
 coverage.xml
 *.cover
 .hypothesis/
+.pytest_cache/
 
 # Translations
 *.mo
@@ -99,3 +100,6 @@ ENV/
 
 # mypy
 .mypy_cache/
+
+# Dev schema
+docs/source/auto*rst

.travis.yml

@@ -0,0 +1,30 @@
+# After changing this file, check it on:
+#   http://lint.travis-ci.org/
+language: python
+
+# Run jobs on container-based infrastructure, can be overridden per job
+sudo: false
+
+matrix:
+  include:
+    - python: 2.7
+    - python: 3.5
+
+before_install:
+  - uname -a
+  - free -m
+  - df -h
+  - ulimit -a
+  - python -V
+  - pip install --upgrade pip setuptools
+  - pip install pytest jsonschema
+  - pip install -e .
+
+script:
+  - make test
+
+after_success:
+  - make docs
+
+notifications:
+    email: false

Makefile

@@ -0,0 +1,11 @@
+.PHONY: install
+install:
+	pip install -e .
+
+.PHONY: test
+test:
+	pytest -v
+
+.PHONY: docs
+docs:
+	cd docs && make html

Topology/README.md

@@ -10,7 +10,7 @@ should likely be handled by a higher level driver and not make the spec more dif
 
 The following molecule specification is used. The required fields are:
 
-  - `symbols` (list) - A list of strings 
+  - `symbols` (list) - A list of strings
   - `geometry` (list) - A 3N XYZ coordinate list of list in bohr, will likely change to encompass decided unit specifications
 
 The following are optional fields and default values (option, more a list of possibilities QM programs would want):
@@ -23,15 +23,15 @@ The following are optional fields and default values (option, more a list of pos
   - `comment` (str) - Any additional comment one would attach to the molecule.
   - `fragments` (list of tuples, `[]`) - A list of indices (0-indexed) for molecular fragments within the topology.
   - `fragment_charges` (list of floats, `[]`) - A list of charges associated with the fragments tuple.
-  - `fragment_multiplicities` (list of ints, `[]`) - A list of multiplicites associated with each fragment. 
+  - `fragment_multiplicities` (list of ints, `[]`) - A list of multiplicites associated with each fragment.
+  - `fix_com` (bool) - whether to adjust to the molecule to the COM or not
+  - `fix_orientation` (bool) - whether to rotate the molecule to a standard orientation or not
   - `provenance` (dict, `{}`) - The provencance of the molecule.
     - `doi` - A doi reference for the molecule.
 
 Other possible quantities:
   - Bonds - Holding data for MM computations
-  - Basis Sets per atom 
-  - `fix_com` (bool) - whether to adjust to the molecule to the COM or not
-  - `fix_orientation` (bool) - whether to rotate the molecule to a standard orientation or not
+  - Basis Sets per atom
   - label (list of str) - Per-atom labels which may be seperate from fragments
   - Extend the `real` quantitity to cover real, ghost, absent, qm/mm region, etc.
-  - EFP quantities `fragment_types`, `coordinate_hints`. This is an example and likely not part of the spec. How would we handle this? 
+  - EFP quantities `fragment_types`, `coordinate_hints`. This is an example and likely not part of the spec. How would we handle this?

docs/Makefile

@@ -0,0 +1,21 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = qc_schema
+SOURCEDIR     = source
+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)
+

docs/README.md

@@ -0,0 +1,16 @@
+# Compiling QC_JSON_Schema's Documentation
+
+The docs for this project are built with [Sphinx](http://www.sphinx-doc.org/en/master/).
+To compile the docs, first ensure that Sphinx and the ReadTheDocs theme are installed.
+
+```bash
+pip install sphinx sphinx_rtd_theme
+```
+
+Once installed, you can use the `Makefile` in this directory to compile static HTML pages by
+```bash
+make html
+```
+
+The compiled docs will be in the `_build` directory and can be viewed by opening `index.html` (which may itself 
+be inside a directory called `html/` depending on what version of Sphinx is installed).

docs/make.bat

@@ -0,0 +1,36 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=_build
+set SPHINXPROJ=qc_schema
+
+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%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

docs/source/conf.py

@@ -0,0 +1,166 @@
+# -*- 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/stable/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 -----------------------------------------------------
+
+# Super hacky auto gen
+import sys
+import os
+sys.path.insert(1, os.path.dirname(__file__))
+import gen_schema_docs
+
+project = 'A schema for Quantum Chemistry'
+copyright = "2018, The Molecular Sciences Software Institute"
+author = 'The Molecular Sciences Software Institute'
+
+# The short X.Y version
+version = ''
+# The full version, including alpha/beta/rc tags
+release = ''
+
+
+# -- 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.mathjax',
+]
+
+# 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 = None
+
+# 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'
+
+
+# -- 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 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']
+
+# 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 = 'QC_JSON_Schemadoc'
+
+
+# -- 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, 'QC_JSON_Schema.tex', 'QC_JSON_Schema Documentation',
+     'QC_JSON_Schema', '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, 'QC_JSON_Schema', 'QC_JSON_Schema 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, 'QC_JSON_Schema', 'QC_JSON_Schema Documentation',
+     author, 'QC_JSON_Schema', 'A schema for Quantum Chemistry',
+     'Miscellaneous'),
+]
+
+
+# -- Extension configuration -------------------------------------------------