Add start of sphinx docs

docs/Makefile

@@ -0,0 +1,55 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help
+help:
+	@echo "Please use \`make <target>' where <target> 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 "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+
+.PHONY: clean
+clean:
+	rm -rf $(BUILDDIR)/*
+
+.PHONY: html
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+.PHONY: singlehtml
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+.PHONY: latex
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+.PHONY: latexpdf
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."

docs/about.rst

@@ -0,0 +1,6 @@
+=====
+About
+=====
+
+Javelin is a moderisation of DISCUS written in the Python programming
+language

docs/conf.py

@@ -0,0 +1,37 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import os
+import sys
+sys.path.insert(0, os.path.abspath('..'))
+
+extensions = [
+    'sphinx.ext.autodoc',
+]
+
+source_suffix = '.rst'
+
+master_doc = 'index'
+
+project = 'Javelin'
+copyright = '2016, Ross Whitfield'
+author = 'Ross Whitfield'
+
+version = '0.1.0'
+release = '0.1.0'
+
+exclude_patterns = ['_build']
+
+pygments_style = 'friendly'
+
+html_theme = 'nature'
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'Javelindoc'
+
+latex_documents = [
+    (master_doc, 'Javelin.tex', 'Javelin Documentation',
+     'Ross Whitfield', 'manual'),
+]
+
+autodoc_default_flags = ['members', 'undoc-members']

docs/index.rst

@@ -0,0 +1,12 @@
+Javelin
+===================================
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+
+   about
+   install
+   tutorials
+   javelin

docs/install.rst

@@ -0,0 +1,67 @@
+============
+Installation
+============
+
+Install the latest release
+==========================
+
+* Update once we have a release
+
+Requirements
+============
+
+* Python 2.7-3.5
+* NumPy
+* h5py_
+* pandas_
+* xarray_
+* periodictable_
+
+Optional:
+
+* ASE_ (to use the ase atoms structue)
+
+.. _h5py: 
+.. _pandas: http://pandas.pydata.org/
+.. _xarray: http://xarray.pydata.org
+.. _periodictable: http://www.reflectometry.org/danse/elements.html
+.. _ASE: https://wiki.fysik.dtu.dk/ase/
+
+Development
+===========
+
+A development enviroment can easily be set up with either conda of PyPI
+
+Using Conda
+===========
+
+.. code:: sh
+
+   conda env create
+   source activate javelin
+   python setup.py install
+
+Using PyPI
+==========
+
+Tests
+=====
+
+The unit tests can be run with pytest_
+
+Install with conda
+------------------
+
+.. code:: sh
+
+   conda install pytest
+
+Install with PyPI
+-----------------
+
+.. code:: sh
+
+   pip install pytest
+
+.. _pytest: http://pytest.org
+

docs/javelin.rst

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+=======
+Modules
+=======
+
+List of javelin modules:
+
+.. toctree::
+   :glob:
+
+   javelin/*

docs/javelin/ase.rst

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+.. automodule:: javelin.ase

docs/javelin/fourier.rst

@@ -0,0 +1 @@
+.. automodule:: javelin.fourier

docs/javelin/grid.rst

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+.. automodule:: javelin.grid

docs/javelin/io.rst

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+.. automodule:: javelin.io

docs/javelin/structure.rst

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+.. automodule:: javelin.structure

docs/javelin/unitcell.rst

@@ -0,0 +1 @@
+.. automodule:: javelin.unitcell

docs/javelin/utils.rst

@@ -0,0 +1 @@
+.. automodule:: javelin.utils

docs/tutorials.rst

@@ -0,0 +1,3 @@
+=========
+Tutorials
+=========

javelin/ase.py

@@ -1,4 +1,9 @@
-"""Theses functions read the legacy DISCUS stru file format in ASE Atoms."""
+"""
+ase
+===
+
+Theses functions read the legacy DISCUS stru file format in ASE Atoms.
+"""
 
 from __future__ import absolute_import
 from ase.atoms import Atoms

javelin/fourier.py

@@ -1,4 +1,9 @@
-"""This module define the Structure object"""
+"""
+fourier
+=======
+
+This module define the Structure object
+"""
 import numpy as np
 import periodictable
 from javelin.grid import Grid

javelin/grid.py

@@ -1,4 +1,8 @@
-"""Grid class to allow the Q-space grid to be definied in different
+"""
+grid
+====
+
+Grid class to allow the Q-space grid to be definied in different
 ways Should allow for corners and bins, or a matrix and the axis to be
 defined.
 

javelin/io.py

@@ -1,3 +1,9 @@
+"""
+io
+====
+"""
+
+
 def read_mantid_MDHisto(filename):
     """Read the saved MDHisto from from Mantid and returns an xarray.DataArray object"""
     import h5py

javelin/structure.py

@@ -1,3 +1,9 @@
+"""
+structure
+=========
+"""
+
+
 import numpy as np
 from pandas import DataFrame
 from javelin.unitcell import UnitCell

javelin/unitcell.py

@@ -1,3 +1,8 @@
+"""
+unitcell
+========
+"""
+
 import numpy as np
 
 
@@ -69,6 +74,7 @@ def cartesian(self, u):
         array([[  2.59807621e+00,  -1.50000000e+00,   3.25954010e-16]])
 
         A array of atoms position can also be passed
+
         >>> positions = [[1,0,0], [0,0,0.5]]
         >>> unitcell.cartesian(positions)
         array([[  2.59807621e+00,  -1.50000000e+00,   3.25954010e-16],
@@ -124,6 +130,7 @@ def fractional(self, u):
         array([[  0.00000000e+00,   1.00000000e+00,  -4.89858720e-17]])
 
         A array of atoms position can also be passed
+
         >>> positions = [[0,2,0], [0,0,5]]
         >>> unitcell.fractional(positions)
         array([[  0.00000000e+00,   5.00000000e-01,  -2.44929360e-17],

javelin/utils.py

@@ -1,3 +1,9 @@
+"""
+utils
+=====
+"""
+
+
 def get_atomic_number_symbol(Z=None, symbol=None):
     import numpy as np
     from periodictable import elements