Merge branch 'MuellerSeb-master'

docs/source/_templates/layout.html

@@ -0,0 +1,7 @@
+{% extends "!layout.html" %}
+
+  {% block menu %}
+    {{ super() }}
+    <a href="py-modindex.html">Python Module Index</a>
+    <a href="genindex.html">Index</a>
+  {% endblock %}

docs/source/conf.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 #
 # GeoStatTools documentation build configuration file, created by
-# sphinx-quickstart on Fri Jan  5 11:25:33 2018.
+# sphinx-quickstart on Fri Jan  5 14:20:43 2018.
 #
 # This file is execfile()d with the current directory set to its
 # containing dir.
@@ -19,13 +19,33 @@
 #
 import os
 import sys
+sys.path.insert(0, os.path.abspath('../../'))
+from gstools import __version__ as ver
 if sys.version_info >= (3, 3):
     from unittest.mock import MagicMock
 else:
     from mock import MagicMock
-sys.path.insert(0, os.path.abspath('../../'))
 
 
+def skip(app, what, name, obj, skip, options):
+    if name in ["__init__", "__call__"]:
+        return False
+    return skip
+
+
+def setup(app):
+    app.connect("autodoc-skip-member", skip)
+
+
+class Mock(MagicMock):
+    @classmethod
+    def __getattr__(clsm, name):
+        return MagicMock()
+
+
+MOCK_MODULES = ['gstools.variogram.estimator']
+sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
+
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -35,14 +55,23 @@
 # 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',
+extensions = [
+    'sphinx.ext.autodoc',
     'sphinx.ext.doctest',
     'sphinx.ext.intersphinx',
     'sphinx.ext.coverage',
-    'sphinx.ext.mathjax',
+    'sphinx.ext.imgmath',
     'sphinx.ext.ifconfig',
+    'sphinx.ext.viewcode',
     'sphinx.ext.githubpages',
-    'sphinx.ext.napoleon']
+    'sphinx.ext.napoleon',
+    'sphinx.ext.autosummary',
+]
+
+autoclass_content = 'class'
+autodoc_member_order = 'groupwise'
+
+numpydoc_show_class_members = False
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -66,9 +95,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.3'
+version = ver
 # The full version, including alpha/beta/rc tags.
-release = '0.3'
+release = ver
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -94,14 +123,31 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
+
+#html_theme = "classic"
+#html_theme = 'sphinxdoc'
 
 # 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_theme_options = {
+#    'canonical_url': '',
+#    'analytics_id': '',
+    'logo_only': False,
+    'display_version': True,
+    'prev_next_buttons_location': 'top',
+#    'style_external_links': False,
+#    'vcs_pageview_mode': '',
+    # Toc options
+    'collapse_navigation': False,
+    'sticky_navigation': True,
+    'navigation_depth': 4,
+    'includehidden': True,
+    'titles_only': 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".
@@ -129,29 +175,16 @@
 # -- 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',
+    'preamble': r'\setcounter{tocdepth}{3}',
+    'pointsize': '9pt',
 }
 
 # 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, 'GeoStatTools.tex', 'GeoStatTools Documentation',
-     'Lennart Schueler', 'manual'),
+     'Lennart Schueler', 'howto'),
 ]
 
 
@@ -177,30 +210,11 @@
 ]
 
 
-# The __call__ special member should be documented.
-
-def skip(app, what, name, obj, skip, options):
-    if name == "__call__":
-        return False
-    return skip
-
-def setup(app):
-    app.connect("autodoc-skip-member", skip)
-
-
-class Mock(MagicMock):
-    @classmethod
-    def __getattr__(clsm, name):
-        return MagicMock()
-
-MOCK_MODULES = ['gstools.variogram.estimator']
-sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
-
-
 # Example configuration for intersphinx: refer to the Python standard library.
-#intersphinx_mapping = {'Python 3.5': ('https://docs.python.org/3.5', None),
-#                       'Python': ('https://docs.python.org/', None),
-#                       'NumPy': ('http://docs.scipy.org/doc/numpy/', None),
-#                       'SciPy': ('http://docs.scipy.org/doc/scipy/reference', None),
-#                       'matplotlib': ('http://matplotlib.org', None),
-#                       'Sphinx': ('http://www.sphinx-doc.org/en/stable/', None),}
+intersphinx_mapping = {
+    'Python 3.6': ('https://docs.python.org/3.6', None),
+    'Python': ('https://docs.python.org/', None),
+    'NumPy': ('http://docs.scipy.org/doc/numpy/', None),
+    'SciPy': ('http://docs.scipy.org/doc/scipy/reference', None),
+    'matplotlib': ('http://matplotlib.org', None),
+    'Sphinx': ('http://www.sphinx-doc.org/en/stable/', None)}

docs/source/field.rst

@@ -0,0 +1,18 @@
+field
+-----
+
+.. automodule:: gstools.field
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   .. only:: html
+
+      .. toctree::
+         :maxdepth: 1
+
+         rng.rst
+         srf.rst
+
+   Details
+   -------

docs/source/index.rst

@@ -1,6 +1,68 @@
-Table of Content
-----------------
+=======================
+Welcome to GeoStatTools
+=======================
+
+.. image:: gstools.png
+   :width: 200px
+   :align: center
+
+About
+-----
+GeoStatTools is a library providing geostatistical tools.
+
+Dependencies
+------------
+- `Numpy <http://www.numpy.org>`_
+- `SciPy <http://www.scipy.org>`_
+
+Installation
+------------
+    ``pip install gstools``
+
+Generation example
+------------------
+This is an example of how to generate a 2 dimensional spatial random field with a Gaussian covariance structure.
+
+.. code-block:: python
+
+   import numpy as np
+   from gstools.field import SRF
+
+   x = np.linspace(0, 10, 120)
+   y = np.linspace(-5, 5, 100)
+
+   cov_model = {'dim': 2, 'var': 1.6, 'len_scale': 4.5, 'model': 'gau', 'mode_no': 1000}
+
+   srf = SRF(**cov_model)
+   field = srf(x, y, seed=19970221, mesh_type='structured')
+
+
+Variogram example
+-----------------
+The spatial structure of a field can be analyzed with the variogram, which contains the same information as the covariance function.
+
+This is an example of how to estimate the variogram of a 2 dimensional unstructured field.
+
+.. code-block:: python
+
+   import numpy as np
+   from gstools.field import SRF
+   from gstools import variogram
+
+   #random samples between 0 <= x, y < 100
+   x = np.random.rand(1000) * 100.
+   y = np.random.rand(1000) * 100.
+
+   srf = SRF(dim=2, var=2, len_scale=30)
+   field = srf(x, y, seed=20011012)
+
+   bins = np.arange(0, 50)
+
+   gamma = variogram.estimate_unstructured(field, bins, x, y)
+
+Modules
+-------
 .. toctree::
-   :maxdepth: 4
+   :maxdepth: 2
 
-   gstools
+   main

docs/source/main.rst

@@ -0,0 +1,7 @@
+.. automodule:: gstools
+
+.. toctree::
+   :maxdepth: 2
+
+   field.rst
+   variogram.rst

docs/source/rng.rst

@@ -0,0 +1,7 @@
+rng
+---
+
+.. automodule:: gstools.field.rng
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/srf.rst

@@ -0,0 +1,7 @@
+srf
+---
+
+.. automodule:: gstools.field.srf
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/variogram.rst

@@ -0,0 +1,10 @@
+variogram
+---------
+
+.. automodule:: gstools.variogram
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   Details
+   -------