Removing faults.py and adding documentation.

docs/source/intro.rst

@@ -35,7 +35,7 @@ The requirements of Geomodelr Query Tool are:
 - Currently, Linux and Mac OS X are supported in Python 2.7 but we plan to support Windows and Python 3.5 in the near future.
 - C++ Build tools that support C++11.
 - Boost Libraries.
-- numpy, scipy and shapely, (pip will install them).
+- numpy, scipy and (pip will install them).
 
 In general, you can install geomodelr by calling::
 

geomodelr/cpp/geomodel.cpp

@@ -168,6 +168,27 @@ BOOST_PYTHON_MODULE(cpp)
 					          "    (double)\n"
 					          "    The signed distance from the unit to the point.\n";
 
+	const char* doc_intersect_planes = "Intersects a set of planes with the faults of the Geological Model.\n"
+        				  "Takes a set of plane represented with its four corners and returns the set\n"
+        				  "of lines that intersect that plane with the faults. The coordinates start from\n"
+        				  "the first plane lower corner, and increase by dist(plane[i][0], plane[i][1]) for the\n"
+        				  "next plane.\n\n"
+        				  "Args:\n"
+        				  "    (list) plane: List with planes. Each plane has a list with four corners\n"
+        				  "    that we want to intersect the fault with.\n"
+        				  "Returns:\n"
+        				  "    (dict): a dictionary with fault names as keys, and lines, (list of points)\n"
+        				  "    as values.\n";
+        const char* doc_intersect_plane = "Intersects a plane with the faults of the Geological Model.\n\n"
+        				  "Takes a plane represented with its four corners and returns the set\n"
+        				  "of lines that intersect that plane with the faults.\n\n"
+        				  "Args:\n"
+        				  "    (list) plane: list with the four corners of the plane that we \n"
+        				  "    want to intersect the fault with.\n\n"
+        				  "Returns:\n"
+        				  "    (dict): a dictionary with fault names as keys, and lines,\n"
+        				  "    (list of points) as values. The coordinates go from the\n"
+        				  "    lower left corner, (0.0, 0.0).\n";
 	// Register exception.
 	python::class_<GeomodelrException> GeomodelrExceptionClass("GeomodelrException", boost::python::init<std::string>());
 
@@ -203,8 +224,8 @@ BOOST_PYTHON_MODULE(cpp)
 					    .def("signed_distance_bounded", &ModelPython::signed_distance_bounded, python::args("unit", "point"), doc_signed_distance_bounded)
 					    .def("signed_distance_unbounded", &ModelPython::signed_distance_unbounded, python::args("unit", "point"), doc_signed_distance_unbounded)
 					    .def("height", &ModelPython::height, python::args("point"), doc_height)
-					    .def("intersect_plane", &ModelPython::intersect_plane)
-					    .def("intersect_planes", &ModelPython::intersect_planes)
+					    .def("intersect_plane", &ModelPython::intersect_plane, doc_intersect_plane)
+					    .def("intersect_planes", &ModelPython::intersect_planes, doc_intersect_planes)
 					    .def("info", &ModelPython::info)
 					    .add_property("bbox", &ModelPython::pybbox)
 					    .add_property("matches", &ModelPython::get_matches, &ModelPython::set_matches)

geomodelr/model.py

@@ -16,7 +16,6 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import shared
-import faults
 import json
 import datetime
 import numpy as np
@@ -254,43 +253,6 @@ def verbose_info(collection):
             print "\tFault names present: %s" % ", ".join(lnames)
             print "\tFault properties present: %s" % ", ".join(lprops)
 
-    #def intersect_plane( self, plane ):
-        """
-        Intersects a plane with the faults of the Geological Model.
-        
-        Takes a plane represented with its four corners and returns the set 
-        of lines that intersect that plane with the faults.
-        
-        Args:
-            (list) plane: list with the four corners of the plane that we 
-            want to intersect the fault with.
-        
-        Returns:
-            (dict): a dictionary with fault names as keys, and lines, 
-            (list of points) as values. The coordinates go from the 
-            lower left corner, (0.0, 0.0).
-        """
-        #return faults.find_faults_plane_intersection( self.faults, plane )
-
-    #def intersect_planes( self, planes ):
-        """
-        Intersects a set of planes with the faults of the Geological Model.
-        
-        Takes a set of plane represented with its four corners and returns the set 
-        of lines that intersect that plane with the faults. The coordinates start from
-        the first plane lower corner, and increase by dist(plane[i][0], plane[i][1]) for the
-        next plane.
-        
-        Args:
-            (list) plane: List with planes. Each plane has a list with four corners 
-            that we want to intersect the fault with.
-        
-        Returns:
-            (dict): a dictionary with fault names as keys, and lines, (list of points) 
-            as values.
-        """
-        #return faults.find_faults_multiple_planes_intersection( self.faults, planes )
-
     def validate( self ):
         """
         Validates that the Geological JSON has correct information.

geomodelr/test.py

@@ -22,7 +22,6 @@
 import os
 import model
 import json
-import faults
 import shared
 import utils
 import isosurfaces
@@ -719,7 +718,7 @@ def test_faults(self):
             for ls in range(faults_size[fp]):
                 self.assertEqual(len(Fault_int.values()[fp][ls]),lines_size[fp][ls])
 
-        Fault_int_py = faults.find_faults_multiple_planes_intersection(geo_model.faults,planes)
+        Fault_int_py = cpp.find_faults_intersection(geo_model.faults,planes)
 
         for name,fault in Fault_int.iteritems():
             flat_fault = np.array([item for sublist in fault for item in sublist])

setup.py

@@ -50,7 +50,7 @@ def if_env(**kwargs):
     license='AGPL',
     packages=['geomodelr'],
     ext_modules=[cppextension],
-    install_requires=['numpy', 'scipy', 'shapely'],# 'scikit-image', 'numpy-stl'],
+    install_requires=['numpy', 'scipy'],# 'scikit-image', 'numpy-stl'],
     keywords=['geology', 'geological modelling', 'cross sections', 'geomodelr'],
     entry_points = {
         'console_scripts': [