python-occ 0.17 compatibility, formatter, documentation and minor fixes (#97)

Author: mtezzele

README.md

@@ -35,7 +35,7 @@ Please see the table below for instructions on how to satisfy the requirements.
 
 | Package | Version  | Comment                                                                    |
 |---------|----------|----------------------------------------------------------------------------|
-| OCC     | >= 0.16  | See pythonocc.org or github.com.tpaviot/pythonocc-core for instructions or `conda install -c https://conda.anaconda.org/dlr-sc pythonocc-core` |
+| OCC     | == 0.17  | See pythonocc.org or github.com.tpaviot/pythonocc-core for instructions or `conda install -c https://conda.anaconda.org/dlr-sc pythonocc-core` |
 | vtk     | >= 5.0   | Simplest solution is `conda install vtk`                                   |
 
 
@@ -133,7 +133,8 @@ just a few small guidelines you need to follow.
      commits related to that bug or feature.
 
   3. To ensure properly formatted code, please make sure to use a tab of 4
-     spaces to indent the code. You should also run [pylint][] over your code.
+     spaces to indent the code. The easy way is to run on your bash the provided
+     script: ./code_formatter.sh. You should also run [pylint][] over your code.
      It's not strictly necessary that your code be completely "lint-free",
      but this will help you find common style issues.
 

code_formatter.sh

@@ -0,0 +1,68 @@
+#!/bin/bash
+
+#######################################
+
+required_command="yapf unexpand"
+code_directories="pygem tests"
+
+#######################################
+
+usage() {
+	echo
+	echo -e "\tUsage: $0 [files]"
+	echo
+	echo -e "\tIf not files are specified, script formats all ".py" files"
+	echo -e "\tin code directories ($code_directories); otherwise, formats"
+	echo -e "\tall given files"
+	echo
+	echo -e "\tRequired command: $required_command"
+	echo
+	exit 0
+}
+
+
+[[ $1 == "-h" ]] && usage
+
+# Test for required program
+for comm in $required_command; do
+	command -v $comm >/dev/null 2>&1 || {
+		echo "I require $comm but it's not installed. Aborting." >&2; 
+		exit 1
+	}
+done
+
+# Find all python files in code directories
+python_files=""
+for dir in $code_directories; do
+	python_files="$python_files `ls $dir/*.py`"
+done
+[[ $# != 0 ]] && python_files=$@
+
+# The files unvhandler.py and params.py can not be formatted because there are
+# strings with spaces inside that otherwise would be converted in tabs.
+python_files_true=""
+for file in $python_files; do
+	if [ $file != "pygem/unvhandler.py" ] && [ $file != "pygem/params.py" ]; then
+		python_files_true="$python_files_true $file"
+	fi
+done
+
+# Here the important part:
+# - first, yapf format the files; it works very well just setting few option
+#		by command line, but at the moment it has bugs for tabs, so uses spaces.
+# - second, convert 4 spaces to tab character
+# - third, you can look a very pretty code 
+for file in $python_files_true; do
+	echo "Making beatiful $file..."
+	[[ ! -f $file ]] && echo "$file does not exist; $0 -h for more info" && exit
+	
+	yapf --style='{
+					based_on_style: pep8, 
+				   	indent_width: 4,
+					dedent_closing_brackets = true,
+					coalesce_brackets = true,
+					column_limit = 80
+			  	  }' -i $file
+	unexpand -t 4 $file > tmp.py
+	mv tmp.py $file
+done

docs/source/code.rst

@@ -1,5 +1,5 @@
 Code Documentation
-==================
+=======================
 
 
 .. toctree::

docs/source/index.rst

@@ -21,11 +21,29 @@ PyGeM is a python library using Free Form Deformation and Radial Basis Functions
 By now, it has been used with meshes with up to 14 milions of cells. Try with more and more complicated input files!
 
 
-Guide
-^^^^^
+Installation
+^^^^^^^^^^^^
+
+To install the pygem package, open the terminal/command line and clone the repository with the command
+::
+
+	 git clone https://github.com/mathLab/PyGeM
+
+For a complete list of dependencies to be installed via conda please refer to the official `repository <https://github.com/mathLab/PyGeM>`_.
+After installing the dependencies you can navigate into the ``PyGeM`` folder (where the ``setup.py`` file is located) and run the command
+::
+
+	 python setup.py install
+
+You should now be able to import the pygem library in Python scripts and interpreters with the command ``import pygem``.
+
+
+
+Developer's Guide
+^^^^^^^^^^^^^^^^^^^^^^^
 
 .. toctree::
-   :maxdepth: 3
+   :maxdepth: 1
 
    code
    contact
@@ -38,10 +56,10 @@ Tutorials
 
 We made some tutorial examples:
 
-- `Tutorial 1 <tutorial1stl.html>`_ shows how to deal with stl files and FFD
-- `Turorial 2 <tutorial2iges.html>`_ shows how to deal with iges files and FFD
-- `Turorial 3 <tutorial3unv.html>`_ shows how to deal with unv files and how to set the desired continuity to the geometry using FFD
-- `Turorial 4 <tutorial4rbf.html>`_ shows how to perform RBF interpolation
+- `Tutorial 1 <tutorial1stl.html>`_ shows how to deal with stl files and FFD.
+- `Turorial 2 <tutorial2iges.html>`_ shows how to deal with iges files and FFD.
+- `Turorial 3 <tutorial3unv.html>`_ shows how to deal with unv files and how to set the desired continuity to the geometry using FFD.
+- `Turorial 4 <tutorial4rbf.html>`_ shows how to perform RBF interpolation.
 
 
 

pygem/__init__.py

@@ -1,5 +1,7 @@
-
-__all__ = ['affine', 'filehandler', 'freeform', 'radial', 'openfhandler', 'params', 'stlhandler', 'unvhandler', 'vtkhandler', 'igeshandler', 'utils', 'gui']
+__all__ = [
+	'affine', 'filehandler', 'freeform', 'radial', 'openfhandler', 'params',
+	'stlhandler', 'unvhandler', 'vtkhandler', 'igeshandler', 'utils', 'gui'
+]
 
 from . import affine
 from . import freeform

pygem/affine.py

@@ -40,15 +40,21 @@ def angles2matrix(rot_z=0, rot_y=0, rot_x=0):
 	if rot_z:
 		cos = math.cos(rot_z)
 		sin = math.sin(rot_z)
-		rot_matrix.append(np.array([cos, -sin, 0, sin, cos, 0, 0, 0, 1]).reshape((3, 3)))
+		rot_matrix.append(
+			np.array([cos, -sin, 0, sin, cos, 0, 0, 0, 1]).reshape((3, 3))
+		)
 	if rot_y:
 		cos = math.cos(rot_y)
 		sin = math.sin(rot_y)
-		rot_matrix.append(np.array([cos, 0, sin, 0, 1, 0, -sin, 0, cos]).reshape((3, 3)))
+		rot_matrix.append(
+			np.array([cos, 0, sin, 0, 1, 0, -sin, 0, cos]).reshape((3, 3))
+		)
 	if rot_x:
 		cos = math.cos(rot_x)
 		sin = math.sin(rot_x)
-		rot_matrix.append(np.array([1, 0, 0, 0, cos, -sin, 0, sin, cos]).reshape((3, 3)))
+		rot_matrix.append(
+			np.array([1, 0, 0, 0, cos, -sin, 0, sin, cos]).reshape((3, 3))
+		)
 	if rot_matrix:
 		return reduce(np.dot, rot_matrix[::-1])
 	return np.eye(3)
@@ -96,7 +102,9 @@ def to_reduced_row_echelon_form(matrix):
 		for i in range(row_count):
 			if i != r:
 				lv = matrix[i][lead]
-				matrix[i] = [iv - lv*rv for rv, iv in zip(matrix[r], matrix[i])]
+				matrix[i] = [
+					iv - lv * rv for rv, iv in zip(matrix[r], matrix[i])
+				]
 		lead += 1
 	return matrix
 
@@ -130,34 +138,36 @@ def affine_points_fit(points_start, points_end):
 
 	dim = len(points_start[0])
 	if len(points_start) < dim:
-		raise RuntimeError("Too few starting points => under-determined system.")
+		raise RuntimeError(
+			"Too few starting points => under-determined system."
+		)
 
 	# Fill an an empty (dim+1) x (dim) matrix
-	c = [[0.0 for a in range(dim)] for i in range(dim+1)]
+	c = [[0.0 for a in range(dim)] for i in range(dim + 1)]
 	for j in range(dim):
-		for k in range(dim+1):
+		for k in range(dim + 1):
 			for i, pnts_i in enumerate(points_start):
 				qt = list(pnts_i) + [1]
 				c[k][j] += qt[k] * points_end[i][j]
 
 	# Fill an an empty (dim+1) x (dim+1) matrix
-	Q = [[0.0 for a in range(dim)] + [0] for i in range(dim+1)]
+	Q = [[0.0 for a in range(dim)] + [0] for i in range(dim + 1)]
 	for qi in points_start:
 		qt = list(qi) + [1]
-		for i in range(dim+1):
-			for j in range(dim+1):
+		for i in range(dim + 1):
+			for j in range(dim + 1):
 				Q[i][j] += qt[i] * qt[j]
 
-
 	# Augement Q with c and get the reduced row echelon form of the result
-	affine_matrix = [Q[i] + c[i] for i in range(dim+1)]
+	affine_matrix = [Q[i] + c[i] for i in range(dim + 1)]
 
-	if np.linalg.cond(affine_matrix) < 1/sys.float_info.epsilon:
+	if np.linalg.cond(affine_matrix) < 1 / sys.float_info.epsilon:
 		rref_aff_matrix = to_reduced_row_echelon_form(affine_matrix)
 		rref_aff_matrix = np.array(rref_aff_matrix)
 	else:
-		raise RuntimeError("Error: singular matrix. Points are probably coplanar.")
-
+		raise RuntimeError(
+			"Error: singular matrix. Points are probably coplanar."
+		)
 
 	def transform_vector(source):
 		"""
@@ -171,9 +181,9 @@ def transform_vector(source):
 		destination = np.zeros(dim)
 		for i in range(dim):
 			for j in range(dim):
-				destination[j] += source[i] * rref_aff_matrix[i][j+dim+1]
+				destination[j] += source[i] * rref_aff_matrix[i][j + dim + 1]
 			# Add the last line of the rref
-			destination[i] += rref_aff_matrix[dim][i+dim+1]
+			destination[i] += rref_aff_matrix[dim][i + dim + 1]
 		return destination
 
 	return transform_vector

pygem/filehandler.py

@@ -3,6 +3,7 @@
 """
 import os
 
+
 class FileHandler(object):
 	"""
 	A base class for file handling.
@@ -12,21 +13,20 @@ class FileHandler(object):
 	:cvar string extension: extension of the input/output files. It is specific for each
 		subclass.
 	"""
+
 	def __init__(self):
 		self.infile = None
 		self.outfile = None
 		self.extension = None
 
-
 	def parse(self, *args):
 		"""
 		Abstract method to parse a specific file.
 
 		Not implemented, it has to be implemented in subclasses.
 		"""
 		raise NotImplementedError("Subclass must implement abstract method " \
-			+ self.__class__.__name__ + ".parse")
-
+		 + self.__class__.__name__ + ".parse")
 
 	def write(self, *args):
 		"""
@@ -35,8 +35,7 @@ def write(self, *args):
 		Not implemented, it has to be implemented in subclasses.
 		"""
 		raise NotImplementedError("Subclass must implement abstract method " \
-			+ self.__class__.__name__ + ".write")
-
+		 + self.__class__.__name__ + ".write")
 
 	def _check_extension(self, filename):
 		"""
@@ -47,9 +46,10 @@ def _check_extension(self, filename):
 		"""
 		__, file_ext = os.path.splitext(filename)
 		if not file_ext in self.extension:
-			raise ValueError('The input file does not have the proper extension. \
-				It is {0!s}, instead of {1!s}.'.format(file_ext, self.extension))
-
+			raise ValueError(
+				'The input file does not have the proper extension. \
+				It is {0!s}, instead of {1!s}.'.format(file_ext, self.extension)
+			)
 
 	@staticmethod
 	def _check_filename_type(filename):
@@ -59,8 +59,9 @@ def _check_filename_type(filename):
 		:param string filename: file to check.
 		"""
 		if not isinstance(filename, basestring):
-			raise TypeError('The given filename ({0!s}) must be a string'.format(filename))
-
+			raise TypeError(
+				'The given filename ({0!s}) must be a string'.format(filename)
+			)
 
 	@staticmethod
 	def _check_infile_instantiation(infile):
@@ -72,4 +73,6 @@ def _check_infile_instantiation(infile):
 		:param string infile: file to check.
 		"""
 		if not infile:
-			raise RuntimeError("You can not write a file without having parsed one.")
+			raise RuntimeError(
+				"You can not write a file without having parsed one."
+			)