Rename files using PEP8 recommendations

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1226 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 4fb27e76a494266c9f79f411c03633f68e2da525

17 files changed, 316 insertions, 56 deletions

diff --git a/src/cython/Makefile b/src/cython/Makefile
index c90135b8..fd7e16e6 100644
--- a/src/cython/Makefile
+++ b/src/cython/Makefile
@@ -2,16 +2,16 @@ ext:
 	python setup.py build_ext --inplace
 
 test:
-	python test/Simplex_tree_UT.py
-	python test/Mini_simplex_tree_UT.py
-	python test/Rips_complex_UT.py
-	python test/Alpha_complex_UT.py
+	python test/test_simplex_tree.py
+	python test/test_mini_simplex_tree.py
+	python test/test_rips_complex.py
+	python test/test_alpha_complex.py
 
 example:
-	python example/Simplex_tree_example.py
-	python example/Mini_simplex_tree_example.py
-	python example/Rips_complex_example.py
-	python example/Alpha_complex_example.py
+	python example/simplex_tree_example.py
+	python example/mini_simplex_tree_example.py
+	python example/rips_complex_example.py
+	python example/alpha_complex_example.py
 
 clean:
 	rm -rf build/ *.o *.so *.cpp
diff --git a/src/cython/example/Rips_complex_example.py b/src/cython/example/Rips_complex_example.py
deleted file mode 100755
index 6a39fc77..00000000
--- a/src/cython/example/Rips_complex_example.py
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env python
-
-import gudhi
-
-print("#####################################################################")
-print("RipsComplex creation from points")
-rips = gudhi.RipsComplex(points=[[0, 0], [1, 0], [0, 1], [1, 1]],
-                         max_dimension=1, max_edge_length=42)
-
-print("filtered_tree=", rips.get_filtered_tree())
-print("star([0])=", rips.get_star_tree([0]))
-print("coface([0], 1)=", rips.get_coface_tree([0], 1))
-
-print("persistence(2)=", rips.persistence(homology_coeff_field=2,
-                                          min_persistence=0))
diff --git a/src/cython/example/Alpha_complex_example.py b/src/cython/example/alpha_complex_example.py
index a724b0c4..6996b692 100755
--- a/src/cython/example/Alpha_complex_example.py
+++ b/src/cython/example/alpha_complex_example.py
@@ -2,6 +2,32 @@
 
 import gudhi
 
+"""This file is part of the Gudhi Library. The Gudhi library
+   (Geometric Understanding in Higher Dimensions) is a generic C++
+   library for computational topology.
+
+   Author(s):       Vincent Rouvreau
+
+   Copyright (C) 2016  INRIA Saclay (France)
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016  INRIA Saclay (France)"
+__license__ = "GPL v3"
+
 print("#####################################################################")
 print("AlphaComplex creation from points")
 alpha_complex = gudhi.AlphaComplex(points=[[0, 0], [1, 0], [0, 1], [1, 1]],
diff --git a/src/cython/example/Mini_simplex_tree_example.py b/src/cython/example/mini_simplex_tree_example.py
index 6cd5bf29..0461a1df 100755
--- a/src/cython/example/Mini_simplex_tree_example.py
+++ b/src/cython/example/mini_simplex_tree_example.py
@@ -2,6 +2,32 @@
 
 import gudhi
 
+"""This file is part of the Gudhi Library. The Gudhi library
+   (Geometric Understanding in Higher Dimensions) is a generic C++
+   library for computational topology.
+
+   Author(s):       Vincent Rouvreau
+
+   Copyright (C) 2016  INRIA Saclay (France)
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016  INRIA Saclay (France)"
+__license__ = "GPL v3"
+
 print("#####################################################################")
 print("MiniSimplexTree creation from insertion")
 
diff --git a/src/cython/example/rips_complex_example.py b/src/cython/example/rips_complex_example.py
new file mode 100755
index 00000000..eba3f298
--- /dev/null
+++ b/src/cython/example/rips_complex_example.py
@@ -0,0 +1,41 @@
+#!/usr/bin/env python
+
+import gudhi
+
+"""This file is part of the Gudhi Library. The Gudhi library
+   (Geometric Understanding in Higher Dimensions) is a generic C++
+   library for computational topology.
+
+   Author(s):       Vincent Rouvreau
+
+   Copyright (C) 2016  INRIA Saclay (France)
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016  INRIA Saclay (France)"
+__license__ = "GPL v3"
+
+print("#####################################################################")
+print("RipsComplex creation from points")
+rips = gudhi.RipsComplex(points=[[0, 0], [1, 0], [0, 1], [1, 1]],
+                         max_dimension=1, max_edge_length=42)
+
+print("filtered_tree=", rips.get_filtered_tree())
+print("star([0])=", rips.get_star_tree([0]))
+print("coface([0], 1)=", rips.get_coface_tree([0], 1))
+
+print("persistence(2)=", rips.persistence(homology_coeff_field=2,
+                                          min_persistence=0))
diff --git a/src/cython/example/Simplex_tree_example.py b/src/cython/example/simplex_tree_example.py
index e8585d83..bdaabca2 100755
--- a/src/cython/example/Simplex_tree_example.py
+++ b/src/cython/example/simplex_tree_example.py
@@ -4,6 +4,32 @@ import gudhi
 
 st = gudhi.SimplexTree()
 
+"""This file is part of the Gudhi Library. The Gudhi library
+   (Geometric Understanding in Higher Dimensions) is a generic C++
+   library for computational topology.
+
+   Author(s):       Vincent Rouvreau
+
+   Copyright (C) 2016  INRIA Saclay (France)
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016  INRIA Saclay (France)"
+__license__ = "GPL v3"
+
 print("#####################################################################")
 print("SimplexTree creation from insertion")
 if st.insert([0, 1]):
diff --git a/src/cython/gudhi.pyx b/src/cython/gudhi.pyx
index 8fcc081a..77b1b4bc 100644
--- a/src/cython/gudhi.pyx
+++ b/src/cython/gudhi.pyx
@@ -1,4 +1,30 @@
-include "src/cython/Simplex_tree.pyx"
-include "src/cython/Mini_simplex_tree.pyx"
-include "src/cython/Rips_complex.pyx"
-include "src/cython/Alpha_complex.pyx"
+"""This file is part of the Gudhi Library. The Gudhi library
+   (Geometric Understanding in Higher Dimensions) is a generic C++
+   library for computational topology.
+
+   Author(s):       Vincent Rouvreau
+
+   Copyright (C) 2016  INRIA Saclay (France)
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016  INRIA Saclay (France)"
+__license__ = "GPL v3"
+
+include "src/cython/simplex_tree.pyx"
+include "src/cython/mini_simplex_tree.pyx"
+include "src/cython/rips_complex.pyx"
+include "src/cython/alpha_complex.pyx"
diff --git a/src/cython/setup.py b/src/cython/setup.py
index 92ed6bbd..5b99ba5f 100644
--- a/src/cython/setup.py
+++ b/src/cython/setup.py
@@ -1,6 +1,32 @@
 from distutils.core import setup, Extension
 from Cython.Build import cythonize
 
+"""This file is part of the Gudhi Library. The Gudhi library
+   (Geometric Understanding in Higher Dimensions) is a generic C++
+   library for computational topology.
+
+   Author(s):       Vincent Rouvreau
+
+   Copyright (C) 2016  INRIA Saclay (France)
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016  INRIA Saclay (France)"
+__license__ = "GPL v3"
+
 gudhi = Extension(
     "gudhi",
     sources = ['gudhi.pyx',],
diff --git a/src/cython/src/cython/Alpha_complex.pyx b/src/cython/src/cython/alpha_complex.pyx
index a06134c8..a06134c8 100644
--- a/src/cython/src/cython/Alpha_complex.pyx
+++ b/src/cython/src/cython/alpha_complex.pyx
diff --git a/src/cython/src/cython/Mini_simplex_tree.pyx b/src/cython/src/cython/mini_simplex_tree.pyx
index b836fb88..b836fb88 100644
--- a/src/cython/src/cython/Mini_simplex_tree.pyx
+++ b/src/cython/src/cython/mini_simplex_tree.pyx
diff --git a/src/cython/src/cython/Rips_complex.pyx b/src/cython/src/cython/rips_complex.pyx
index 3ca890d9..3ca890d9 100644
--- a/src/cython/src/cython/Rips_complex.pyx
+++ b/src/cython/src/cython/rips_complex.pyx
diff --git a/src/cython/src/cython/Simplex_tree.pyx b/src/cython/src/cython/simplex_tree.pyx
index e3cdc27b..e3cdc27b 100644
--- a/src/cython/src/cython/Simplex_tree.pyx
+++ b/src/cython/src/cython/simplex_tree.pyx
diff --git a/src/cython/test/Mini_simplex_tree_UT.py b/src/cython/test/Mini_simplex_tree_UT.py
deleted file mode 100755
index 8f2f56df..00000000
--- a/src/cython/test/Mini_simplex_tree_UT.py
+++ /dev/null
@@ -1,29 +0,0 @@
-import unittest
-
-import gudhi
-
-
-class TestMiniSimplexTree(unittest.TestCase):
-
-    def test_mini(self):
-        triangle012 = [0, 1, 2]
-        edge03 = [0, 3]
-        mini_st = gudhi.MiniSimplexTree()
-        self.assertTrue(mini_st.insert(triangle012))
-        self.assertTrue(mini_st.insert(edge03))
-        # FIXME: Remove this line
-        mini_st.set_dimension(2)
-
-        edge02 = [0, 2]
-        self.assertTrue(mini_st.find(edge02))
-        self.assertEqual(mini_st.get_coface_tree(edge02, 1),
-                         [([0, 1, 2], 0.0)])
-
-        # remove_maximal_simplex test
-        self.assertEqual(mini_st.get_coface_tree(triangle012, 1), [])
-        mini_st.remove_maximal_simplex(triangle012)
-        self.assertTrue(mini_st.find(edge02))
-        self.assertFalse(mini_st.find(triangle012))
-
-if __name__ == '__main__':
-    unittest.main()
diff --git a/src/cython/test/Alpha_complex_UT.py b/src/cython/test/test_alpha_complex.py
index c14c43e2..8a346bb9 100755
--- a/src/cython/test/Alpha_complex_UT.py
+++ b/src/cython/test/test_alpha_complex.py
@@ -2,6 +2,32 @@ import unittest
 
 import gudhi
 
+"""This file is part of the Gudhi Library. The Gudhi library
+   (Geometric Understanding in Higher Dimensions) is a generic C++
+   library for computational topology.
+
+   Author(s):       Vincent Rouvreau
+
+   Copyright (C) 2016  INRIA Saclay (France)
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016  INRIA Saclay (France)"
+__license__ = "GPL v3"
+
 
 class TestAlphaComplex(unittest.TestCase):
 
diff --git a/src/cython/test/test_mini_simplex_tree.py b/src/cython/test/test_mini_simplex_tree.py
new file mode 100755
index 00000000..6622fa57
--- /dev/null
+++ b/src/cython/test/test_mini_simplex_tree.py
@@ -0,0 +1,55 @@
+import unittest
+
+import gudhi
+
+"""This file is part of the Gudhi Library. The Gudhi library
+   (Geometric Understanding in Higher Dimensions) is a generic C++
+   library for computational topology.
+
+   Author(s):       Vincent Rouvreau
+
+   Copyright (C) 2016  INRIA Saclay (France)
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016  INRIA Saclay (France)"
+__license__ = "GPL v3"
+
+
+class TestMiniSimplexTree(unittest.TestCase):
+
+    def test_mini(self):
+        triangle012 = [0, 1, 2]
+        edge03 = [0, 3]
+        mini_st = gudhi.MiniSimplexTree()
+        self.assertTrue(mini_st.insert(triangle012))
+        self.assertTrue(mini_st.insert(edge03))
+        # FIXME: Remove this line
+        mini_st.set_dimension(2)
+
+        edge02 = [0, 2]
+        self.assertTrue(mini_st.find(edge02))
+        self.assertEqual(mini_st.get_coface_tree(edge02, 1),
+                         [([0, 1, 2], 0.0)])
+
+        # remove_maximal_simplex test
+        self.assertEqual(mini_st.get_coface_tree(triangle012, 1), [])
+        mini_st.remove_maximal_simplex(triangle012)
+        self.assertTrue(mini_st.find(edge02))
+        self.assertFalse(mini_st.find(triangle012))
+
+if __name__ == '__main__':
+    unittest.main()
diff --git a/src/cython/test/Rips_complex_UT.py b/src/cython/test/test_rips_complex.py
index ccff5c2d..3ad26b53 100755
--- a/src/cython/test/Rips_complex_UT.py
+++ b/src/cython/test/test_rips_complex.py
@@ -2,6 +2,32 @@ import unittest
 
 import gudhi
 
+"""This file is part of the Gudhi Library. The Gudhi library
+   (Geometric Understanding in Higher Dimensions) is a generic C++
+   library for computational topology.
+
+   Author(s):       Vincent Rouvreau
+
+   Copyright (C) 2016  INRIA Saclay (France)
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016  INRIA Saclay (France)"
+__license__ = "GPL v3"
+
 
 class TestRipsComplex(unittest.TestCase):
 
diff --git a/src/cython/test/Simplex_tree_UT.py b/src/cython/test/test_simplex_tree.py
index 392c6d71..3451ca4b 100755
--- a/src/cython/test/Simplex_tree_UT.py
+++ b/src/cython/test/test_simplex_tree.py
@@ -2,6 +2,32 @@ import unittest
 
 import gudhi
 
+"""This file is part of the Gudhi Library. The Gudhi library
+   (Geometric Understanding in Higher Dimensions) is a generic C++
+   library for computational topology.
+
+   Author(s):       Vincent Rouvreau
+
+   Copyright (C) 2016  INRIA Saclay (France)
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   This program is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU General Public License for more details.
+
+   You should have received a copy of the GNU General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+__author__ = "Vincent Rouvreau"
+__copyright__ = "Copyright (C) 2016  INRIA Saclay (France)"
+__license__ = "GPL v3"
+
 
 class TestSimplexTree(unittest.TestCase):