Merge pull request #529 from marscher/lgpl

LGPLv3 headers

doc/source/conf.py

@@ -1,3 +1,4 @@
+
 # -*- coding: utf-8 -*-
 #
 # EMMA documentation build configuration file, created by

pyemma/__init__.py

@@ -1,26 +1,21 @@
-# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University
-# Berlin, 14195 Berlin, Germany.
-# All rights reserved.
+
+# This file is part of PyEMMA.
+#
+# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
 #
-# Redistribution and use in source and binary forms, with or without modification,
-# are permitted provided that the following conditions are met:
+# PyEMMA is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
 #
-#  * Redistributions of source code must retain the above copyright notice, this
-# list of conditions and the following disclaimer.
-#  * Redistributions in binary form must reproduce the above copyright notice,
-# this list of conditions and the following disclaimer in the documentation and/or
-# other materials provided with the distribution.
+# 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.
 #
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS''
-# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
-# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
-# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 r"""
 =======================================
 PyEMMA - Emma's Markov Model Algorithms
@@ -36,4 +31,4 @@
 
 from ._version import get_versions
 __version__ = get_versions()['version']
-del get_versions
+del get_versions

pyemma/_base/__init__.py

@@ -1 +1,19 @@
+
+# This file is part of PyEMMA.
+#
+# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
+#
+# PyEMMA is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser 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 Lesser General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 __author__ = 'noe'

pyemma/_base/estimator.py

@@ -1,3 +1,21 @@
+
+# This file is part of PyEMMA.
+#
+# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
+#
+# PyEMMA is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser 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 Lesser General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 from __future__ import absolute_import, print_function
 
 from six.moves import range
@@ -335,4 +353,4 @@ def model(self):
             return self._model
         except AttributeError:
             raise AttributeError(
-                'Model has not yet been estimated. Call estimate(X) or fit(X) first')
+                'Model has not yet been estimated. Call estimate(X) or fit(X) first')

pyemma/_base/model.py

@@ -1,3 +1,21 @@
+
+# This file is part of PyEMMA.
+#
+# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
+#
+# PyEMMA is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser 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 Lesser General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 from __future__ import absolute_import
 import numpy as _np
 import inspect
@@ -157,4 +175,4 @@ def sample_std(self, f, *args, **kw):
 
     def sample_conf(self, f, *args, **kw):
         vals = self.sample_f(f, *args, **kw)
-        return confidence_interval(vals, conf=self.conf)
+        return confidence_interval(vals, conf=self.conf)

pyemma/_base/progress/__init__.py

@@ -1 +1,19 @@
+
+# This file is part of PyEMMA.
+#
+# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
+#
+# PyEMMA is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser 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 Lesser General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 from .reporter import ProgressReporter

pyemma/_base/progress/bar/__init__.py

@@ -1,2 +1,20 @@
+
+# This file is part of PyEMMA.
+#
+# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
+#
+# PyEMMA is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser 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 Lesser General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 from ._impl import ProgressBar
 from .gui import show_progressbar

pyemma/_base/progress/bar/_impl.py

@@ -1,3 +1,21 @@
+
+# This file is part of PyEMMA.
+#
+# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
+#
+# PyEMMA is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser 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 Lesser General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 """Easy to use ETA calculation. Used by etaprogress.progress.
 taken from:
 
@@ -490,4 +508,4 @@ def get_remaining_width(sample_string, max_terminal_width=None):
         available_width = min(terminal_width(), max_terminal_width)
     else:
         available_width = terminal_width()
-    return available_width - len(sample_string)
+    return available_width - len(sample_string)

pyemma/_base/progress/bar/gui.py

@@ -1,3 +1,21 @@
+
+# This file is part of PyEMMA.
+#
+# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
+#
+# PyEMMA is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser 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 Lesser General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 '''
 Created on 24.04.2015
 
@@ -106,4 +124,4 @@ def show_progressbar(bar, show_eta=True):
         widget.children[1].value = bar.percent
     else:
         sys.stdout.write("\r" + str(bar))
-        sys.stdout.flush()
+        sys.stdout.flush()

pyemma/_base/progress/bar/misc.py

@@ -1,3 +1,21 @@
+
+# This file is part of PyEMMA.
+#
+# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
+#
+# PyEMMA is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser 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 Lesser General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 '''
 Created on 21.04.2015
 
@@ -132,5 +150,4 @@ def terminal_width():
             return _WindowsCSBI.get_info(_WindowsCSBI.HANDLE_STDOUT)['terminal_width']
         return struct.unpack('hhhh', fcntl.ioctl(0, termios.TIOCGWINSZ, '\000' * 8))[1]
     except IOError:
-        return 80
-
+        return 80

pyemma/_base/progress/reporter.py

@@ -1,3 +1,21 @@
+
+# This file is part of PyEMMA.
+#
+# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
+#
+# PyEMMA is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser 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 Lesser General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 '''
 Created on 16.07.2015
 
@@ -124,4 +142,4 @@ def _progress_force_finish(self, stage=0):
         pg.numerator = pg.denominator
         pg._eta.eta_epoch = 0
         _show_progressbar(pg)
-        _hide_progressbar(pg)
+        _hide_progressbar(pg)

pyemma/_base/tests/__init__.py

@@ -0,0 +1,18 @@
+
+# This file is part of PyEMMA.
+#
+# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
+#
+# PyEMMA is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser 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 Lesser General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+

pyemma/_base/tests/test_progress.py

@@ -1,3 +1,21 @@
+
+# This file is part of PyEMMA.
+#
+# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
+#
+# PyEMMA is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser 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 Lesser General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 '''
 Created on 29.07.2015
 
@@ -80,4 +98,4 @@ def work(self, count):
         self.assertEqual(self.has_been_called, expected_calls)
 
 if __name__ == "__main__":
-    unittest.main()
+    unittest.main()

pyemma/_ext/__init__.py

@@ -1 +1,19 @@
+
+# This file is part of PyEMMA.
+#
+# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
+#
+# PyEMMA is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser 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 Lesser General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 __author__ = 'noe'

pyemma/_ext/sklearn/__init__.py

@@ -1 +1,19 @@
+
+# This file is part of PyEMMA.
+#
+# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
+#
+# PyEMMA is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser 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 Lesser General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 __author__ = 'noe'

pyemma/_ext/sklearn/base.py

@@ -1,3 +1,21 @@
+
+# This file is part of PyEMMA.
+#
+# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
+#
+# PyEMMA is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser 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 Lesser General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 """
 --------------------------------------------------------------------------------------------
 Extracted from skikit-learn to ensure basic compatibility