Updated LICENSE and AUTHOR info regarding xdrfile (closes #679)

Rebranded our xdrlib with cython bindings as libmdaxdr. Further standardized XDR error message reporting and exceptions (now mostly IOError). Removed reference to the old SWIG numpy.i in the credits. Made logo LICENSE info consistent
MDAnalysis · Feb 8, 2016 · c3b838f · c3b838f
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diff --git a/LICENSE b/LICENSE
@@ -346,6 +346,43 @@ Public License instead of this License.
 
 
 ==========================================================================
+
+Gromacs xdrfile library for reading XTC/TRR trajectories
+  - lib/formats/src/xdrfile.c
+  - lib/formats/src/xdrfile_xtc.c
+  - lib/formats/src/xdrfile_trr.c
+  - lib/formats/include/xdrfile.h
+  - lib/formats/include/xdrfile_xtc.h
+  - lib/formats/include/xdrfile_trr.h
+
+Copyright (c) 2009-2014, Erik Lindahl & David van der Spoel
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+this
+list of conditions and the following disclaimer.
+
+2. 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 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.
+
+==========================================================================
+
 CatDCD is released under the UIUC Open Source License:
 http://www.ks.uiuc.edu/Development/MDTools/catdcd/license.html
 
@@ -526,15 +563,22 @@ PyQCPROT
 
 MDAnalysis logo (see doc/sphinx/source/logos)
 
+The MDAnalysis 'Atom' logo was created by Christian Beckstein and is
+
+Copyright (c) 2011 Christian Beckstein
+
 MDAnalysis Logo 'Atom' by Christian Beckstein is licensed under a
 Creative Commons Attribution-NoDerivs 3.0 Unported License.
+To view a copy of this license, visit
+http://creativecommons.org/licenses/by-nd/3.0/ or send a letter to Creative
+Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.
 
-http://creativecommons.org/licenses/by-nd/3.0/
+The logo is contained in the file 'mdanalysis-logo.png'.
 
-See the file LICENSE in the logo directory for the full text of the
-license.
+Derivatives in the files 'mdanalysis-logo-127x55.png',
+'mdanalysis-logo-200x150.png', 'mdanalysis-logo.ico' were created for
+inclusion in MDAnalysis and on websites related to MDAnalysis. They
+are distributed under the same license as the 'Atom' logo.
 
 ==========================================================================
 
-
-
diff --git a/package/AUTHORS b/package/AUTHORS
@@ -73,14 +73,22 @@ External code
 External code (under a GPL-compatible licence) was obtained from
 various sources. The authors (as far as we know them) are listed here.
 
-libxdrfile
-  - David van der Spoel <[email protected]>
-  - Erik Lindahl <[email protected]>
-  As of MDAnalysis version 0.8.0 libxdrfile is no longer used, having
-  been replaced by libxdrfile2, a GPLv2 derivative of libxdrfile.
-
-numpy.i
-  - Bill Spotz
+xdrfile
+  - David van der Spoel <[email protected]>
+  - Erik Lindahl <[email protected]>
+  - Frans van Hoesel <[email protected]> (not listed as an xdrfile
+    author, but the original author of the XTC coordinate compression code)
+
+  The Gromacs libxdrfile (LGPL-licensed) was used before MDAnalysis
+   version 0.8.0.
+  Between MDAnalysis versions 0.8.0 and 0.13.0 libxdrfile was replaced by
+   libxdrfile2, our GPLv2 enhanced derivative of libxdrfile.
+  Since version 0.14.0 xdr enhanecments were rebased onto Gromacs'
+   xdrfile 1.1.4 code (now BSD-licensed). Our contributions remain GPLv2
+   and were split into files xtc_seek.c, trr_seek.c, xtc_seek.h, and
+   trr_seek.h, for clarity (xdrfile 1.1.4 code is distributed with minor
+   modifications). Also for clarity we now name the resulting enhanced
+   xdr-reading library, complete with cython bindings, 'libmdaxdr'.
 
 KDTree
   - Thomas Hamelryck <[email protected]>

diff --git a/package/CHANGELOG b/package/CHANGELOG
@@ -34,6 +34,7 @@ Enhancement
 
 Changes
 
+  * xdrlib was rebranded limdaxdr. (Issue #679)
   * xdrlib has been ported to cython. (Issue #441)
   * util.NamedStream no longer inherits from basestring (Issue #649)
   * Short TRZ titles are striped from trailing spaces. A friendlier error

diff --git a/package/LICENSE b/package/LICENSE
@@ -346,6 +346,43 @@ Public License instead of this License.
 
 
 ==========================================================================
+
+Gromacs xdrfile library for reading XTC/TRR trajectories
+  - lib/formats/src/xdrfile.c
+  - lib/formats/src/xdrfile_xtc.c
+  - lib/formats/src/xdrfile_trr.c
+  - lib/formats/include/xdrfile.h
+  - lib/formats/include/xdrfile_xtc.h
+  - lib/formats/include/xdrfile_trr.h
+
+Copyright (c) 2009-2014, Erik Lindahl & David van der Spoel
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+this
+list of conditions and the following disclaimer.
+
+2. 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 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.
+
+==========================================================================
+
 CatDCD is released under the UIUC Open Source License:
 http://www.ks.uiuc.edu/Development/MDTools/catdcd/license.html
 
@@ -526,15 +563,22 @@ PyQCPROT
 
 MDAnalysis logo (see doc/sphinx/source/logos)
 
+The MDAnalysis 'Atom' logo was created by Christian Beckstein and is
+
+Copyright (c) 2011 Christian Beckstein
+
 MDAnalysis Logo 'Atom' by Christian Beckstein is licensed under a
 Creative Commons Attribution-NoDerivs 3.0 Unported License.
+To view a copy of this license, visit
+http://creativecommons.org/licenses/by-nd/3.0/ or send a letter to Creative
+Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.
 
-http://creativecommons.org/licenses/by-nd/3.0/
+The logo is contained in the file 'mdanalysis-logo.png'.
 
-See the file LICENSE in the logo directory for the full text of the
-license.
+Derivatives in the files 'mdanalysis-logo-127x55.png',
+'mdanalysis-logo-200x150.png', 'mdanalysis-logo.ico' were created for
+inclusion in MDAnalysis and on websites related to MDAnalysis. They
+are distributed under the same license as the 'Atom' logo.
 
 ==========================================================================
 
-
-
diff --git a/package/MDAnalysis/coordinates/TRR.py b/package/MDAnalysis/coordinates/TRR.py
@@ -14,7 +14,7 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 from .XDR import XDRBaseReader, XDRBaseWriter
-from ..lib.formats.xdrlib import TRRFile
+from ..lib.formats.libmdaxdr import TRRFile
 from ..lib.mdamath import triclinic_vectors
 
 

diff --git a/package/MDAnalysis/coordinates/XDR.py b/package/MDAnalysis/coordinates/XDR.py
@@ -62,7 +62,7 @@ def read_numpy_offsets(filename):
 
 
 class XDRBaseReader(base.Reader):
-    """Base class for xdrlib file formats xtc and trr"""
+    """Base class for libmdaxdr file formats xtc and trr"""
     def __init__(self, filename, convert_units=True, sub=None,
                  refresh_offsets=False, **kwargs):
         super(XDRBaseReader, self).__init__(filename,
@@ -191,7 +191,7 @@ def Writer(self, filename, n_atoms=None, **kwargs):
 
 
 class XDRBaseWriter(base.Writer):
-    """Base class for xdrlib file formats xtc and trr"""
+    """Base class for libmdaxdr file formats xtc and trr"""
 
     def __init__(self, filename, n_atoms, convert_units=True, **kwargs):
         self.filename = filename

diff --git a/package/MDAnalysis/coordinates/XTC.py b/package/MDAnalysis/coordinates/XTC.py
@@ -14,7 +14,7 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 from .XDR import XDRBaseReader, XDRBaseWriter
-from ..lib.formats.xdrlib import XTCFile
+from ..lib.formats.libmdaxdr import XTCFile
 from ..lib.mdamath import triclinic_vectors
 
 
@@ -69,7 +69,7 @@ def write_next_timestep(self, ts):
             dimensions = self.convert_dimensions_to_unitcell(ts, inplace=False)
 
         box = triclinic_vectors(dimensions)
-        # xdrlib will multiply the coordinated by precision. This means for a
+        # libmdaxdr will multiply the coordinates by precision. This means for a
         # precision of 3 decimal places we need to pass 1000.0 to the xdr
         # library.
         precision = 10.0 ** self.precision

diff --git a/package/MDAnalysis/lib/formats/__init__.py b/package/MDAnalysis/lib/formats/__init__.py
@@ -13,6 +13,6 @@
 # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
-from . import xdrlib
+from . import libmdaxdr
 
-__all__ = ['xdrlib']
+__all__ = ['libmdaxdr']
diff --git a/package/MDAnalysis/lib/formats/xdrlib.pyx → package/MDAnalysis/lib/formats/libmdaxdr.pyx b/package/MDAnalysis/lib/formats/xdrlib.pyx → package/MDAnalysis/lib/formats/libmdaxdr.pyx
@@ -150,7 +150,7 @@ cdef class _XDRFile:
             res = xdrfile_close(self.xfp)
             self.is_open = False
             if res != EOK:
-                raise IOError('Couldn\'t close file: {}, Error = XDRLIB-{}'.format(
+                raise IOError('Couldn\'t close file: {}  XDR error = {}'.format(
                     self.fname, error_message[res]))
         # forget old offsets in case we open a different file with the same instance.
         self._has_offsets = False
@@ -198,15 +198,15 @@ cdef class _XDRFile:
             return_code, self.n_atoms = self._calc_natoms(fname);
 
             if return_code != EOK:
-                raise IOError('XDRLIB read error: {}'.format(
+                raise IOError('XDR read error = {}'.format(
                     error_message[return_code]))
             if self.n_atoms <= 0:
                 raise IOError('Couldn\'t read number of atoms: {}'.format(
                     fname))
 
         self.xfp = xdrfile_open(fname, opening_mode)
         if self.xfp is NULL:
-            raise IOError('error opening xtf file: {}'.format(self.fname))
+            raise IOError('Error opening XTC/TRR file: {}'.format(self.fname))
         self.is_open = True
 
     def __enter__(self):
@@ -362,7 +362,7 @@ cdef class TRRFile(_XDRFile):
 
     Examples
     --------
-    >>> from MDAnalysis.lib.formats.xdrlib import TRRFile
+    >>> from MDAnalysis.lib.formats.libmdaxdr import TRRFile
     >>> with TRRFile('foo.trr') as f:
     >>>     for frame in f:
     >>>         print(frame.x)
@@ -383,8 +383,8 @@ cdef class TRRFile(_XDRFile):
         cdef int64_t* offsets = NULL
         ok = read_trr_n_frames(self.fname, &n_frames, &est_nframes, &offsets);
         if ok != EOK:
-            raise RuntimeError("TRR couldn't calculate offsets, error={}".format(
-                error_message[ok]))
+            raise RuntimeError("TRR couldn't calculate offsets. "
+                               "XDR error = {}".format(error_message[ok]))
         # the read_xtc_n_frames allocates memory for the offsets with an
         # overestimation. This number is saved in est_nframes and we need to
         # tell the new numpy array about the whole allocated memory to avoid
@@ -399,7 +399,7 @@ cdef class TRRFile(_XDRFile):
 
         Returns
         -------
-        frame : xdrlib.TRRFrame
+        frame : libmdaxdr.TRRFrame
             namedtuple with frame information
 
         See Also
@@ -444,7 +444,7 @@ cdef class TRRFile(_XDRFile):
         # produced by different codes (Gromacs, ...).
         if return_code != EOK and return_code != EENDOFFILE \
            and return_code != EINTEGER:
-            raise RuntimeError('TRR Read Error occured: {}'.format(
+            raise IOError('TRR read error = {}'.format(
                 error_message[return_code]))
 
         # In a trr the integer error seems to indicate that the file is ending.
@@ -549,7 +549,7 @@ cdef class TRRFile(_XDRFile):
                                        <rvec*> velocity_ptr,
                                        <rvec*> forces_ptr)
         if return_code != EOK:
-            raise RuntimeError('TRR write error: {}'.format(
+            raise IOError('TRR write error = {}'.format(
                 error_message[return_code]))
 
         self.current_frame += 1
@@ -574,7 +574,7 @@ cdef class XTCFile(_XDRFile):
 
     Examples
     --------
-    >>> from MDAnalysis.lib.formats.xdrlib import XTCFile
+    >>> from MDAnalysis.lib.formats.libmdaxdr import XTCFile
     >>> with XTCFile('foo.trr') as f:
     >>>     for frame in f:
     >>>         print(frame.x)
@@ -596,8 +596,8 @@ cdef class XTCFile(_XDRFile):
         cdef int64_t* offsets = NULL
         ok = read_xtc_n_frames(self.fname, &n_frames, &est_nframes, &offsets);
         if ok != EOK:
-            raise RuntimeError("XTC couldn't calculate offsets, error={}".format(
-                error_message[ok]))
+            raise RuntimeError("XTC couldn't calculate offsets. "
+                               "XDR error = {}".format(error_message[ok]))
         # the read_xtc_n_frames allocates memory for the offsets with an
         # overestimation. This number is saved in est_nframes and we need to
         # tell the new numpy array about the whole allocated memory to avoid
@@ -612,7 +612,7 @@ cdef class XTCFile(_XDRFile):
 
         Returns
         -------
-        frame : xdrlib.XTCFrame
+        frame : libmdaxdr.XTCFrame
             namedtuple with frame information
 
         See Also
@@ -644,7 +644,7 @@ cdef class XTCFile(_XDRFile):
                                       &time, <matrix>box.data,
                                       <rvec*>xyz.data, <float*> &prec)
         if return_code != EOK and return_code != EENDOFFILE:
-            raise RuntimeError('XTC Read Error occured: {}'.format(
+            raise IOError('XTC read error = {}'.format(
                 error_message[return_code]))
 
         if return_code == EENDOFFILE:
@@ -715,7 +715,7 @@ cdef class XTCFile(_XDRFile):
                                        <matrix>&box_view[0, 0],
                                        <rvec*>&xyz_view[0, 0], precision)
         if return_code != EOK:
-            raise RuntimeError('XTC write error: {}'.format(
+            raise IOError('XTC write error = {}'.format(
                 error_message[return_code]))
 
         self.current_frame += 1