From 4c8883155e009f1db8580edfe5ad44c2fa228e0a Mon Sep 17 00:00:00 2001 From: Jonathan Barnoud Date: Thu, 28 Jan 2016 21:51:52 +0100 Subject: [PATCH 1/5] Fix python 3 compatibility issues Mostly bytes/strings issues --- package/MDAnalysis/analysis/density.py | 2 +- .../analysis/hbonds/hbond_analysis.py | 12 +- package/MDAnalysis/analysis/leaflet.py | 7 +- package/MDAnalysis/coordinates/CRD.py | 4 +- package/MDAnalysis/coordinates/GMS.py | 4 +- package/MDAnalysis/coordinates/GRO.py | 4 +- package/MDAnalysis/coordinates/PDB.py | 6 +- package/MDAnalysis/coordinates/XDR.py | 12 +- package/MDAnalysis/coordinates/XYZ.py | 2 +- package/MDAnalysis/coordinates/base.py | 2 +- package/MDAnalysis/core/Selection.py | 10 +- package/MDAnalysis/lib/formats/xdrlib.c | 980 +++++++++--------- package/MDAnalysis/lib/formats/xdrlib.pyx | 2 +- package/MDAnalysis/lib/util.py | 16 +- package/MDAnalysis/topology/GMSParser.py | 2 +- package/MDAnalysis/topology/GROParser.py | 2 +- package/MDAnalysis/topology/PSFParser.py | 3 +- package/MDAnalysis/topology/TOPParser.py | 4 +- .../MDAnalysisTests/analysis/test_hbonds.py | 4 +- .../MDAnalysisTests/coordinates/test_gro.py | 4 +- .../coordinates/test_reader_api.py | 4 + .../MDAnalysisTests/coordinates/test_xdr.py | 10 +- testsuite/MDAnalysisTests/test_streamio.py | 8 +- 23 files changed, 580 insertions(+), 524 deletions(-) diff --git a/package/MDAnalysis/analysis/density.py b/package/MDAnalysis/analysis/density.py index cac0ba1b5b5..489451d660b 100644 --- a/package/MDAnalysis/analysis/density.py +++ b/package/MDAnalysis/analysis/density.py @@ -306,7 +306,7 @@ def make_density(self): warnings.warn(msg) return - dedges = map(np.diff, self.edges) + dedges = list(map(np.diff, self.edges)) D = len(self.edges) for i in range(D): shape = np.ones(D, int) diff --git a/package/MDAnalysis/analysis/hbonds/hbond_analysis.py b/package/MDAnalysis/analysis/hbonds/hbond_analysis.py index 206bc8ac66a..6b2b84a0d23 100644 --- a/package/MDAnalysis/analysis/hbonds/hbond_analysis.py +++ b/package/MDAnalysis/analysis/hbonds/hbond_analysis.py @@ -958,8 +958,8 @@ def generate_table(self): # build empty output table dtype = [ ("time", float), ("donor_idx", int), ("acceptor_idx", int), - ("donor_resnm", "|S4"), ("donor_resid", int), ("donor_atom", "|S4"), - ("acceptor_resnm", "|S4"), ("acceptor_resid", int), ("acceptor_atom", "|S4"), + ("donor_resnm", "|U4"), ("donor_resid", int), ("donor_atom", "|U4"), + ("acceptor_resnm", "|U4"), ("acceptor_resid", int), ("acceptor_atom", "|U4"), ("distance", float), ("angle", float)] # according to Lukas' notes below, using a recarray at this stage is ineffective # and speedups of ~x10 can be achieved by filling a standard array, like this: @@ -1040,8 +1040,8 @@ def count_by_type(self): # build empty output table dtype = [ ('donor_idx', int), ('acceptor_idx', int), - ('donor_resnm', 'S4'), ('donor_resid', int), ('donor_heavy_atom', 'S4'), ('donor_atom', 'S4'), - ('acceptor_resnm', 'S4'), ('acceptor_resid', int), ('acceptor_atom', 'S4'), + ('donor_resnm', 'U4'), ('donor_resid', int), ('donor_heavy_atom', 'U4'), ('donor_atom', 'U4'), + ('acceptor_resnm', 'U4'), ('acceptor_resid', int), ('acceptor_atom', 'U4'), ('frequency', float) ] out = np.empty((len(hbonds),), dtype=dtype) @@ -1101,8 +1101,8 @@ def timesteps_by_type(self): # build empty output table dtype = [ ('donor_idx', int), ('acceptor_idx', int), - ('donor_resnm', 'S4'), ('donor_resid', int), ('donor_heavy_atom', 'S4'), ('donor_atom', 'S4'), - ('acceptor_resnm', 'S4'), ('acceptor_resid', int), ('acceptor_atom', 'S4'), + ('donor_resnm', 'U4'), ('donor_resid', int), ('donor_heavy_atom', 'U4'), ('donor_atom', 'U4'), + ('acceptor_resnm', 'U4'), ('acceptor_resid', int), ('acceptor_atom', 'U4'), ('time', float)] out = np.empty((out_nrows,), dtype=dtype) diff --git a/package/MDAnalysis/analysis/leaflet.py b/package/MDAnalysis/analysis/leaflet.py index 086e698890e..e857e458bef 100644 --- a/package/MDAnalysis/analysis/leaflet.py +++ b/package/MDAnalysis/analysis/leaflet.py @@ -54,11 +54,12 @@ from six.moves import range +import warnings + import numpy as np -import MDAnalysis import networkx as NX -import distances -import warnings +import MDAnalysis +from . import distances class LeafletFinder(object): diff --git a/package/MDAnalysis/coordinates/CRD.py b/package/MDAnalysis/coordinates/CRD.py index a5bcf98ae3e..78ad91443c6 100644 --- a/package/MDAnalysis/coordinates/CRD.py +++ b/package/MDAnalysis/coordinates/CRD.py @@ -64,9 +64,9 @@ def _read_first_frame(self): # process coordinates try: if extended: - coords_list.append(np.array(map(float, line[45:100].split()[0:3]))) + coords_list.append(np.array(line[45:100].split()[0:3], dtype=float)) else: - coords_list.append(np.array(map(float, line[20:50].split()[0:3]))) + coords_list.append(np.array(line[20:50].split()[0:3], dtype=float)) except: raise ValueError("Check CRD format at line {0}: {1}" "".format(linenum, line.rstrip())) diff --git a/package/MDAnalysis/coordinates/GMS.py b/package/MDAnalysis/coordinates/GMS.py index 9c79bd3163b..5073607f5a9 100644 --- a/package/MDAnalysis/coordinates/GMS.py +++ b/package/MDAnalysis/coordinates/GMS.py @@ -66,7 +66,7 @@ def __init__(self, outfilename, **kwargs): super(GMSReader, self).__init__(outfilename, **kwargs) # the filename has been parsed to be either b(g)zipped or not - self.outfile = util.anyopen(self.filename, 'r') + self.outfile = util.anyopen(self.filename, 'rt') # note that, like for xtc and trr files, _n_atoms and _n_frames are used quasi-private variables # to prevent the properties being recalculated @@ -242,7 +242,7 @@ def open_trajectory(self): # must check; otherwise might segmentation fault raise IOError(errno.ENOENT, 'GMS file not found', self.filename) - self.outfile = util.anyopen(self.filename, 'r') + self.outfile = util.anyopen(self.filename, 'rt') # reset ts ts = self.ts diff --git a/package/MDAnalysis/coordinates/GRO.py b/package/MDAnalysis/coordinates/GRO.py index d48a9257be1..4ba180fd3bd 100644 --- a/package/MDAnalysis/coordinates/GRO.py +++ b/package/MDAnalysis/coordinates/GRO.py @@ -122,7 +122,7 @@ class GROReader(base.SingleFrameReader): _Timestep = Timestep def _read_first_frame(self): - with util.openany(self.filename, 'r') as grofile: + with util.openany(self.filename, 'rt') as grofile: # Read first two lines to get number of atoms grofile.readline() self.n_atoms = n_atoms = int(grofile.readline()) @@ -281,7 +281,7 @@ def write(self, selection, frame=None): "".format(self.gro_coor_limits["min"], self.gro_coor_limits["max"])) - with util.openany(self.filename, 'w') as output_gro: + with util.openany(self.filename, 'wt') as output_gro: # Header output_gro.write('Written by MDAnalysis\n') output_gro.write(self.fmt['n_atoms'].format(len(atoms))) diff --git a/package/MDAnalysis/coordinates/PDB.py b/package/MDAnalysis/coordinates/PDB.py index 84417b3dd13..dc45c7275e1 100644 --- a/package/MDAnalysis/coordinates/PDB.py +++ b/package/MDAnalysis/coordinates/PDB.py @@ -475,7 +475,7 @@ def __init__(self, filename, **kwargs): pos = 0 # atom position for filling coordinates array occupancy = np.ones(self._n_atoms) - with util.openany(filename, 'r') as pdbfile: + with util.openany(filename, 'rt') as pdbfile: for i, line in enumerate(pdbfile): line = line.strip() # Remove extra spaces if len(line) == 0: # Skip line if empty @@ -594,7 +594,7 @@ def _read_frame(self, frame): # forth; should improve performance substantially pos = 0 occupancy = np.ones(self._n_atoms) - with util.openany(self.filename, 'r') as f: + with util.openany(self.filename, 'rt') as f: for i in range(line): next(f) # forward to frame for line in f: @@ -776,7 +776,7 @@ def __init__(self, filename, bonds="conect", n_atoms=None, start=0, step=1, self.step = step self.remarks = remarks - self.pdbfile = util.anyopen(self.filename, 'w') # open file on init + self.pdbfile = util.anyopen(self.filename, 'wt') # open file on init self.has_END = False def close(self): diff --git a/package/MDAnalysis/coordinates/XDR.py b/package/MDAnalysis/coordinates/XDR.py index bdc1dda60fb..1c9f36c6442 100644 --- a/package/MDAnalysis/coordinates/XDR.py +++ b/package/MDAnalysis/coordinates/XDR.py @@ -93,7 +93,7 @@ def _load_offsets(self): self._read_offsets(store=True) return - with open(fname) as f: + with open(fname, 'rb') as f: data = {k: v for k, v in six.iteritems(np.load(f))} ctime_ok = getctime(self.filename) == data['ctime'] @@ -116,8 +116,12 @@ def _read_offsets(self, store=False): np.savez(offsets_filename(self.filename), offsets=offsets, size=size, ctime=ctime) except Exception as e: - warnings.warn("Couldn't save offsets because: {}".format( - e.message)) + try: + warnings.warn("Couldn't save offsets because: {}".format( + e.message)) + except AttributeError: + warnings.warn("Couldn't save offsets because: {}".format(e)) + def rewind(self): """Read the first frame again""" @@ -133,7 +137,7 @@ def _reopen(self): self.ts.frame = 0 self._frame = -1 self._xdr.close() - self._xdr.open(self.filename, 'r') + self._xdr.open(self.filename.encode('utf-8'), 'r') def _read_frame(self, i): """read frame i""" diff --git a/package/MDAnalysis/coordinates/XYZ.py b/package/MDAnalysis/coordinates/XYZ.py index ecb13c96a78..c2c796e714f 100644 --- a/package/MDAnalysis/coordinates/XYZ.py +++ b/package/MDAnalysis/coordinates/XYZ.py @@ -139,7 +139,7 @@ def __init__(self, filename, n_atoms=None, atoms='X', convert_units=None, self.__class__.__name__, __version__) self.remark = default_remark if remark == 'default' else remark # can also be gz, bz2 - self._xyz = util.anyopen(self.filename, 'w') + self._xyz = util.anyopen(self.filename, 'wt') def _get_atomnames(self, atoms): """Return a list of atom names""" diff --git a/package/MDAnalysis/coordinates/base.py b/package/MDAnalysis/coordinates/base.py index a949575c932..ea0fb6384bd 100644 --- a/package/MDAnalysis/coordinates/base.py +++ b/package/MDAnalysis/coordinates/base.py @@ -1165,7 +1165,7 @@ def apply_limits(frame): elif isinstance(frame, (list, np.ndarray)): def listiter(frames): for f in frames: - if not isinstance(f, int): + if not isinstance(f, (int, np.integer)): raise TypeError("Frames indices must be integers") yield self._read_frame(apply_limits(f)) return listiter(frame) diff --git a/package/MDAnalysis/core/Selection.py b/package/MDAnalysis/core/Selection.py index fe74df3f229..b3fadf4c56b 100644 --- a/package/MDAnalysis/core/Selection.py +++ b/package/MDAnalysis/core/Selection.py @@ -29,15 +29,17 @@ This is all invisible to the user through ag.select_atoms """ +import six +from six.moves import zip import collections import re +import functools +import warnings + import numpy as np from numpy.lib.utils import deprecate from Bio.KDTree import KDTree -import warnings -import six -from six.moves import zip from MDAnalysis.core import flags from ..lib import distances @@ -909,7 +911,7 @@ def apply(self, group): if self.prop == 'fragment': # Combine all fragments together, then check where group # indices are same as fragment(s) indices - allfrags = reduce(lambda x, y: x + y, res.fragments) + allfrags = functools.reduce(lambda x, y: x + y, res.fragments) mask = np.in1d(group.indices, allfrags.indices) return unique(group[mask]) diff --git a/package/MDAnalysis/lib/formats/xdrlib.c b/package/MDAnalysis/lib/formats/xdrlib.c index d53d9211cd2..52d8f3f0d97 100644 --- a/package/MDAnalysis/lib/formats/xdrlib.c +++ b/package/MDAnalysis/lib/formats/xdrlib.c @@ -1,4 +1,4 @@ -/* Generated by Cython 0.23.2 */ +/* Generated by Cython 0.23.4 */ /* BEGIN: Cython Metadata { @@ -18,8 +18,8 @@ ] ], "depends": [ - "/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h", - "/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ufuncobject.h", + "/home/jon/Envs/mda2/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h", + "/home/jon/Envs/mda2/local/lib/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h", "MDAnalysis/lib/formats/include/trr_seek.h", "MDAnalysis/lib/formats/include/xdrfile.h", "MDAnalysis/lib/formats/include/xdrfile_trr.h", @@ -27,7 +27,7 @@ "MDAnalysis/lib/formats/include/xtc_seek.h" ], "include_dirs": [ - "/usr/local/lib/python2.7/dist-packages/numpy/core/include", + "/home/jon/Envs/mda2/local/lib/python2.7/site-packages/numpy/core/include", "MDAnalysis/lib/formats/include", "MDAnalysis/lib/formats" ] @@ -42,7 +42,7 @@ END: Cython Metadata */ #elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) #error Cython requires Python 2.6+ or Python 3.2+. #else -#define CYTHON_ABI "0_23_2" +#define CYTHON_ABI "0_23_4" #include #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) @@ -224,7 +224,7 @@ typedef struct { #define CYTHON_RESTRICT #endif #endif -#define __Pyx_void_to_None(void_result) (void_result, Py_INCREF(Py_None), Py_None) +#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) #ifndef CYTHON_INLINE #if defined(__GNUC__) @@ -339,10 +339,10 @@ typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding; #define __Pyx_sst_abs(value) abs(value) #elif SIZEOF_LONG >= SIZEOF_SIZE_T #define __Pyx_sst_abs(value) labs(value) -#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define __Pyx_sst_abs(value) llabs(value) #elif defined (_MSC_VER) && defined (_M_X64) #define __Pyx_sst_abs(value) _abs64(value) +#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define __Pyx_sst_abs(value) llabs(value) #elif defined (__GNUC__) #define __Pyx_sst_abs(value) __builtin_llabs(value) #else @@ -611,7 +611,7 @@ typedef volatile __pyx_atomic_int_type __pyx_atomic_int; #endif -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":725 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":725 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -620,7 +620,7 @@ typedef volatile __pyx_atomic_int_type __pyx_atomic_int; */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":726 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -629,7 +629,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":727 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":727 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -638,7 +638,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":728 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":728 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -647,7 +647,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":732 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":732 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -656,7 +656,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":733 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -665,7 +665,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":734 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":734 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -674,7 +674,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":735 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":735 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -683,7 +683,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":739 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":739 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -692,7 +692,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":740 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":740 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -701,7 +701,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":749 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":749 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -710,7 +710,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":750 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":750 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -719,7 +719,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":751 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":751 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -728,7 +728,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":753 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":753 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -737,7 +737,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":754 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":754 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -746,7 +746,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":755 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":755 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -755,7 +755,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":757 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":757 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -764,7 +764,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":758 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -773,7 +773,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":760 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":760 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # 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<<<<<<<<<<<<<< - * self.fname = fname + * self.fname = fname.encode('utf-8') * self.is_open = False */ @@ -3930,7 +3938,7 @@ static Py_ssize_t __pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_16__len_ * return self.offsets.size * */ - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple_, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__2, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -4079,7 +4087,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_8_XDRFile_18seek(st * offset = self.offsets[frame] * self.reached_eof = False */ - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__2, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_IOError, __pyx_tuple__3, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; @@ -5521,7 +5529,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru * if not self.is_open: * raise RuntimeError('No file opened') */ - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__3, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__4, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -5553,7 +5561,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru * if self.mode != 'r': * raise RuntimeError('File opened in mode: {}. Reading only allow ' */ - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__4, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 418; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__5, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 418; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -5588,7 +5596,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_4read(stru */ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_File_opened_in_mode_Reading_only, __pyx_n_s_format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__5, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__6, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -6361,7 +6369,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7TRRFile_6write(str */ __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_File_opened_in_mode_Writing_only, __pyx_n_s_format); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 494; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__6, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 494; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__7, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 494; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; @@ -7833,7 +7841,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru * if not self.is_open: * raise RuntimeError('No file opened') */ - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__7, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 629; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__8, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 629; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -7865,7 +7873,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru * if self.mode != 'r': * raise RuntimeError('File opened in mode: {}. Reading only allow ' */ - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__8, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__9, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_Raise(__pyx_t_2, 0, 0, 0); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -7900,7 +7908,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_4read(stru */ __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_File_opened_in_mode_Reading_only, __pyx_n_s_format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__9, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__10, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; @@ -8431,7 +8439,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str */ __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_File_opened_in_mode_Writing_only, __pyx_n_s_format); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__10, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__11, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; @@ -9070,7 +9078,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_6xdrlib_7XTCFile_6write(str return __pyx_r; } -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":197 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":197 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -9120,7 +9128,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_GIVEREF(__pyx_v_info->obj); } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":203 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":203 * # of flags * * if info == NULL: return # <<<<<<<<<<<<<< @@ -9133,7 +9141,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L0; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":206 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":206 * * cdef int copy_shape, i, ndim * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -9142,7 +9150,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_endian_detector = 1; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":207 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":207 * cdef int copy_shape, i, ndim * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< @@ -9151,7 +9159,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":209 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":209 * cdef bint little_endian = ((&endian_detector)[0] != 0) * * ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<< @@ -9160,7 +9168,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_ndim = PyArray_NDIM(__pyx_v_self); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":211 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":211 * ndim = PyArray_NDIM(self) * * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -9170,7 +9178,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":212 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":212 * * if sizeof(npy_intp) != sizeof(Py_ssize_t): * copy_shape = 1 # <<<<<<<<<<<<<< @@ -9179,7 +9187,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_copy_shape = 1; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":211 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":211 * ndim = PyArray_NDIM(self) * * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -9189,7 +9197,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L4; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":214 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":214 * copy_shape = 1 * else: * copy_shape = 0 # <<<<<<<<<<<<<< @@ -9201,7 +9209,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L4:; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":216 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":216 * copy_shape = 0 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -9215,7 +9223,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L6_bool_binop_done; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":217 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":217 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -9226,7 +9234,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L6_bool_binop_done:; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":216 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":216 * copy_shape = 0 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -9235,20 +9243,20 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (__pyx_t_1) { - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":218 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":218 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__11, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__12, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":216 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":216 * copy_shape = 0 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -9257,7 +9265,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":220 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":220 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -9271,7 +9279,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L9_bool_binop_done; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":221 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":221 * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -9282,7 +9290,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L9_bool_binop_done:; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":220 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":220 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -9291,20 +9299,20 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (__pyx_t_1) { - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":222 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":222 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< * * info.buf = PyArray_DATA(self) */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__12, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__13, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":220 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":220 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -9313,7 +9321,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":224 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":224 * raise ValueError(u"ndarray is not Fortran contiguous") * * info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<< @@ -9322,7 +9330,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->buf = PyArray_DATA(__pyx_v_self); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":225 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":225 * * info.buf = PyArray_DATA(self) * info.ndim = ndim # <<<<<<<<<<<<<< @@ -9331,7 +9339,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->ndim = __pyx_v_ndim; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":226 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":226 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if copy_shape: # <<<<<<<<<<<<<< @@ -9341,7 +9349,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = (__pyx_v_copy_shape != 0); if (__pyx_t_1) { - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":229 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":229 * # Allocate new buffer for strides and shape info. * # This is allocated as one block, strides first. * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) # <<<<<<<<<<<<<< @@ -9350,7 +9358,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->strides = ((Py_ssize_t *)malloc((((sizeof(Py_ssize_t)) * ((size_t)__pyx_v_ndim)) * 2))); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":230 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":230 * # This is allocated as one block, strides first. * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) * info.shape = info.strides + ndim # <<<<<<<<<<<<<< @@ -9359,7 +9367,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":231 * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) * info.shape = info.strides + ndim * for i in range(ndim): # <<<<<<<<<<<<<< @@ -9370,7 +9378,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { __pyx_v_i = __pyx_t_5; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":232 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":232 * info.shape = info.strides + ndim * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< @@ -9379,7 +9387,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":233 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":233 * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< @@ -9389,7 +9397,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(__pyx_v_self)[__pyx_v_i]); } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":226 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":226 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if copy_shape: # <<<<<<<<<<<<<< @@ -9399,7 +9407,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L11; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":235 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":235 * info.shape[i] = PyArray_DIMS(self)[i] * else: * info.strides = PyArray_STRIDES(self) # <<<<<<<<<<<<<< @@ -9409,7 +9417,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self)); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":236 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":236 * else: * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -9420,7 +9428,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L11:; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":237 * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL # <<<<<<<<<<<<<< @@ -9429,7 +9437,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->suboffsets = NULL; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":238 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":238 * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<< @@ -9438,7 +9446,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":239 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":239 * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) * info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<< @@ -9447,7 +9455,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":242 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":242 * * cdef int t * cdef char* f = NULL # <<<<<<<<<<<<<< @@ -9456,7 +9464,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_f = NULL; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":243 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":243 * cdef int t * cdef char* f = NULL * cdef dtype descr = self.descr # <<<<<<<<<<<<<< @@ -9468,7 +9476,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3); __pyx_t_3 = 0; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":246 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":246 * cdef int offset * * cdef bint hasfields = PyDataType_HASFIELDS(descr) # <<<<<<<<<<<<<< @@ -9477,7 +9485,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_hasfields = PyDataType_HASFIELDS(__pyx_v_descr); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":248 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":248 * cdef bint hasfields = PyDataType_HASFIELDS(descr) * * if not hasfields and not copy_shape: # <<<<<<<<<<<<<< @@ -9495,7 +9503,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_L15_bool_binop_done:; if (__pyx_t_1) { - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":250 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":250 * if not hasfields and not copy_shape: * # do not call releasebuffer * info.obj = None # <<<<<<<<<<<<<< @@ -9508,7 +9516,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = Py_None; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":248 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":248 * cdef bint hasfields = PyDataType_HASFIELDS(descr) * * if not hasfields and not copy_shape: # <<<<<<<<<<<<<< @@ -9518,7 +9526,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L14; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":253 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":253 * else: * # need to call releasebuffer * info.obj = self # <<<<<<<<<<<<<< @@ -9534,7 +9542,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L14:; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":255 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":255 * info.obj = self * * if not hasfields: # <<<<<<<<<<<<<< @@ -9544,7 +9552,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = ((!(__pyx_v_hasfields != 0)) != 0); if (__pyx_t_1) { - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":256 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":256 * * if not hasfields: * t = descr.type_num # <<<<<<<<<<<<<< @@ -9554,7 +9562,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_4 = __pyx_v_descr->type_num; __pyx_v_t = __pyx_t_4; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257 * if not hasfields: * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -9574,7 +9582,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L20_next_or:; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":258 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":258 * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -9591,7 +9599,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L19_bool_binop_done:; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257 * if not hasfields: * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -9600,20 +9608,20 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (__pyx_t_1) { - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":259 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__13, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__14, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257 * if not hasfields: * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -9622,7 +9630,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":260 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":260 * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< @@ -9634,7 +9642,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_b; break; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":261 * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< @@ -9645,7 +9653,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_B; break; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":262 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":262 * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< @@ -9656,7 +9664,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_h; break; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":263 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":263 * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< @@ -9667,7 +9675,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_H; break; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":264 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":264 * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< @@ -9678,7 +9686,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_i; break; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":265 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":265 * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< @@ -9689,7 +9697,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_I; break; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":266 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":266 * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< @@ -9700,7 +9708,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_l; break; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":267 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":267 * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< @@ -9711,7 +9719,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_L; break; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":268 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":268 * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< @@ -9722,7 +9730,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_q; break; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":269 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":269 * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< @@ -9733,7 +9741,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Q; break; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270 * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< @@ -9744,7 +9752,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_f; break; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":271 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":271 * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< @@ -9755,7 +9763,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_d; break; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":272 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":272 * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< @@ -9766,7 +9774,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_g; break; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":273 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":273 * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<< @@ -9777,7 +9785,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Zf; break; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274 * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<< @@ -9788,7 +9796,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Zd; break; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":275 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":275 * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<< @@ -9799,7 +9807,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Zg; break; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":276 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":276 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< @@ -9811,7 +9819,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; default: - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":278 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":278 * elif t == NPY_OBJECT: f = "O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -9837,7 +9845,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":279 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":279 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f # <<<<<<<<<<<<<< @@ -9846,7 +9854,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->format = __pyx_v_f; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":280 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":280 * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f * return # <<<<<<<<<<<<<< @@ -9856,7 +9864,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_r = 0; goto __pyx_L0; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":255 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":255 * info.obj = self * * if not hasfields: # <<<<<<<<<<<<<< @@ -9865,7 +9873,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":282 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":282 * return * else: * info.format = stdlib.malloc(_buffer_format_string_len) # <<<<<<<<<<<<<< @@ -9875,7 +9883,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->format = ((char *)malloc(0xFF)); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":283 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":283 * else: * info.format = stdlib.malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<< @@ -9884,7 +9892,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->format[0]) = '^'; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":284 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":284 * info.format = stdlib.malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 # <<<<<<<<<<<<<< @@ -9893,7 +9901,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_offset = 0; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":285 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":285 * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 * f = _util_dtypestring(descr, info.format + 1, # <<<<<<<<<<<<<< @@ -9903,7 +9911,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_7 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 0xFF), (&__pyx_v_offset)); 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__pyx_t_3 = 0; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":795 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":795 * * for childname in descr.names: * fields = descr.fields[childname] # <<<<<<<<<<<<<< @@ -10377,7 +10385,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_fields, ((PyObject*)__pyx_t_3)); __pyx_t_3 = 0; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":796 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":796 * for childname in descr.names: * fields = descr.fields[childname] * child, new_offset = fields # <<<<<<<<<<<<<< @@ -10416,7 +10424,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_new_offset, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":798 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":798 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -10433,20 +10441,20 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((((__pyx_v_end - __pyx_v_f) - ((int)__pyx_t_5)) < 15) != 0); if (__pyx_t_6) { - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":799 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":799 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< * * if ((child.byteorder == c'>' and little_endian) or */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__14, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__15, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":798 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":798 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -10455,7 +10463,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":801 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":801 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -10475,7 +10483,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L8_next_or:; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":802 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":802 * * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -10492,7 +10500,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = __pyx_t_7; __pyx_L7_bool_binop_done:; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":801 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":801 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -10501,20 +10509,20 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ if (__pyx_t_6) { - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":803 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":803 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< * # One could encode it in the format string and have Cython * # complain instead, BUT: < and > in format strings also imply */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__15, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__16, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":801 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":801 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -10523,7 +10531,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":813 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":813 * * # Output padding bytes * while offset[0] < new_offset: # <<<<<<<<<<<<<< @@ -10539,7 +10547,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (!__pyx_t_6) break; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":814 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":814 * # Output padding bytes * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<< @@ -10548,7 +10556,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ (__pyx_v_f[0]) = 0x78; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":815 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":815 * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte * f += 1 # <<<<<<<<<<<<<< @@ -10557,7 +10565,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":816 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":816 * f[0] = 120 # "x"; pad byte * f += 1 * offset[0] += 1 # <<<<<<<<<<<<<< @@ -10568,7 +10576,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + 1); } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":818 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":818 * offset[0] += 1 * * offset[0] += child.itemsize # <<<<<<<<<<<<<< @@ -10578,7 +10586,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_8 = 0; (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":820 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":820 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -10588,7 +10596,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0); if (__pyx_t_6) { - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":821 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":821 * * if not PyDataType_HASFIELDS(child): * t = child.type_num # <<<<<<<<<<<<<< @@ -10600,7 +10608,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":822 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":822 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -10610,20 +10618,20 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = (((__pyx_v_end - __pyx_v_f) < 5) != 0); if (__pyx_t_6) { - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":823 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":823 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< * * # Until ticket #99 is fixed, use integers to avoid warnings */ - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__16, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_RuntimeError, __pyx_tuple__17, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_Raise(__pyx_t_4, 0, 0, 0); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":822 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":822 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -10632,7 +10640,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":826 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":826 * * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<< @@ -10650,7 +10658,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":827 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":827 * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<< @@ -10668,7 +10676,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":828 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":828 * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<< @@ -10686,7 +10694,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":829 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":829 * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<< @@ -10704,7 +10712,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":830 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":830 * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<< @@ -10722,7 +10730,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":831 * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<< @@ -10740,7 +10748,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":832 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":832 * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<< @@ -10758,7 +10766,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":833 * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<< @@ -10776,7 +10784,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":834 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":834 * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<< @@ -10794,7 +10802,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":835 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":835 * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<< @@ -10812,7 +10820,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":836 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":836 * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<< @@ -10830,7 +10838,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":837 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":837 * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<< @@ -10848,7 +10856,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":838 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":838 * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<< @@ -10866,7 +10874,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":839 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":839 * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<< @@ -10886,7 +10894,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":840 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":840 * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<< @@ -10906,7 +10914,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":841 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":841 * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<< @@ -10926,7 +10934,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":842 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":842 * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg * elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<< @@ -10944,7 +10952,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":844 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":844 * elif t == NPY_OBJECT: f[0] = 79 #"O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -10968,7 +10976,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L15:; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":845 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":845 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * f += 1 # <<<<<<<<<<<<<< @@ -10977,7 +10985,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":820 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":820 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -10987,7 +10995,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L13; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":849 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":849 * # Cython ignores struct boundary information ("T{...}"), * # so don't output it * f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<< @@ -11000,7 +11008,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L13:; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":794 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":794 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -11010,7 +11018,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":850 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":850 * # so don't output it * f = _util_dtypestring(child, f, end, offset) * return f # <<<<<<<<<<<<<< @@ -11020,7 +11028,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_r = __pyx_v_f; goto __pyx_L0; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":785 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":785 * return PyArray_MultiIterNew(5, a, b, c, d, e) * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -11045,7 +11053,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx return __pyx_r; } -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":966 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":966 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -11060,7 +11068,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a int __pyx_t_2; __Pyx_RefNannySetupContext("set_array_base", 0); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":968 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":968 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -11071,7 +11079,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":969 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":969 * cdef PyObject* baseptr * if base is None: * baseptr = NULL # <<<<<<<<<<<<<< @@ -11080,7 +11088,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_baseptr = NULL; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":968 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":968 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -11090,7 +11098,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a goto __pyx_L3; } - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":971 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":971 * baseptr = NULL * else: * Py_INCREF(base) # important to do this before decref below! # <<<<<<<<<<<<<< @@ -11100,7 +11108,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a /*else*/ { Py_INCREF(__pyx_v_base); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":972 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":972 * else: * Py_INCREF(base) # important to do this before decref below! * baseptr = base # <<<<<<<<<<<<<< @@ -11111,7 +11119,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a } __pyx_L3:; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":973 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":973 * Py_INCREF(base) # important to do this before decref below! * baseptr = base * Py_XDECREF(arr.base) # <<<<<<<<<<<<<< @@ -11120,7 +11128,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ Py_XDECREF(__pyx_v_arr->base); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":974 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":974 * baseptr = base * Py_XDECREF(arr.base) * arr.base = baseptr # <<<<<<<<<<<<<< @@ -11129,7 +11137,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_arr->base = __pyx_v_baseptr; - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":966 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":966 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -11141,7 +11149,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __Pyx_RefNannyFinishContext(); } -/* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":976 +/* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":976 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -11155,7 +11163,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py int __pyx_t_1; __Pyx_RefNannySetupContext("get_array_base", 0); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":977 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":977 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< @@ -11165,7 +11173,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_t_1 = ((__pyx_v_arr->base == NULL) != 0); if (__pyx_t_1) { - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":978 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":978 * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: * return None # <<<<<<<<<<<<<< @@ -11177,7 +11185,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = Py_None; 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if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__18, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; @@ -11436,7 +11444,7 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __ * * if not isinstance(format, bytes): */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__18, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__19, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; @@ -11471,7 +11479,7 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __ */ __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_v_format, __pyx_n_s_encode); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__19, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__20, NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF_SET(__pyx_v_format, __pyx_t_5); @@ -11547,7 +11555,7 @@ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __ * * */ - __pyx_t_5 = __Pyx_PyObject_Call(__pyx_builtin_MemoryError, __pyx_tuple__20, NULL); 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__pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__2); + __Pyx_GIVEREF(__pyx_tuple__2); /* "MDAnalysis/lib/formats/xdrlib.pyx":260 * else: @@ -23961,9 +23981,9 @@ static int __Pyx_InitCachedConstants(void) { * offset = self.offsets[frame] * self.reached_eof = False */ - __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_s_Trying_to_seek_over_max_number_o); if (unlikely(!__pyx_tuple__2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__2); - __Pyx_GIVEREF(__pyx_tuple__2); + __pyx_tuple__3 = PyTuple_Pack(1, __pyx_kp_s_Trying_to_seek_over_max_number_o); if (unlikely(!__pyx_tuple__3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__3); + __Pyx_GIVEREF(__pyx_tuple__3); /* "MDAnalysis/lib/formats/xdrlib.pyx":416 * """ @@ -23972,9 +23992,9 @@ static int __Pyx_InitCachedConstants(void) { * if not self.is_open: * raise RuntimeError('No file opened') */ - __pyx_tuple__3 = PyTuple_Pack(1, __pyx_kp_s_Reached_last_frame_in_TRR_seek_t); if (unlikely(!__pyx_tuple__3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__3); - __Pyx_GIVEREF(__pyx_tuple__3); + __pyx_tuple__4 = PyTuple_Pack(1, __pyx_kp_s_Reached_last_frame_in_TRR_seek_t); if (unlikely(!__pyx_tuple__4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__4); + __Pyx_GIVEREF(__pyx_tuple__4); /* "MDAnalysis/lib/formats/xdrlib.pyx":418 * raise RuntimeError('Reached last frame in TRR, seek to 0') @@ -23983,9 +24003,9 @@ static int __Pyx_InitCachedConstants(void) { * if self.mode != 'r': * raise RuntimeError('File opened in mode: {}. 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Reading only allow ' */ - __pyx_tuple__8 = PyTuple_Pack(1, __pyx_kp_s_No_file_opened); if (unlikely(!__pyx_tuple__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__8); - __Pyx_GIVEREF(__pyx_tuple__8); + __pyx_tuple__9 = PyTuple_Pack(1, __pyx_kp_s_No_file_opened); if (unlikely(!__pyx_tuple__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__9); + __Pyx_GIVEREF(__pyx_tuple__9); /* "MDAnalysis/lib/formats/xdrlib.pyx":634 * if self.mode != 'r': @@ -24038,9 +24058,9 @@ static int __Pyx_InitCachedConstants(void) { * * return_code = 1 */ - __pyx_tuple__9 = PyTuple_Pack(1, __pyx_kp_s_self_mode); if (unlikely(!__pyx_tuple__9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__9); - __Pyx_GIVEREF(__pyx_tuple__9); + __pyx_tuple__10 = PyTuple_Pack(1, __pyx_kp_s_self_mode); if (unlikely(!__pyx_tuple__10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__10); + __Pyx_GIVEREF(__pyx_tuple__10); /* "MDAnalysis/lib/formats/xdrlib.pyx":691 * if self.mode != 'w': @@ -24049,75 +24069,75 @@ static int __Pyx_InitCachedConstants(void) { * * cdef DTYPE_T[:, ::1] xyz_view = np.ascontiguousarray(xyz, dtype=DTYPE) */ - __pyx_tuple__10 = PyTuple_Pack(1, __pyx_kp_s_self_mode); if (unlikely(!__pyx_tuple__10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__10); - __Pyx_GIVEREF(__pyx_tuple__10); + __pyx_tuple__11 = PyTuple_Pack(1, __pyx_kp_s_self_mode); if (unlikely(!__pyx_tuple__11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__11); + __Pyx_GIVEREF(__pyx_tuple__11); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":218 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":218 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) */ - __pyx_tuple__11 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_C_contiguous); if (unlikely(!__pyx_tuple__11)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__11); - __Pyx_GIVEREF(__pyx_tuple__11); + __pyx_tuple__12 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_C_contiguous); if (unlikely(!__pyx_tuple__12)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__12); + __Pyx_GIVEREF(__pyx_tuple__12); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":222 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":222 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< * * info.buf = PyArray_DATA(self) */ - __pyx_tuple__12 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_Fortran_contiguou); if (unlikely(!__pyx_tuple__12)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__12); - __Pyx_GIVEREF(__pyx_tuple__12); + __pyx_tuple__13 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_Fortran_contiguou); if (unlikely(!__pyx_tuple__13)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__13); + __Pyx_GIVEREF(__pyx_tuple__13); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":259 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" */ - __pyx_tuple__13 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__13)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__13); - __Pyx_GIVEREF(__pyx_tuple__13); + __pyx_tuple__14 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__14)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__14); + __Pyx_GIVEREF(__pyx_tuple__14); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":799 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":799 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< * * if ((child.byteorder == c'>' and little_endian) or */ - __pyx_tuple__14 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor); if (unlikely(!__pyx_tuple__14)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__14); - __Pyx_GIVEREF(__pyx_tuple__14); + __pyx_tuple__15 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor); if (unlikely(!__pyx_tuple__15)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__15); + __Pyx_GIVEREF(__pyx_tuple__15); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":803 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":803 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< * # One could encode it in the format string and have Cython * # complain instead, BUT: < and > in format strings also imply */ - __pyx_tuple__15 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__15)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__15); - __Pyx_GIVEREF(__pyx_tuple__15); + __pyx_tuple__16 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__16)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__16); + __Pyx_GIVEREF(__pyx_tuple__16); - /* "../../../../../../usr/local/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":823 + /* "../../../Envs/mda2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":823 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< * * # Until ticket #99 is fixed, use integers to avoid warnings */ - __pyx_tuple__16 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor_2); if (unlikely(!__pyx_tuple__16)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__16); - __Pyx_GIVEREF(__pyx_tuple__16); + __pyx_tuple__17 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor_2); if (unlikely(!__pyx_tuple__17)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__17); + __Pyx_GIVEREF(__pyx_tuple__17); /* "View.MemoryView":129 * @@ -24126,9 +24146,9 @@ static int __Pyx_InitCachedConstants(void) { * * if itemsize <= 0: */ - __pyx_tuple__17 = PyTuple_Pack(1, __pyx_kp_s_Empty_shape_tuple_for_cython_arr); if (unlikely(!__pyx_tuple__17)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__17); - __Pyx_GIVEREF(__pyx_tuple__17); + __pyx_tuple__18 = PyTuple_Pack(1, __pyx_kp_s_Empty_shape_tuple_for_cython_arr); if (unlikely(!__pyx_tuple__18)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__18); + __Pyx_GIVEREF(__pyx_tuple__18); /* "View.MemoryView":132 * @@ -24137,9 +24157,9 @@ static int __Pyx_InitCachedConstants(void) { * * if not isinstance(format, bytes): */ - __pyx_tuple__18 = PyTuple_Pack(1, __pyx_kp_s_itemsize_0_for_cython_array); if (unlikely(!__pyx_tuple__18)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__18); - __Pyx_GIVEREF(__pyx_tuple__18); + __pyx_tuple__19 = PyTuple_Pack(1, __pyx_kp_s_itemsize_0_for_cython_array); if (unlikely(!__pyx_tuple__19)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__19); + __Pyx_GIVEREF(__pyx_tuple__19); /* "View.MemoryView":135 * @@ -24148,9 +24168,9 @@ static int __Pyx_InitCachedConstants(void) { * self._format = format # keep a reference to the byte string * self.format = self._format */ - __pyx_tuple__19 = PyTuple_Pack(1, __pyx_n_s_ASCII); if (unlikely(!__pyx_tuple__19)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__19); - __Pyx_GIVEREF(__pyx_tuple__19); + __pyx_tuple__20 = PyTuple_Pack(1, __pyx_n_s_ASCII); if (unlikely(!__pyx_tuple__20)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__20); + __Pyx_GIVEREF(__pyx_tuple__20); /* "View.MemoryView":144 * @@ -24159,9 +24179,9 @@ static int __Pyx_InitCachedConstants(void) { * * */ - __pyx_tuple__20 = PyTuple_Pack(1, __pyx_kp_s_unable_to_allocate_shape_and_str); if (unlikely(!__pyx_tuple__20)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__20); - __Pyx_GIVEREF(__pyx_tuple__20); + __pyx_tuple__21 = PyTuple_Pack(1, __pyx_kp_s_unable_to_allocate_shape_and_str); if (unlikely(!__pyx_tuple__21)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__21); + __Pyx_GIVEREF(__pyx_tuple__21); /* "View.MemoryView":172 * self.data = malloc(self.len) @@ -24170,9 +24190,9 @@ static int __Pyx_InitCachedConstants(void) { * * if self.dtype_is_object: */ - __pyx_tuple__21 = PyTuple_Pack(1, __pyx_kp_s_unable_to_allocate_array_data); if (unlikely(!__pyx_tuple__21)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__21); - __Pyx_GIVEREF(__pyx_tuple__21); + __pyx_tuple__22 = PyTuple_Pack(1, __pyx_kp_s_unable_to_allocate_array_data); if (unlikely(!__pyx_tuple__22)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__22); + __Pyx_GIVEREF(__pyx_tuple__22); /* "View.MemoryView":188 * bufmode = PyBUF_F_CONTIGUOUS | PyBUF_ANY_CONTIGUOUS @@ -24181,9 +24201,9 @@ static int __Pyx_InitCachedConstants(void) { * info.buf = self.data * info.len = self.len */ - __pyx_tuple__22 = PyTuple_Pack(1, __pyx_kp_s_Can_only_create_a_buffer_that_is); if (unlikely(!__pyx_tuple__22)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__22); - __Pyx_GIVEREF(__pyx_tuple__22); + __pyx_tuple__23 = PyTuple_Pack(1, __pyx_kp_s_Can_only_create_a_buffer_that_is); if (unlikely(!__pyx_tuple__23)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__23); + __Pyx_GIVEREF(__pyx_tuple__23); /* "View.MemoryView":447 * result = struct.unpack(self.view.format, bytesitem) @@ -24192,9 +24212,9 @@ static int __Pyx_InitCachedConstants(void) { * else: * if len(self.view.format) == 1: */ - __pyx_tuple__23 = PyTuple_Pack(1, __pyx_kp_s_Unable_to_convert_item_to_object); if (unlikely(!__pyx_tuple__23)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__23); - __Pyx_GIVEREF(__pyx_tuple__23); + __pyx_tuple__24 = PyTuple_Pack(1, __pyx_kp_s_Unable_to_convert_item_to_object); if (unlikely(!__pyx_tuple__24)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__24); + __Pyx_GIVEREF(__pyx_tuple__24); /* "View.MemoryView":523 * if self.view.strides == NULL: @@ -24203,9 +24223,9 @@ static int __Pyx_InitCachedConstants(void) { * * return tuple([stride for stride in self.view.strides[:self.view.ndim]]) */ - __pyx_tuple__24 = PyTuple_Pack(1, __pyx_kp_s_Buffer_view_does_not_expose_stri); if (unlikely(!__pyx_tuple__24)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 523; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__24); - __Pyx_GIVEREF(__pyx_tuple__24); + __pyx_tuple__25 = PyTuple_Pack(1, __pyx_kp_s_Buffer_view_does_not_expose_stri); if (unlikely(!__pyx_tuple__25)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 523; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__25); + __Pyx_GIVEREF(__pyx_tuple__25); /* "View.MemoryView":531 * def __get__(self): @@ -24214,12 +24234,12 @@ static int __Pyx_InitCachedConstants(void) { * * return tuple([suboffset for suboffset in self.view.suboffsets[:self.view.ndim]]) */ - __pyx_tuple__25 = PyTuple_New(1); if (unlikely(!__pyx_tuple__25)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 531; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__25); + __pyx_tuple__26 = PyTuple_New(1); if (unlikely(!__pyx_tuple__26)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 531; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__26); __Pyx_INCREF(__pyx_int_neg_1); __Pyx_GIVEREF(__pyx_int_neg_1); - PyTuple_SET_ITEM(__pyx_tuple__25, 0, __pyx_int_neg_1); - __Pyx_GIVEREF(__pyx_tuple__25); + PyTuple_SET_ITEM(__pyx_tuple__26, 0, __pyx_int_neg_1); + __Pyx_GIVEREF(__pyx_tuple__26); /* "View.MemoryView":640 * if item is Ellipsis: @@ -24228,9 +24248,9 @@ static int __Pyx_InitCachedConstants(void) { * seen_ellipsis = True * else: */ - __pyx_slice__26 = PySlice_New(Py_None, Py_None, Py_None); if (unlikely(!__pyx_slice__26)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_slice__26); - __Pyx_GIVEREF(__pyx_slice__26); + __pyx_slice__27 = PySlice_New(Py_None, Py_None, Py_None); if (unlikely(!__pyx_slice__27)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_slice__27); + __Pyx_GIVEREF(__pyx_slice__27); /* "View.MemoryView":643 * seen_ellipsis = True @@ -24239,9 +24259,9 @@ static int __Pyx_InitCachedConstants(void) { * have_slices = True * else: */ - __pyx_slice__27 = PySlice_New(Py_None, Py_None, Py_None); if (unlikely(!__pyx_slice__27)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_slice__27); - __Pyx_GIVEREF(__pyx_slice__27); + __pyx_slice__28 = PySlice_New(Py_None, Py_None, Py_None); if (unlikely(!__pyx_slice__28)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_slice__28); + __Pyx_GIVEREF(__pyx_slice__28); /* "View.MemoryView":654 * nslices = ndim - len(result) @@ -24250,9 +24270,9 @@ static int __Pyx_InitCachedConstants(void) { * * return have_slices or nslices, tuple(result) */ - __pyx_slice__28 = PySlice_New(Py_None, Py_None, Py_None); if (unlikely(!__pyx_slice__28)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_slice__28); - __Pyx_GIVEREF(__pyx_slice__28); + __pyx_slice__29 = PySlice_New(Py_None, Py_None, Py_None); if (unlikely(!__pyx_slice__29)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_slice__29); + __Pyx_GIVEREF(__pyx_slice__29); /* "View.MemoryView":661 * for suboffset in suboffsets[:ndim]: @@ -24261,9 +24281,9 @@ static int __Pyx_InitCachedConstants(void) { * * */ - __pyx_tuple__29 = PyTuple_Pack(1, __pyx_kp_s_Indirect_dimensions_not_supporte); if (unlikely(!__pyx_tuple__29)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__29); - __Pyx_GIVEREF(__pyx_tuple__29); + __pyx_tuple__30 = PyTuple_Pack(1, __pyx_kp_s_Indirect_dimensions_not_supporte); if (unlikely(!__pyx_tuple__30)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__30); + __Pyx_GIVEREF(__pyx_tuple__30); /* "MDAnalysis/lib/formats/xdrlib.pyx":346 * @@ -24272,9 +24292,9 @@ static int __Pyx_InitCachedConstants(void) { * * */ - __pyx_tuple__30 = PyTuple_Pack(2, __pyx_n_s_TRRFrame, __pyx_kp_s_x_v_f_box_step_time_lmbda_hasx_h); if (unlikely(!__pyx_tuple__30)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 346; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__30); - __Pyx_GIVEREF(__pyx_tuple__30); + __pyx_tuple__31 = PyTuple_Pack(2, __pyx_n_s_TRRFrame, __pyx_kp_s_x_v_f_box_step_time_lmbda_hasx_h); if (unlikely(!__pyx_tuple__31)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 346; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__31); + __Pyx_GIVEREF(__pyx_tuple__31); /* "MDAnalysis/lib/formats/xdrlib.pyx":558 * @@ -24283,9 +24303,9 @@ static int __Pyx_InitCachedConstants(void) { * * */ - __pyx_tuple__31 = PyTuple_Pack(2, __pyx_n_s_XTCFrame, __pyx_kp_s_x_box_step_time_prec); if (unlikely(!__pyx_tuple__31)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 558; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__31); - __Pyx_GIVEREF(__pyx_tuple__31); + __pyx_tuple__32 = PyTuple_Pack(2, __pyx_n_s_XTCFrame, __pyx_kp_s_x_box_step_time_prec); if (unlikely(!__pyx_tuple__32)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 558; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__32); + __Pyx_GIVEREF(__pyx_tuple__32); /* "View.MemoryView":278 * return self.name @@ -24294,9 +24314,9 @@ static int __Pyx_InitCachedConstants(void) { * cdef strided = Enum("") # default * cdef indirect = Enum("") */ - __pyx_tuple__32 = PyTuple_Pack(1, __pyx_kp_s_strided_and_direct_or_indirect); if (unlikely(!__pyx_tuple__32)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__32); - __Pyx_GIVEREF(__pyx_tuple__32); + __pyx_tuple__33 = PyTuple_Pack(1, __pyx_kp_s_strided_and_direct_or_indirect); if (unlikely(!__pyx_tuple__33)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__33); + __Pyx_GIVEREF(__pyx_tuple__33); /* "View.MemoryView":279 * @@ -24305,9 +24325,9 @@ static int __Pyx_InitCachedConstants(void) { * cdef indirect = Enum("") * */ - __pyx_tuple__33 = PyTuple_Pack(1, __pyx_kp_s_strided_and_direct); if (unlikely(!__pyx_tuple__33)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__33); - __Pyx_GIVEREF(__pyx_tuple__33); + __pyx_tuple__34 = PyTuple_Pack(1, __pyx_kp_s_strided_and_direct); if (unlikely(!__pyx_tuple__34)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__34); + __Pyx_GIVEREF(__pyx_tuple__34); /* "View.MemoryView":280 * cdef generic = Enum("") @@ -24316,9 +24336,9 @@ static int __Pyx_InitCachedConstants(void) { * * */ - __pyx_tuple__34 = PyTuple_Pack(1, __pyx_kp_s_strided_and_indirect); if (unlikely(!__pyx_tuple__34)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 280; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__34); - __Pyx_GIVEREF(__pyx_tuple__34); + __pyx_tuple__35 = PyTuple_Pack(1, __pyx_kp_s_strided_and_indirect); if (unlikely(!__pyx_tuple__35)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 280; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__35); + __Pyx_GIVEREF(__pyx_tuple__35); /* "View.MemoryView":283 * @@ -24327,9 +24347,9 @@ static int __Pyx_InitCachedConstants(void) { * cdef indirect_contiguous = Enum("") * */ - __pyx_tuple__35 = PyTuple_Pack(1, __pyx_kp_s_contiguous_and_direct); if (unlikely(!__pyx_tuple__35)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__35); - __Pyx_GIVEREF(__pyx_tuple__35); + __pyx_tuple__36 = PyTuple_Pack(1, __pyx_kp_s_contiguous_and_direct); if (unlikely(!__pyx_tuple__36)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__36); + __Pyx_GIVEREF(__pyx_tuple__36); /* "View.MemoryView":284 * @@ -24338,9 +24358,9 @@ static int __Pyx_InitCachedConstants(void) { * * */ - __pyx_tuple__36 = PyTuple_Pack(1, __pyx_kp_s_contiguous_and_indirect); if (unlikely(!__pyx_tuple__36)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__36); - __Pyx_GIVEREF(__pyx_tuple__36); + __pyx_tuple__37 = PyTuple_Pack(1, __pyx_kp_s_contiguous_and_indirect); if (unlikely(!__pyx_tuple__37)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__37); + __Pyx_GIVEREF(__pyx_tuple__37); __Pyx_RefNannyFinishContext(); return 0; __pyx_L1_error:; @@ -24743,7 +24763,7 @@ PyMODINIT_FUNC PyInit_xdrlib(void) */ __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_namedtuple); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 346; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__30, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 346; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_tuple__31, NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 346; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (PyDict_SetItem(__pyx_d, __pyx_n_s_TRRFrame, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 346; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -24758,7 +24778,7 @@ PyMODINIT_FUNC PyInit_xdrlib(void) */ __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_namedtuple); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 558; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__31, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 558; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_tuple__32, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 558; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; if (PyDict_SetItem(__pyx_d, __pyx_n_s_XTCFrame, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 558; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -24794,7 +24814,7 @@ PyMODINIT_FUNC PyInit_xdrlib(void) * cdef strided = Enum("") # default * cdef indirect = Enum("") */ - __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__32, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__33, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_XGOTREF(generic); __Pyx_DECREF_SET(generic, __pyx_t_3); @@ -24808,7 +24828,7 @@ PyMODINIT_FUNC PyInit_xdrlib(void) * cdef indirect = Enum("") * */ - __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__33, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__34, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_XGOTREF(strided); __Pyx_DECREF_SET(strided, __pyx_t_3); @@ -24822,7 +24842,7 @@ PyMODINIT_FUNC PyInit_xdrlib(void) * * */ - __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__34, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 280; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__35, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 280; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_XGOTREF(indirect); __Pyx_DECREF_SET(indirect, __pyx_t_3); @@ -24836,7 +24856,7 @@ PyMODINIT_FUNC PyInit_xdrlib(void) * cdef indirect_contiguous = Enum("") * */ - __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__35, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__36, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_XGOTREF(contiguous); __Pyx_DECREF_SET(contiguous, __pyx_t_3); @@ -24850,7 +24870,7 @@ PyMODINIT_FUNC PyInit_xdrlib(void) * * */ - __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__36, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(((PyObject *)__pyx_MemviewEnum_type), __pyx_tuple__37, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_XGOTREF(indirect_contiguous); __Pyx_DECREF_SET(indirect_contiguous, __pyx_t_3); @@ -25147,8 +25167,12 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObjec } #else static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject* args = PyTuple_Pack(1, arg); - return (likely(args)) ? __Pyx_PyObject_Call(func, args, NULL) : NULL; + PyObject *result; + PyObject *args = PyTuple_Pack(1, arg); + if (unlikely(!args)) return NULL; + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; } #endif @@ -25701,32 +25725,32 @@ static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED switch (size) { case -2: if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0])); + a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); break; } case 2: if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0])); + a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); break; } case -3: if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); break; } case 3: if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); break; } case -4: if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); break; } case 4: if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); break; } #if PyLong_SHIFT < 30 && PyLong_SHIFT != 15 @@ -26696,7 +26720,13 @@ static CYTHON_INLINE PyObject* __Pyx_decode_c_string( PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { Py_ssize_t length; if (unlikely((start < 0) | (stop < 0))) { - length = strlen(cstring); + size_t slen = strlen(cstring); + if (unlikely(slen > (size_t) PY_SSIZE_T_MAX)) { + PyErr_SetString(PyExc_OverflowError, + "c-string too long to convert to Python"); + return NULL; + } + length = (Py_ssize_t) slen; if (start < 0) { start += length; if (start < 0) @@ -26836,50 +26866,50 @@ static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED switch (size) { case -2: if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0])); + a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); break; } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | digits[0])); + lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); goto long_long; } case 2: if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0])); + a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); break; } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | digits[0])); + lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); goto long_long; } case -3: if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); break; } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); goto long_long; } case 3: if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); break; } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); goto long_long; } case -4: if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); break; } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); goto long_long; } case 4: if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); break; } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); goto long_long; } default: return PyLong_Type.tp_as_number->nb_add(op1, op2); @@ -27209,27 +27239,27 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { case 2: if (8 * sizeof(int) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | digits[0])); + return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); } } break; case 3: if (8 * sizeof(int) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); } } break; case 4: if (8 * sizeof(int) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); } } break; @@ -27263,54 +27293,54 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { case -2: if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) -(((((int)digits[1]) << PyLong_SHIFT) | digits[0])); + return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } } break; case 2: if (8 * sizeof(int) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | digits[0])); + return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } } break; case -3: if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) -(((((((int)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } } break; case 3: if (8 * sizeof(int) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } } break; case -4: if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) -(((((((((int)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } } break; case 4: if (8 * sizeof(int) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); } } break; @@ -27419,27 +27449,27 @@ static CYTHON_INLINE int64_t __Pyx_PyInt_As_int64_t(PyObject *x) { case 2: if (8 * sizeof(int64_t) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(int64_t) >= 2 * PyLong_SHIFT) { - return (int64_t) (((((int64_t)digits[1]) << PyLong_SHIFT) | digits[0])); + return (int64_t) (((((int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])); } } break; case 3: if (8 * sizeof(int64_t) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(int64_t) >= 3 * PyLong_SHIFT) { - return (int64_t) (((((((int64_t)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (int64_t) (((((((int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])); } } break; case 4: if (8 * sizeof(int64_t) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(int64_t) >= 4 * PyLong_SHIFT) { - return (int64_t) (((((((((int64_t)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (int64_t) (((((((((int64_t)digits[3]) << PyLong_SHIFT) | (int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0])); } } break; @@ -27473,54 +27503,54 @@ static CYTHON_INLINE int64_t __Pyx_PyInt_As_int64_t(PyObject *x) { case -2: if (8 * sizeof(int64_t) - 1 > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT) { - return (int64_t) -(((((int64_t)digits[1]) << PyLong_SHIFT) | digits[0])); + return (int64_t) (((int64_t)-1)*(((((int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); } } break; case 2: if (8 * sizeof(int64_t) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT) { - return (int64_t) (((((int64_t)digits[1]) << PyLong_SHIFT) | digits[0])); + return (int64_t) ((((((int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); } } break; case -3: if (8 * sizeof(int64_t) - 1 > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT) { - return (int64_t) -(((((((int64_t)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (int64_t) (((int64_t)-1)*(((((((int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); } } break; case 3: if (8 * sizeof(int64_t) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT) { - return (int64_t) (((((((int64_t)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (int64_t) ((((((((int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); } } break; case -4: if (8 * sizeof(int64_t) - 1 > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(int64_t, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(int64_t) - 1 > 4 * PyLong_SHIFT) { - return (int64_t) -(((((((((int64_t)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (int64_t) (((int64_t)-1)*(((((((((int64_t)digits[3]) << PyLong_SHIFT) | (int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); } } break; case 4: if (8 * sizeof(int64_t) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(int64_t, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(int64_t) - 1 > 4 * PyLong_SHIFT) { - return (int64_t) (((((((((int64_t)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (int64_t) ((((((((((int64_t)digits[3]) << PyLong_SHIFT) | (int64_t)digits[2]) << PyLong_SHIFT) | (int64_t)digits[1]) << PyLong_SHIFT) | (int64_t)digits[0]))); } } break; @@ -28030,27 +28060,27 @@ static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { case 2: if (8 * sizeof(char) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(char) >= 2 * PyLong_SHIFT) { - return (char) (((((char)digits[1]) << PyLong_SHIFT) | digits[0])); + return (char) (((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); } } break; case 3: if (8 * sizeof(char) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(char) >= 3 * PyLong_SHIFT) { - return (char) (((((((char)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (char) (((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); } } break; case 4: if (8 * sizeof(char) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(char) >= 4 * PyLong_SHIFT) { - return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0])); } } break; @@ -28084,54 +28114,54 @@ static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { case -2: if (8 * sizeof(char) - 1 > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) -(((((char)digits[1]) << PyLong_SHIFT) | digits[0])); + return (char) (((char)-1)*(((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); } } break; case 2: if (8 * sizeof(char) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { - return (char) (((((char)digits[1]) << PyLong_SHIFT) | digits[0])); + return (char) ((((((char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); } } break; case -3: if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) -(((((((char)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (char) (((char)-1)*(((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); } } break; case 3: if (8 * sizeof(char) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { - return (char) (((((((char)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (char) ((((((((char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); } } break; case -4: if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) -(((((((((char)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (char) (((char)-1)*(((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); } } break; case 4: if (8 * sizeof(char) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { - return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (char) ((((((((((char)digits[3]) << PyLong_SHIFT) | (char)digits[2]) << PyLong_SHIFT) | (char)digits[1]) << PyLong_SHIFT) | (char)digits[0]))); } } break; @@ -28214,27 +28244,27 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { case 2: if (8 * sizeof(long) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | digits[0])); + return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); } } break; case 3: if (8 * sizeof(long) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); } } break; case 4: if (8 * sizeof(long) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); } } break; @@ -28268,54 +28298,54 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { case -2: if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) -(((((long)digits[1]) << PyLong_SHIFT) | digits[0])); + return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } } break; case 2: if (8 * sizeof(long) > 1 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | digits[0])); + return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } } break; case -3: if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) -(((((((long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } } break; case 3: if (8 * sizeof(long) > 2 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } } break; case -4: if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) -(((((((((long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } } break; case 4: if (8 * sizeof(long) > 3 * PyLong_SHIFT) { if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); } } break; @@ -28954,32 +28984,32 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { switch (size) { case 2: if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | digits[0])); + return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); } break; case -2: if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | digits[0])); + return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); } break; case 3: if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); } break; case -3: if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); } break; case 4: if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); } break; case -4: if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); } break; } diff --git a/package/MDAnalysis/lib/formats/xdrlib.pyx b/package/MDAnalysis/lib/formats/xdrlib.pyx index f7dd7e6ab59..828843df72e 100644 --- a/package/MDAnalysis/lib/formats/xdrlib.pyx +++ b/package/MDAnalysis/lib/formats/xdrlib.pyx @@ -130,7 +130,7 @@ cdef class _XDRFile: cdef int _has_offsets def __cinit__(self, fname, mode='r'): - self.fname = fname + self.fname = fname.encode('utf-8') self.is_open = False self.open(self.fname, mode) diff --git a/package/MDAnalysis/lib/util.py b/package/MDAnalysis/lib/util.py index 79467106876..e6210dc58aa 100644 --- a/package/MDAnalysis/lib/util.py +++ b/package/MDAnalysis/lib/util.py @@ -257,6 +257,20 @@ def openany(datasource, mode='r', reset=True): stream.close() +def _bz2_open_py2(filename, mode): + mode = mode.replace('t', '').replace('b', '') + return bz2.BZ2File(filename, mode) + +try: + bz2.open +except AttributeError: + # We are on python 2 and bz2.open is not available + bz2_open = _bz2_open_py2 +else: + # We are on python 3 so we can use bz2.open + bz2_open = bz2.open + + def anyopen(datasource, mode='r', reset=True): """Open datasource (gzipped, bzipped, uncompressed) and return a stream. @@ -285,7 +299,7 @@ def anyopen(datasource, mode='r', reset=True): Only returns the ``stream`` and tries to set ``stream.name = filename`` instead of the previous behavior to return a tuple ``(stream, filename)``. """ - handlers = {'bz2': bz2.BZ2File, 'gz': gzip.open, '': open} + handlers = {'bz2': bz2_open, 'gz': gzip.open, '': open} if mode.startswith('r'): if isstream(datasource): diff --git a/package/MDAnalysis/topology/GMSParser.py b/package/MDAnalysis/topology/GMSParser.py index 0662ac65c79..9ccde57d3c9 100644 --- a/package/MDAnalysis/topology/GMSParser.py +++ b/package/MDAnalysis/topology/GMSParser.py @@ -57,7 +57,7 @@ class GMSParser(TopologyReader): def parse(self): """Read list of atoms from a GAMESS file.""" - with openany(self.filename, 'r') as inf: + with openany(self.filename, 'rt') as inf: natoms = 0 while True: line = inf.readline() diff --git a/package/MDAnalysis/topology/GROParser.py b/package/MDAnalysis/topology/GROParser.py index 3854dd72a41..af25d61a8fb 100644 --- a/package/MDAnalysis/topology/GROParser.py +++ b/package/MDAnalysis/topology/GROParser.py @@ -57,7 +57,7 @@ def parse(self): """ segid = "SYSTEM" atoms = [] - with openany(self.filename, "r") as grofile: + with openany(self.filename, "rt") as grofile: grofile.readline() natoms = int(grofile.readline()) for atom_iter in range(natoms): diff --git a/package/MDAnalysis/topology/PSFParser.py b/package/MDAnalysis/topology/PSFParser.py index 1a796dff174..cb9077dd7b7 100644 --- a/package/MDAnalysis/topology/PSFParser.py +++ b/package/MDAnalysis/topology/PSFParser.py @@ -61,7 +61,8 @@ def parse(self): :Returns: MDAnalysis internal *structure* dict as defined here. """ # Open and check psf validity - with openany(self.filename, 'r') as psffile: + with openany(self.filename, 'rt') as psffile: + print(type(psffile)) header = next(psffile) if header[:3] != "PSF": err = ("{0} is not valid PSF file (header = {1})" diff --git a/package/MDAnalysis/topology/TOPParser.py b/package/MDAnalysis/topology/TOPParser.py index c5b843c76c2..a1a78d2ae89 100644 --- a/package/MDAnalysis/topology/TOPParser.py +++ b/package/MDAnalysis/topology/TOPParser.py @@ -79,7 +79,7 @@ def parse(self): :Returns: MDAnalysis internal *structure* dict. """ formatversion = 10 - with openany(self.filename) as topfile: + with openany(self.filename, 'rt') as topfile: for line in topfile: if line.startswith("%FLAG ATOMIC_NUMBER"): formatversion = 12 @@ -142,7 +142,7 @@ def parse(self): # Open and check top validity # Reading header info POINTERS - with openany(self.filename) as topfile: + with openany(self.filename, 'rt') as topfile: next_line = functools.partial(next, topfile) header = next_line() if header[:3] != "%VE": diff --git a/testsuite/MDAnalysisTests/analysis/test_hbonds.py b/testsuite/MDAnalysisTests/analysis/test_hbonds.py index 3c6bf4de109..db244f14fb4 100644 --- a/testsuite/MDAnalysisTests/analysis/test_hbonds.py +++ b/testsuite/MDAnalysisTests/analysis/test_hbonds.py @@ -43,7 +43,7 @@ def setUp(self): self.values = { 'num_bb_hbonds': u.atoms.n_residues - u.SYSTEM.PRO.n_residues - 4, 'donor_resid': np.array([5, 6, 8, 9, 10, 11, 12, 13]), - 'acceptor_resnm': np.array(['ALA', 'ALA', 'ALA', 'ALA', 'ALA', 'PRO', 'ALA', 'ALA']), + 'acceptor_resnm': np.array(['ALA', 'ALA', 'ALA', 'ALA', 'ALA', 'PRO', 'ALA', 'ALA'], dtype='U4'), } def _run(self, **kwargs): @@ -109,7 +109,7 @@ def setUp(self): self.kwargs["distance"] = 3.0 self.values['num_bb_hbonds'] = 0 # no H-bonds with a D-A distance < 3.0 A (they start at 3.05 A) self.values['donor_resid'] = np.array([]) - self.values['acceptor_resnm'] = np.array([], dtype="|S3") + self.values['acceptor_resnm'] = np.array([], dtype=" Date: Sun, 31 Jan 2016 12:37:06 +0100 Subject: [PATCH 2/5] Remove debug lines --- testsuite/MDAnalysisTests/coordinates/test_reader_api.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/testsuite/MDAnalysisTests/coordinates/test_reader_api.py b/testsuite/MDAnalysisTests/coordinates/test_reader_api.py index e651c9f5690..8c6ba432c1e 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_reader_api.py +++ b/testsuite/MDAnalysisTests/coordinates/test_reader_api.py @@ -171,10 +171,6 @@ def sl(): assert_raises(TypeError, sl) def _check_getitem(self, sl): - try: - print(sl.dtype) - except AttributeError: - pass res = [ts.frame for ts in self.reader[sl]] ref = self.reference[sl] From 081e5ca8e91b29f9eac4b5f5a532d3b4ce335844 Mon Sep 17 00:00:00 2001 From: Jonathan Barnoud Date: Sun, 31 Jan 2016 12:45:55 +0100 Subject: [PATCH 3/5] Move the definition of bz2_open in the try/except Following suggestion by @richardjgowers in #683 review. --- package/MDAnalysis/lib/util.py | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/package/MDAnalysis/lib/util.py b/package/MDAnalysis/lib/util.py index e6210dc58aa..da7faf3f10b 100644 --- a/package/MDAnalysis/lib/util.py +++ b/package/MDAnalysis/lib/util.py @@ -257,15 +257,20 @@ def openany(datasource, mode='r', reset=True): stream.close() -def _bz2_open_py2(filename, mode): - mode = mode.replace('t', '').replace('b', '') - return bz2.BZ2File(filename, mode) - +# On python 3, we want to use bz2.open to open and uncompress bz2 files. That +# function allows to specify the type of the uncompressed file (bytes ot text). +# The function does not exist in python 2, thus we must use bz2.BZFile to +# which we cannot tell if the uncompressed file contains bytes or text. +# Therefore, on python 2 we use a proxy function that removes the type of the +# uncompressed file from the `mode` argument. try: bz2.open except AttributeError: # We are on python 2 and bz2.open is not available - bz2_open = _bz2_open_py2 + def bz2_open(filename, mode): + """Open and uncompress a BZ2 file""" + mode = mode.replace('t', '').replace('b', '') + return bz2.BZ2File(filename, mode) else: # We are on python 3 so we can use bz2.open bz2_open = bz2.open From 317d8035131e30834309a71164a6608fa9ff3c1e Mon Sep 17 00:00:00 2001 From: Jonathan Barnoud Date: Sun, 31 Jan 2016 12:48:11 +0100 Subject: [PATCH 4/5] Simplify a list(map()) into a list comprehension Following a suggestion by @kain88-de on #683 review. --- package/MDAnalysis/analysis/density.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package/MDAnalysis/analysis/density.py b/package/MDAnalysis/analysis/density.py index 489451d660b..7e597c8deb8 100644 --- a/package/MDAnalysis/analysis/density.py +++ b/package/MDAnalysis/analysis/density.py @@ -306,7 +306,7 @@ def make_density(self): warnings.warn(msg) return - dedges = list(map(np.diff, self.edges)) + dedges = [np.diff(edge) for edge in self.edges] D = len(self.edges) for i in range(D): shape = np.ones(D, int) From 2cdcb2ad67bb4a352b65821053fa7c3a985aca90 Mon Sep 17 00:00:00 2001 From: Jonathan Barnoud Date: Sun, 31 Jan 2016 16:20:46 +0100 Subject: [PATCH 5/5] Remove a forgotten debug line --- package/MDAnalysis/topology/PSFParser.py | 1 - 1 file changed, 1 deletion(-) diff --git a/package/MDAnalysis/topology/PSFParser.py b/package/MDAnalysis/topology/PSFParser.py index cb9077dd7b7..ae5a5d0afe2 100644 --- a/package/MDAnalysis/topology/PSFParser.py +++ b/package/MDAnalysis/topology/PSFParser.py @@ -62,7 +62,6 @@ def parse(self): """ # Open and check psf validity with openany(self.filename, 'rt') as psffile: - print(type(psffile)) header = next(psffile) if header[:3] != "PSF": err = ("{0} is not valid PSF file (header = {1})"