From 793d85d696d359bc7f0c93c12cc3ec6b8e538aed Mon Sep 17 00:00:00 2001 From: Max Linke Date: Mon, 2 Nov 2015 08:21:21 +0100 Subject: [PATCH] Check that box in trr is only close and not completely the same. This is a small sanity check that people will use the same data --- package/MDAnalysis/lib/formats/trr.c | 548 ++++++++++++------------- package/MDAnalysis/lib/formats/trr.pyx | 2 +- 2 files changed, 272 insertions(+), 278 deletions(-) diff --git a/package/MDAnalysis/lib/formats/trr.c b/package/MDAnalysis/lib/formats/trr.c index 6512af44b1e..1eee42d3d05 100644 --- a/package/MDAnalysis/lib/formats/trr.c +++ b/package/MDAnalysis/lib/formats/trr.c @@ -1,4 +1,4 @@ -/* Generated by Cython 0.23.4 */ +/* Generated by Cython 0.23.3 */ #define PY_SSIZE_T_CLEAN #include "Python.h" @@ -7,7 +7,7 @@ #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_4" +#define CYTHON_ABI "0_23_3" #include #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) @@ -189,7 +189,7 @@ typedef struct { #define CYTHON_RESTRICT #endif #endif -#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) +#define __Pyx_void_to_None(void_result) (void_result, Py_INCREF(Py_None), Py_None) #ifndef CYTHON_INLINE #if defined(__GNUC__) @@ -301,10 +301,10 @@ 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 (_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 (_MSC_VER) && defined (_M_X64) + #define __Pyx_sst_abs(value) _abs64(value) #elif defined (__GNUC__) #define __Pyx_sst_abs(value) __builtin_llabs(value) #else @@ -573,7 +573,7 @@ typedef volatile __pyx_atomic_int_type __pyx_atomic_int; #endif -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":725 +/* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -582,7 +582,7 @@ typedef volatile __pyx_atomic_int_type __pyx_atomic_int; */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726 +/* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -591,7 +591,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":727 +/* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -600,7 +600,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":728 +/* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -609,7 +609,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":732 +/* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":732 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -618,7 +618,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733 +/* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -627,7 +627,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":734 +/* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -636,7 +636,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":735 +/* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -645,7 +645,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":739 +/* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":739 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -654,7 +654,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":740 +/* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":740 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -663,7 +663,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":749 +/* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -672,7 +672,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":750 +/* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -681,7 +681,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":751 +/* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -690,7 +690,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":753 +/* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":753 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -699,7 +699,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":754 +/* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":754 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -708,7 +708,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":755 +/* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -717,7 +717,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":757 +/* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":757 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -726,7 +726,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758 +/* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -735,7 +735,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":760 +/* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":760 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -744,7 +744,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":761 +/* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":761 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -753,7 +753,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":762 +/* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":762 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -798,7 +798,7 @@ struct __pyx_MemviewEnum_obj; struct __pyx_memoryview_obj; struct __pyx_memoryviewslice_obj; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":764 +/* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":764 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -807,7 +807,7 @@ struct __pyx_memoryviewslice_obj; */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":765 +/* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":765 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -816,7 +816,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":766 +/* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":766 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -825,7 +825,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":768 +/* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":768 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -1632,11 +1632,11 @@ static char __pyx_k_Zf[] = "Zf"; static char __pyx_k_Zg[] = "Zg"; static char __pyx_k_id[] = "id"; static char __pyx_k_np[] = "np"; -static char __pyx_k_all[] = "all"; static char __pyx_k_box[] = "box"; static char __pyx_k_end[] = "end"; static char __pyx_k_obj[] = "obj"; static char __pyx_k_xyz[] = "xyz"; +static char __pyx_k_atol[] = "atol"; static char __pyx_k_base[] = "base"; static char __pyx_k_file[] = "file"; static char __pyx_k_main[] = "__main__"; @@ -1646,6 +1646,7 @@ static char __pyx_k_ndim[] = "ndim"; static char __pyx_k_open[] = "open"; static char __pyx_k_pack[] = "pack"; static char __pyx_k_read[] = "read"; +static char __pyx_k_rtol[] = "rtol"; static char __pyx_k_seek[] = "seek"; static char __pyx_k_size[] = "size"; static char __pyx_k_step[] = "step"; @@ -1684,6 +1685,7 @@ static char __pyx_k_fortran[] = "fortran"; static char __pyx_k_memview[] = "memview"; static char __pyx_k_os_path[] = "os.path"; static char __pyx_k_Ellipsis[] = "Ellipsis"; +static char __pyx_k_allclose[] = "allclose"; static char __pyx_k_exc_type[] = "exc_type"; static char __pyx_k_itemsize[] = "itemsize"; static char __pyx_k_velocity[] = "velocity"; @@ -1787,10 +1789,11 @@ static PyObject *__pyx_kp_s_Trying_to_seek_over_max_number_o; static PyObject *__pyx_n_s_TypeError; static PyObject *__pyx_kp_s_Unable_to_convert_item_to_object; static PyObject *__pyx_n_s_ValueError; -static PyObject *__pyx_n_s_all; +static PyObject *__pyx_n_s_allclose; static PyObject *__pyx_n_s_allocate_buffer; static PyObject *__pyx_n_s_asarray; static PyObject *__pyx_n_s_ascontiguousarray; +static PyObject *__pyx_n_s_atol; static PyObject *__pyx_n_s_base; static PyObject *__pyx_n_s_box; static PyObject *__pyx_n_s_c; @@ -1847,6 +1850,7 @@ static PyObject *__pyx_n_b_r; static PyObject *__pyx_n_s_r; static PyObject *__pyx_n_s_range; static PyObject *__pyx_n_s_read; +static PyObject *__pyx_n_s_rtol; static PyObject *__pyx_n_s_seek; static PyObject *__pyx_kp_s_self_mode; static PyObject *__pyx_n_s_shape; @@ -1924,6 +1928,7 @@ static PyObject *__pyx_tp_new_memoryview(PyTypeObject *t, PyObject *a, PyObject static PyObject *__pyx_tp_new__memoryviewslice(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_int_0; static PyObject *__pyx_int_1; +static PyObject *__pyx_int_8; static PyObject *__pyx_int_neg_1; static PyObject *__pyx_tuple_; static PyObject *__pyx_tuple__2; @@ -5451,7 +5456,7 @@ static PyObject *__pyx_pf_3lib_7formats_3trr_7TRRFile_24write(struct __pyx_obj_3 * raise ValueError('Previous frames contained {} atoms. You ' * 'are trying to write {} atoms.'.format( # <<<<<<<<<<<<<< * self.n_atoms, xyz.shape[1])) - * if not np.all(self.box == box): + * if not np.allclose(self.box, box, rtol=0, atol=8): */ __pyx_t_5 = __Pyx_PyObject_GetAttrStr(__pyx_kp_s_Previous_frames_contained_atoms, __pyx_n_s_format); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 293; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); @@ -5460,7 +5465,7 @@ static PyObject *__pyx_pf_3lib_7formats_3trr_7TRRFile_24write(struct __pyx_obj_3 * raise ValueError('Previous frames contained {} atoms. You ' * 'are trying to write {} atoms.'.format( * self.n_atoms, xyz.shape[1])) # <<<<<<<<<<<<<< - * if not np.all(self.box == box): + * if not np.allclose(self.box, box, rtol=0, atol=8): * raise ValueError('Previous frames contained {} box. You ' */ __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_self->n_atoms); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 294; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -5529,49 +5534,39 @@ static PyObject *__pyx_pf_3lib_7formats_3trr_7TRRFile_24write(struct __pyx_obj_3 /* "lib/formats/trr.pyx":295 * 'are trying to write {} atoms.'.format( * self.n_atoms, xyz.shape[1])) - * if not np.all(self.box == box): # <<<<<<<<<<<<<< + * if not np.allclose(self.box, box, rtol=0, atol=8): # <<<<<<<<<<<<<< * raise ValueError('Previous frames contained {} box. 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} - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":203 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":203 * # of flags * * if info == NULL: return # <<<<<<<<<<<<<< @@ -5999,7 +5994,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L0; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":206 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":206 * * cdef int copy_shape, i, ndim * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -6008,7 +6003,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_endian_detector = 1; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":207 + /* "../../../../.virtualenvs/mda-py2/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) # <<<<<<<<<<<<<< @@ -6017,7 +6012,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":209 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":209 * cdef bint little_endian = ((&endian_detector)[0] != 0) * * ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<< @@ -6026,7 +6021,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_ndim = PyArray_NDIM(__pyx_v_self); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":211 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":211 * ndim = PyArray_NDIM(self) * * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -6036,7 +6031,7 @@ 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) { - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":212 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":212 * * if sizeof(npy_intp) != sizeof(Py_ssize_t): * copy_shape = 1 # <<<<<<<<<<<<<< @@ -6045,7 +6040,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_copy_shape = 1; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":211 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":211 * ndim = PyArray_NDIM(self) * * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -6055,7 +6050,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L4; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":214 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":214 * copy_shape = 1 * else: * copy_shape = 0 # <<<<<<<<<<<<<< @@ -6067,7 +6062,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L4:; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":216 + /* "../../../../.virtualenvs/mda-py2/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) # <<<<<<<<<<<<<< @@ -6081,7 +6076,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L6_bool_binop_done; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":217 + /* "../../../../.virtualenvs/mda-py2/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)): # <<<<<<<<<<<<<< @@ -6092,7 +6087,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L6_bool_binop_done:; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":216 + /* "../../../../.virtualenvs/mda-py2/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) # <<<<<<<<<<<<<< @@ -6101,7 +6096,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (__pyx_t_1) { - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":218 + /* "../../../../.virtualenvs/mda-py2/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") # <<<<<<<<<<<<<< @@ -6114,7 +6109,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":216 + /* "../../../../.virtualenvs/mda-py2/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) # <<<<<<<<<<<<<< @@ -6123,7 +6118,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":220 + /* "../../../../.virtualenvs/mda-py2/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) # <<<<<<<<<<<<<< @@ -6137,7 +6132,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L9_bool_binop_done; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":221 + /* "../../../../.virtualenvs/mda-py2/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)): # <<<<<<<<<<<<<< @@ -6148,7 +6143,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L9_bool_binop_done:; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":220 + /* "../../../../.virtualenvs/mda-py2/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) # <<<<<<<<<<<<<< @@ -6157,7 +6152,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (__pyx_t_1) { - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":222 + /* "../../../../.virtualenvs/mda-py2/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") # <<<<<<<<<<<<<< @@ -6170,7 +6165,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":220 + /* "../../../../.virtualenvs/mda-py2/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) # <<<<<<<<<<<<<< @@ -6179,7 +6174,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":224 + /* "../../../../.virtualenvs/mda-py2/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) # <<<<<<<<<<<<<< @@ -6188,7 +6183,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->buf = PyArray_DATA(__pyx_v_self); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":225 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":225 * * info.buf = PyArray_DATA(self) * info.ndim = ndim # <<<<<<<<<<<<<< @@ -6197,7 +6192,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->ndim = __pyx_v_ndim; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":226 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":226 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if copy_shape: # <<<<<<<<<<<<<< @@ -6207,7 +6202,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = (__pyx_v_copy_shape != 0); if (__pyx_t_1) { - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":229 + /* "../../../../.virtualenvs/mda-py2/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) # <<<<<<<<<<<<<< @@ -6216,7 +6211,7 @@ 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))); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":230 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -6225,7 +6220,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../../.virtualenvs/mda-py2/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): # <<<<<<<<<<<<<< @@ -6236,7 +6231,7 @@ 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; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":232 + /* "../../../../.virtualenvs/mda-py2/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] # <<<<<<<<<<<<<< @@ -6245,7 +6240,7 @@ 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]); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":233 + /* "../../../../.virtualenvs/mda-py2/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] # <<<<<<<<<<<<<< @@ -6255,7 +6250,7 @@ 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]); } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":226 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":226 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if copy_shape: # <<<<<<<<<<<<<< @@ -6265,7 +6260,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L11; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":235 + /* "../../../../.virtualenvs/mda-py2/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) # <<<<<<<<<<<<<< @@ -6275,7 +6270,7 @@ 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)); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":236 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":236 * else: * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -6286,7 +6281,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L11:; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -6295,7 +6290,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->suboffsets = NULL; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":238 + /* "../../../../.virtualenvs/mda-py2/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) # <<<<<<<<<<<<<< @@ -6304,7 +6299,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":239 + /* "../../../../.virtualenvs/mda-py2/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) # <<<<<<<<<<<<<< @@ -6313,7 +6308,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":242 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":242 * * cdef int t * cdef char* f = NULL # <<<<<<<<<<<<<< @@ -6322,7 +6317,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_f = NULL; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":243 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":243 * cdef int t * cdef char* f = NULL * cdef dtype descr = self.descr # <<<<<<<<<<<<<< @@ -6334,7 +6329,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3); __pyx_t_3 = 0; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":246 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":246 * cdef int offset * * cdef bint hasfields = PyDataType_HASFIELDS(descr) # <<<<<<<<<<<<<< @@ -6343,7 +6338,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_hasfields = PyDataType_HASFIELDS(__pyx_v_descr); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":248 + /* "../../../../.virtualenvs/mda-py2/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: # <<<<<<<<<<<<<< @@ -6361,7 +6356,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_L15_bool_binop_done:; if (__pyx_t_1) { - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":250 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -6374,7 +6369,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = Py_None; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":248 + /* "../../../../.virtualenvs/mda-py2/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: # <<<<<<<<<<<<<< @@ -6384,7 +6379,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L14; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":253 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":253 * else: * # need to call releasebuffer * info.obj = self # <<<<<<<<<<<<<< @@ -6400,7 +6395,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L14:; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":255 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":255 * info.obj = self * * if not hasfields: # <<<<<<<<<<<<<< @@ -6410,7 +6405,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = ((!(__pyx_v_hasfields != 0)) != 0); if (__pyx_t_1) { - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":256 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":256 * * if not hasfields: * t = descr.type_num # <<<<<<<<<<<<<< @@ -6420,7 +6415,7 @@ 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; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -6440,7 +6435,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L20_next_or:; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":258 + /* "../../../../.virtualenvs/mda-py2/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)): # <<<<<<<<<<<<<< @@ -6457,7 +6452,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = __pyx_t_2; __pyx_L19_bool_binop_done:; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -6466,7 +6461,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ if (__pyx_t_1) { - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../../.virtualenvs/mda-py2/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") # <<<<<<<<<<<<<< @@ -6479,7 +6474,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -6488,7 +6483,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":260 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -6500,7 +6495,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_b; break; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -6511,7 +6506,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_B; break; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":262 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -6522,7 +6517,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_h; break; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":263 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -6533,7 +6528,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_H; break; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":264 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -6544,7 +6539,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_i; break; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":265 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -6555,7 +6550,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_I; break; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":266 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -6566,7 +6561,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_l; break; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":267 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -6577,7 +6572,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_L; break; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":268 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -6588,7 +6583,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_q; break; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":269 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -6599,7 +6594,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Q; break; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -6610,7 +6605,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_f; break; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":271 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -6621,7 +6616,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_d; break; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":272 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -6632,7 +6627,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_g; break; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":273 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -6643,7 +6638,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Zf; break; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -6654,7 +6649,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Zd; break; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":275 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -6665,7 +6660,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Zg; break; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":276 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -6677,7 +6672,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; default: - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":278 + /* "../../../../.virtualenvs/mda-py2/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) # <<<<<<<<<<<<<< @@ -6703,7 +6698,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":279 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -6712,7 +6707,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->format = __pyx_v_f; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":280 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -6722,7 +6717,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_r = 0; goto __pyx_L0; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":255 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":255 * info.obj = self * * if not hasfields: # <<<<<<<<<<<<<< @@ -6731,7 +6726,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":282 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":282 * return * else: * info.format = stdlib.malloc(_buffer_format_string_len) # <<<<<<<<<<<<<< @@ -6741,7 +6736,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P /*else*/ { __pyx_v_info->format = ((char *)malloc(0xFF)); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":283 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -6750,7 +6745,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->format[0]) = '^'; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":284 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -6759,7 +6754,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_offset = 0; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":285 + /* "../../../../.virtualenvs/mda-py2/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, # <<<<<<<<<<<<<< @@ -6769,7 +6764,7 @@ 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)); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 285; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_f = __pyx_t_7; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":288 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":288 * info.format + _buffer_format_string_len, * &offset) * f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<< @@ -6779,7 +6774,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_f[0]) = '\x00'; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":197 + /* "../../../../.virtualenvs/mda-py2/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): # <<<<<<<<<<<<<< @@ -6811,7 +6806,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P return __pyx_r; } -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":290 +/* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":290 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -6835,7 +6830,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s int __pyx_t_1; __Pyx_RefNannySetupContext("__releasebuffer__", 0); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":291 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":291 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -6845,7 +6840,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (PyArray_HASFIELDS(__pyx_v_self) != 0); if (__pyx_t_1) { - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":292 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":292 * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): * stdlib.free(info.format) # <<<<<<<<<<<<<< @@ -6854,7 +6849,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ free(__pyx_v_info->format); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":291 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":291 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -6863,7 +6858,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":293 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":293 * if PyArray_HASFIELDS(self): * stdlib.free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -6873,7 +6868,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":294 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":294 * stdlib.free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): * stdlib.free(info.strides) # <<<<<<<<<<<<<< @@ -6882,7 +6877,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ free(__pyx_v_info->strides); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":293 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":293 * if PyArray_HASFIELDS(self): * stdlib.free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -6891,7 +6886,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s */ } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":290 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":290 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -6903,7 +6898,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __Pyx_RefNannyFinishContext(); } -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":770 +/* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":770 * ctypedef npy_cdouble complex_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< @@ -6920,7 +6915,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ int __pyx_clineno = 0; 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__pyx_t_3 = 0; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":795 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":795 * * for childname in descr.names: * fields = descr.fields[childname] # <<<<<<<<<<<<<< @@ -7243,7 +7238,7 @@ 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; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":796 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -7282,7 +7277,7 @@ 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; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":798 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":798 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -7299,7 +7294,7 @@ 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) { - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":799 + /* "../../../../.virtualenvs/mda-py2/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") # <<<<<<<<<<<<<< @@ -7312,7 +7307,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":798 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":798 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -7321,7 +7316,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":801 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -7341,7 +7336,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L8_next_or:; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":802 + /* "../../../../.virtualenvs/mda-py2/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)): # <<<<<<<<<<<<<< @@ -7358,7 +7353,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = __pyx_t_7; __pyx_L7_bool_binop_done:; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":801 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -7367,7 +7362,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ if (__pyx_t_6) { - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":803 + /* "../../../../.virtualenvs/mda-py2/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") # <<<<<<<<<<<<<< @@ -7380,7 +7375,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":801 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -7389,7 +7384,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":813 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":813 * * # Output padding bytes * while offset[0] < new_offset: # <<<<<<<<<<<<<< @@ -7405,7 +7400,7 @@ 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; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":814 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -7414,7 +7409,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ (__pyx_v_f[0]) = 0x78; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":815 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -7423,7 +7418,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":816 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":816 * f[0] = 120 # "x"; pad byte * f += 1 * offset[0] += 1 # <<<<<<<<<<<<<< @@ -7434,7 +7429,7 @@ 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); } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":818 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":818 * offset[0] += 1 * * offset[0] += child.itemsize # <<<<<<<<<<<<<< @@ -7444,7 +7439,7 @@ 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); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":820 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":820 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -7454,7 +7449,7 @@ 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) { - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":821 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":821 * * if not PyDataType_HASFIELDS(child): * t = child.type_num # <<<<<<<<<<<<<< @@ -7466,7 +7461,7 @@ 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; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":822 + /* "../../../../.virtualenvs/mda-py2/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: # <<<<<<<<<<<<<< @@ -7476,7 +7471,7 @@ 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) { - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":823 + /* "../../../../.virtualenvs/mda-py2/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.") # <<<<<<<<<<<<<< @@ -7489,7 +7484,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":822 + /* "../../../../.virtualenvs/mda-py2/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: # <<<<<<<<<<<<<< @@ -7498,7 +7493,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":826 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -7516,7 +7511,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":827 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -7534,7 +7529,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":828 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -7552,7 +7547,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":829 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -7570,7 +7565,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":830 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -7588,7 +7583,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -7606,7 +7601,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":832 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -7624,7 +7619,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -7642,7 +7637,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":834 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -7660,7 +7655,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":835 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -7678,7 +7673,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":836 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -7696,7 +7691,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":837 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -7714,7 +7709,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":838 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -7732,7 +7727,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":839 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -7752,7 +7747,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":840 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -7772,7 +7767,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":841 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -7792,7 +7787,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":842 + /* "../../../../.virtualenvs/mda-py2/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" # <<<<<<<<<<<<<< @@ -7810,7 +7805,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":844 + /* "../../../../.virtualenvs/mda-py2/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) # <<<<<<<<<<<<<< @@ -7834,7 +7829,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L15:; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":845 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -7843,7 +7838,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":820 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":820 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -7853,7 +7848,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L13; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":849 + /* "../../../../.virtualenvs/mda-py2/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) # <<<<<<<<<<<<<< @@ -7866,7 +7861,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __pyx_L13:; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":794 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":794 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -7876,7 +7871,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":850 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -7886,7 +7881,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_r = __pyx_v_f; goto __pyx_L0; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":785 + /* "../../../../.virtualenvs/mda-py2/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: # <<<<<<<<<<<<<< @@ -7911,7 +7906,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx return __pyx_r; } -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":966 +/* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":966 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -7926,7 +7921,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a int __pyx_t_2; __Pyx_RefNannySetupContext("set_array_base", 0); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":968 + /* "../../../../.virtualenvs/mda-py2/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: # <<<<<<<<<<<<<< @@ -7937,7 +7932,7 @@ 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) { - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":969 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":969 * cdef PyObject* baseptr * if base is None: * baseptr = NULL # <<<<<<<<<<<<<< @@ -7946,7 +7941,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_baseptr = NULL; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":968 + /* "../../../../.virtualenvs/mda-py2/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: # <<<<<<<<<<<<<< @@ -7956,7 +7951,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a goto __pyx_L3; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":971 + /* "../../../../.virtualenvs/mda-py2/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! # <<<<<<<<<<<<<< @@ -7966,7 +7961,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a /*else*/ { Py_INCREF(__pyx_v_base); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":972 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -7977,7 +7972,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a } __pyx_L3:; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":973 + /* "../../../../.virtualenvs/mda-py2/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) # <<<<<<<<<<<<<< @@ -7986,7 +7981,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ Py_XDECREF(__pyx_v_arr->base); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":974 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":974 * baseptr = base * Py_XDECREF(arr.base) * arr.base = baseptr # <<<<<<<<<<<<<< @@ -7995,7 +7990,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_arr->base = __pyx_v_baseptr; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":966 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":966 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -8007,7 +8002,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __Pyx_RefNannyFinishContext(); } -/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":976 +/* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":976 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -8021,7 +8016,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py int __pyx_t_1; __Pyx_RefNannySetupContext("get_array_base", 0); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":977 + /* "../../../../.virtualenvs/mda-py2/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: # <<<<<<<<<<<<<< @@ -8031,7 +8026,7 @@ 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) { - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":978 + /* "../../../../.virtualenvs/mda-py2/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 # <<<<<<<<<<<<<< @@ -8043,7 +8038,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py __pyx_r = Py_None; goto __pyx_L0; - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":977 + /* "../../../../.virtualenvs/mda-py2/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: # <<<<<<<<<<<<<< @@ -8052,7 +8047,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py */ } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":980 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":980 * return None * else: * return arr.base # <<<<<<<<<<<<<< @@ -8064,7 +8059,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py goto __pyx_L0; } - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":976 + /* "../../../../.virtualenvs/mda-py2/local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":976 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -20484,10 +20479,11 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_TypeError, __pyx_k_TypeError, sizeof(__pyx_k_TypeError), 0, 0, 1, 1}, {&__pyx_kp_s_Unable_to_convert_item_to_object, __pyx_k_Unable_to_convert_item_to_object, sizeof(__pyx_k_Unable_to_convert_item_to_object), 0, 0, 1, 0}, {&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1}, - {&__pyx_n_s_all, __pyx_k_all, sizeof(__pyx_k_all), 0, 0, 1, 1}, + {&__pyx_n_s_allclose, __pyx_k_allclose, sizeof(__pyx_k_allclose), 0, 0, 1, 1}, {&__pyx_n_s_allocate_buffer, __pyx_k_allocate_buffer, sizeof(__pyx_k_allocate_buffer), 0, 0, 1, 1}, {&__pyx_n_s_asarray, __pyx_k_asarray, sizeof(__pyx_k_asarray), 0, 0, 1, 1}, {&__pyx_n_s_ascontiguousarray, __pyx_k_ascontiguousarray, sizeof(__pyx_k_ascontiguousarray), 0, 0, 1, 1}, + {&__pyx_n_s_atol, __pyx_k_atol, sizeof(__pyx_k_atol), 0, 0, 1, 1}, {&__pyx_n_s_base, __pyx_k_base, sizeof(__pyx_k_base), 0, 0, 1, 1}, {&__pyx_n_s_box, __pyx_k_box, sizeof(__pyx_k_box), 0, 0, 1, 1}, {&__pyx_n_s_c, __pyx_k_c, sizeof(__pyx_k_c), 0, 0, 1, 1}, @@ -20544,6 +20540,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_r, __pyx_k_r, sizeof(__pyx_k_r), 0, 0, 1, 1}, {&__pyx_n_s_range, __pyx_k_range, sizeof(__pyx_k_range), 0, 0, 1, 1}, {&__pyx_n_s_read, __pyx_k_read, sizeof(__pyx_k_read), 0, 0, 1, 1}, + {&__pyx_n_s_rtol, __pyx_k_rtol, sizeof(__pyx_k_rtol), 0, 0, 1, 1}, {&__pyx_n_s_seek, __pyx_k_seek, sizeof(__pyx_k_seek), 0, 0, 1, 1}, {&__pyx_kp_s_self_mode, __pyx_k_self_mode, sizeof(__pyx_k_self_mode), 0, 0, 1, 0}, {&__pyx_n_s_shape, __pyx_k_shape, sizeof(__pyx_k_shape), 0, 0, 1, 1}, @@ -20654,7 +20651,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__6); __Pyx_GIVEREF(__pyx_tuple__6); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":218 + /* "../../../../.virtualenvs/mda-py2/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") # <<<<<<<<<<<<<< @@ -20665,7 +20662,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__7); __Pyx_GIVEREF(__pyx_tuple__7); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":222 + /* "../../../../.virtualenvs/mda-py2/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") # <<<<<<<<<<<<<< @@ -20676,7 +20673,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__8); __Pyx_GIVEREF(__pyx_tuple__8); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../../.virtualenvs/mda-py2/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") # <<<<<<<<<<<<<< @@ -20687,7 +20684,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__9); __Pyx_GIVEREF(__pyx_tuple__9); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":799 + /* "../../../../.virtualenvs/mda-py2/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") # <<<<<<<<<<<<<< @@ -20698,7 +20695,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__10); __Pyx_GIVEREF(__pyx_tuple__10); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":803 + /* "../../../../.virtualenvs/mda-py2/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") # <<<<<<<<<<<<<< @@ -20709,7 +20706,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__11); __Pyx_GIVEREF(__pyx_tuple__11); - /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":823 + /* "../../../../.virtualenvs/mda-py2/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.") # <<<<<<<<<<<<<< @@ -20931,6 +20928,7 @@ static int __Pyx_InitGlobals(void) { if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __pyx_int_0 = PyInt_FromLong(0); if (unlikely(!__pyx_int_0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_int_8 = PyInt_FromLong(8); if (unlikely(!__pyx_int_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_int_neg_1 = PyInt_FromLong(-1); if (unlikely(!__pyx_int_neg_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} return 0; __pyx_L1_error:; @@ -21528,12 +21526,8 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObjec } #else static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { - 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; + PyObject* args = PyTuple_Pack(1, arg); + return (likely(args)) ? __Pyx_PyObject_Call(func, args, NULL) : NULL; } #endif diff --git a/package/MDAnalysis/lib/formats/trr.pyx b/package/MDAnalysis/lib/formats/trr.pyx index 5650f5fe943..532b023169a 100644 --- a/package/MDAnalysis/lib/formats/trr.pyx +++ b/package/MDAnalysis/lib/formats/trr.pyx @@ -292,7 +292,7 @@ cdef class TRRFile: raise ValueError('Previous frames contained {} atoms. You ' 'are trying to write {} atoms.'.format( self.n_atoms, xyz.shape[1])) - if not np.all(self.box == box): + if not np.allclose(self.box, box, rtol=0, atol=8): raise ValueError('Previous frames contained {} box. You ' 'are trying to write {} box.'.format( self.box, box))