From 716a722f7d59a2d9ecb4208dc9dae0fae421c1ce Mon Sep 17 00:00:00 2001 From: singjc Date: Sun, 8 Mar 2026 11:00:07 -0400 Subject: [PATCH 1/4] Update log messages to reflect OSW file reading instead of Parquet --- pyprophet/io/export/osw.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pyprophet/io/export/osw.py b/pyprophet/io/export/osw.py index 57ce93ae..3039a906 100644 --- a/pyprophet/io/export/osw.py +++ b/pyprophet/io/export/osw.py @@ -127,19 +127,19 @@ def _read_sqlite(self, con): ) if self._is_unscored_file(con): - logger.info("Reading unscored data from Parquet file.") + logger.info("Reading unscored data from OSW file.") return self._read_unscored_data(con) ipf_present = self._check_ipf_presence(con, cfg) if ipf_present and cfg.ipf == "peptidoform": - logger.info("Reading peptidoform IPF data from Parquet file.") + logger.info("Reading peptidoform IPF data from OSW file.") data = self._read_peptidoform_data(con, cfg) elif ipf_present and cfg.ipf == "augmented": - logger.info("Reading augmented data with IPF from Parquet file.") + logger.info("Reading augmented data with IPF from OSW file.") data = self._read_augmented_data(con, cfg) else: - logger.info("Reading standard OpenSWATH data from Parquet file.") + logger.info("Reading standard OpenSWATH data from OSW file.") data = self._read_standard_data(con, cfg) # Apply common augmentations to all scored data types From f64afea3b90681cc18d05ef7190d09d712d74cc1 Mon Sep 17 00:00:00 2001 From: singjc Date: Sun, 8 Mar 2026 16:05:38 -0400 Subject: [PATCH 2/4] Add debug and trace logging for data reading in OSWReader --- pyprophet/io/export/osw.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/pyprophet/io/export/osw.py b/pyprophet/io/export/osw.py index 3039a906..88789093 100644 --- a/pyprophet/io/export/osw.py +++ b/pyprophet/io/export/osw.py @@ -141,6 +141,7 @@ def _read_sqlite(self, con): else: logger.info("Reading standard OpenSWATH data from OSW file.") data = self._read_standard_data(con, cfg) + logger.debug(f"Base data read with {len(data)} rows") # Apply common augmentations to all scored data types return self._augment_data(data, con, cfg) @@ -493,6 +494,10 @@ def _read_standard_data(self, con, cfg): ORDER BY transition_group_id, peak_group_rank; """ data = pd.read_sql_query(query, con) + logger.trace( + f"Initial standard data read with {len(data)} rows and columns: {data.columns.tolist()}" + ) + print(query) # Ensure id column is Int64 to preserve precision for large feature IDs if "id" in data.columns: @@ -656,6 +661,10 @@ def _read_standard_data(self, con, cfg): f"Assigned alignment_group_id to {mask.sum()} reference features" ) + logger.trace( + f"Data after merging alignment features has {len(data)} rows and columns: {data.columns.tolist()}" + ) + return data def _augment_data(self, data, con, cfg): From 86356be11a6fd09b5e6e51c865d55409ef42a437 Mon Sep 17 00:00:00 2001 From: singjc Date: Wed, 25 Mar 2026 22:58:11 -0400 Subject: [PATCH 3/4] Add utility function for writable C-contiguous arrays and update scoring methods - Introduced `_to_writable_c_array` to create writable, C-contiguous numpy arrays for Cython memoryviews. - Updated `Experiment` class methods to use the new utility function for handling `tg_num_id` and score arrays. - Enhanced tests to verify the functionality of `_to_writable_c_array` with read-only input. --- pyprophet/scoring/_optimized.c | 990 +++++++++++++++-------------- pyprophet/scoring/data_handling.py | 19 +- tests/test_data_handling.py | 15 + 3 files changed, 549 insertions(+), 475 deletions(-) diff --git a/pyprophet/scoring/_optimized.c b/pyprophet/scoring/_optimized.c index 9360c473..577348cf 100644 --- a/pyprophet/scoring/_optimized.c +++ b/pyprophet/scoring/_optimized.c @@ -1,4 +1,4 @@ -/* Generated by Cython 3.2.1 */ +/* Generated by Cython 3.2.4 */ /* BEGIN: Cython Metadata { @@ -35,8 +35,8 @@ END: Cython Metadata */ #elif PY_VERSION_HEX < 0x03080000 #error Cython requires Python 3.8+. #else -#define __PYX_ABI_VERSION "3_2_1" -#define CYTHON_HEX_VERSION 0x030201F0 +#define __PYX_ABI_VERSION "3_2_4" +#define CYTHON_HEX_VERSION 0x030204F0 #define CYTHON_FUTURE_DIVISION 1 /* CModulePreamble */ #include @@ -1150,6 +1150,15 @@ static int __Pyx_init_co_variables(void) { #define CYTHON_WITHOUT_ASSERTIONS #endif +#ifdef CYTHON_FREETHREADING_COMPATIBLE +#if CYTHON_FREETHREADING_COMPATIBLE +#define __Pyx_FREETHREADING_COMPATIBLE Py_MOD_GIL_NOT_USED +#else +#define __Pyx_FREETHREADING_COMPATIBLE Py_MOD_GIL_USED +#endif +#else +#define __Pyx_FREETHREADING_COMPATIBLE Py_MOD_GIL_USED +#endif #define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 #define __PYX_DEFAULT_STRING_ENCODING_IS_UTF8 0 #define __PYX_DEFAULT_STRING_ENCODING "" @@ -1373,7 +1382,7 @@ static const char *__pyx_filename; static const char* const __pyx_f[] = { "pyprophet/scoring/_optimized.pyx", "", - "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd", + "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd", "cpython/type.pxd", }; /* #### Code section: utility_code_proto_before_types ### */ @@ -1626,7 +1635,7 @@ typedef struct { /* #### Code section: numeric_typedefs ### */ -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":743 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":770 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -1635,7 +1644,7 @@ typedef struct { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":744 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":771 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -1644,26 +1653,26 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":745 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":772 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< * ctypedef npy_int64 int64_t - * + * #ctypedef npy_int96 int96_t */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":746 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":773 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< - * - * ctypedef npy_uint8 uint8_t + * #ctypedef npy_int96 int96_t + * #ctypedef npy_int128 int128_t */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":748 - * ctypedef npy_int64 int64_t +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":777 + * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< * ctypedef npy_uint16 uint16_t @@ -1671,7 +1680,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":749 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":778 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -1680,26 +1689,26 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":750 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":779 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< * ctypedef npy_uint64 uint64_t - * + * #ctypedef npy_uint96 uint96_t */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":751 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":780 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< - * - * ctypedef npy_float32 float32_t + * #ctypedef npy_uint96 uint96_t + * #ctypedef npy_uint128 uint128_t */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":753 - * ctypedef npy_uint64 uint64_t +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":784 + * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< * ctypedef npy_float64 float64_t @@ -1707,7 +1716,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":754 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":785 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -1716,7 +1725,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":761 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":792 * ctypedef double complex complex128_t * * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -1725,7 +1734,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":762 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":793 * * ctypedef npy_longlong longlong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -1734,7 +1743,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":764 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":795 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -1743,7 +1752,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":765 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":796 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -1752,7 +1761,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":767 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":798 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -1761,7 +1770,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":768 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":799 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -1770,7 +1779,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":769 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":800 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -1832,6 +1841,24 @@ struct __pyx_MemviewEnum_obj; struct __pyx_memoryview_obj; struct __pyx_memoryviewslice_obj; +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1096 + * + * # Iterator API added in v1.6 + * ctypedef int (*NpyIter_IterNextFunc)(NpyIter* it) noexcept nogil # <<<<<<<<<<<<<< + * ctypedef void (*NpyIter_GetMultiIndexFunc)(NpyIter* it, npy_intp* outcoords) noexcept nogil + * +*/ +typedef int (*__pyx_t_5numpy_NpyIter_IterNextFunc)(NpyIter *); + +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1097 + * # Iterator API added in v1.6 + * ctypedef int (*NpyIter_IterNextFunc)(NpyIter* it) noexcept nogil + * ctypedef void (*NpyIter_GetMultiIndexFunc)(NpyIter* it, npy_intp* outcoords) noexcept nogil # <<<<<<<<<<<<<< + * + * cdef extern from "numpy/arrayobject.h": +*/ +typedef void (*__pyx_t_5numpy_NpyIter_GetMultiIndexFunc)(NpyIter *, npy_intp *); + /* "View.MemoryView":110 * * @@ -2472,6 +2499,9 @@ static CYTHON_INLINE PyObject *__Pyx__GetModuleGlobalName(PyObject *name); #if CYTHON_COMPILING_IN_LIMITED_API || PY_VERSION_HEX >= 0x030C0000 static int __pyx_assertions_enabled_flag; #define __pyx_assertions_enabled() (__pyx_assertions_enabled_flag) + #if __clang__ || __GNUC__ + __attribute__((no_sanitize("thread"))) + #endif static int __Pyx_init_assertions_enabled(void) { PyObject *builtins, *debug, *debug_str; int flag; @@ -2604,7 +2634,11 @@ static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { /* PySequenceMultiply.proto */ #define __Pyx_PySequence_Multiply_Left(mul, seq) __Pyx_PySequence_Multiply(seq, mul) +#if !CYTHON_USE_TYPE_SLOTS +#define __Pyx_PySequence_Multiply PySequence_Repeat +#else static CYTHON_INLINE PyObject* __Pyx_PySequence_Multiply(PyObject *seq, Py_ssize_t mul); +#endif /* PyObjectFormatAndDecref.proto */ static CYTHON_INLINE PyObject* __Pyx_PyObject_FormatSimpleAndDecref(PyObject* s, PyObject* f); @@ -2718,22 +2752,22 @@ static int __Pyx__DelItemOnTypeDict(PyTypeObject *tp, PyObject *k); static int __Pyx_setup_reduce(PyObject* type_obj); /* TypeImport.proto */ -#ifndef __PYX_HAVE_RT_ImportType_proto_3_2_1 -#define __PYX_HAVE_RT_ImportType_proto_3_2_1 +#ifndef __PYX_HAVE_RT_ImportType_proto_3_2_4 +#define __PYX_HAVE_RT_ImportType_proto_3_2_4 #if defined (__STDC_VERSION__) && __STDC_VERSION__ >= 201112L #include #endif #if (defined (__STDC_VERSION__) && __STDC_VERSION__ >= 201112L) || __cplusplus >= 201103L -#define __PYX_GET_STRUCT_ALIGNMENT_3_2_1(s) alignof(s) +#define __PYX_GET_STRUCT_ALIGNMENT_3_2_4(s) alignof(s) #else -#define __PYX_GET_STRUCT_ALIGNMENT_3_2_1(s) sizeof(void*) +#define __PYX_GET_STRUCT_ALIGNMENT_3_2_4(s) sizeof(void*) #endif -enum __Pyx_ImportType_CheckSize_3_2_1 { - __Pyx_ImportType_CheckSize_Error_3_2_1 = 0, - __Pyx_ImportType_CheckSize_Warn_3_2_1 = 1, - __Pyx_ImportType_CheckSize_Ignore_3_2_1 = 2 +enum __Pyx_ImportType_CheckSize_3_2_4 { + __Pyx_ImportType_CheckSize_Error_3_2_4 = 0, + __Pyx_ImportType_CheckSize_Warn_3_2_4 = 1, + __Pyx_ImportType_CheckSize_Ignore_3_2_4 = 2 }; -static PyTypeObject *__Pyx_ImportType_3_2_1(PyObject* module, const char *module_name, const char *class_name, size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_2_1 check_size); +static PyTypeObject *__Pyx_ImportType_3_2_4(PyObject* module, const char *module_name, const char *class_name, size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_2_4 check_size); #endif /* dict_setdefault.proto (used by FetchCommonType) */ @@ -3351,6 +3385,9 @@ static PyObject *__pyx_builtin_enumerate; static PyObject *__pyx_builtin_Ellipsis; static PyObject *__pyx_builtin_id; /* #### Code section: string_decls ### */ +static const char __pyx_k_c[] = "c"; +static const char __pyx_k_name[] = "name"; +static const char __pyx_k_fortran[] = "fortran"; /* #### Code section: decls ### */ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ @@ -3451,9 +3488,9 @@ typedef struct { __Pyx_CachedCFunction __pyx_umethod_PyDict_Type_pop; __Pyx_CachedCFunction __pyx_umethod_PyDict_Type_values; PyObject *__pyx_slice[1]; - PyObject *__pyx_tuple[3]; + PyObject *__pyx_tuple[2]; PyObject *__pyx_codeobj_tab[6]; - PyObject *__pyx_string_tab[179]; + PyObject *__pyx_string_tab[178]; PyObject *__pyx_number_tab[4]; /* #### Code section: module_state_contents ### */ /* CommonTypesMetaclass.module_state_decls */ @@ -3537,143 +3574,142 @@ static __pyx_mstatetype * const __pyx_mstate_global = &__pyx_mstate_global_stati #define __pyx_kp_u_numpy__core_umath_failed_to_impo __pyx_string_tab[39] #define __pyx_kp_u_object __pyx_string_tab[40] #define __pyx_kp_u_pyprophet_scoring__optimized_pyx __pyx_string_tab[41] -#define __pyx_kp_u_self_name_is_not_None __pyx_string_tab[42] -#define __pyx_kp_u_strided_and_direct __pyx_string_tab[43] -#define __pyx_kp_u_strided_and_direct_or_indirect __pyx_string_tab[44] -#define __pyx_kp_u_strided_and_indirect __pyx_string_tab[45] -#define __pyx_kp_u_unable_to_allocate_array_data __pyx_string_tab[46] -#define __pyx_kp_u_unable_to_allocate_shape_and_str __pyx_string_tab[47] -#define __pyx_n_u_ASCII __pyx_string_tab[48] -#define __pyx_n_u_Ellipsis __pyx_string_tab[49] -#define __pyx_n_u_Pyx_PyDict_NextRef __pyx_string_tab[50] -#define __pyx_n_u_Sequence __pyx_string_tab[51] -#define __pyx_n_u_View_MemoryView __pyx_string_tab[52] -#define __pyx_n_u_abc __pyx_string_tab[53] -#define __pyx_n_u_af __pyx_string_tab[54] -#define __pyx_n_u_allocate_buffer __pyx_string_tab[55] -#define __pyx_n_u_asyncio_coroutines __pyx_string_tab[56] -#define __pyx_n_u_base __pyx_string_tab[57] -#define __pyx_n_u_basis __pyx_string_tab[58] -#define __pyx_n_u_best_dist __pyx_string_tab[59] -#define __pyx_n_u_best_j __pyx_string_tab[60] -#define __pyx_n_u_c __pyx_string_tab[61] -#define __pyx_n_u_class __pyx_string_tab[62] -#define __pyx_n_u_class_getitem __pyx_string_tab[63] -#define __pyx_n_u_cline_in_traceback __pyx_string_tab[64] -#define __pyx_n_u_count __pyx_string_tab[65] -#define __pyx_n_u_count_num_positives __pyx_string_tab[66] -#define __pyx_n_u_cresult __pyx_string_tab[67] -#define __pyx_n_u_current_imax __pyx_string_tab[68] -#define __pyx_n_u_current_max __pyx_string_tab[69] -#define __pyx_n_u_current_tg_id __pyx_string_tab[70] -#define __pyx_n_u_current_write_i __pyx_string_tab[71] -#define __pyx_n_u_dict __pyx_string_tab[72] -#define __pyx_n_u_dist __pyx_string_tab[73] -#define __pyx_n_u_dtype __pyx_string_tab[74] -#define __pyx_n_u_dtype_is_object __pyx_string_tab[75] -#define __pyx_n_u_encode __pyx_string_tab[76] -#define __pyx_n_u_enumerate __pyx_string_tab[77] -#define __pyx_n_u_error __pyx_string_tab[78] -#define __pyx_n_u_final_val __pyx_string_tab[79] -#define __pyx_n_u_find_nearest_matches __pyx_string_tab[80] -#define __pyx_n_u_find_top_ranked __pyx_string_tab[81] -#define __pyx_n_u_flags __pyx_string_tab[82] -#define __pyx_n_u_float64 __pyx_string_tab[83] -#define __pyx_n_u_format __pyx_string_tab[84] -#define __pyx_n_u_fortran __pyx_string_tab[85] -#define __pyx_n_u_func __pyx_string_tab[86] -#define __pyx_n_u_g0 __pyx_string_tab[87] -#define __pyx_n_u_getstate __pyx_string_tab[88] -#define __pyx_n_u_high __pyx_string_tab[89] -#define __pyx_n_u_i __pyx_string_tab[90] -#define __pyx_n_u_i0 __pyx_string_tab[91] -#define __pyx_n_u_i1 __pyx_string_tab[92] -#define __pyx_n_u_id __pyx_string_tab[93] -#define __pyx_n_u_id_2 __pyx_string_tab[94] -#define __pyx_n_u_imax __pyx_string_tab[95] -#define __pyx_n_u_imin __pyx_string_tab[96] -#define __pyx_n_u_import __pyx_string_tab[97] -#define __pyx_n_u_index __pyx_string_tab[98] -#define __pyx_n_u_inp_view __pyx_string_tab[99] -#define __pyx_n_u_int64 __pyx_string_tab[100] -#define __pyx_n_u_inv_pg_pp_true __pyx_string_tab[101] -#define __pyx_n_u_is_coroutine __pyx_string_tab[102] -#define __pyx_n_u_items __pyx_string_tab[103] -#define __pyx_n_u_itemsize __pyx_string_tab[104] -#define __pyx_n_u_ix __pyx_string_tab[105] -#define __pyx_n_u_j __pyx_string_tab[106] -#define __pyx_n_u_low __pyx_string_tab[107] -#define __pyx_n_u_main __pyx_string_tab[108] -#define __pyx_n_u_memview __pyx_string_tab[109] -#define __pyx_n_u_mid __pyx_string_tab[110] -#define __pyx_n_u_mode __pyx_string_tab[111] -#define __pyx_n_u_module __pyx_string_tab[112] -#define __pyx_n_u_n __pyx_string_tab[113] -#define __pyx_n_u_name __pyx_string_tab[114] -#define __pyx_n_u_name_2 __pyx_string_tab[115] -#define __pyx_n_u_ndim __pyx_string_tab[116] -#define __pyx_n_u_new __pyx_string_tab[117] -#define __pyx_n_u_np __pyx_string_tab[118] -#define __pyx_n_u_num_basis __pyx_string_tab[119] -#define __pyx_n_u_num_samples __pyx_string_tab[120] -#define __pyx_n_u_numpy __pyx_string_tab[121] -#define __pyx_n_u_obj __pyx_string_tab[122] -#define __pyx_n_u_operator __pyx_string_tab[123] -#define __pyx_n_u_pack __pyx_string_tab[124] -#define __pyx_n_u_pop __pyx_string_tab[125] -#define __pyx_n_u_prior_chrom_null __pyx_string_tab[126] -#define __pyx_n_u_prior_pg_true __pyx_string_tab[127] -#define __pyx_n_u_pyprophet_scoring__optimized __pyx_string_tab[128] -#define __pyx_n_u_pyx_checksum __pyx_string_tab[129] -#define __pyx_n_u_pyx_state __pyx_string_tab[130] -#define __pyx_n_u_pyx_type __pyx_string_tab[131] -#define __pyx_n_u_pyx_unpickle_Enum __pyx_string_tab[132] -#define __pyx_n_u_pyx_vtable __pyx_string_tab[133] -#define __pyx_n_u_qualname __pyx_string_tab[134] -#define __pyx_n_u_rank __pyx_string_tab[135] -#define __pyx_n_u_rank32 __pyx_string_tab[136] -#define __pyx_n_u_ranks __pyx_string_tab[137] -#define __pyx_n_u_reduce __pyx_string_tab[138] -#define __pyx_n_u_reduce_cython __pyx_string_tab[139] -#define __pyx_n_u_reduce_ex __pyx_string_tab[140] -#define __pyx_n_u_register __pyx_string_tab[141] -#define __pyx_n_u_res_view __pyx_string_tab[142] -#define __pyx_n_u_result __pyx_string_tab[143] -#define __pyx_n_u_sample_points __pyx_string_tab[144] -#define __pyx_n_u_sc __pyx_string_tab[145] -#define __pyx_n_u_scores __pyx_string_tab[146] -#define __pyx_n_u_set_name __pyx_string_tab[147] -#define __pyx_n_u_setdefault __pyx_string_tab[148] -#define __pyx_n_u_setstate __pyx_string_tab[149] -#define __pyx_n_u_setstate_cython __pyx_string_tab[150] -#define __pyx_n_u_shape __pyx_string_tab[151] -#define __pyx_n_u_single_chromatogram_hypothesis_f __pyx_string_tab[152] -#define __pyx_n_u_size __pyx_string_tab[153] -#define __pyx_n_u_sort_order __pyx_string_tab[154] -#define __pyx_n_u_sp_i __pyx_string_tab[155] -#define __pyx_n_u_start __pyx_string_tab[156] -#define __pyx_n_u_step __pyx_string_tab[157] -#define __pyx_n_u_stop __pyx_string_tab[158] -#define __pyx_n_u_struct __pyx_string_tab[159] -#define __pyx_n_u_sum_all __pyx_string_tab[160] -#define __pyx_n_u_test __pyx_string_tab[161] -#define __pyx_n_u_tg_ids __pyx_string_tab[162] -#define __pyx_n_u_uint32 __pyx_string_tab[163] -#define __pyx_n_u_unpack __pyx_string_tab[164] -#define __pyx_n_u_update __pyx_string_tab[165] -#define __pyx_n_u_use_sort_order __pyx_string_tab[166] -#define __pyx_n_u_val __pyx_string_tab[167] -#define __pyx_n_u_values __pyx_string_tab[168] -#define __pyx_n_u_view __pyx_string_tab[169] -#define __pyx_n_u_x __pyx_string_tab[170] -#define __pyx_n_u_zeros __pyx_string_tab[171] -#define __pyx_n_u_zeros_like __pyx_string_tab[172] -#define __pyx_kp_b_iso88591_8_q_Rq_F_RvRuF_A_q_r_uBa_V1A_e2 __pyx_string_tab[173] -#define __pyx_kp_b_iso88591_F_A_R_86_1_a_Rq_c_2T_c_AV1_Q_a __pyx_string_tab[174] -#define __pyx_kp_b_iso88591_F_BfBe6_1_a_q_q_aq_U_6_q_fAQ_V1 __pyx_string_tab[175] -#define __pyx_kp_b_iso88591_IJ_E_q_m6_RvR_fBa_a_t1_E_aq_Q_1 __pyx_string_tab[176] -#define __pyx_kp_b_iso88591_N_RvRq_fBa_1_Q_Ba_nAQ_Q_1E_Ba_B __pyx_string_tab[177] -#define __pyx_n_b_O __pyx_string_tab[178] +#define __pyx_kp_u_strided_and_direct __pyx_string_tab[42] +#define __pyx_kp_u_strided_and_direct_or_indirect __pyx_string_tab[43] +#define __pyx_kp_u_strided_and_indirect __pyx_string_tab[44] +#define __pyx_kp_u_unable_to_allocate_array_data __pyx_string_tab[45] +#define __pyx_kp_u_unable_to_allocate_shape_and_str __pyx_string_tab[46] +#define __pyx_n_u_ASCII __pyx_string_tab[47] +#define __pyx_n_u_Ellipsis __pyx_string_tab[48] +#define __pyx_n_u_Pyx_PyDict_NextRef __pyx_string_tab[49] +#define __pyx_n_u_Sequence __pyx_string_tab[50] +#define __pyx_n_u_View_MemoryView __pyx_string_tab[51] +#define __pyx_n_u_abc __pyx_string_tab[52] +#define __pyx_n_u_af __pyx_string_tab[53] +#define __pyx_n_u_allocate_buffer __pyx_string_tab[54] +#define __pyx_n_u_asyncio_coroutines __pyx_string_tab[55] +#define __pyx_n_u_base __pyx_string_tab[56] +#define __pyx_n_u_basis __pyx_string_tab[57] +#define __pyx_n_u_best_dist __pyx_string_tab[58] +#define __pyx_n_u_best_j __pyx_string_tab[59] +#define __pyx_n_u_c __pyx_string_tab[60] +#define __pyx_n_u_class __pyx_string_tab[61] +#define __pyx_n_u_class_getitem __pyx_string_tab[62] +#define __pyx_n_u_cline_in_traceback __pyx_string_tab[63] +#define __pyx_n_u_count __pyx_string_tab[64] +#define __pyx_n_u_count_num_positives __pyx_string_tab[65] +#define __pyx_n_u_cresult __pyx_string_tab[66] +#define __pyx_n_u_current_imax __pyx_string_tab[67] +#define __pyx_n_u_current_max __pyx_string_tab[68] +#define __pyx_n_u_current_tg_id __pyx_string_tab[69] +#define __pyx_n_u_current_write_i __pyx_string_tab[70] +#define __pyx_n_u_dict __pyx_string_tab[71] +#define __pyx_n_u_dist __pyx_string_tab[72] +#define __pyx_n_u_dtype __pyx_string_tab[73] +#define __pyx_n_u_dtype_is_object __pyx_string_tab[74] +#define __pyx_n_u_encode __pyx_string_tab[75] +#define __pyx_n_u_enumerate __pyx_string_tab[76] +#define __pyx_n_u_error __pyx_string_tab[77] +#define __pyx_n_u_final_val __pyx_string_tab[78] +#define __pyx_n_u_find_nearest_matches __pyx_string_tab[79] +#define __pyx_n_u_find_top_ranked __pyx_string_tab[80] +#define __pyx_n_u_flags __pyx_string_tab[81] +#define __pyx_n_u_float64 __pyx_string_tab[82] +#define __pyx_n_u_format __pyx_string_tab[83] +#define __pyx_n_u_fortran __pyx_string_tab[84] +#define __pyx_n_u_func __pyx_string_tab[85] +#define __pyx_n_u_g0 __pyx_string_tab[86] +#define __pyx_n_u_getstate __pyx_string_tab[87] +#define __pyx_n_u_high __pyx_string_tab[88] +#define __pyx_n_u_i __pyx_string_tab[89] +#define __pyx_n_u_i0 __pyx_string_tab[90] +#define __pyx_n_u_i1 __pyx_string_tab[91] +#define __pyx_n_u_id __pyx_string_tab[92] +#define __pyx_n_u_id_2 __pyx_string_tab[93] +#define __pyx_n_u_imax __pyx_string_tab[94] +#define __pyx_n_u_imin __pyx_string_tab[95] +#define __pyx_n_u_import __pyx_string_tab[96] +#define __pyx_n_u_index __pyx_string_tab[97] +#define __pyx_n_u_inp_view __pyx_string_tab[98] +#define __pyx_n_u_int64 __pyx_string_tab[99] +#define __pyx_n_u_inv_pg_pp_true __pyx_string_tab[100] +#define __pyx_n_u_is_coroutine __pyx_string_tab[101] +#define __pyx_n_u_items __pyx_string_tab[102] +#define __pyx_n_u_itemsize __pyx_string_tab[103] +#define __pyx_n_u_ix __pyx_string_tab[104] +#define __pyx_n_u_j __pyx_string_tab[105] +#define __pyx_n_u_low __pyx_string_tab[106] +#define __pyx_n_u_main __pyx_string_tab[107] +#define __pyx_n_u_memview __pyx_string_tab[108] +#define __pyx_n_u_mid __pyx_string_tab[109] +#define __pyx_n_u_mode __pyx_string_tab[110] +#define __pyx_n_u_module __pyx_string_tab[111] +#define __pyx_n_u_n __pyx_string_tab[112] +#define __pyx_n_u_name __pyx_string_tab[113] +#define __pyx_n_u_name_2 __pyx_string_tab[114] +#define __pyx_n_u_ndim __pyx_string_tab[115] +#define __pyx_n_u_new __pyx_string_tab[116] +#define __pyx_n_u_np __pyx_string_tab[117] +#define __pyx_n_u_num_basis __pyx_string_tab[118] +#define __pyx_n_u_num_samples __pyx_string_tab[119] +#define __pyx_n_u_numpy __pyx_string_tab[120] +#define __pyx_n_u_obj __pyx_string_tab[121] +#define __pyx_n_u_operator __pyx_string_tab[122] +#define __pyx_n_u_pack __pyx_string_tab[123] +#define __pyx_n_u_pop __pyx_string_tab[124] +#define __pyx_n_u_prior_chrom_null __pyx_string_tab[125] +#define __pyx_n_u_prior_pg_true __pyx_string_tab[126] +#define __pyx_n_u_pyprophet_scoring__optimized __pyx_string_tab[127] +#define __pyx_n_u_pyx_checksum __pyx_string_tab[128] +#define __pyx_n_u_pyx_state __pyx_string_tab[129] +#define __pyx_n_u_pyx_type __pyx_string_tab[130] +#define __pyx_n_u_pyx_unpickle_Enum __pyx_string_tab[131] +#define __pyx_n_u_pyx_vtable __pyx_string_tab[132] +#define __pyx_n_u_qualname __pyx_string_tab[133] +#define __pyx_n_u_rank __pyx_string_tab[134] +#define __pyx_n_u_rank32 __pyx_string_tab[135] +#define __pyx_n_u_ranks __pyx_string_tab[136] +#define __pyx_n_u_reduce __pyx_string_tab[137] +#define __pyx_n_u_reduce_cython __pyx_string_tab[138] +#define __pyx_n_u_reduce_ex __pyx_string_tab[139] +#define __pyx_n_u_register __pyx_string_tab[140] +#define __pyx_n_u_res_view __pyx_string_tab[141] +#define __pyx_n_u_result __pyx_string_tab[142] +#define __pyx_n_u_sample_points __pyx_string_tab[143] +#define __pyx_n_u_sc __pyx_string_tab[144] +#define __pyx_n_u_scores __pyx_string_tab[145] +#define __pyx_n_u_set_name __pyx_string_tab[146] +#define __pyx_n_u_setdefault __pyx_string_tab[147] +#define __pyx_n_u_setstate __pyx_string_tab[148] +#define __pyx_n_u_setstate_cython __pyx_string_tab[149] +#define __pyx_n_u_shape __pyx_string_tab[150] +#define __pyx_n_u_single_chromatogram_hypothesis_f __pyx_string_tab[151] +#define __pyx_n_u_size __pyx_string_tab[152] +#define __pyx_n_u_sort_order __pyx_string_tab[153] +#define __pyx_n_u_sp_i __pyx_string_tab[154] +#define __pyx_n_u_start __pyx_string_tab[155] +#define __pyx_n_u_step __pyx_string_tab[156] +#define __pyx_n_u_stop __pyx_string_tab[157] +#define __pyx_n_u_struct __pyx_string_tab[158] +#define __pyx_n_u_sum_all __pyx_string_tab[159] +#define __pyx_n_u_test __pyx_string_tab[160] +#define __pyx_n_u_tg_ids __pyx_string_tab[161] +#define __pyx_n_u_uint32 __pyx_string_tab[162] +#define __pyx_n_u_unpack __pyx_string_tab[163] +#define __pyx_n_u_update __pyx_string_tab[164] +#define __pyx_n_u_use_sort_order __pyx_string_tab[165] +#define __pyx_n_u_val __pyx_string_tab[166] +#define __pyx_n_u_values __pyx_string_tab[167] +#define __pyx_n_u_view __pyx_string_tab[168] +#define __pyx_n_u_x __pyx_string_tab[169] +#define __pyx_n_u_zeros __pyx_string_tab[170] +#define __pyx_n_u_zeros_like __pyx_string_tab[171] +#define __pyx_kp_b_iso88591_8_q_Rq_F_RvRuF_A_q_r_uBa_V1A_e2 __pyx_string_tab[172] +#define __pyx_kp_b_iso88591_F_A_R_86_1_a_Rq_c_2T_c_AV1_Q_a __pyx_string_tab[173] +#define __pyx_kp_b_iso88591_F_BfBe6_1_a_q_q_aq_U_6_q_fAQ_V1 __pyx_string_tab[174] +#define __pyx_kp_b_iso88591_IJ_E_q_m6_RvR_fBa_a_t1_E_aq_Q_1 __pyx_string_tab[175] +#define __pyx_kp_b_iso88591_N_RvRq_fBa_1_Q_Ba_nAQ_Q_1E_Ba_B __pyx_string_tab[176] +#define __pyx_n_b_O __pyx_string_tab[177] #define __pyx_int_0 __pyx_number_tab[0] #define __pyx_int_neg_1 __pyx_number_tab[1] #define __pyx_int_1 __pyx_number_tab[2] @@ -3717,9 +3753,9 @@ static CYTHON_SMALL_CODE int __pyx_m_clear(PyObject *m) { Py_CLEAR(clear_module_state->__pyx_memoryviewslice_type); Py_CLEAR(clear_module_state->__pyx_type___pyx_memoryviewslice); for (int i=0; i<1; ++i) { Py_CLEAR(clear_module_state->__pyx_slice[i]); } - for (int i=0; i<3; ++i) { Py_CLEAR(clear_module_state->__pyx_tuple[i]); } + for (int i=0; i<2; ++i) { Py_CLEAR(clear_module_state->__pyx_tuple[i]); } for (int i=0; i<6; ++i) { Py_CLEAR(clear_module_state->__pyx_codeobj_tab[i]); } - for (int i=0; i<179; ++i) { Py_CLEAR(clear_module_state->__pyx_string_tab[i]); } + for (int i=0; i<178; ++i) { Py_CLEAR(clear_module_state->__pyx_string_tab[i]); } for (int i=0; i<4; ++i) { Py_CLEAR(clear_module_state->__pyx_number_tab[i]); } /* #### Code section: module_state_clear_contents ### */ /* CommonTypesMetaclass.module_state_clear */ @@ -3768,9 +3804,9 @@ static CYTHON_SMALL_CODE int __pyx_m_traverse(PyObject *m, visitproc visit, void Py_VISIT(traverse_module_state->__pyx_memoryviewslice_type); Py_VISIT(traverse_module_state->__pyx_type___pyx_memoryviewslice); for (int i=0; i<1; ++i) { __Pyx_VISIT_CONST(traverse_module_state->__pyx_slice[i]); } - for (int i=0; i<3; ++i) { __Pyx_VISIT_CONST(traverse_module_state->__pyx_tuple[i]); } + for (int i=0; i<2; ++i) { __Pyx_VISIT_CONST(traverse_module_state->__pyx_tuple[i]); } for (int i=0; i<6; ++i) { __Pyx_VISIT_CONST(traverse_module_state->__pyx_codeobj_tab[i]); } - for (int i=0; i<179; ++i) { __Pyx_VISIT_CONST(traverse_module_state->__pyx_string_tab[i]); } + for (int i=0; i<178; ++i) { __Pyx_VISIT_CONST(traverse_module_state->__pyx_string_tab[i]); } for (int i=0; i<4; ++i) { __Pyx_VISIT_CONST(traverse_module_state->__pyx_number_tab[i]); } /* #### Code section: module_state_traverse_contents ### */ /* CommonTypesMetaclass.module_state_traverse */ @@ -6148,7 +6184,7 @@ static PyObject *__pyx_pf___pyx_MemviewEnum___reduce_cython__(struct __pyx_Memvi * state += (_dict,) * use_setstate = True # <<<<<<<<<<<<<< * else: - * use_setstate = ('self.name is not None',) + * use_setstate = self.name is not None */ __pyx_v_use_setstate = 1; @@ -6165,19 +6201,19 @@ static PyObject *__pyx_pf___pyx_MemviewEnum___reduce_cython__(struct __pyx_Memvi /* "(tree fragment)":11 * use_setstate = True * else: - * use_setstate = ('self.name is not None',) # <<<<<<<<<<<<<< + * use_setstate = self.name is not None # <<<<<<<<<<<<<< * if use_setstate: * return __pyx_unpickle_Enum, (type(self), 0x82a3537, None), state */ /*else*/ { - __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_mstate_global->__pyx_tuple[0]); if (unlikely((__pyx_t_2 == (int)-1) && PyErr_Occurred())) __PYX_ERR(1, 11, __pyx_L1_error) + __pyx_t_2 = (__pyx_v_self->name != Py_None); __pyx_v_use_setstate = __pyx_t_2; } __pyx_L3:; /* "(tree fragment)":12 * else: - * use_setstate = ('self.name is not None',) + * use_setstate = self.name is not None * if use_setstate: # <<<<<<<<<<<<<< * return __pyx_unpickle_Enum, (type(self), 0x82a3537, None), state * else: @@ -6185,7 +6221,7 @@ static PyObject *__pyx_pf___pyx_MemviewEnum___reduce_cython__(struct __pyx_Memvi if (__pyx_v_use_setstate) { /* "(tree fragment)":13 - * use_setstate = ('self.name is not None',) + * use_setstate = self.name is not None * if use_setstate: * return __pyx_unpickle_Enum, (type(self), 0x82a3537, None), state # <<<<<<<<<<<<<< * else: @@ -6222,7 +6258,7 @@ static PyObject *__pyx_pf___pyx_MemviewEnum___reduce_cython__(struct __pyx_Memvi /* "(tree fragment)":12 * else: - * use_setstate = ('self.name is not None',) + * use_setstate = self.name is not None * if use_setstate: # <<<<<<<<<<<<<< * return __pyx_unpickle_Enum, (type(self), 0x82a3537, None), state * else: @@ -9519,7 +9555,7 @@ static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_10suboffsets___get_ * return tuple([suboffset for suboffset in self.view.suboffsets[:self.view.ndim]]) */ __Pyx_XDECREF(__pyx_r); - __pyx_t_2 = __Pyx_PySequence_Multiply(__pyx_mstate_global->__pyx_tuple[1], __pyx_v_self->view.ndim); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 583, __pyx_L1_error) + __pyx_t_2 = __Pyx_PySequence_Multiply(__pyx_mstate_global->__pyx_tuple[0], __pyx_v_self->view.ndim); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 583, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __pyx_r = __pyx_t_2; __pyx_t_2 = 0; @@ -10495,7 +10531,7 @@ static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_20 * self.view.itemsize, * flags|PyBUF_C_CONTIGUOUS, */ - __pyx_t_1 = __pyx_memoryview_copy_new_contig((&__pyx_v_mslice), ((char const *)"c"), __pyx_v_self->view.ndim, __pyx_v_self->view.itemsize, (__pyx_v_flags | PyBUF_C_CONTIGUOUS), __pyx_v_self->dtype_is_object); if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 642, __pyx_L1_error) + __pyx_t_1 = __pyx_memoryview_copy_new_contig((&__pyx_v_mslice), __pyx_k_c, __pyx_v_self->view.ndim, __pyx_v_self->view.itemsize, (__pyx_v_flags | PyBUF_C_CONTIGUOUS), __pyx_v_self->dtype_is_object); if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 642, __pyx_L1_error) __pyx_v_mslice = __pyx_t_1; /* "View.MemoryView":647 @@ -10618,7 +10654,7 @@ static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_22 * self.view.itemsize, * flags|PyBUF_F_CONTIGUOUS, */ - __pyx_t_1 = __pyx_memoryview_copy_new_contig((&__pyx_v_src), ((char const *)"fortran"), __pyx_v_self->view.ndim, __pyx_v_self->view.itemsize, (__pyx_v_flags | PyBUF_F_CONTIGUOUS), __pyx_v_self->dtype_is_object); if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 654, __pyx_L1_error) + __pyx_t_1 = __pyx_memoryview_copy_new_contig((&__pyx_v_src), __pyx_k_fortran, __pyx_v_self->view.ndim, __pyx_v_self->view.itemsize, (__pyx_v_flags | PyBUF_F_CONTIGUOUS), __pyx_v_self->dtype_is_object); if (unlikely(PyErr_Occurred())) __PYX_ERR(1, 654, __pyx_L1_error) __pyx_v_dst = __pyx_t_1; /* "View.MemoryView":659 @@ -16903,7 +16939,7 @@ static PyObject *__pyx_pf_15View_dot_MemoryView___pyx_unpickle_Enum(CYTHON_UNUSE * __pyx_result = Enum.__new__(__pyx_type) * if __pyx_state is not None: */ - __pyx_t_1 = __Pyx_CheckUnpickleChecksum(__pyx_v___pyx_checksum, 0x82a3537, 0x6ae9995, 0xb068931, ((char const *)"name")); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(1, 6, __pyx_L1_error) + __pyx_t_1 = __Pyx_CheckUnpickleChecksum(__pyx_v___pyx_checksum, 0x82a3537, 0x6ae9995, 0xb068931, __pyx_k_name); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(1, 6, __pyx_L1_error) /* "(tree fragment)":7 * cdef object __pyx_result @@ -17052,7 +17088,7 @@ static PyObject *__pyx_unpickle_Enum__set_state(struct __pyx_MemviewEnum_obj *__ return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":242 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":285 * cdef int type_num * * @property # <<<<<<<<<<<<<< @@ -17063,7 +17099,7 @@ static PyObject *__pyx_unpickle_Enum__set_state(struct __pyx_MemviewEnum_obj *__ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_8itemsize_itemsize(PyArray_Descr *__pyx_v_self) { npy_intp __pyx_r; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":244 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":287 * @property * cdef inline npy_intp itemsize(self) noexcept nogil: * return PyDataType_ELSIZE(self) # <<<<<<<<<<<<<< @@ -17073,7 +17109,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_8itemsize_itemsize(PyArray_D __pyx_r = PyDataType_ELSIZE(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":242 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":285 * cdef int type_num * * @property # <<<<<<<<<<<<<< @@ -17086,7 +17122,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_8itemsize_itemsize(PyArray_D return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":246 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":289 * return PyDataType_ELSIZE(self) * * @property # <<<<<<<<<<<<<< @@ -17097,7 +17133,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_8itemsize_itemsize(PyArray_D static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_9alignment_alignment(PyArray_Descr *__pyx_v_self) { npy_intp __pyx_r; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":248 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":291 * @property * cdef inline npy_intp alignment(self) noexcept nogil: * return PyDataType_ALIGNMENT(self) # <<<<<<<<<<<<<< @@ -17107,7 +17143,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_9alignment_alignment(PyArray __pyx_r = PyDataType_ALIGNMENT(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":246 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":289 * return PyDataType_ELSIZE(self) * * @property # <<<<<<<<<<<<<< @@ -17120,7 +17156,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_5dtype_9alignment_alignment(PyArray return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":252 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":295 * # Use fields/names with care as they may be NULL. You must check * # for this using PyDataType_HASFIELDS. * @property # <<<<<<<<<<<<<< @@ -17134,7 +17170,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_6fields_fields(PyArray_Desc PyObject *__pyx_t_1; __Pyx_RefNannySetupContext("fields", 0); - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":254 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":297 * @property * cdef inline object fields(self): * return PyDataType_FIELDS(self) # <<<<<<<<<<<<<< @@ -17147,7 +17183,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_6fields_fields(PyArray_Desc __pyx_r = ((PyObject *)__pyx_t_1); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":252 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":295 * # Use fields/names with care as they may be NULL. You must check * # for this using PyDataType_HASFIELDS. * @property # <<<<<<<<<<<<<< @@ -17162,7 +17198,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_6fields_fields(PyArray_Desc return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":256 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":299 * return PyDataType_FIELDS(self) * * @property # <<<<<<<<<<<<<< @@ -17176,7 +17212,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_5names_names(PyArray_Descr PyObject *__pyx_t_1; __Pyx_RefNannySetupContext("names", 0); - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":258 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":301 * @property * cdef inline tuple names(self): * return PyDataType_NAMES(self) # <<<<<<<<<<<<<< @@ -17189,7 +17225,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_5names_names(PyArray_Descr __pyx_r = ((PyObject*)__pyx_t_1); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":256 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":299 * return PyDataType_FIELDS(self) * * @property # <<<<<<<<<<<<<< @@ -17204,7 +17240,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_5names_names(PyArray_Descr return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":263 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":306 * # valid (the pointer can be NULL). Most users should access * # this field via the inline helper method PyDataType_SHAPE. * @property # <<<<<<<<<<<<<< @@ -17215,7 +17251,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_5dtype_5names_names(PyArray_Descr static CYTHON_INLINE PyArray_ArrayDescr *__pyx_f_5numpy_5dtype_8subarray_subarray(PyArray_Descr *__pyx_v_self) { PyArray_ArrayDescr *__pyx_r; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":265 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":308 * @property * cdef inline PyArray_ArrayDescr* subarray(self) noexcept nogil: * return PyDataType_SUBARRAY(self) # <<<<<<<<<<<<<< @@ -17225,7 +17261,7 @@ static CYTHON_INLINE PyArray_ArrayDescr *__pyx_f_5numpy_5dtype_8subarray_subarra __pyx_r = PyDataType_SUBARRAY(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":263 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":306 * # valid (the pointer can be NULL). Most users should access * # this field via the inline helper method PyDataType_SHAPE. * @property # <<<<<<<<<<<<<< @@ -17238,7 +17274,7 @@ static CYTHON_INLINE PyArray_ArrayDescr *__pyx_f_5numpy_5dtype_8subarray_subarra return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":267 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":310 * return PyDataType_SUBARRAY(self) * * @property # <<<<<<<<<<<<<< @@ -17249,7 +17285,7 @@ static CYTHON_INLINE PyArray_ArrayDescr *__pyx_f_5numpy_5dtype_8subarray_subarra static CYTHON_INLINE npy_uint64 __pyx_f_5numpy_5dtype_5flags_flags(PyArray_Descr *__pyx_v_self) { npy_uint64 __pyx_r; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":270 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":313 * cdef inline npy_uint64 flags(self) noexcept nogil: * """The data types flags.""" * return PyDataType_FLAGS(self) # <<<<<<<<<<<<<< @@ -17259,7 +17295,7 @@ static CYTHON_INLINE npy_uint64 __pyx_f_5numpy_5dtype_5flags_flags(PyArray_Descr __pyx_r = PyDataType_FLAGS(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":267 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":310 * return PyDataType_SUBARRAY(self) * * @property # <<<<<<<<<<<<<< @@ -17272,7 +17308,7 @@ static CYTHON_INLINE npy_uint64 __pyx_f_5numpy_5dtype_5flags_flags(PyArray_Descr return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":279 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":322 * ctypedef class numpy.broadcast [object PyArrayMultiIterObject, check_size ignore]: * * @property # <<<<<<<<<<<<<< @@ -17283,7 +17319,7 @@ static CYTHON_INLINE npy_uint64 __pyx_f_5numpy_5dtype_5flags_flags(PyArray_Descr static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_7numiter_numiter(PyArrayMultiIterObject *__pyx_v_self) { int __pyx_r; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":282 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":325 * cdef inline int numiter(self) noexcept nogil: * """The number of arrays that need to be broadcast to the same shape.""" * return PyArray_MultiIter_NUMITER(self) # <<<<<<<<<<<<<< @@ -17293,7 +17329,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_7numiter_numiter(PyArrayMulti __pyx_r = PyArray_MultiIter_NUMITER(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":279 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":322 * ctypedef class numpy.broadcast [object PyArrayMultiIterObject, check_size ignore]: * * @property # <<<<<<<<<<<<<< @@ -17306,7 +17342,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_7numiter_numiter(PyArrayMulti return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":284 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":327 * return PyArray_MultiIter_NUMITER(self) * * @property # <<<<<<<<<<<<<< @@ -17317,7 +17353,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_7numiter_numiter(PyArrayMulti static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_4size_size(PyArrayMultiIterObject *__pyx_v_self) { npy_intp __pyx_r; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":287 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":330 * cdef inline npy_intp size(self) noexcept nogil: * """The total broadcasted size.""" * return PyArray_MultiIter_SIZE(self) # <<<<<<<<<<<<<< @@ -17327,7 +17363,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_4size_size(PyArrayMultiI __pyx_r = PyArray_MultiIter_SIZE(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":284 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":327 * return PyArray_MultiIter_NUMITER(self) * * @property # <<<<<<<<<<<<<< @@ -17340,7 +17376,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_4size_size(PyArrayMultiI return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":289 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":332 * return PyArray_MultiIter_SIZE(self) * * @property # <<<<<<<<<<<<<< @@ -17351,7 +17387,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_4size_size(PyArrayMultiI static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_5index_index(PyArrayMultiIterObject *__pyx_v_self) { npy_intp __pyx_r; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":292 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":335 * cdef inline npy_intp index(self) noexcept nogil: * """The current (1-d) index into the broadcasted result.""" * return PyArray_MultiIter_INDEX(self) # <<<<<<<<<<<<<< @@ -17361,7 +17397,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_5index_index(PyArrayMult __pyx_r = PyArray_MultiIter_INDEX(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":289 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":332 * return PyArray_MultiIter_SIZE(self) * * @property # <<<<<<<<<<<<<< @@ -17374,7 +17410,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_5index_index(PyArrayMult return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":294 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":337 * return PyArray_MultiIter_INDEX(self) * * @property # <<<<<<<<<<<<<< @@ -17385,7 +17421,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_9broadcast_5index_index(PyArrayMult static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_2nd_nd(PyArrayMultiIterObject *__pyx_v_self) { int __pyx_r; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":297 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":340 * cdef inline int nd(self) noexcept nogil: * """The number of dimensions in the broadcasted result.""" * return PyArray_MultiIter_NDIM(self) # <<<<<<<<<<<<<< @@ -17395,7 +17431,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_2nd_nd(PyArrayMultiIterObject __pyx_r = PyArray_MultiIter_NDIM(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":294 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":337 * return PyArray_MultiIter_INDEX(self) * * @property # <<<<<<<<<<<<<< @@ -17408,7 +17444,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_2nd_nd(PyArrayMultiIterObject return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":299 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":342 * return PyArray_MultiIter_NDIM(self) * * @property # <<<<<<<<<<<<<< @@ -17419,7 +17455,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_9broadcast_2nd_nd(PyArrayMultiIterObject static CYTHON_INLINE npy_intp *__pyx_f_5numpy_9broadcast_10dimensions_dimensions(PyArrayMultiIterObject *__pyx_v_self) { npy_intp *__pyx_r; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":302 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":345 * cdef inline npy_intp* dimensions(self) noexcept nogil: * """The shape of the broadcasted result.""" * return PyArray_MultiIter_DIMS(self) # <<<<<<<<<<<<<< @@ -17429,7 +17465,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_9broadcast_10dimensions_dimensions __pyx_r = PyArray_MultiIter_DIMS(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":299 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":342 * return PyArray_MultiIter_NDIM(self) * * @property # <<<<<<<<<<<<<< @@ -17442,7 +17478,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_9broadcast_10dimensions_dimensions return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":304 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":347 * return PyArray_MultiIter_DIMS(self) * * @property # <<<<<<<<<<<<<< @@ -17453,7 +17489,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_9broadcast_10dimensions_dimensions static CYTHON_INLINE void **__pyx_f_5numpy_9broadcast_5iters_iters(PyArrayMultiIterObject *__pyx_v_self) { void **__pyx_r; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":308 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":351 * """An array of iterator objects that holds the iterators for the arrays to be broadcast together. * On return, the iterators are adjusted for broadcasting.""" * return PyArray_MultiIter_ITERS(self) # <<<<<<<<<<<<<< @@ -17463,7 +17499,7 @@ static CYTHON_INLINE void **__pyx_f_5numpy_9broadcast_5iters_iters(PyArrayMultiI __pyx_r = PyArray_MultiIter_ITERS(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":304 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":347 * return PyArray_MultiIter_DIMS(self) * * @property # <<<<<<<<<<<<<< @@ -17476,7 +17512,7 @@ static CYTHON_INLINE void **__pyx_f_5numpy_9broadcast_5iters_iters(PyArrayMultiI return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":322 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":365 * # Instead, we use properties that map to the corresponding C-API functions. * * @property # <<<<<<<<<<<<<< @@ -17487,7 +17523,7 @@ static CYTHON_INLINE void **__pyx_f_5numpy_9broadcast_5iters_iters(PyArrayMultiI static CYTHON_INLINE PyObject *__pyx_f_5numpy_7ndarray_4base_base(PyArrayObject *__pyx_v_self) { PyObject *__pyx_r; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":326 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":369 * """Returns a borrowed reference to the object owning the data/memory. * """ * return PyArray_BASE(self) # <<<<<<<<<<<<<< @@ -17497,7 +17533,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_7ndarray_4base_base(PyArrayObject __pyx_r = PyArray_BASE(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":322 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":365 * # Instead, we use properties that map to the corresponding C-API functions. * * @property # <<<<<<<<<<<<<< @@ -17510,7 +17546,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_7ndarray_4base_base(PyArrayObject return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":328 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":371 * return PyArray_BASE(self) * * @property # <<<<<<<<<<<<<< @@ -17524,7 +17560,7 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray PyArray_Descr *__pyx_t_1; __Pyx_RefNannySetupContext("descr", 0); - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":332 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":375 * """Returns an owned reference to the dtype of the array. * """ * return PyArray_DESCR(self) # <<<<<<<<<<<<<< @@ -17537,7 +17573,7 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray __pyx_r = ((PyArray_Descr *)__pyx_t_1); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":328 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":371 * return PyArray_BASE(self) * * @property # <<<<<<<<<<<<<< @@ -17552,7 +17588,7 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":334 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":377 * return PyArray_DESCR(self) * * @property # <<<<<<<<<<<<<< @@ -17563,7 +17599,7 @@ static CYTHON_INLINE PyArray_Descr *__pyx_f_5numpy_7ndarray_5descr_descr(PyArray static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx_v_self) { int __pyx_r; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":338 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":381 * """Returns the number of dimensions in the array. * """ * return PyArray_NDIM(self) # <<<<<<<<<<<<<< @@ -17573,7 +17609,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx __pyx_r = PyArray_NDIM(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":334 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":377 * return PyArray_DESCR(self) * * @property # <<<<<<<<<<<<<< @@ -17586,7 +17622,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":340 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":383 * return PyArray_NDIM(self) * * @property # <<<<<<<<<<<<<< @@ -17597,7 +17633,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_7ndarray_4ndim_ndim(PyArrayObject *__pyx static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObject *__pyx_v_self) { npy_intp *__pyx_r; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":346 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":389 * Can return NULL for 0-dimensional arrays. * """ * return PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -17607,7 +17643,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObjec __pyx_r = PyArray_DIMS(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":340 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":383 * return PyArray_NDIM(self) * * @property # <<<<<<<<<<<<<< @@ -17620,7 +17656,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObjec return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":348 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":391 * return PyArray_DIMS(self) * * @property # <<<<<<<<<<<<<< @@ -17631,7 +17667,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_5shape_shape(PyArrayObjec static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayObject *__pyx_v_self) { npy_intp *__pyx_r; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":353 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":396 * The number of elements matches the number of dimensions of the array (ndim). * """ * return PyArray_STRIDES(self) # <<<<<<<<<<<<<< @@ -17641,7 +17677,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayO __pyx_r = PyArray_STRIDES(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":348 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":391 * return PyArray_DIMS(self) * * @property # <<<<<<<<<<<<<< @@ -17654,7 +17690,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayO return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":355 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":398 * return PyArray_STRIDES(self) * * @property # <<<<<<<<<<<<<< @@ -17665,7 +17701,7 @@ static CYTHON_INLINE npy_intp *__pyx_f_5numpy_7ndarray_7strides_strides(PyArrayO static CYTHON_INLINE npy_intp __pyx_f_5numpy_7ndarray_4size_size(PyArrayObject *__pyx_v_self) { npy_intp __pyx_r; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":359 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":402 * """Returns the total size (in number of elements) of the array. * """ * return PyArray_SIZE(self) # <<<<<<<<<<<<<< @@ -17675,7 +17711,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_7ndarray_4size_size(PyArrayObject * __pyx_r = PyArray_SIZE(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":355 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":398 * return PyArray_STRIDES(self) * * @property # <<<<<<<<<<<<<< @@ -17688,7 +17724,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_7ndarray_4size_size(PyArrayObject * return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":361 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":404 * return PyArray_SIZE(self) * * @property # <<<<<<<<<<<<<< @@ -17699,7 +17735,7 @@ static CYTHON_INLINE npy_intp __pyx_f_5numpy_7ndarray_4size_size(PyArrayObject * static CYTHON_INLINE char *__pyx_f_5numpy_7ndarray_4data_data(PyArrayObject *__pyx_v_self) { char *__pyx_r; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":368 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":411 * of `PyArray_DATA()` instead, which returns a 'void*'. * """ * return PyArray_BYTES(self) # <<<<<<<<<<<<<< @@ -17709,7 +17745,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy_7ndarray_4data_data(PyArrayObject *__p __pyx_r = PyArray_BYTES(__pyx_v_self); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":361 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":404 * return PyArray_SIZE(self) * * @property # <<<<<<<<<<<<<< @@ -17722,7 +17758,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy_7ndarray_4data_data(PyArrayObject *__p return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":776 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":807 * ctypedef long double complex clongdouble_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< @@ -17739,7 +17775,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew1", 0); - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":777 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":808 * * cdef inline object PyArray_MultiIterNew1(a): * return PyArray_MultiIterNew(1, a) # <<<<<<<<<<<<<< @@ -17747,13 +17783,13 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ * cdef inline object PyArray_MultiIterNew2(a, b): */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = PyArray_MultiIterNew(1, ((void *)__pyx_v_a)); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 777, __pyx_L1_error) + __pyx_t_1 = PyArray_MultiIterNew(1, ((void *)__pyx_v_a)); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 808, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":776 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":807 * ctypedef long double complex clongdouble_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< @@ -17772,7 +17808,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ return __pyx_r; 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} -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1006 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1022 * # Versions of the import_* functions which are more suitable for * # Cython code. * cdef inline int import_array() except -1: # <<<<<<<<<<<<<< @@ -18202,7 +18238,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { int __pyx_clineno = 0; __Pyx_RefNannySetupContext("import_array", 0); - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1007 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1023 * # Cython code. * cdef inline int import_array() except -1: * try: # <<<<<<<<<<<<<< @@ -18218,16 +18254,16 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_array(void) { __Pyx_XGOTREF(__pyx_t_3); /*try:*/ { - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1008 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1024 * cdef inline int import_array() except -1: * try: * __pyx_import_array() # <<<<<<<<<<<<<< * except Exception: * raise ImportError("numpy._core.multiarray failed to import") */ - __pyx_t_4 = _import_array(); 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if (__pyx_t_4) { __Pyx_AddTraceback("numpy.import_ufunc", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(2, 1021, __pyx_L5_except_error) + if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(2, 1037, __pyx_L5_except_error) __Pyx_XGOTREF(__pyx_t_5); __Pyx_XGOTREF(__pyx_t_6); __Pyx_XGOTREF(__pyx_t_7); - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1022 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1038 * _import_umath() * except Exception: * raise ImportError("numpy._core.umath failed to import") # <<<<<<<<<<<<<< @@ -18553,16 +18589,16 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { PyObject *__pyx_callargs[2] = {__pyx_t_9, __pyx_mstate_global->__pyx_kp_u_numpy__core_umath_failed_to_impo}; __pyx_t_8 = __Pyx_PyObject_FastCall((PyObject*)(((PyTypeObject*)PyExc_ImportError)), __pyx_callargs+__pyx_t_10, (2-__pyx_t_10) | (__pyx_t_10*__Pyx_PY_VECTORCALL_ARGUMENTS_OFFSET)); __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0; - if (unlikely(!__pyx_t_8)) __PYX_ERR(2, 1022, __pyx_L5_except_error) + if (unlikely(!__pyx_t_8)) __PYX_ERR(2, 1038, __pyx_L5_except_error) __Pyx_GOTREF(__pyx_t_8); } __Pyx_Raise(__pyx_t_8, 0, 0, 0); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; - __PYX_ERR(2, 1022, __pyx_L5_except_error) + __PYX_ERR(2, 1038, __pyx_L5_except_error) } goto __pyx_L5_except_error; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1019 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1035 * * cdef inline int import_ufunc() except -1: * try: # <<<<<<<<<<<<<< @@ -18578,7 +18614,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { __pyx_L8_try_end:; } - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1018 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1034 * raise ImportError("numpy._core.umath failed to import") * * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< @@ -18602,7 +18638,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1025 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1041 * * * cdef inline bint is_timedelta64_object(object obj) noexcept: # <<<<<<<<<<<<<< @@ -18613,7 +18649,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_import_ufunc(void) { static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_obj) { int __pyx_r; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1037 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1053 * bool * """ * return PyObject_TypeCheck(obj, &PyTimedeltaArrType_Type) # <<<<<<<<<<<<<< @@ -18623,7 +18659,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_ __pyx_r = PyObject_TypeCheck(__pyx_v_obj, (&PyTimedeltaArrType_Type)); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1025 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1041 * * * cdef inline bint is_timedelta64_object(object obj) noexcept: # <<<<<<<<<<<<<< @@ -18636,7 +18672,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_ return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1040 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1056 * * * cdef inline bint is_datetime64_object(object obj) noexcept: # <<<<<<<<<<<<<< @@ -18647,7 +18683,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_timedelta64_object(PyObject *__pyx_v_ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_obj) { int __pyx_r; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1052 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1068 * bool * """ * return PyObject_TypeCheck(obj, &PyDatetimeArrType_Type) # <<<<<<<<<<<<<< @@ -18657,7 +18693,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_o __pyx_r = PyObject_TypeCheck(__pyx_v_obj, (&PyDatetimeArrType_Type)); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1040 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1056 * * * cdef inline bint is_datetime64_object(object obj) noexcept: # <<<<<<<<<<<<<< @@ -18670,7 +18706,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_o return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1055 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1071 * * * cdef inline npy_datetime get_datetime64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< @@ -18681,7 +18717,7 @@ static CYTHON_INLINE int __pyx_f_5numpy_is_datetime64_object(PyObject *__pyx_v_o static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject *__pyx_v_obj) { npy_datetime __pyx_r; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1062 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1078 * also needed. That can be found using `get_datetime64_unit`. * """ * return (obj).obval # <<<<<<<<<<<<<< @@ -18691,7 +18727,7 @@ static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject * __pyx_r = ((PyDatetimeScalarObject *)__pyx_v_obj)->obval; goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1055 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1071 * * * cdef inline npy_datetime get_datetime64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< @@ -18704,7 +18740,7 @@ static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject * return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1065 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1081 * * * cdef inline npy_timedelta get_timedelta64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< @@ -18715,7 +18751,7 @@ static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject * static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject *__pyx_v_obj) { npy_timedelta __pyx_r; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1069 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1085 * returns the int64 value underlying scalar numpy timedelta64 object * """ * return (obj).obval # <<<<<<<<<<<<<< @@ -18725,7 +18761,7 @@ static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject __pyx_r = ((PyTimedeltaScalarObject *)__pyx_v_obj)->obval; goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1065 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1081 * * * cdef inline npy_timedelta get_timedelta64_value(object obj) noexcept nogil: # <<<<<<<<<<<<<< @@ -18738,7 +18774,7 @@ static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject return __pyx_r; } -/* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1072 +/* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1088 * * * cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) noexcept nogil: # <<<<<<<<<<<<<< @@ -18749,7 +18785,7 @@ static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject static CYTHON_INLINE NPY_DATETIMEUNIT __pyx_f_5numpy_get_datetime64_unit(PyObject *__pyx_v_obj) { NPY_DATETIMEUNIT __pyx_r; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1076 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1092 * returns the unit part of the dtype for a numpy datetime64 object. * """ * return (obj).obmeta.base # <<<<<<<<<<<<<< @@ -18759,7 +18795,7 @@ static CYTHON_INLINE NPY_DATETIMEUNIT __pyx_f_5numpy_get_datetime64_unit(PyObjec __pyx_r = ((NPY_DATETIMEUNIT)((PyDatetimeScalarObject *)__pyx_v_obj)->obmeta.base); goto __pyx_L0; - /* "../../../../../tmp/pip-build-env-bryxb9us/overlay/local/lib/python3.12/dist-packages/numpy/__init__.cython-30.pxd":1072 + /* "../../../../../tmp/pip-build-env-_q1myxj8/overlay/lib/python3.9/site-packages/numpy/__init__.cython-30.pxd":1088 * * * cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) noexcept nogil: # <<<<<<<<<<<<<< @@ -23552,153 +23588,153 @@ static int __Pyx_modinit_type_import_code(__pyx_mstatetype 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PyObject *data = NULL; CYTHON_UNUSED_VAR(__Pyx_DecompressString); #endif PyObject **stringtab = __pyx_mstate->__pyx_string_tab; Py_ssize_t pos = 0; - for (int i = 0; i < 173; i++) { + for (int i = 0; i < 172; i++) { Py_ssize_t bytes_length = index[i].length; PyObject *string = PyUnicode_DecodeUTF8(bytes + pos, bytes_length, NULL); - if (likely(string) && i >= 48) PyUnicode_InternInPlace(&string); + if (likely(string) && i >= 47) PyUnicode_InternInPlace(&string); if (unlikely(!string)) { Py_XDECREF(data); __PYX_ERR(0, 1, __pyx_L1_error) @@ -24792,7 +24831,7 @@ const char* const bytes = ": All dimensions preceding dimension %d must be index stringtab[i] = string; pos += bytes_length; } - for (int i = 173; i < 179; i++) { + for (int i = 172; i < 178; i++) { Py_ssize_t bytes_length = index[i].length; PyObject *string = PyBytes_FromStringAndSize(bytes + pos, bytes_length); stringtab[i] = string; @@ -24803,17 +24842,24 @@ const char* const bytes = ": All dimensions preceding dimension %d must be index } } Py_XDECREF(data); - for (Py_ssize_t i = 0; i < 179; i++) { + for (Py_ssize_t i = 0; i < 178; i++) { if (unlikely(PyObject_Hash(stringtab[i]) == -1)) { __PYX_ERR(0, 1, __pyx_L1_error) } } #if CYTHON_IMMORTAL_CONSTANTS { - PyObject **table = stringtab + 173; + PyObject **table = stringtab + 172; for (Py_ssize_t i=0; i<6; ++i) { #if CYTHON_COMPILING_IN_CPYTHON_FREETHREADING - Py_SET_REFCNT(table[i], _Py_IMMORTAL_REFCNT_LOCAL); + #if PY_VERSION_HEX < 0x030E0000 + if (_Py_IsOwnedByCurrentThread(table[i]) && Py_REFCNT(table[i]) == 1) + #else + if (PyUnstable_Object_IsUniquelyReferenced(table[i])) + #endif + { + Py_SET_REFCNT(table[i], _Py_IMMORTAL_REFCNT_LOCAL); + } #else Py_SET_REFCNT(table[i], _Py_IMMORTAL_INITIAL_REFCNT); #endif @@ -24835,7 +24881,14 @@ const char* const bytes = ": All dimensions preceding dimension %d must be index PyObject **table = __pyx_mstate->__pyx_number_tab; for (Py_ssize_t i=0; i<4; ++i) { #if CYTHON_COMPILING_IN_CPYTHON_FREETHREADING - Py_SET_REFCNT(table[i], _Py_IMMORTAL_REFCNT_LOCAL); + #if PY_VERSION_HEX < 0x030E0000 + if (_Py_IsOwnedByCurrentThread(table[i]) && Py_REFCNT(table[i]) == 1) + #else + if (PyUnstable_Object_IsUniquelyReferenced(table[i])) + #endif + { + Py_SET_REFCNT(table[i], _Py_IMMORTAL_REFCNT_LOCAL); + } #else Py_SET_REFCNT(table[i], _Py_IMMORTAL_INITIAL_REFCNT); #endif @@ -27570,6 +27623,7 @@ static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObj #endif /* PySequenceMultiply */ +#if CYTHON_USE_TYPE_SLOTS static PyObject* __Pyx_PySequence_Multiply_Generic(PyObject *seq, Py_ssize_t mul) { PyObject *result, *pymul = PyLong_FromSsize_t(mul); if (unlikely(!pymul)) @@ -27579,16 +27633,14 @@ static PyObject* __Pyx_PySequence_Multiply_Generic(PyObject *seq, Py_ssize_t mul return result; } static CYTHON_INLINE PyObject* __Pyx_PySequence_Multiply(PyObject *seq, Py_ssize_t mul) { -#if CYTHON_USE_TYPE_SLOTS PyTypeObject *type = Py_TYPE(seq); if (likely(type->tp_as_sequence && type->tp_as_sequence->sq_repeat)) { return type->tp_as_sequence->sq_repeat(seq, mul); - } else -#endif - { + } else { return __Pyx_PySequence_Multiply_Generic(seq, mul); } } +#endif /* PyObjectFormatAndDecref */ static CYTHON_INLINE PyObject* __Pyx_PyObject_FormatSimpleAndDecref(PyObject* s, PyObject* f) { @@ -28497,10 +28549,10 @@ static int __Pyx_setup_reduce(PyObject* type_obj) { } /* TypeImport */ -#ifndef __PYX_HAVE_RT_ImportType_3_2_1 -#define __PYX_HAVE_RT_ImportType_3_2_1 -static PyTypeObject *__Pyx_ImportType_3_2_1(PyObject *module, const char *module_name, const char *class_name, - size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_2_1 check_size) +#ifndef __PYX_HAVE_RT_ImportType_3_2_4 +#define __PYX_HAVE_RT_ImportType_3_2_4 +static PyTypeObject *__Pyx_ImportType_3_2_4(PyObject *module, const char *module_name, const char *class_name, + size_t size, size_t alignment, enum __Pyx_ImportType_CheckSize_3_2_4 check_size) { PyObject *result = 0; Py_ssize_t basicsize; @@ -28556,7 +28608,7 @@ static PyTypeObject *__Pyx_ImportType_3_2_1(PyObject *module, const char *module module_name, class_name, size, basicsize+itemsize); goto bad; } - if (check_size == __Pyx_ImportType_CheckSize_Error_3_2_1 && + if (check_size == __Pyx_ImportType_CheckSize_Error_3_2_4 && ((size_t)basicsize > size || (size_t)(basicsize + itemsize) < size)) { PyErr_Format(PyExc_ValueError, "%.200s.%.200s size changed, may indicate binary incompatibility. " @@ -28564,7 +28616,7 @@ static PyTypeObject *__Pyx_ImportType_3_2_1(PyObject *module, const char *module module_name, class_name, size, basicsize, basicsize+itemsize); goto bad; } - else if (check_size == __Pyx_ImportType_CheckSize_Warn_3_2_1 && (size_t)basicsize > size) { + else if (check_size == __Pyx_ImportType_CheckSize_Warn_3_2_4 && (size_t)basicsize > size) { if (PyErr_WarnFormat(NULL, 0, "%.200s.%.200s size changed, may indicate binary incompatibility. " "Expected %zd from C header, got %zd from PyObject", @@ -28582,13 +28634,13 @@ static PyTypeObject *__Pyx_ImportType_3_2_1(PyObject *module, const char *module /* dict_setdefault (used by FetchCommonType) */ static CYTHON_INLINE PyObject *__Pyx_PyDict_SetDefault(PyObject *d, PyObject *key, PyObject *default_value) { PyObject* value; -#if CYTHON_COMPILING_IN_LIMITED_API && __PYX_LIMITED_VERSION_HEX >= 0x030C0000 +#if __PYX_LIMITED_VERSION_HEX >= 0x030F0000 || (!CYTHON_COMPILING_IN_LIMITED_API && PY_VERSION_HEX >= 0x030d00A4) + PyDict_SetDefaultRef(d, key, default_value, &value); +#elif CYTHON_COMPILING_IN_LIMITED_API && __PYX_LIMITED_VERSION_HEX >= 0x030C0000 PyObject *args[] = {d, key, default_value}; value = PyObject_VectorcallMethod(__pyx_mstate_global->__pyx_n_u_setdefault, args, 3 | PY_VECTORCALL_ARGUMENTS_OFFSET, NULL); #elif CYTHON_COMPILING_IN_LIMITED_API value = PyObject_CallMethodObjArgs(d, __pyx_mstate_global->__pyx_n_u_setdefault, key, default_value, NULL); -#elif PY_VERSION_HEX >= 0x030d0000 - PyDict_SetDefaultRef(d, key, default_value, &value); #else value = PyDict_SetDefault(d, key, default_value); if (unlikely(!value)) return NULL; @@ -33565,14 +33617,14 @@ static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const cha /* DecompressString */ static PyObject *__Pyx_DecompressString(const char *s, Py_ssize_t length, int algo) { - PyObject *module, *decompress, *compressed_bytes, *decompressed; + PyObject *module = NULL, *decompress, *compressed_bytes, *decompressed; const char* module_name = algo == 3 ? "compression.zstd" : algo == 2 ? "bz2" : "zlib"; PyObject *methodname = PyUnicode_FromString("decompress"); if (unlikely(!methodname)) return NULL; #if __PYX_LIMITED_VERSION_HEX >= 0x030e0000 if (algo == 3) { PyObject *fromlist = Py_BuildValue("[O]", methodname); - if (unlikely(!fromlist)) return NULL; + if (unlikely(!fromlist)) goto bad; module = PyImport_ImportModuleLevel("compression.zstd", NULL, NULL, fromlist, 0); Py_DECREF(fromlist); } else diff --git a/pyprophet/scoring/data_handling.py b/pyprophet/scoring/data_handling.py index c0881bd8..cacff214 100644 --- a/pyprophet/scoring/data_handling.py +++ b/pyprophet/scoring/data_handling.py @@ -77,6 +77,12 @@ def check_for_unique_blocks(tg_ids): return True +def _to_writable_c_array(values, dtype): + """Return a writable, C-contiguous numpy array for Cython memoryviews.""" + arr = np.asarray(values, dtype=dtype) + return np.require(arr, dtype=dtype, requirements=["C", "W"]) + + @profile def cleanup_and_check(df): """ @@ -435,10 +441,11 @@ def rank_by(self, score_col_name): Args: score_col_name (str): Name of the score column to rank by. """ - flags = find_top_ranked( - self.df.tg_num_id.values, - self.df[score_col_name].values.astype(np.float32, copy=False), + tg_ids = _to_writable_c_array(self.df.tg_num_id.to_numpy(copy=False), np.int64) + scores = _to_writable_c_array( + self.df[score_col_name].to_numpy(copy=False), np.float32 ) + flags = find_top_ranked(tg_ids, scores) self.df.is_top_peak = flags def get_top_test_peaks(self): @@ -537,9 +544,9 @@ def add_peak_group_rank(self): """ Adds a peak group rank column to the data. """ - ids = self.df.tg_num_id.values - scores = self.df.d_score.values - peak_group_ranks = rank(ids, scores.astype(np.float32, copy=False)) + ids = _to_writable_c_array(self.df.tg_num_id.to_numpy(copy=False), np.int64) + scores = _to_writable_c_array(self.df.d_score.to_numpy(copy=False), np.float32) + peak_group_ranks = rank(ids, scores) self.df["peak_group_rank"] = peak_group_ranks @profile diff --git a/tests/test_data_handling.py b/tests/test_data_handling.py index c9356d6a..08e4fd7c 100644 --- a/tests/test_data_handling.py +++ b/tests/test_data_handling.py @@ -1,7 +1,10 @@ # encoding: utf-8 from __future__ import print_function +import numpy as np + from pyprophet.scoring.data_handling import check_for_unique_blocks +from pyprophet.scoring.data_handling import _to_writable_c_array def test_ok(): @@ -46,3 +49,15 @@ def test_not_ok(): assert check_for_unique_blocks(map(str, [1, 2, 2, 2, 1])) is False assert check_for_unique_blocks(map(str, [1, 1, 2, 2, 3, 3, 4, 4, 3])) is False assert check_for_unique_blocks(map(str, [1, 1, 2, 2, 3, 3, 4, 4, 5, 4])) is False + + +def test_to_writable_c_array_handles_read_only_input(): + source = np.array([1.0, 2.0, 3.0], dtype=np.float32) + source.setflags(write=False) + + out = _to_writable_c_array(source, np.float32) + + assert out.flags.writeable is True + assert out.flags.c_contiguous is True + out[0] = 42.0 + assert out[0] == 42.0 From 80fc438b2b7b9c4bc15cffaf56408fc399692f17 Mon Sep 17 00:00:00 2001 From: singjc Date: Wed, 25 Mar 2026 22:59:44 -0400 Subject: [PATCH 4/4] Remove print statement for query in OSWReader's data reading method --- pyprophet/io/export/osw.py | 1 - 1 file changed, 1 deletion(-) diff --git a/pyprophet/io/export/osw.py b/pyprophet/io/export/osw.py index 88789093..435fa8db 100644 --- a/pyprophet/io/export/osw.py +++ b/pyprophet/io/export/osw.py @@ -497,7 +497,6 @@ def _read_standard_data(self, con, cfg): logger.trace( f"Initial standard data read with {len(data)} rows and columns: {data.columns.tolist()}" ) - print(query) # Ensure id column is Int64 to preserve precision for large feature IDs if "id" in data.columns: