From b06431a722fdd620a237e6f52456ffd31984c304 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20Elvira?= <clement.elvira@centralesupelec.fr>
Date: Thu, 10 Nov 2022 11:18:53 +0100
Subject: [PATCH] new namespace + missing information in setup.py
---
experiments/SIAM/increasingball.py | 2 +-
experiments/SIAM/slopepb.py | 4 +-
.../SIAM/xp_1_balls/xp_a_accuracy_sol.py | 12 +-
experiments/SIAM/xp_1_balls/xp_b_screening.py | 12 +-
.../SIAM/xp_2_bench_time/get_algs_params.py | 6 +-
.../SIAM/xp_2_bench_time/xp_a_get_state.py | 2 +-
.../SIAM/xp_2_bench_time/xp_b_get_budget.py | 12 +-
.../SIAM/xp_2_bench_time/xp_c_results_time.py | 10 +-
experiments/utils/increasingball.py | 2 +-
experiments/utils/slopepb.py | 4 +-
requirements.txt | 19 +-
setup.py | 11 +-
slopescreening/__init__.py | 3 +
{src => slopescreening}/__version.py | 0
{src => slopescreening}/dictionaries.py | 0
{src => slopescreening}/screening/__init__.py | 0
.../screening/ascreening.py | 0
.../screening/gap_test_all.c | 851 +++++++++++-------
.../screening/gap_test_all.pyx | 2 +-
.../screening/gap_test_p_1.c | 825 ++++++++++-------
.../screening/gap_test_p_1.pyx | 2 +-
.../screening/gap_test_p_q.py | 2 +-
{src => slopescreening}/screening/utils.c | 748 +++++++++------
{src => slopescreening}/screening/utils.pyx | 0
{src => slopescreening}/solver/parameters.py | 2 +-
{src => slopescreening}/solver/prox.py | 0
{src => slopescreening}/solver/slope.py | 4 +-
{src => slopescreening}/utils.py | 0
src/__init__.py | 3 -
tests/test_solver.py | 8 +-
tests/test_utils.py | 6 +-
31 files changed, 1589 insertions(+), 963 deletions(-)
create mode 100755 slopescreening/__init__.py
rename {src => slopescreening}/__version.py (100%)
rename {src => slopescreening}/dictionaries.py (100%)
rename {src => slopescreening}/screening/__init__.py (100%)
rename {src => slopescreening}/screening/ascreening.py (100%)
rename {src => slopescreening}/screening/gap_test_all.c (90%)
rename {src => slopescreening}/screening/gap_test_all.pyx (98%)
rename {src => slopescreening}/screening/gap_test_p_1.c (89%)
rename {src => slopescreening}/screening/gap_test_p_1.pyx (98%)
rename {src => slopescreening}/screening/gap_test_p_q.py (95%)
rename {src => slopescreening}/screening/utils.c (91%)
rename {src => slopescreening}/screening/utils.pyx (100%)
rename {src => slopescreening}/solver/parameters.py (94%)
rename {src => slopescreening}/solver/prox.py (100%)
rename {src => slopescreening}/solver/slope.py (98%)
rename {src => slopescreening}/utils.py (100%)
delete mode 100755 src/__init__.py
diff --git a/experiments/SIAM/increasingball.py b/experiments/SIAM/increasingball.py
index fdbc7d0..ba797c4 100644
--- a/experiments/SIAM/increasingball.py
+++ b/experiments/SIAM/increasingball.py
@@ -2,7 +2,7 @@ import time
import numpy as np
-from src.utils import get_lambda_max
+from slopescreening.utils import get_lambda_max
def test_increasing_ball(list_tests, vec_offsets, slopepb, vecx):
diff --git a/experiments/SIAM/slopepb.py b/experiments/SIAM/slopepb.py
index c301bd6..d902d87 100644
--- a/experiments/SIAM/slopepb.py
+++ b/experiments/SIAM/slopepb.py
@@ -1,7 +1,7 @@
import numpy as np
-from src.solver.slope import primal_func, dual_func
-from src.utils import get_lambda_max
+from slopescreening.solver.slope import primal_func, dual_func
+from slopescreening.utils import get_lambda_max
class SlopePb(object):
diff --git a/experiments/SIAM/xp_1_balls/xp_a_accuracy_sol.py b/experiments/SIAM/xp_1_balls/xp_a_accuracy_sol.py
index aba6721..1bbd67c 100755
--- a/experiments/SIAM/xp_1_balls/xp_a_accuracy_sol.py
+++ b/experiments/SIAM/xp_1_balls/xp_a_accuracy_sol.py
@@ -5,16 +5,16 @@ from pathlib import Path
import numpy as np
# Algorithm import
-from src import __version__
-from src.solver.parameters import SlopeParameters, EnumLipchitzOptions
-from src.solver.slope import primal_func, dual_func, slope_gp
+from slopescreening import __version__
+from slopescreening.solver.parameters import SlopeParameters, EnumLipchitzOptions
+from slopescreening.solver.slope import primal_func, dual_func, slope_gp
# Generative models
-from src.utils import get_lambda_max, gamma_sequence_generator
-from src.dictionaries import generate_dic
+from slopescreening.utils import get_lambda_max, gamma_sequence_generator
+from slopescreening.dictionaries import generate_dic
# Screening
-from src.screening.gap_test_all import GapTestAll
+from slopescreening.screening.gap_test_all import GapTestAll
# XP import
from experiments.SIAM.slopepb import SlopePb
diff --git a/experiments/SIAM/xp_1_balls/xp_b_screening.py b/experiments/SIAM/xp_1_balls/xp_b_screening.py
index 5d24334..574fa28 100644
--- a/experiments/SIAM/xp_1_balls/xp_b_screening.py
+++ b/experiments/SIAM/xp_1_balls/xp_b_screening.py
@@ -4,14 +4,14 @@ import argparse
import numpy as np
# Algorithm import
-from src import __version__
-from src.dictionaries import generate_dic
-from src.utils import get_lambda_max, gamma_sequence_generator
+from slopescreening import __version__
+from slopescreening.dictionaries import generate_dic
+from slopescreening.utils import get_lambda_max, gamma_sequence_generator
# Screening
-from src.screening.gap_test_p_1 import GapTestPequalOne
-from src.screening.gap_test_p_q import GapTestPequalQ
-from src.screening.gap_test_all import GapTestAll
+from slopescreening.screening.gap_test_p_1 import GapTestPequalOne
+from slopescreening.screening.gap_test_p_q import GapTestPequalQ
+from slopescreening.screening.gap_test_all import GapTestAll
# XP import
from experiments.SIAM.slopepb import SlopePb
diff --git a/experiments/SIAM/xp_2_bench_time/get_algs_params.py b/experiments/SIAM/xp_2_bench_time/get_algs_params.py
index 1602fbd..028fb9c 100644
--- a/experiments/SIAM/xp_2_bench_time/get_algs_params.py
+++ b/experiments/SIAM/xp_2_bench_time/get_algs_params.py
@@ -1,9 +1,9 @@
import numpy as np
-from src.solver.parameters import SlopeParameters, EnumLipchitzOptions, DualScalingOptions
+from slopescreening.solver.parameters import SlopeParameters, EnumLipchitzOptions, DualScalingOptions
-from src.screening.gap_test_p_q import GapTestPequalQ
-from src.screening.gap_test_all import GapTestAll
+from slopescreening.screening.gap_test_p_q import GapTestPequalQ
+from slopescreening.screening.gap_test_all import GapTestAll
nb_algs = 4
diff --git a/experiments/SIAM/xp_2_bench_time/xp_a_get_state.py b/experiments/SIAM/xp_2_bench_time/xp_a_get_state.py
index e037bf5..9fd3f09 100644
--- a/experiments/SIAM/xp_2_bench_time/xp_a_get_state.py
+++ b/experiments/SIAM/xp_2_bench_time/xp_a_get_state.py
@@ -3,7 +3,7 @@ import argparse, sys
from pathlib import Path
import numpy as np
-from src import __version__
+from slopescreening import __version__
from experiments.SIAM.setup import Setup
from get_algs_params import get_alg_params, get_nb_algs
diff --git a/experiments/SIAM/xp_2_bench_time/xp_b_get_budget.py b/experiments/SIAM/xp_2_bench_time/xp_b_get_budget.py
index 4207b54..8fa0f86 100755
--- a/experiments/SIAM/xp_2_bench_time/xp_b_get_budget.py
+++ b/experiments/SIAM/xp_2_bench_time/xp_b_get_budget.py
@@ -3,13 +3,13 @@ import argparse, sys
import numpy as np
-from src import __version__
-from src.solver.slope import slope_gp
-from src.utils import get_lambda_max, gamma_sequence_generator
-from src.dictionaries import generate_dic
+from slopescreening import __version__
+from slopescreening.solver.slope import slope_gp
+from slopescreening.utils import get_lambda_max, gamma_sequence_generator
+from slopescreening.dictionaries import generate_dic
-from src.solver.parameters import SlopeParameters, EnumLipchitzOptions
-from src.screening.gap_test_all import GapTestAll
+from slopescreening.solver.parameters import SlopeParameters, EnumLipchitzOptions
+from slopescreening.screening.gap_test_all import GapTestAll
from experiments.SIAM.setup import Setup
diff --git a/experiments/SIAM/xp_2_bench_time/xp_c_results_time.py b/experiments/SIAM/xp_2_bench_time/xp_c_results_time.py
index 8921d7a..1c58aca 100644
--- a/experiments/SIAM/xp_2_bench_time/xp_c_results_time.py
+++ b/experiments/SIAM/xp_2_bench_time/xp_c_results_time.py
@@ -3,11 +3,11 @@ import argparse, sys
import numpy as np
-from src import __version__
-from src.solver.slope import slope_gp
-from src.solver.parameters import SlopeParameters, EnumLipchitzOptions
-from src.utils import get_lambda_max, gamma_sequence_generator
-from src.dictionaries import generate_dic
+from slopescreening import __version__
+from slopescreening.solver.slope import slope_gp
+from slopescreening.solver.parameters import SlopeParameters, EnumLipchitzOptions
+from slopescreening.utils import get_lambda_max, gamma_sequence_generator
+from slopescreening.dictionaries import generate_dic
from experiments.SIAM.setup import Setup
from experiments.SIAM.slopepb import SlopePb
diff --git a/experiments/utils/increasingball.py b/experiments/utils/increasingball.py
index fdbc7d0..ba797c4 100644
--- a/experiments/utils/increasingball.py
+++ b/experiments/utils/increasingball.py
@@ -2,7 +2,7 @@ import time
import numpy as np
-from src.utils import get_lambda_max
+from slopescreening.utils import get_lambda_max
def test_increasing_ball(list_tests, vec_offsets, slopepb, vecx):
diff --git a/experiments/utils/slopepb.py b/experiments/utils/slopepb.py
index 55f6562..ff3de6a 100644
--- a/experiments/utils/slopepb.py
+++ b/experiments/utils/slopepb.py
@@ -1,7 +1,7 @@
import numpy as np
-from src.slope import primal_func, dual_func
-from src.utils import get_lambda_max
+from slopescreening.slope import primal_func, dual_func
+from slopescreening.utils import get_lambda_max
class SlopePb(object):
diff --git a/requirements.txt b/requirements.txt
index e29e904..900f6ea 100755
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,16 +1,7 @@
-coverage==5.5
-cycler==0.10.0
-Cython==0.29.24
-joblib==1.0.1
-kiwisolver==1.3.2
-matplotlib==3.4.3
-numpy==1.21.2
-Pillow==8.3.2
-pybind11==2.7.1
+numpy>=1.21.2
+scipy>=1.7.1
+matplotlib>=3.4.3
+Cython>=0.29.24
pyparsing==2.4.7
python-dateutil==2.8.2
-scikit-learn==0.24.2
-scipy==1.7.1
-six==1.16.0
-sklearn==0.0
-threadpoolctl==2.2.0
+scikit-learn>=0.24.2
diff --git a/setup.py b/setup.py
index 1e4fe3a..64551fc 100755
--- a/setup.py
+++ b/setup.py
@@ -2,8 +2,9 @@
from setuptools import setup, find_packages
from Cython.Build import cythonize
+import numpy as np
-from src import __version__
+from slopescreening import __version__
with open('README.md') as f:
readme = f.read()
@@ -22,9 +23,9 @@ setup(
license=license,
packages=find_packages(exclude=('tests', 'docs')),
ext_modules=cythonize([
- "src/screening/utils.pyx",
- "src/screening/gap_test_all.pyx",
- "src/screening/gap_test_p_1.pyx",
+ "slopescreening/screening/utils.pyx",
+ "slopescreening/screening/gap_test_all.pyx",
+ "slopescreening/screening/gap_test_p_1.pyx",
]),
+ include_dirs=[np.get_include()],
)
-
diff --git a/slopescreening/__init__.py b/slopescreening/__init__.py
new file mode 100755
index 0000000..dd651f8
--- /dev/null
+++ b/slopescreening/__init__.py
@@ -0,0 +1,3 @@
+# -*- coding: utf-8 -*-
+
+from slopescreening.__version import __version__
\ No newline at end of file
diff --git a/src/__version.py b/slopescreening/__version.py
similarity index 100%
rename from src/__version.py
rename to slopescreening/__version.py
diff --git a/src/dictionaries.py b/slopescreening/dictionaries.py
similarity index 100%
rename from src/dictionaries.py
rename to slopescreening/dictionaries.py
diff --git a/src/screening/__init__.py b/slopescreening/screening/__init__.py
similarity index 100%
rename from src/screening/__init__.py
rename to slopescreening/screening/__init__.py
diff --git a/src/screening/ascreening.py b/slopescreening/screening/ascreening.py
similarity index 100%
rename from src/screening/ascreening.py
rename to slopescreening/screening/ascreening.py
diff --git a/src/screening/gap_test_all.c b/slopescreening/screening/gap_test_all.c
similarity index 90%
rename from src/screening/gap_test_all.c
rename to slopescreening/screening/gap_test_all.c
index df03365..f883f34 100644
--- a/src/screening/gap_test_all.c
+++ b/slopescreening/screening/gap_test_all.c
@@ -1,15 +1,15 @@
-/* Generated by Cython 0.29.24 */
+/* Generated by Cython 0.29.32 */
/* BEGIN: Cython Metadata
{
"distutils": {
"depends": [],
- "name": "src.screening.gap_test_all",
+ "name": "slopescreening.screening.gap_test_all",
"sources": [
- "src/screening/gap_test_all.pyx"
+ "slopescreening/screening/gap_test_all.pyx"
]
},
- "module_name": "src.screening.gap_test_all"
+ "module_name": "slopescreening.screening.gap_test_all"
}
END: Cython Metadata */
@@ -22,8 +22,8 @@ END: Cython Metadata */
#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000)
#error Cython requires Python 2.6+ or Python 3.3+.
#else
-#define CYTHON_ABI "0_29_24"
-#define CYTHON_HEX_VERSION 0x001D18F0
+#define CYTHON_ABI "0_29_32"
+#define CYTHON_HEX_VERSION 0x001D20F0
#define CYTHON_FUTURE_DIVISION 0
#include <stddef.h>
#ifndef offsetof
@@ -62,6 +62,7 @@ END: Cython Metadata */
#define CYTHON_COMPILING_IN_PYPY 1
#define CYTHON_COMPILING_IN_PYSTON 0
#define CYTHON_COMPILING_IN_CPYTHON 0
+ #define CYTHON_COMPILING_IN_NOGIL 0
#undef CYTHON_USE_TYPE_SLOTS
#define CYTHON_USE_TYPE_SLOTS 0
#undef CYTHON_USE_PYTYPE_LOOKUP
@@ -98,10 +99,14 @@ END: Cython Metadata */
#define CYTHON_USE_DICT_VERSIONS 0
#undef CYTHON_USE_EXC_INFO_STACK
#define CYTHON_USE_EXC_INFO_STACK 0
+ #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
+ #define CYTHON_UPDATE_DESCRIPTOR_DOC (PYPY_VERSION_HEX >= 0x07030900)
+ #endif
#elif defined(PYSTON_VERSION)
#define CYTHON_COMPILING_IN_PYPY 0
#define CYTHON_COMPILING_IN_PYSTON 1
#define CYTHON_COMPILING_IN_CPYTHON 0
+ #define CYTHON_COMPILING_IN_NOGIL 0
#ifndef CYTHON_USE_TYPE_SLOTS
#define CYTHON_USE_TYPE_SLOTS 1
#endif
@@ -139,10 +144,59 @@ END: Cython Metadata */
#define CYTHON_USE_DICT_VERSIONS 0
#undef CYTHON_USE_EXC_INFO_STACK
#define CYTHON_USE_EXC_INFO_STACK 0
+ #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
+ #define CYTHON_UPDATE_DESCRIPTOR_DOC 0
+ #endif
+#elif defined(PY_NOGIL)
+ #define CYTHON_COMPILING_IN_PYPY 0
+ #define CYTHON_COMPILING_IN_PYSTON 0
+ #define CYTHON_COMPILING_IN_CPYTHON 0
+ #define CYTHON_COMPILING_IN_NOGIL 1
+ #ifndef CYTHON_USE_TYPE_SLOTS
+ #define CYTHON_USE_TYPE_SLOTS 1
+ #endif
+ #undef CYTHON_USE_PYTYPE_LOOKUP
+ #define CYTHON_USE_PYTYPE_LOOKUP 0
+ #ifndef CYTHON_USE_ASYNC_SLOTS
+ #define CYTHON_USE_ASYNC_SLOTS 1
+ #endif
+ #undef CYTHON_USE_PYLIST_INTERNALS
+ #define CYTHON_USE_PYLIST_INTERNALS 0
+ #ifndef CYTHON_USE_UNICODE_INTERNALS
+ #define CYTHON_USE_UNICODE_INTERNALS 1
+ #endif
+ #undef CYTHON_USE_UNICODE_WRITER
+ #define CYTHON_USE_UNICODE_WRITER 0
+ #undef CYTHON_USE_PYLONG_INTERNALS
+ #define CYTHON_USE_PYLONG_INTERNALS 0
+ #ifndef CYTHON_AVOID_BORROWED_REFS
+ #define CYTHON_AVOID_BORROWED_REFS 0
+ #endif
+ #ifndef CYTHON_ASSUME_SAFE_MACROS
+ #define CYTHON_ASSUME_SAFE_MACROS 1
+ #endif
+ #ifndef CYTHON_UNPACK_METHODS
+ #define CYTHON_UNPACK_METHODS 1
+ #endif
+ #undef CYTHON_FAST_THREAD_STATE
+ #define CYTHON_FAST_THREAD_STATE 0
+ #undef CYTHON_FAST_PYCALL
+ #define CYTHON_FAST_PYCALL 0
+ #ifndef CYTHON_PEP489_MULTI_PHASE_INIT
+ #define CYTHON_PEP489_MULTI_PHASE_INIT 1
+ #endif
+ #ifndef CYTHON_USE_TP_FINALIZE
+ #define CYTHON_USE_TP_FINALIZE 1
+ #endif
+ #undef CYTHON_USE_DICT_VERSIONS
+ #define CYTHON_USE_DICT_VERSIONS 0
+ #undef CYTHON_USE_EXC_INFO_STACK
+ #define CYTHON_USE_EXC_INFO_STACK 0
#else
#define CYTHON_COMPILING_IN_PYPY 0
#define CYTHON_COMPILING_IN_PYSTON 0
#define CYTHON_COMPILING_IN_CPYTHON 1
+ #define CYTHON_COMPILING_IN_NOGIL 0
#ifndef CYTHON_USE_TYPE_SLOTS
#define CYTHON_USE_TYPE_SLOTS 1
#endif
@@ -170,7 +224,7 @@ END: Cython Metadata */
#ifndef CYTHON_USE_UNICODE_INTERNALS
#define CYTHON_USE_UNICODE_INTERNALS 1
#endif
- #if PY_VERSION_HEX < 0x030300F0
+ #if PY_VERSION_HEX < 0x030300F0 || PY_VERSION_HEX >= 0x030B00A2
#undef CYTHON_USE_UNICODE_WRITER
#define CYTHON_USE_UNICODE_WRITER 0
#elif !defined(CYTHON_USE_UNICODE_WRITER)
@@ -185,11 +239,14 @@ END: Cython Metadata */
#ifndef CYTHON_UNPACK_METHODS
#define CYTHON_UNPACK_METHODS 1
#endif
- #ifndef CYTHON_FAST_THREAD_STATE
+ #if PY_VERSION_HEX >= 0x030B00A4
+ #undef CYTHON_FAST_THREAD_STATE
+ #define CYTHON_FAST_THREAD_STATE 0
+ #elif !defined(CYTHON_FAST_THREAD_STATE)
#define CYTHON_FAST_THREAD_STATE 1
#endif
#ifndef CYTHON_FAST_PYCALL
- #define CYTHON_FAST_PYCALL 1
+ #define CYTHON_FAST_PYCALL (PY_VERSION_HEX < 0x030A0000)
#endif
#ifndef CYTHON_PEP489_MULTI_PHASE_INIT
#define CYTHON_PEP489_MULTI_PHASE_INIT (PY_VERSION_HEX >= 0x03050000)
@@ -200,15 +257,23 @@ END: Cython Metadata */
#ifndef CYTHON_USE_DICT_VERSIONS
#define CYTHON_USE_DICT_VERSIONS (PY_VERSION_HEX >= 0x030600B1)
#endif
- #ifndef CYTHON_USE_EXC_INFO_STACK
+ #if PY_VERSION_HEX >= 0x030B00A4
+ #undef CYTHON_USE_EXC_INFO_STACK
+ #define CYTHON_USE_EXC_INFO_STACK 0
+ #elif !defined(CYTHON_USE_EXC_INFO_STACK)
#define CYTHON_USE_EXC_INFO_STACK (PY_VERSION_HEX >= 0x030700A3)
#endif
+ #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
+ #define CYTHON_UPDATE_DESCRIPTOR_DOC 1
+ #endif
#endif
#if !defined(CYTHON_FAST_PYCCALL)
#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1)
#endif
#if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
+ #if PY_MAJOR_VERSION < 3
+ #include "longintrepr.h"
+ #endif
#undef SHIFT
#undef BASE
#undef MASK
@@ -325,9 +390,68 @@ END: Cython Metadata */
#define __Pyx_DefaultClassType PyClass_Type
#else
#define __Pyx_BUILTIN_MODULE_NAME "builtins"
-#if PY_VERSION_HEX >= 0x030800A4 && PY_VERSION_HEX < 0x030800B2
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
- PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
+ #define __Pyx_DefaultClassType PyType_Type
+#if PY_VERSION_HEX >= 0x030B00A1
+ static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, int k, int l, int s, int f,
+ PyObject *code, PyObject *c, PyObject* n, PyObject *v,
+ PyObject *fv, PyObject *cell, PyObject* fn,
+ PyObject *name, int fline, PyObject *lnos) {
+ PyObject *kwds=NULL, *argcount=NULL, *posonlyargcount=NULL, *kwonlyargcount=NULL;
+ PyObject *nlocals=NULL, *stacksize=NULL, *flags=NULL, *replace=NULL, *call_result=NULL, *empty=NULL;
+ const char *fn_cstr=NULL;
+ const char *name_cstr=NULL;
+ PyCodeObject* co=NULL;
+ PyObject *type, *value, *traceback;
+ PyErr_Fetch(&type, &value, &traceback);
+ if (!(kwds=PyDict_New())) goto end;
+ if (!(argcount=PyLong_FromLong(a))) goto end;
+ if (PyDict_SetItemString(kwds, "co_argcount", argcount) != 0) goto end;
+ if (!(posonlyargcount=PyLong_FromLong(0))) goto end;
+ if (PyDict_SetItemString(kwds, "co_posonlyargcount", posonlyargcount) != 0) goto end;
+ if (!(kwonlyargcount=PyLong_FromLong(k))) goto end;
+ if (PyDict_SetItemString(kwds, "co_kwonlyargcount", kwonlyargcount) != 0) goto end;
+ if (!(nlocals=PyLong_FromLong(l))) goto end;
+ if (PyDict_SetItemString(kwds, "co_nlocals", nlocals) != 0) goto end;
+ if (!(stacksize=PyLong_FromLong(s))) goto end;
+ if (PyDict_SetItemString(kwds, "co_stacksize", stacksize) != 0) goto end;
+ if (!(flags=PyLong_FromLong(f))) goto end;
+ if (PyDict_SetItemString(kwds, "co_flags", flags) != 0) goto end;
+ if (PyDict_SetItemString(kwds, "co_code", code) != 0) goto end;
+ if (PyDict_SetItemString(kwds, "co_consts", c) != 0) goto end;
+ if (PyDict_SetItemString(kwds, "co_names", n) != 0) goto end;
+ if (PyDict_SetItemString(kwds, "co_varnames", v) != 0) goto end;
+ if (PyDict_SetItemString(kwds, "co_freevars", fv) != 0) goto end;
+ if (PyDict_SetItemString(kwds, "co_cellvars", cell) != 0) goto end;
+ if (PyDict_SetItemString(kwds, "co_linetable", lnos) != 0) goto end;
+ if (!(fn_cstr=PyUnicode_AsUTF8AndSize(fn, NULL))) goto end;
+ if (!(name_cstr=PyUnicode_AsUTF8AndSize(name, NULL))) goto end;
+ if (!(co = PyCode_NewEmpty(fn_cstr, name_cstr, fline))) goto end;
+ if (!(replace = PyObject_GetAttrString((PyObject*)co, "replace"))) goto cleanup_code_too;
+ if (!(empty = PyTuple_New(0))) goto cleanup_code_too; // unfortunately __pyx_empty_tuple isn't available here
+ if (!(call_result = PyObject_Call(replace, empty, kwds))) goto cleanup_code_too;
+ Py_XDECREF((PyObject*)co);
+ co = (PyCodeObject*)call_result;
+ call_result = NULL;
+ if (0) {
+ cleanup_code_too:
+ Py_XDECREF((PyObject*)co);
+ co = NULL;
+ }
+ end:
+ Py_XDECREF(kwds);
+ Py_XDECREF(argcount);
+ Py_XDECREF(posonlyargcount);
+ Py_XDECREF(kwonlyargcount);
+ Py_XDECREF(nlocals);
+ Py_XDECREF(stacksize);
+ Py_XDECREF(replace);
+ Py_XDECREF(call_result);
+ Py_XDECREF(empty);
+ if (type) {
+ PyErr_Restore(type, value, traceback);
+ }
+ return co;
+ }
#else
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
@@ -565,10 +689,10 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) {
#if PY_VERSION_HEX < 0x030200A4
typedef long Py_hash_t;
#define __Pyx_PyInt_FromHash_t PyInt_FromLong
- #define __Pyx_PyInt_AsHash_t PyInt_AsLong
+ #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsHash_t
#else
#define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
- #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
+ #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsSsize_t
#endif
#if PY_MAJOR_VERSION >= 3
#define __Pyx_PyMethod_New(func, self, klass) ((self) ? ((void)(klass), PyMethod_New(func, self)) : __Pyx_NewRef(func))
@@ -593,8 +717,10 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) {
} __Pyx_PyAsyncMethodsStruct;
#endif
-#if defined(WIN32) || defined(MS_WINDOWS)
- #define _USE_MATH_DEFINES
+#if defined(_WIN32) || defined(WIN32) || defined(MS_WINDOWS)
+ #if !defined(_USE_MATH_DEFINES)
+ #define _USE_MATH_DEFINES
+ #endif
#endif
#include <math.h>
#ifdef NAN
@@ -625,8 +751,8 @@ static CYTHON_INLINE float __PYX_NAN() {
#endif
#endif
-#define __PYX_HAVE__src__screening__gap_test_all
-#define __PYX_HAVE_API__src__screening__gap_test_all
+#define __PYX_HAVE__slopescreening__screening__gap_test_all
+#define __PYX_HAVE_API__slopescreening__screening__gap_test_all
/* Early includes */
#include <string.h>
#include <stdio.h>
@@ -734,6 +860,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x);
(likely(PyTuple_CheckExact(obj)) ? __Pyx_NewRef(obj) : PySequence_Tuple(obj))
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
+static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject*);
#if CYTHON_ASSUME_SAFE_MACROS
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
#else
@@ -868,10 +995,10 @@ static const char *__pyx_filename;
static const char *__pyx_f[] = {
- "src/screening/gap_test_all.pyx",
+ "slopescreening/screening/gap_test_all.pyx",
"stringsource",
- "venv/lib/python3.8/site-packages/numpy/__init__.pxd",
- "venv/lib/python3.8/site-packages/Cython/Includes/cpython/type.pxd",
+ "venv/lib/python3.10/site-packages/numpy/__init__.pxd",
+ "venv/lib/python3.10/site-packages/Cython/Includes/cpython/type.pxd",
};
/* BufferFormatStructs.proto */
#define IS_UNSIGNED(type) (((type) -1) > 0)
@@ -910,7 +1037,7 @@ typedef struct {
} __Pyx_BufFmt_Context;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":690
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":689
* # in Cython to enable them only on the right systems.
*
* ctypedef npy_int8 int8_t # <<<<<<<<<<<<<<
@@ -919,7 +1046,7 @@ typedef struct {
*/
typedef npy_int8 __pyx_t_5numpy_int8_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":691
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":690
*
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t # <<<<<<<<<<<<<<
@@ -928,7 +1055,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t;
*/
typedef npy_int16 __pyx_t_5numpy_int16_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":692
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":691
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t # <<<<<<<<<<<<<<
@@ -937,7 +1064,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t;
*/
typedef npy_int32 __pyx_t_5numpy_int32_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":693
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":692
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t
* ctypedef npy_int64 int64_t # <<<<<<<<<<<<<<
@@ -946,7 +1073,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t;
*/
typedef npy_int64 __pyx_t_5numpy_int64_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":697
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":696
* #ctypedef npy_int128 int128_t
*
* ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<<
@@ -955,7 +1082,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t;
*/
typedef npy_uint8 __pyx_t_5numpy_uint8_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":698
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":697
*
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<<
@@ -964,7 +1091,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t;
*/
typedef npy_uint16 __pyx_t_5numpy_uint16_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":699
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":698
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<<
@@ -973,7 +1100,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t;
*/
typedef npy_uint32 __pyx_t_5numpy_uint32_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":700
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":699
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t
* ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<<
@@ -982,7 +1109,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t;
*/
typedef npy_uint64 __pyx_t_5numpy_uint64_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":704
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":703
* #ctypedef npy_uint128 uint128_t
*
* ctypedef npy_float32 float32_t # <<<<<<<<<<<<<<
@@ -991,7 +1118,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t;
*/
typedef npy_float32 __pyx_t_5numpy_float32_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":705
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":704
*
* ctypedef npy_float32 float32_t
* ctypedef npy_float64 float64_t # <<<<<<<<<<<<<<
@@ -1000,7 +1127,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t;
*/
typedef npy_float64 __pyx_t_5numpy_float64_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":714
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":713
* # The int types are mapped a bit surprising --
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t # <<<<<<<<<<<<<<
@@ -1009,7 +1136,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t;
*/
typedef npy_long __pyx_t_5numpy_int_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":715
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":714
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t # <<<<<<<<<<<<<<
@@ -1018,7 +1145,7 @@ typedef npy_long __pyx_t_5numpy_int_t;
*/
typedef npy_longlong __pyx_t_5numpy_long_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":716
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":715
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t
* ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<<
@@ -1027,7 +1154,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t;
*/
typedef npy_longlong __pyx_t_5numpy_longlong_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":718
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":717
* ctypedef npy_longlong longlong_t
*
* ctypedef npy_ulong uint_t # <<<<<<<<<<<<<<
@@ -1036,7 +1163,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t;
*/
typedef npy_ulong __pyx_t_5numpy_uint_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":719
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":718
*
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<<
@@ -1045,7 +1172,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t;
*/
typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":720
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":719
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t
* ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<<
@@ -1054,7 +1181,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
*/
typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":722
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":721
* ctypedef npy_ulonglong ulonglong_t
*
* ctypedef npy_intp intp_t # <<<<<<<<<<<<<<
@@ -1063,7 +1190,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
*/
typedef npy_intp __pyx_t_5numpy_intp_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":723
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":722
*
* ctypedef npy_intp intp_t
* ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<<
@@ -1072,7 +1199,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t;
*/
typedef npy_uintp __pyx_t_5numpy_uintp_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":725
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":724
* ctypedef npy_uintp uintp_t
*
* ctypedef npy_double float_t # <<<<<<<<<<<<<<
@@ -1081,7 +1208,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t;
*/
typedef npy_double __pyx_t_5numpy_float_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":726
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":725
*
* ctypedef npy_double float_t
* ctypedef npy_double double_t # <<<<<<<<<<<<<<
@@ -1090,7 +1217,7 @@ typedef npy_double __pyx_t_5numpy_float_t;
*/
typedef npy_double __pyx_t_5numpy_double_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":727
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":726
* ctypedef npy_double float_t
* ctypedef npy_double double_t
* ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<<
@@ -1099,14 +1226,14 @@ typedef npy_double __pyx_t_5numpy_double_t;
*/
typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
-/* "src/screening/gap_test_all.pyx":18
+/* "slopescreening/screening/gap_test_all.pyx":18
* from cpython.mem cimport PyMem_Malloc, PyMem_Realloc, PyMem_Free
*
* ctypedef np.npy_bool bool_t # <<<<<<<<<<<<<<
*
*
*/
-typedef npy_bool __pyx_t_3src_9screening_12gap_test_all_bool_t;
+typedef npy_bool __pyx_t_14slopescreening_9screening_12gap_test_all_bool_t;
/* Declarations.proto */
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
@@ -1133,9 +1260,9 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do
/*--- Type declarations ---*/
-struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll;
+struct __pyx_obj_14slopescreening_9screening_12gap_test_all_GapTestAll;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":729
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":728
* ctypedef npy_longdouble longdouble_t
*
* ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<<
@@ -1144,7 +1271,7 @@ struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll;
*/
typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":730
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":729
*
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<<
@@ -1153,7 +1280,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
*/
typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":731
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":730
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t
* ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<<
@@ -1162,7 +1289,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
*/
typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":733
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":732
* ctypedef npy_clongdouble clongdouble_t
*
* ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<<
@@ -1171,14 +1298,14 @@ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
*/
typedef npy_cdouble __pyx_t_5numpy_complex_t;
-/* "src/screening/gap_test_all.pyx":21
+/* "slopescreening/screening/gap_test_all.pyx":21
*
*
* cdef class GapTestAll: # <<<<<<<<<<<<<<
* """ Generalized test
* """
*/
-struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll {
+struct __pyx_obj_14slopescreening_9screening_12gap_test_all_GapTestAll {
PyObject_HEAD
double *vec_cumsum_gammas;
char *name;
@@ -1403,13 +1530,21 @@ static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args,
#ifndef Py_MEMBER_SIZE
#define Py_MEMBER_SIZE(type, member) sizeof(((type *)0)->member)
#endif
+#if CYTHON_FAST_PYCALL
static size_t __pyx_pyframe_localsplus_offset = 0;
#include "frameobject.h"
+#if PY_VERSION_HEX >= 0x030b00a6
+ #ifndef Py_BUILD_CORE
+ #define Py_BUILD_CORE 1
+ #endif
+ #include "internal/pycore_frame.h"
+#endif
#define __Pxy_PyFrame_Initialize_Offsets()\
((void)__Pyx_BUILD_ASSERT_EXPR(sizeof(PyFrameObject) == offsetof(PyFrameObject, f_localsplus) + Py_MEMBER_SIZE(PyFrameObject, f_localsplus)),\
(void)(__pyx_pyframe_localsplus_offset = ((size_t)PyFrame_Type.tp_basicsize) - Py_MEMBER_SIZE(PyFrameObject, f_localsplus)))
#define __Pyx_PyFrame_GetLocalsplus(frame)\
(assert(__pyx_pyframe_localsplus_offset), (PyObject **)(((char *)(frame)) + __pyx_pyframe_localsplus_offset))
+#endif // CYTHON_FAST_PYCALL
#endif
/* PyObjectCall.proto */
@@ -1775,17 +1910,17 @@ static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0;
/* Module declarations from 'cython' */
-/* Module declarations from 'src.screening.gap_test_all' */
-static PyTypeObject *__pyx_ptype_3src_9screening_12gap_test_all_GapTestAll = 0;
+/* Module declarations from 'slopescreening.screening.gap_test_all' */
+static PyTypeObject *__pyx_ptype_14slopescreening_9screening_12gap_test_all_GapTestAll = 0;
static __Pyx_TypeInfo __Pyx_TypeInfo_nn_npy_double = { "npy_double", NULL, sizeof(npy_double), { 0 }, 0, 'R', 0, 0 };
static __Pyx_TypeInfo __Pyx_TypeInfo_long = { "long", NULL, sizeof(long), { 0 }, 0, IS_UNSIGNED(long) ? 'U' : 'I', IS_UNSIGNED(long), 0 };
static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_int_t = { "int_t", NULL, sizeof(__pyx_t_5numpy_int_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_5numpy_int_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_5numpy_int_t), 0 };
static __Pyx_TypeInfo __Pyx_TypeInfo_nn_npy_bool = { "npy_bool", NULL, sizeof(npy_bool), { 0 }, 0, IS_UNSIGNED(npy_bool) ? 'U' : 'I', IS_UNSIGNED(npy_bool), 0 };
-#define __Pyx_MODULE_NAME "src.screening.gap_test_all"
-extern int __pyx_module_is_main_src__screening__gap_test_all;
-int __pyx_module_is_main_src__screening__gap_test_all = 0;
+#define __Pyx_MODULE_NAME "slopescreening.screening.gap_test_all"
+extern int __pyx_module_is_main_slopescreening__screening__gap_test_all;
+int __pyx_module_is_main_slopescreening__screening__gap_test_all = 0;
-/* Implementation of 'src.screening.gap_test_all' */
+/* Implementation of 'slopescreening.screening.gap_test_all' */
static PyObject *__pyx_builtin_range;
static PyObject *__pyx_builtin_TypeError;
static PyObject *__pyx_builtin_ImportError;
@@ -1820,10 +1955,10 @@ static const char __pyx_k_setstate_cython[] = "__setstate_cython__";
static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback";
static const char __pyx_k_coeff_dual_scaling[] = "coeff_dual_scaling";
static const char __pyx_k_AbstractGapScreening[] = "AbstractGapScreening";
-static const char __pyx_k_src_screening_ascreening[] = "src.screening.ascreening";
static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import";
static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import";
static const char __pyx_k_self_vec_cumsum_gammas_cannot_be[] = "self.vec_cumsum_gammas cannot be converted to a Python object for pickling";
+static const char __pyx_k_slopescreening_screening_ascreen[] = "slopescreening.screening.ascreening";
static PyObject *__pyx_n_s_AbstractGapScreening;
static PyObject *__pyx_n_s_Atcabs;
static PyObject *__pyx_n_s_GapTestAll;
@@ -1854,17 +1989,17 @@ static PyObject *__pyx_n_s_reduce_ex;
static PyObject *__pyx_kp_s_self_vec_cumsum_gammas_cannot_be;
static PyObject *__pyx_n_s_setstate;
static PyObject *__pyx_n_s_setstate_cython;
+static PyObject *__pyx_n_s_slopescreening_screening_ascreen;
static PyObject *__pyx_n_s_sqrt;
-static PyObject *__pyx_n_s_src_screening_ascreening;
static PyObject *__pyx_n_s_test;
static PyObject *__pyx_n_s_vec_gammas;
static PyObject *__pyx_n_s_zeros;
-static int __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll___init__(struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *__pyx_v_self, PyArrayObject *__pyx_v_vec_gammas); /* proto */
-static void __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_2__dealloc__(struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_test(CYTHON_UNUSED struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *__pyx_v_self, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_gap, double __pyx_v_lbd, PyArrayObject *__pyx_v_vec_gammas, double __pyx_v_coeff_dual_scaling, double __pyx_v_offset_radius, PyArrayObject *__pyx_v_index); /* proto */
-static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_6__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_8__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
-static PyObject *__pyx_tp_new_3src_9screening_12gap_test_all_GapTestAll(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
+static int __pyx_pf_14slopescreening_9screening_12gap_test_all_10GapTestAll___init__(struct __pyx_obj_14slopescreening_9screening_12gap_test_all_GapTestAll *__pyx_v_self, PyArrayObject *__pyx_v_vec_gammas); /* proto */
+static void __pyx_pf_14slopescreening_9screening_12gap_test_all_10GapTestAll_2__dealloc__(struct __pyx_obj_14slopescreening_9screening_12gap_test_all_GapTestAll *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_14slopescreening_9screening_12gap_test_all_10GapTestAll_4apply_test(CYTHON_UNUSED struct __pyx_obj_14slopescreening_9screening_12gap_test_all_GapTestAll *__pyx_v_self, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_gap, double __pyx_v_lbd, PyArrayObject *__pyx_v_vec_gammas, double __pyx_v_coeff_dual_scaling, double __pyx_v_offset_radius, PyArrayObject *__pyx_v_index); /* proto */
+static PyObject *__pyx_pf_14slopescreening_9screening_12gap_test_all_10GapTestAll_6__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_14slopescreening_9screening_12gap_test_all_GapTestAll *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_14slopescreening_9screening_12gap_test_all_10GapTestAll_8__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_14slopescreening_9screening_12gap_test_all_GapTestAll *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
+static PyObject *__pyx_tp_new_14slopescreening_9screening_12gap_test_all_GapTestAll(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_int_0;
static PyObject *__pyx_int_1;
static PyObject *__pyx_int_neg_1;
@@ -1875,7 +2010,7 @@ static PyObject *__pyx_tuple__4;
static PyObject *__pyx_tuple__5;
/* Late includes */
-/* "src/screening/gap_test_all.pyx":30
+/* "slopescreening/screening/gap_test_all.pyx":30
* @cython.boundscheck(False) # turn off bounds-checking for entire function
* @cython.wraparound(False) # turn off negative index wrapping for entire function
* def __init__( # <<<<<<<<<<<<<<
@@ -1884,8 +2019,8 @@ static PyObject *__pyx_tuple__5;
*/
/* Python wrapper */
-static int __pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static int __pyx_pw_14slopescreening_9screening_12gap_test_all_10GapTestAll_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_14slopescreening_9screening_12gap_test_all_10GapTestAll_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyArrayObject *__pyx_v_vec_gammas = 0;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
@@ -1925,12 +2060,12 @@ static int __pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_1__init__(PyObje
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 30, __pyx_L3_error)
__pyx_L3_error:;
- __Pyx_AddTraceback("src.screening.gap_test_all.GapTestAll.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("slopescreening.screening.gap_test_all.GapTestAll.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_vec_gammas), __pyx_ptype_5numpy_ndarray, 1, "vec_gammas", 0))) __PYX_ERR(0, 31, __pyx_L1_error)
- __pyx_r = __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll___init__(((struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *)__pyx_v_self), __pyx_v_vec_gammas);
+ __pyx_r = __pyx_pf_14slopescreening_9screening_12gap_test_all_10GapTestAll___init__(((struct __pyx_obj_14slopescreening_9screening_12gap_test_all_GapTestAll *)__pyx_v_self), __pyx_v_vec_gammas);
/* function exit code */
goto __pyx_L0;
@@ -1941,7 +2076,7 @@ static int __pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_1__init__(PyObje
return __pyx_r;
}
-static int __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll___init__(struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *__pyx_v_self, PyArrayObject *__pyx_v_vec_gammas) {
+static int __pyx_pf_14slopescreening_9screening_12gap_test_all_10GapTestAll___init__(struct __pyx_obj_14slopescreening_9screening_12gap_test_all_GapTestAll *__pyx_v_self, PyArrayObject *__pyx_v_vec_gammas) {
int __pyx_v_n;
int __pyx_v_i;
__Pyx_LocalBuf_ND __pyx_pybuffernd_vec_gammas;
@@ -1966,7 +2101,7 @@ static int __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll___init__(struct
}
__pyx_pybuffernd_vec_gammas.diminfo[0].strides = __pyx_pybuffernd_vec_gammas.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_vec_gammas.diminfo[0].shape = __pyx_pybuffernd_vec_gammas.rcbuffer->pybuffer.shape[0];
- /* "src/screening/gap_test_all.pyx":34
+ /* "slopescreening/screening/gap_test_all.pyx":34
* ):
*
* cdef int n = vec_gammas.shape[0] # <<<<<<<<<<<<<<
@@ -1975,7 +2110,7 @@ static int __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll___init__(struct
*/
__pyx_v_n = (__pyx_v_vec_gammas->dimensions[0]);
- /* "src/screening/gap_test_all.pyx":37
+ /* "slopescreening/screening/gap_test_all.pyx":37
* cdef int i
*
* self.vec_cumsum_gammas = <double*> PyMem_Malloc((n+1) * sizeof(double)) # <<<<<<<<<<<<<<
@@ -1984,7 +2119,7 @@ static int __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll___init__(struct
*/
__pyx_v_self->vec_cumsum_gammas = ((double *)PyMem_Malloc(((__pyx_v_n + 1) * (sizeof(double)))));
- /* "src/screening/gap_test_all.pyx":38
+ /* "slopescreening/screening/gap_test_all.pyx":38
*
* self.vec_cumsum_gammas = <double*> PyMem_Malloc((n+1) * sizeof(double))
* self.vec_cumsum_gammas[0] = 0 # <<<<<<<<<<<<<<
@@ -1993,7 +2128,7 @@ static int __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll___init__(struct
*/
(__pyx_v_self->vec_cumsum_gammas[0]) = 0.0;
- /* "src/screening/gap_test_all.pyx":40
+ /* "slopescreening/screening/gap_test_all.pyx":40
* self.vec_cumsum_gammas[0] = 0
*
* for i in range(n): # <<<<<<<<<<<<<<
@@ -2005,7 +2140,7 @@ static int __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll___init__(struct
for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
__pyx_v_i = __pyx_t_3;
- /* "src/screening/gap_test_all.pyx":41
+ /* "slopescreening/screening/gap_test_all.pyx":41
*
* for i in range(n):
* self.vec_cumsum_gammas[i+1] = self.vec_cumsum_gammas[i] + vec_gammas[i] # <<<<<<<<<<<<<<
@@ -2016,7 +2151,7 @@ static int __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll___init__(struct
(__pyx_v_self->vec_cumsum_gammas[(__pyx_v_i + 1)]) = ((__pyx_v_self->vec_cumsum_gammas[__pyx_v_i]) + (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_gammas.rcbuffer->pybuffer.buf, __pyx_t_4, __pyx_pybuffernd_vec_gammas.diminfo[0].strides)));
}
- /* "src/screening/gap_test_all.pyx":49
+ /* "slopescreening/screening/gap_test_all.pyx":49
* # self.vec_cumsum_gammas = &buf[0]
*
* self.name = "GAP test-all (cython)" # <<<<<<<<<<<<<<
@@ -2025,7 +2160,7 @@ static int __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll___init__(struct
*/
__pyx_v_self->name = ((char *)"GAP test-all (cython)");
- /* "src/screening/gap_test_all.pyx":30
+ /* "slopescreening/screening/gap_test_all.pyx":30
* @cython.boundscheck(False) # turn off bounds-checking for entire function
* @cython.wraparound(False) # turn off negative index wrapping for entire function
* def __init__( # <<<<<<<<<<<<<<
@@ -2043,7 +2178,7 @@ static int __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll___init__(struct
__Pyx_ErrFetch(&__pyx_type, &__pyx_value, &__pyx_tb);
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_vec_gammas.rcbuffer->pybuffer);
__Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);}
- __Pyx_AddTraceback("src.screening.gap_test_all.GapTestAll.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("slopescreening.screening.gap_test_all.GapTestAll.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
goto __pyx_L2;
__pyx_L0:;
@@ -2053,7 +2188,7 @@ static int __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll___init__(struct
return __pyx_r;
}
-/* "src/screening/gap_test_all.pyx":52
+/* "slopescreening/screening/gap_test_all.pyx":52
*
*
* def __dealloc__(self): # <<<<<<<<<<<<<<
@@ -2062,21 +2197,21 @@ static int __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll___init__(struct
*/
/* Python wrapper */
-static void __pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_3__dealloc__(PyObject *__pyx_v_self) {
+static void __pyx_pw_14slopescreening_9screening_12gap_test_all_10GapTestAll_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_14slopescreening_9screening_12gap_test_all_10GapTestAll_3__dealloc__(PyObject *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
- __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_2__dealloc__(((struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *)__pyx_v_self));
+ __pyx_pf_14slopescreening_9screening_12gap_test_all_10GapTestAll_2__dealloc__(((struct __pyx_obj_14slopescreening_9screening_12gap_test_all_GapTestAll *)__pyx_v_self));
/* function exit code */
__Pyx_RefNannyFinishContext();
}
-static void __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_2__dealloc__(struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *__pyx_v_self) {
+static void __pyx_pf_14slopescreening_9screening_12gap_test_all_10GapTestAll_2__dealloc__(struct __pyx_obj_14slopescreening_9screening_12gap_test_all_GapTestAll *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__dealloc__", 0);
- /* "src/screening/gap_test_all.pyx":53
+ /* "slopescreening/screening/gap_test_all.pyx":53
*
* def __dealloc__(self):
* PyMem_Free(self.vec_cumsum_gammas) # no-op if self.data is NULL # <<<<<<<<<<<<<<
@@ -2085,7 +2220,7 @@ static void __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_2__dealloc__(st
*/
PyMem_Free(__pyx_v_self->vec_cumsum_gammas);
- /* "src/screening/gap_test_all.pyx":52
+ /* "slopescreening/screening/gap_test_all.pyx":52
*
*
* def __dealloc__(self): # <<<<<<<<<<<<<<
@@ -2097,7 +2232,7 @@ static void __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_2__dealloc__(st
__Pyx_RefNannyFinishContext();
}
-/* "src/screening/gap_test_all.pyx":58
+/* "slopescreening/screening/gap_test_all.pyx":58
* @cython.boundscheck(False) # turn off bounds-checking for entire function
* # @cython.wraparound(False) # turn off negative index wrapping for entire function
* def apply_test(self, # <<<<<<<<<<<<<<
@@ -2106,9 +2241,9 @@ static void __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_2__dealloc__(st
*/
/* Python wrapper */
-static PyObject *__pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_5apply_test(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_3src_9screening_12gap_test_all_10GapTestAll_4apply_test[] = " Apply the Gap safe sphere screening test\n\n Implementation of the safe screening test\n \n Parameters\n ----------\n Atcabs : np.ndarray\n vector matA.T @ vecc where vec is dual admissible in absolute value\n size [n]\n gap : positive float\n duality gap\n lbd : positive float\n regularization parameters\n vec_gammas : np.ndarray\n slope parameters\n size [n,]\n coeff_dual_scaling : positif float\n If coeff_dual_scaling is not feasible, dual scaling factor\n such taht vecu / coeff_dual_scaling os dual feasible\n Here for code optimization purposes\n Default value is 1. (vecu is feasible)\n offset_radius : float\n additive term added to the redius\n default is 0\n index : np.ndarray\n Array of indices that sort Atu in absolute value\n default is None\n \n Returns\n -------\n calI_screen : np.ndarray\n vector of boolean\n True if screening test passes and False otherwise\n size [n,]\n ";
-static PyObject *__pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_5apply_test(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pw_14slopescreening_9screening_12gap_test_all_10GapTestAll_5apply_test(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_14slopescreening_9screening_12gap_test_all_10GapTestAll_4apply_test[] = " Apply the Gap safe sphere screening test\n\n Implementation of the safe screening test\n \n Parameters\n ----------\n Atcabs : np.ndarray\n vector matA.T @ vecc where vec is dual admissible in absolute value\n size [n]\n gap : positive float\n duality gap\n lbd : positive float\n regularization parameters\n vec_gammas : np.ndarray\n slope parameters\n size [n,]\n coeff_dual_scaling : positif float\n If coeff_dual_scaling is not feasible, dual scaling factor\n such taht vecu / coeff_dual_scaling os dual feasible\n Here for code optimization purposes\n Default value is 1. (vecu is feasible)\n offset_radius : float\n additive term added to the redius\n default is 0\n index : np.ndarray\n Array of indices that sort Atu in absolute value\n default is None\n \n Returns\n -------\n calI_screen : np.ndarray\n vector of boolean\n True if screening test passes and False otherwise\n size [n,]\n ";
+static PyObject *__pyx_pw_14slopescreening_9screening_12gap_test_all_10GapTestAll_5apply_test(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyArrayObject *__pyx_v_Atcabs = 0;
double __pyx_v_gap;
double __pyx_v_lbd;
@@ -2126,7 +2261,7 @@ static PyObject *__pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_5apply_tes
static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_Atcabs,&__pyx_n_s_gap,&__pyx_n_s_lbd,&__pyx_n_s_vec_gammas,&__pyx_n_s_coeff_dual_scaling,&__pyx_n_s_offset_radius,&__pyx_n_s_index,0};
PyObject* values[7] = {0,0,0,0,0,0,0};
- /* "src/screening/gap_test_all.pyx":65
+ /* "slopescreening/screening/gap_test_all.pyx":65
* double coeff_dual_scaling =1.,
* double offset_radius=0.,
* np.ndarray[long, ndim=1] index=None # <<<<<<<<<<<<<<
@@ -2236,16 +2371,16 @@ static PyObject *__pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_5apply_tes
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("apply_test", 0, 4, 7, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 58, __pyx_L3_error)
__pyx_L3_error:;
- __Pyx_AddTraceback("src.screening.gap_test_all.GapTestAll.apply_test", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("slopescreening.screening.gap_test_all.GapTestAll.apply_test", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_Atcabs), __pyx_ptype_5numpy_ndarray, 1, "Atcabs", 0))) __PYX_ERR(0, 59, __pyx_L1_error)
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_vec_gammas), __pyx_ptype_5numpy_ndarray, 1, "vec_gammas", 0))) __PYX_ERR(0, 62, __pyx_L1_error)
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_index), __pyx_ptype_5numpy_ndarray, 1, "index", 0))) __PYX_ERR(0, 65, __pyx_L1_error)
- __pyx_r = __pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_test(((struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *)__pyx_v_self), __pyx_v_Atcabs, __pyx_v_gap, __pyx_v_lbd, __pyx_v_vec_gammas, __pyx_v_coeff_dual_scaling, __pyx_v_offset_radius, __pyx_v_index);
+ __pyx_r = __pyx_pf_14slopescreening_9screening_12gap_test_all_10GapTestAll_4apply_test(((struct __pyx_obj_14slopescreening_9screening_12gap_test_all_GapTestAll *)__pyx_v_self), __pyx_v_Atcabs, __pyx_v_gap, __pyx_v_lbd, __pyx_v_vec_gammas, __pyx_v_coeff_dual_scaling, __pyx_v_offset_radius, __pyx_v_index);
- /* "src/screening/gap_test_all.pyx":58
+ /* "slopescreening/screening/gap_test_all.pyx":58
* @cython.boundscheck(False) # turn off bounds-checking for entire function
* # @cython.wraparound(False) # turn off negative index wrapping for entire function
* def apply_test(self, # <<<<<<<<<<<<<<
@@ -2262,7 +2397,7 @@ static PyObject *__pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_5apply_tes
return __pyx_r;
}
-static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_test(CYTHON_UNUSED struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll *__pyx_v_self, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_gap, double __pyx_v_lbd, PyArrayObject *__pyx_v_vec_gammas, double __pyx_v_coeff_dual_scaling, double __pyx_v_offset_radius, PyArrayObject *__pyx_v_index) {
+static PyObject *__pyx_pf_14slopescreening_9screening_12gap_test_all_10GapTestAll_4apply_test(CYTHON_UNUSED struct __pyx_obj_14slopescreening_9screening_12gap_test_all_GapTestAll *__pyx_v_self, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_gap, double __pyx_v_lbd, PyArrayObject *__pyx_v_vec_gammas, double __pyx_v_coeff_dual_scaling, double __pyx_v_offset_radius, PyArrayObject *__pyx_v_index) {
double __pyx_v_radius;
PyArrayObject *__pyx_v_coeff_lbd_gamma = 0;
int __pyx_v_n;
@@ -2374,7 +2509,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
}
__pyx_pybuffernd_index.diminfo[0].strides = __pyx_pybuffernd_index.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_index.diminfo[0].shape = __pyx_pybuffernd_index.rcbuffer->pybuffer.shape[0];
- /* "src/screening/gap_test_all.pyx":107
+ /* "slopescreening/screening/gap_test_all.pyx":107
* # in order to match the paper indexation rules
*
* cdef double radius = coeff_dual_scaling * np.sqrt(2 * gap) + offset_radius # <<<<<<<<<<<<<<
@@ -2420,7 +2555,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_radius = __pyx_t_6;
- /* "src/screening/gap_test_all.pyx":109
+ /* "slopescreening/screening/gap_test_all.pyx":109
* cdef double radius = coeff_dual_scaling * np.sqrt(2 * gap) + offset_radius
* # cdef double lbd_aug = coeff_dual_scaling * lbd
* cdef np.ndarray[np.npy_double, ndim=1] coeff_lbd_gamma = coeff_dual_scaling * lbd * vec_gammas # <<<<<<<<<<<<<<
@@ -2446,7 +2581,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
__pyx_v_coeff_lbd_gamma = ((PyArrayObject *)__pyx_t_2);
__pyx_t_2 = 0;
- /* "src/screening/gap_test_all.pyx":111
+ /* "slopescreening/screening/gap_test_all.pyx":111
* cdef np.ndarray[np.npy_double, ndim=1] coeff_lbd_gamma = coeff_dual_scaling * lbd * vec_gammas
*
* cdef int n = Atcabs.shape[0] # <<<<<<<<<<<<<<
@@ -2455,7 +2590,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
*/
__pyx_v_n = (__pyx_v_Atcabs->dimensions[0]);
- /* "src/screening/gap_test_all.pyx":113
+ /* "slopescreening/screening/gap_test_all.pyx":113
* cdef int n = Atcabs.shape[0]
* cdef int k, q, r
* cdef double tau = 0 # <<<<<<<<<<<<<<
@@ -2464,7 +2599,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
*/
__pyx_v_tau = 0.0;
- /* "src/screening/gap_test_all.pyx":117
+ /* "slopescreening/screening/gap_test_all.pyx":117
*
* # arange because I want entries 0, 1 being 0 and 1!
* cdef np.ndarray[np.int_t, ndim=1] vec_p_star = np.arange(n+1, dtype=long) # <<<<<<<<<<<<<<
@@ -2505,7 +2640,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
__pyx_v_vec_p_star = ((PyArrayObject *)__pyx_t_3);
__pyx_t_3 = 0;
- /* "src/screening/gap_test_all.pyx":118
+ /* "slopescreening/screening/gap_test_all.pyx":118
* # arange because I want entries 0, 1 being 0 and 1!
* cdef np.ndarray[np.int_t, ndim=1] vec_p_star = np.arange(n+1, dtype=long)
* cdef np.ndarray[np.int_t, ndim=1] vec_q_star = np.arange(n+1, dtype=long) # <<<<<<<<<<<<<<
@@ -2546,7 +2681,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
__pyx_v_vec_q_star = ((PyArrayObject *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "src/screening/gap_test_all.pyx":121
+ /* "slopescreening/screening/gap_test_all.pyx":121
*
* # output
* cdef np.ndarray[np.npy_bool, ndim=1] calI_screen = np.zeros(n, dtype=bool) # <<<<<<<<<<<<<<
@@ -2587,7 +2722,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
__pyx_v_calI_screen = ((PyArrayObject *)__pyx_t_2);
__pyx_t_2 = 0;
- /* "src/screening/gap_test_all.pyx":124
+ /* "slopescreening/screening/gap_test_all.pyx":124
*
* # 1. Sort in descending order
* if index is None: # <<<<<<<<<<<<<<
@@ -2598,7 +2733,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
__pyx_t_12 = (__pyx_t_11 != 0);
if (__pyx_t_12) {
- /* "src/screening/gap_test_all.pyx":125
+ /* "slopescreening/screening/gap_test_all.pyx":125
* # 1. Sort in descending order
* if index is None:
* index = np.argsort(Atcabs)[::-1] # <<<<<<<<<<<<<<
@@ -2651,7 +2786,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
__Pyx_DECREF_SET(__pyx_v_index, ((PyArrayObject *)__pyx_t_4));
__pyx_t_4 = 0;
- /* "src/screening/gap_test_all.pyx":124
+ /* "slopescreening/screening/gap_test_all.pyx":124
*
* # 1. Sort in descending order
* if index is None: # <<<<<<<<<<<<<<
@@ -2660,7 +2795,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
*/
}
- /* "src/screening/gap_test_all.pyx":128
+ /* "slopescreening/screening/gap_test_all.pyx":128
*
* # 2. Precomputing quantities
* cdef np.ndarray[np.npy_double, ndim=1] vec_f = np.cumsum( # <<<<<<<<<<<<<<
@@ -2673,7 +2808,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "src/screening/gap_test_all.pyx":129
+ /* "slopescreening/screening/gap_test_all.pyx":129
* # 2. Precomputing quantities
* cdef np.ndarray[np.npy_double, ndim=1] vec_f = np.cumsum(
* coeff_lbd_gamma[::-1] - Atcabs[index[::-1]] - radius # <<<<<<<<<<<<<<
@@ -2714,7 +2849,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "src/screening/gap_test_all.pyx":130
+ /* "slopescreening/screening/gap_test_all.pyx":130
* cdef np.ndarray[np.npy_double, ndim=1] vec_f = np.cumsum(
* coeff_lbd_gamma[::-1] - Atcabs[index[::-1]] - radius
* )[::-1] # <<<<<<<<<<<<<<
@@ -2738,7 +2873,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
__pyx_v_vec_f = ((PyArrayObject *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "src/screening/gap_test_all.pyx":132
+ /* "slopescreening/screening/gap_test_all.pyx":132
* )[::-1]
*
* cdef double best_bound_q = vec_f[0] - coeff_lbd_gamma[0] # <<<<<<<<<<<<<<
@@ -2751,7 +2886,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_pybuffernd_coeff_lbd_gamma.diminfo[0].shape;
__pyx_v_best_bound_q = ((*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_f.rcbuffer->pybuffer.buf, __pyx_t_19, __pyx_pybuffernd_vec_f.diminfo[0].strides)) - (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_coeff_lbd_gamma.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_coeff_lbd_gamma.diminfo[0].strides)));
- /* "src/screening/gap_test_all.pyx":133
+ /* "slopescreening/screening/gap_test_all.pyx":133
*
* cdef double best_bound_q = vec_f[0] - coeff_lbd_gamma[0]
* cdef double curr_bound_q = 0. # <<<<<<<<<<<<<<
@@ -2760,7 +2895,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
*/
__pyx_v_curr_bound_q = 0.;
- /* "src/screening/gap_test_all.pyx":134
+ /* "slopescreening/screening/gap_test_all.pyx":134
* cdef double best_bound_q = vec_f[0] - coeff_lbd_gamma[0]
* cdef double curr_bound_q = 0.
* cdef double best_bound_p = vec_f[0] # <<<<<<<<<<<<<<
@@ -2771,7 +2906,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_pybuffernd_vec_f.diminfo[0].shape;
__pyx_v_best_bound_p = (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_f.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_vec_f.diminfo[0].strides));
- /* "src/screening/gap_test_all.pyx":135
+ /* "slopescreening/screening/gap_test_all.pyx":135
* cdef double curr_bound_q = 0.
* cdef double best_bound_p = vec_f[0]
* cdef double curr_bound_p = 0. # <<<<<<<<<<<<<<
@@ -2780,7 +2915,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
*/
__pyx_v_curr_bound_p = 0.;
- /* "src/screening/gap_test_all.pyx":136
+ /* "slopescreening/screening/gap_test_all.pyx":136
* cdef double best_bound_p = vec_f[0]
* cdef double curr_bound_p = 0.
* for k in range(2, n+1): # <<<<<<<<<<<<<<
@@ -2792,7 +2927,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
for (__pyx_t_14 = 2; __pyx_t_14 < __pyx_t_22; __pyx_t_14+=1) {
__pyx_v_k = __pyx_t_14;
- /* "src/screening/gap_test_all.pyx":140
+ /* "slopescreening/screening/gap_test_all.pyx":140
*
* # 1. Evaluate p*
* curr_bound_p = vec_f[k-1] # <<<<<<<<<<<<<<
@@ -2803,7 +2938,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_pybuffernd_vec_f.diminfo[0].shape;
__pyx_v_curr_bound_p = (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_f.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_vec_f.diminfo[0].strides));
- /* "src/screening/gap_test_all.pyx":141
+ /* "slopescreening/screening/gap_test_all.pyx":141
* # 1. Evaluate p*
* curr_bound_p = vec_f[k-1]
* if curr_bound_p > best_bound_p: # <<<<<<<<<<<<<<
@@ -2813,7 +2948,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
__pyx_t_12 = ((__pyx_v_curr_bound_p > __pyx_v_best_bound_p) != 0);
if (__pyx_t_12) {
- /* "src/screening/gap_test_all.pyx":142
+ /* "slopescreening/screening/gap_test_all.pyx":142
* curr_bound_p = vec_f[k-1]
* if curr_bound_p > best_bound_p:
* best_bound_p = curr_bound_p # <<<<<<<<<<<<<<
@@ -2822,7 +2957,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
*/
__pyx_v_best_bound_p = __pyx_v_curr_bound_p;
- /* "src/screening/gap_test_all.pyx":143
+ /* "slopescreening/screening/gap_test_all.pyx":143
* if curr_bound_p > best_bound_p:
* best_bound_p = curr_bound_p
* vec_p_star[k] = k # <<<<<<<<<<<<<<
@@ -2833,7 +2968,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_pybuffernd_vec_p_star.diminfo[0].shape;
*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int_t *, __pyx_pybuffernd_vec_p_star.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_vec_p_star.diminfo[0].strides) = __pyx_v_k;
- /* "src/screening/gap_test_all.pyx":141
+ /* "slopescreening/screening/gap_test_all.pyx":141
* # 1. Evaluate p*
* curr_bound_p = vec_f[k-1]
* if curr_bound_p > best_bound_p: # <<<<<<<<<<<<<<
@@ -2843,7 +2978,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
goto __pyx_L6;
}
- /* "src/screening/gap_test_all.pyx":145
+ /* "slopescreening/screening/gap_test_all.pyx":145
* vec_p_star[k] = k
* else:
* vec_p_star[k] = vec_p_star[k-1] # <<<<<<<<<<<<<<
@@ -2859,7 +2994,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
}
__pyx_L6:;
- /* "src/screening/gap_test_all.pyx":148
+ /* "slopescreening/screening/gap_test_all.pyx":148
*
* # 1. Evaluate q*
* curr_bound_q = vec_f[k-1] - coeff_lbd_gamma[k-1] # <<<<<<<<<<<<<<
@@ -2872,7 +3007,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
if (__pyx_t_19 < 0) __pyx_t_19 += __pyx_pybuffernd_coeff_lbd_gamma.diminfo[0].shape;
__pyx_v_curr_bound_q = ((*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_f.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_vec_f.diminfo[0].strides)) - (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_coeff_lbd_gamma.rcbuffer->pybuffer.buf, __pyx_t_19, __pyx_pybuffernd_coeff_lbd_gamma.diminfo[0].strides)));
- /* "src/screening/gap_test_all.pyx":149
+ /* "slopescreening/screening/gap_test_all.pyx":149
* # 1. Evaluate q*
* curr_bound_q = vec_f[k-1] - coeff_lbd_gamma[k-1]
* if curr_bound_q > best_bound_q: # <<<<<<<<<<<<<<
@@ -2882,7 +3017,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
__pyx_t_12 = ((__pyx_v_curr_bound_q > __pyx_v_best_bound_q) != 0);
if (__pyx_t_12) {
- /* "src/screening/gap_test_all.pyx":150
+ /* "slopescreening/screening/gap_test_all.pyx":150
* curr_bound_q = vec_f[k-1] - coeff_lbd_gamma[k-1]
* if curr_bound_q > best_bound_q:
* best_bound_q = curr_bound_q # <<<<<<<<<<<<<<
@@ -2891,7 +3026,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
*/
__pyx_v_best_bound_q = __pyx_v_curr_bound_q;
- /* "src/screening/gap_test_all.pyx":151
+ /* "slopescreening/screening/gap_test_all.pyx":151
* if curr_bound_q > best_bound_q:
* best_bound_q = curr_bound_q
* vec_q_star[k] = k # <<<<<<<<<<<<<<
@@ -2902,7 +3037,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
if (__pyx_t_19 < 0) __pyx_t_19 += __pyx_pybuffernd_vec_q_star.diminfo[0].shape;
*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int_t *, __pyx_pybuffernd_vec_q_star.rcbuffer->pybuffer.buf, __pyx_t_19, __pyx_pybuffernd_vec_q_star.diminfo[0].strides) = __pyx_v_k;
- /* "src/screening/gap_test_all.pyx":149
+ /* "slopescreening/screening/gap_test_all.pyx":149
* # 1. Evaluate q*
* curr_bound_q = vec_f[k-1] - coeff_lbd_gamma[k-1]
* if curr_bound_q > best_bound_q: # <<<<<<<<<<<<<<
@@ -2912,7 +3047,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
goto __pyx_L7;
}
- /* "src/screening/gap_test_all.pyx":153
+ /* "slopescreening/screening/gap_test_all.pyx":153
* vec_q_star[k] = k
* else:
* vec_q_star[k] = vec_q_star[k-1] # <<<<<<<<<<<<<<
@@ -2929,7 +3064,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
__pyx_L7:;
}
- /* "src/screening/gap_test_all.pyx":156
+ /* "slopescreening/screening/gap_test_all.pyx":156
*
* # 3. Tests
* for l in range(n, 0, -1): # <<<<<<<<<<<<<<
@@ -2995,7 +3130,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
__Pyx_XDECREF_SET(__pyx_v_l, __pyx_t_1);
__pyx_t_1 = 0;
- /* "src/screening/gap_test_all.pyx":157
+ /* "slopescreening/screening/gap_test_all.pyx":157
* # 3. Tests
* for l in range(n, 0, -1):
* q = vec_q_star[l] # <<<<<<<<<<<<<<
@@ -3008,7 +3143,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_q = __pyx_t_14;
- /* "src/screening/gap_test_all.pyx":158
+ /* "slopescreening/screening/gap_test_all.pyx":158
* for l in range(n, 0, -1):
* q = vec_q_star[l]
* while q >= 1: # <<<<<<<<<<<<<<
@@ -3019,7 +3154,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
__pyx_t_12 = ((__pyx_v_q >= 1) != 0);
if (!__pyx_t_12) break;
- /* "src/screening/gap_test_all.pyx":160
+ /* "slopescreening/screening/gap_test_all.pyx":160
* while q >= 1:
* # Implicit definition of the best value of p given q
* p = vec_p_star[q] # <<<<<<<<<<<<<<
@@ -3033,7 +3168,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
__Pyx_XDECREF_SET(__pyx_v_p, __pyx_t_1);
__pyx_t_1 = 0;
- /* "src/screening/gap_test_all.pyx":163
+ /* "slopescreening/screening/gap_test_all.pyx":163
*
* # Evaluation of the threshold
* tau = vec_f[p-1] - vec_f[q-1] + (coeff_lbd_gamma[q-1] - radius) # <<<<<<<<<<<<<<
@@ -3065,7 +3200,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_v_tau = __pyx_t_6;
- /* "src/screening/gap_test_all.pyx":166
+ /* "slopescreening/screening/gap_test_all.pyx":166
*
* # Test
* if Atcabs[index[l-1]] >= tau: # <<<<<<<<<<<<<<
@@ -3089,7 +3224,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_12) {
- /* "src/screening/gap_test_all.pyx":167
+ /* "slopescreening/screening/gap_test_all.pyx":167
* # Test
* if Atcabs[index[l-1]] >= tau:
* calI_screen[index[l:]] = True # <<<<<<<<<<<<<<
@@ -3104,7 +3239,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
if (unlikely(PyObject_SetItem(((PyObject *)__pyx_v_calI_screen), __pyx_t_1, Py_True) < 0)) __PYX_ERR(0, 167, __pyx_L1_error)
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "src/screening/gap_test_all.pyx":168
+ /* "slopescreening/screening/gap_test_all.pyx":168
* if Atcabs[index[l-1]] >= tau:
* calI_screen[index[l:]] = True
* return calI_screen # <<<<<<<<<<<<<<
@@ -3117,7 +3252,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
goto __pyx_L0;
- /* "src/screening/gap_test_all.pyx":166
+ /* "slopescreening/screening/gap_test_all.pyx":166
*
* # Test
* if Atcabs[index[l-1]] >= tau: # <<<<<<<<<<<<<<
@@ -3126,7 +3261,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
*/
}
- /* "src/screening/gap_test_all.pyx":171
+ /* "slopescreening/screening/gap_test_all.pyx":171
*
* # Next critical point
* q = vec_q_star[p-1] # <<<<<<<<<<<<<<
@@ -3143,7 +3278,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
__pyx_v_q = __pyx_t_14;
}
- /* "src/screening/gap_test_all.pyx":156
+ /* "slopescreening/screening/gap_test_all.pyx":156
*
* # 3. Tests
* for l in range(n, 0, -1): # <<<<<<<<<<<<<<
@@ -3153,7 +3288,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "src/screening/gap_test_all.pyx":174
+ /* "slopescreening/screening/gap_test_all.pyx":174
*
*
* calI_screen[index[l:]] = True # <<<<<<<<<<<<<<
@@ -3168,7 +3303,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_all_10GapTestAll_4apply_tes
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@@ -4273,7 +4408,7 @@ 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;
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":1004
+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":1003
* also needed. That can be found using `get_datetime64_unit`.
* """
* return (<PyDatetimeScalarObject*>obj).obval # <<<<<<<<<<<<<<
@@ -4283,7 +4418,7 @@ static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject *
__pyx_r = ((PyDatetimeScalarObject *)__pyx_v_obj)->obval;
goto __pyx_L0;
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":997
+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":996
*
*
* cdef inline npy_datetime get_datetime64_value(object obj) nogil: # <<<<<<<<<<<<<<
@@ -4296,7 +4431,7 @@ static CYTHON_INLINE npy_datetime __pyx_f_5numpy_get_datetime64_value(PyObject *
return __pyx_r;
}
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":1007
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":1006
*
*
* cdef inline npy_timedelta get_timedelta64_value(object obj) nogil: # <<<<<<<<<<<<<<
@@ -4307,7 +4442,7 @@ 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;
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":1011
+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":1010
* returns the int64 value underlying scalar numpy timedelta64 object
* """
* return (<PyTimedeltaScalarObject*>obj).obval # <<<<<<<<<<<<<<
@@ -4317,7 +4452,7 @@ static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject
__pyx_r = ((PyTimedeltaScalarObject *)__pyx_v_obj)->obval;
goto __pyx_L0;
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":1007
+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":1006
*
*
* cdef inline npy_timedelta get_timedelta64_value(object obj) nogil: # <<<<<<<<<<<<<<
@@ -4330,7 +4465,7 @@ static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject
return __pyx_r;
}
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":1014
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":1013
*
*
* cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) nogil: # <<<<<<<<<<<<<<
@@ -4341,7 +4476,7 @@ 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;
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":1018
+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":1017
* returns the unit part of the dtype for a numpy datetime64 object.
* """
* return <NPY_DATETIMEUNIT>(<PyDatetimeScalarObject*>obj).obmeta.base # <<<<<<<<<<<<<<
@@ -4349,7 +4484,7 @@ 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;
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":1014
+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":1013
*
*
* cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) nogil: # <<<<<<<<<<<<<<
@@ -4362,7 +4497,7 @@ static CYTHON_INLINE NPY_DATETIMEUNIT __pyx_f_5numpy_get_datetime64_unit(PyObjec
return __pyx_r;
}
-static PyObject *__pyx_tp_new_3src_9screening_12gap_test_all_GapTestAll(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_14slopescreening_9screening_12gap_test_all_GapTestAll(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
PyObject *o;
if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
o = (*t->tp_alloc)(t, 0);
@@ -4373,7 +4508,7 @@ static PyObject *__pyx_tp_new_3src_9screening_12gap_test_all_GapTestAll(PyTypeOb
return o;
}
-static void __pyx_tp_dealloc_3src_9screening_12gap_test_all_GapTestAll(PyObject *o) {
+static void __pyx_tp_dealloc_14slopescreening_9screening_12gap_test_all_GapTestAll(PyObject *o) {
#if CYTHON_USE_TP_FINALIZE
if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) {
if (PyObject_CallFinalizerFromDealloc(o)) return;
@@ -4383,26 +4518,26 @@ static void __pyx_tp_dealloc_3src_9screening_12gap_test_all_GapTestAll(PyObject
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
__Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1);
- __pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_3__dealloc__(o);
+ __pyx_pw_14slopescreening_9screening_12gap_test_all_10GapTestAll_3__dealloc__(o);
__Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1);
PyErr_Restore(etype, eval, etb);
}
(*Py_TYPE(o)->tp_free)(o);
}
-static PyMethodDef __pyx_methods_3src_9screening_12gap_test_all_GapTestAll[] = {
- {"apply_test", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_5apply_test, METH_VARARGS|METH_KEYWORDS, __pyx_doc_3src_9screening_12gap_test_all_10GapTestAll_4apply_test},
- {"__reduce_cython__", (PyCFunction)__pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_7__reduce_cython__, METH_NOARGS, 0},
- {"__setstate_cython__", (PyCFunction)__pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_9__setstate_cython__, METH_O, 0},
+static PyMethodDef __pyx_methods_14slopescreening_9screening_12gap_test_all_GapTestAll[] = {
+ {"apply_test", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_14slopescreening_9screening_12gap_test_all_10GapTestAll_5apply_test, METH_VARARGS|METH_KEYWORDS, __pyx_doc_14slopescreening_9screening_12gap_test_all_10GapTestAll_4apply_test},
+ {"__reduce_cython__", (PyCFunction)__pyx_pw_14slopescreening_9screening_12gap_test_all_10GapTestAll_7__reduce_cython__, METH_NOARGS, 0},
+ {"__setstate_cython__", (PyCFunction)__pyx_pw_14slopescreening_9screening_12gap_test_all_10GapTestAll_9__setstate_cython__, METH_O, 0},
{0, 0, 0, 0}
};
-static PyTypeObject __pyx_type_3src_9screening_12gap_test_all_GapTestAll = {
+static PyTypeObject __pyx_type_14slopescreening_9screening_12gap_test_all_GapTestAll = {
PyVarObject_HEAD_INIT(0, 0)
- "src.screening.gap_test_all.GapTestAll", /*tp_name*/
- sizeof(struct __pyx_obj_3src_9screening_12gap_test_all_GapTestAll), /*tp_basicsize*/
+ "slopescreening.screening.gap_test_all.GapTestAll", /*tp_name*/
+ sizeof(struct __pyx_obj_14slopescreening_9screening_12gap_test_all_GapTestAll), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_3src_9screening_12gap_test_all_GapTestAll, /*tp_dealloc*/
+ __pyx_tp_dealloc_14slopescreening_9screening_12gap_test_all_GapTestAll, /*tp_dealloc*/
#if PY_VERSION_HEX < 0x030800b4
0, /*tp_print*/
#endif
@@ -4435,7 +4570,7 @@ static PyTypeObject __pyx_type_3src_9screening_12gap_test_all_GapTestAll = {
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_3src_9screening_12gap_test_all_GapTestAll, /*tp_methods*/
+ __pyx_methods_14slopescreening_9screening_12gap_test_all_GapTestAll, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -4443,9 +4578,9 @@ static PyTypeObject __pyx_type_3src_9screening_12gap_test_all_GapTestAll = {
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pw_3src_9screening_12gap_test_all_10GapTestAll_1__init__, /*tp_init*/
+ __pyx_pw_14slopescreening_9screening_12gap_test_all_10GapTestAll_1__init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_3src_9screening_12gap_test_all_GapTestAll, /*tp_new*/
+ __pyx_tp_new_14slopescreening_9screening_12gap_test_all_GapTestAll, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -4458,12 +4593,15 @@ static PyTypeObject __pyx_type_3src_9screening_12gap_test_all_GapTestAll = {
#if PY_VERSION_HEX >= 0x030400a1
0, /*tp_finalize*/
#endif
- #if PY_VERSION_HEX >= 0x030800b1
+ #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
0, /*tp_vectorcall*/
#endif
#if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000
0, /*tp_print*/
#endif
+ #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000
+ 0, /*tp_pypy_flags*/
+ #endif
};
static PyMethodDef __pyx_methods[] = {
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{&__pyx_n_s_setstate, __pyx_k_setstate, sizeof(__pyx_k_setstate), 0, 0, 1, 1},
{&__pyx_n_s_setstate_cython, __pyx_k_setstate_cython, sizeof(__pyx_k_setstate_cython), 0, 0, 1, 1},
+ {&__pyx_n_s_slopescreening_screening_ascreen, __pyx_k_slopescreening_screening_ascreen, sizeof(__pyx_k_slopescreening_screening_ascreen), 0, 0, 1, 1},
{&__pyx_n_s_sqrt, __pyx_k_sqrt, sizeof(__pyx_k_sqrt), 0, 0, 1, 1},
- {&__pyx_n_s_src_screening_ascreening, __pyx_k_src_screening_ascreening, sizeof(__pyx_k_src_screening_ascreening), 0, 0, 1, 1},
{&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1},
{&__pyx_n_s_vec_gammas, __pyx_k_vec_gammas, sizeof(__pyx_k_vec_gammas), 0, 0, 1, 1},
{&__pyx_n_s_zeros, __pyx_k_zeros, sizeof(__pyx_k_zeros), 0, 0, 1, 1},
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__pyx_builtin_TypeError = __Pyx_GetBuiltinName(__pyx_n_s_TypeError); if (!__pyx_builtin_TypeError) __PYX_ERR(1, 2, __pyx_L1_error)
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+ __pyx_builtin_ImportError = __Pyx_GetBuiltinName(__pyx_n_s_ImportError); if (!__pyx_builtin_ImportError) __PYX_ERR(2, 944, __pyx_L1_error)
return 0;
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__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);
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__Pyx_GIVEREF(__pyx_tuple__3);
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":945
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* cdef inline int import_umath() except -1:
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+ __pyx_tuple__4 = PyTuple_Pack(1, __pyx_kp_s_numpy_core_multiarray_failed_to); if (unlikely(!__pyx_tuple__4)) __PYX_ERR(2, 944, __pyx_L1_error)
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__Pyx_GIVEREF(__pyx_tuple__4);
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":951
+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":950
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@@ -4669,16 +4807,16 @@ static int __Pyx_modinit_type_init_code(void) {
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#if PY_VERSION_HEX < 0x030800B1
- __pyx_type_3src_9screening_12gap_test_all_GapTestAll.tp_print = 0;
+ __pyx_type_14slopescreening_9screening_12gap_test_all_GapTestAll.tp_print = 0;
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- if ((CYTHON_USE_TYPE_SLOTS && CYTHON_USE_PYTYPE_LOOKUP) && likely(!__pyx_type_3src_9screening_12gap_test_all_GapTestAll.tp_dictoffset && __pyx_type_3src_9screening_12gap_test_all_GapTestAll.tp_getattro == PyObject_GenericGetAttr)) {
- __pyx_type_3src_9screening_12gap_test_all_GapTestAll.tp_getattro = __Pyx_PyObject_GenericGetAttr;
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+ if (!__pyx_ptype_5numpy_floating) __PYX_ERR(2, 782, __pyx_L1_error)
__pyx_ptype_5numpy_complexfloating = __Pyx_ImportType(__pyx_t_1, "numpy", "complexfloating", sizeof(PyObject), __Pyx_ImportType_CheckSize_Warn);
- if (!__pyx_ptype_5numpy_complexfloating) __PYX_ERR(2, 785, __pyx_L1_error)
+ if (!__pyx_ptype_5numpy_complexfloating) __PYX_ERR(2, 784, __pyx_L1_error)
__pyx_ptype_5numpy_flexible = __Pyx_ImportType(__pyx_t_1, "numpy", "flexible", sizeof(PyObject), __Pyx_ImportType_CheckSize_Warn);
- if (!__pyx_ptype_5numpy_flexible) __PYX_ERR(2, 787, __pyx_L1_error)
+ if (!__pyx_ptype_5numpy_flexible) __PYX_ERR(2, 786, __pyx_L1_error)
__pyx_ptype_5numpy_character = __Pyx_ImportType(__pyx_t_1, "numpy", "character", sizeof(PyObject), __Pyx_ImportType_CheckSize_Warn);
- if (!__pyx_ptype_5numpy_character) __PYX_ERR(2, 789, __pyx_L1_error)
+ if (!__pyx_ptype_5numpy_character) __PYX_ERR(2, 788, __pyx_L1_error)
__pyx_ptype_5numpy_ufunc = __Pyx_ImportType(__pyx_t_1, "numpy", "ufunc", sizeof(PyUFuncObject), __Pyx_ImportType_CheckSize_Ignore);
- if (!__pyx_ptype_5numpy_ufunc) __PYX_ERR(2, 827, __pyx_L1_error)
+ if (!__pyx_ptype_5numpy_ufunc) __PYX_ERR(2, 826, __pyx_L1_error)
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_RefNannyFinishContext();
return 0;
@@ -4935,14 +5073,14 @@ if (!__Pyx_RefNanny) {
#if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT)
if (__Pyx_init_sys_getdefaultencoding_params() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
#endif
- if (__pyx_module_is_main_src__screening__gap_test_all) {
+ if (__pyx_module_is_main_slopescreening__screening__gap_test_all) {
if (PyObject_SetAttr(__pyx_m, __pyx_n_s_name, __pyx_n_s_main) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
}
#if PY_MAJOR_VERSION >= 3
{
PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) __PYX_ERR(0, 1, __pyx_L1_error)
- if (!PyDict_GetItemString(modules, "src.screening.gap_test_all")) {
- if (unlikely(PyDict_SetItemString(modules, "src.screening.gap_test_all", __pyx_m) < 0)) __PYX_ERR(0, 1, __pyx_L1_error)
+ if (!PyDict_GetItemString(modules, "slopescreening.screening.gap_test_all")) {
+ if (unlikely(PyDict_SetItemString(modules, "slopescreening.screening.gap_test_all", __pyx_m) < 0)) __PYX_ERR(0, 1, __pyx_L1_error)
}
}
#endif
@@ -4963,22 +5101,22 @@ if (!__Pyx_RefNanny) {
if (__Pyx_patch_abc() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
#endif
- /* "src/screening/gap_test_all.pyx":4
+ /* "slopescreening/screening/gap_test_all.pyx":4
* # Based on https://cython.readthedocs.io/en/latest/src/tutorial/numpy.html
* # https://cython.readthedocs.io/en/latest/src/tutorial/memory_allocation.html
* import numpy as np # <<<<<<<<<<<<<<
*
- * from src.screening.ascreening import AbstractGapScreening
+ * from slopescreening.screening.ascreening import AbstractGapScreening
*/
__pyx_t_1 = __Pyx_Import(__pyx_n_s_numpy, 0, -1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 4, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_1);
if (PyDict_SetItem(__pyx_d, __pyx_n_s_np, __pyx_t_1) < 0) __PYX_ERR(0, 4, __pyx_L1_error)
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "src/screening/gap_test_all.pyx":6
+ /* "slopescreening/screening/gap_test_all.pyx":6
* import numpy as np
*
- * from src.screening.ascreening import AbstractGapScreening # <<<<<<<<<<<<<<
+ * from slopescreening.screening.ascreening import AbstractGapScreening # <<<<<<<<<<<<<<
*
*
*/
@@ -4987,7 +5125,7 @@ if (!__Pyx_RefNanny) {
__Pyx_INCREF(__pyx_n_s_AbstractGapScreening);
__Pyx_GIVEREF(__pyx_n_s_AbstractGapScreening);
PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_AbstractGapScreening);
- __pyx_t_2 = __Pyx_Import(__pyx_n_s_src_screening_ascreening, __pyx_t_1, -1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 6, __pyx_L1_error)
+ __pyx_t_2 = __Pyx_Import(__pyx_n_s_slopescreening_screening_ascreen, __pyx_t_1, -1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 6, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_1 = __Pyx_ImportFrom(__pyx_t_2, __pyx_n_s_AbstractGapScreening); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 6, __pyx_L1_error)
@@ -4996,7 +5134,7 @@ if (!__Pyx_RefNanny) {
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "src/screening/gap_test_all.pyx":1
+ /* "slopescreening/screening/gap_test_all.pyx":1
* # -*- coding: utf-8 -*- # <<<<<<<<<<<<<<
* # Based on https://cython.readthedocs.io/en/latest/src/tutorial/numpy.html
* # https://cython.readthedocs.io/en/latest/src/tutorial/memory_allocation.html
@@ -5006,7 +5144,7 @@ if (!__Pyx_RefNanny) {
if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_2) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":1014
+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":1013
*
*
* cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) nogil: # <<<<<<<<<<<<<<
@@ -5022,11 +5160,11 @@ if (!__Pyx_RefNanny) {
__Pyx_XDECREF(__pyx_t_2);
if (__pyx_m) {
if (__pyx_d) {
- __Pyx_AddTraceback("init src.screening.gap_test_all", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("init slopescreening.screening.gap_test_all", __pyx_clineno, __pyx_lineno, __pyx_filename);
}
Py_CLEAR(__pyx_m);
} else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_ImportError, "init src.screening.gap_test_all");
+ PyErr_SetString(PyExc_ImportError, "init slopescreening.screening.gap_test_all");
}
__pyx_L0:;
__Pyx_RefNannyFinishContext();
@@ -6814,17 +6952,35 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, P
static int __Pyx_setup_reduce(PyObject* type_obj) {
int ret = 0;
PyObject *object_reduce = NULL;
+ PyObject *object_getstate = NULL;
PyObject *object_reduce_ex = NULL;
PyObject *reduce = NULL;
PyObject *reduce_ex = NULL;
PyObject *reduce_cython = NULL;
PyObject *setstate = NULL;
PyObject *setstate_cython = NULL;
+ PyObject *getstate = NULL;
#if CYTHON_USE_PYTYPE_LOOKUP
- if (_PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate)) goto __PYX_GOOD;
+ getstate = _PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate);
#else
- if (PyObject_HasAttr(type_obj, __pyx_n_s_getstate)) goto __PYX_GOOD;
+ getstate = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_getstate);
+ if (!getstate && PyErr_Occurred()) {
+ goto __PYX_BAD;
+ }
#endif
+ if (getstate) {
+#if CYTHON_USE_PYTYPE_LOOKUP
+ object_getstate = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_getstate);
+#else
+ object_getstate = __Pyx_PyObject_GetAttrStrNoError((PyObject*)&PyBaseObject_Type, __pyx_n_s_getstate);
+ if (!object_getstate && PyErr_Occurred()) {
+ goto __PYX_BAD;
+ }
+#endif
+ if (object_getstate != getstate) {
+ goto __PYX_GOOD;
+ }
+ }
#if CYTHON_USE_PYTYPE_LOOKUP
object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD;
#else
@@ -6869,6 +7025,8 @@ __PYX_GOOD:
#if !CYTHON_USE_PYTYPE_LOOKUP
Py_XDECREF(object_reduce);
Py_XDECREF(object_reduce_ex);
+ Py_XDECREF(object_getstate);
+ Py_XDECREF(getstate);
#endif
Py_XDECREF(reduce);
Py_XDECREF(reduce_ex);
@@ -7050,7 +7208,7 @@ static int __Pyx_CLineForTraceback(CYTHON_NCP_UNUSED PyThreadState *tstate, int
}
if (!use_cline) {
c_line = 0;
- PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False);
+ (void) PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False);
}
else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) {
c_line = 0;
@@ -7144,33 +7302,40 @@ static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
#include "compile.h"
#include "frameobject.h"
#include "traceback.h"
+#if PY_VERSION_HEX >= 0x030b00a6
+ #ifndef Py_BUILD_CORE
+ #define Py_BUILD_CORE 1
+ #endif
+ #include "internal/pycore_frame.h"
+#endif
static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
const char *funcname, int c_line,
int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
+ PyCodeObject *py_code = NULL;
+ PyObject *py_funcname = NULL;
#if PY_MAJOR_VERSION < 3
+ PyObject *py_srcfile = NULL;
py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
if (!py_srcfile) goto bad;
+ #endif
if (c_line) {
#if PY_MAJOR_VERSION < 3
py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
+ if (!py_funcname) goto bad;
#else
py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
+ if (!py_funcname) goto bad;
+ funcname = PyUnicode_AsUTF8(py_funcname);
+ if (!funcname) goto bad;
#endif
}
else {
#if PY_MAJOR_VERSION < 3
py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
+ if (!py_funcname) goto bad;
#endif
}
- if (!py_funcname) goto bad;
+ #if PY_MAJOR_VERSION < 3
py_code = __Pyx_PyCode_New(
0,
0,
@@ -7189,11 +7354,16 @@ static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
__pyx_empty_bytes /*PyObject *lnotab*/
);
Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
+ #else
+ py_code = PyCode_NewEmpty(filename, funcname, py_line);
+ #endif
+ Py_XDECREF(py_funcname); // XDECREF since it's only set on Py3 if cline
return py_code;
bad:
- Py_XDECREF(py_srcfile);
Py_XDECREF(py_funcname);
+ #if PY_MAJOR_VERSION < 3
+ Py_XDECREF(py_srcfile);
+ #endif
return NULL;
}
static void __Pyx_AddTraceback(const char *funcname, int c_line,
@@ -7201,14 +7371,24 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line,
PyCodeObject *py_code = 0;
PyFrameObject *py_frame = 0;
PyThreadState *tstate = __Pyx_PyThreadState_Current;
+ PyObject *ptype, *pvalue, *ptraceback;
if (c_line) {
c_line = __Pyx_CLineForTraceback(tstate, c_line);
}
py_code = __pyx_find_code_object(c_line ? -c_line : py_line);
if (!py_code) {
+ __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback);
py_code = __Pyx_CreateCodeObjectForTraceback(
funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
+ if (!py_code) {
+ /* If the code object creation fails, then we should clear the
+ fetched exception references and propagate the new exception */
+ Py_XDECREF(ptype);
+ Py_XDECREF(pvalue);
+ Py_XDECREF(ptraceback);
+ goto bad;
+ }
+ __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback);
__pyx_insert_code_object(c_line ? -c_line : py_line, py_code);
}
py_frame = PyFrame_New(
@@ -8183,11 +8363,33 @@ static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObj
/* CheckBinaryVersion */
static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
+ char ctversion[5];
+ int same=1, i, found_dot;
+ const char* rt_from_call = Py_GetVersion();
+ PyOS_snprintf(ctversion, 5, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
+ found_dot = 0;
+ for (i = 0; i < 4; i++) {
+ if (!ctversion[i]) {
+ same = (rt_from_call[i] < '0' || rt_from_call[i] > '9');
+ break;
+ }
+ if (rt_from_call[i] != ctversion[i]) {
+ same = 0;
+ break;
+ }
+ }
+ if (!same) {
+ char rtversion[5] = {'\0'};
char message[200];
+ for (i=0; i<4; ++i) {
+ if (rt_from_call[i] == '.') {
+ if (found_dot) break;
+ found_dot = 1;
+ } else if (rt_from_call[i] < '0' || rt_from_call[i] > '9') {
+ break;
+ }
+ rtversion[i] = rt_from_call[i];
+ }
PyOS_snprintf(message, sizeof(message),
"compiletime version %s of module '%.100s' "
"does not match runtime version %s",
@@ -8445,6 +8647,23 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
Py_DECREF(x);
return ival;
}
+static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject* o) {
+ if (sizeof(Py_hash_t) == sizeof(Py_ssize_t)) {
+ return (Py_hash_t) __Pyx_PyIndex_AsSsize_t(o);
+#if PY_MAJOR_VERSION < 3
+ } else if (likely(PyInt_CheckExact(o))) {
+ return PyInt_AS_LONG(o);
+#endif
+ } else {
+ Py_ssize_t ival;
+ PyObject *x;
+ x = PyNumber_Index(o);
+ if (!x) return -1;
+ ival = PyInt_AsLong(x);
+ Py_DECREF(x);
+ return ival;
+ }
+}
static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b) {
return b ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False);
}
diff --git a/src/screening/gap_test_all.pyx b/slopescreening/screening/gap_test_all.pyx
similarity index 98%
rename from src/screening/gap_test_all.pyx
rename to slopescreening/screening/gap_test_all.pyx
index b172470..b5534f0 100644
--- a/src/screening/gap_test_all.pyx
+++ b/slopescreening/screening/gap_test_all.pyx
@@ -3,7 +3,7 @@
# https://cython.readthedocs.io/en/latest/src/tutorial/memory_allocation.html
import numpy as np
-from src.screening.ascreening import AbstractGapScreening
+from slopescreening.screening.ascreening import AbstractGapScreening
# "cimport" is used to import special compile-time information
diff --git a/src/screening/gap_test_p_1.c b/slopescreening/screening/gap_test_p_1.c
similarity index 89%
rename from src/screening/gap_test_p_1.c
rename to slopescreening/screening/gap_test_p_1.c
index 595c769..97c5c3c 100644
--- a/src/screening/gap_test_p_1.c
+++ b/slopescreening/screening/gap_test_p_1.c
@@ -1,15 +1,15 @@
-/* Generated by Cython 0.29.24 */
+/* Generated by Cython 0.29.32 */
/* BEGIN: Cython Metadata
{
"distutils": {
"depends": [],
- "name": "src.screening.gap_test_p_1",
+ "name": "slopescreening.screening.gap_test_p_1",
"sources": [
- "src/screening/gap_test_p_1.pyx"
+ "slopescreening/screening/gap_test_p_1.pyx"
]
},
- "module_name": "src.screening.gap_test_p_1"
+ "module_name": "slopescreening.screening.gap_test_p_1"
}
END: Cython Metadata */
@@ -22,8 +22,8 @@ END: Cython Metadata */
#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000)
#error Cython requires Python 2.6+ or Python 3.3+.
#else
-#define CYTHON_ABI "0_29_24"
-#define CYTHON_HEX_VERSION 0x001D18F0
+#define CYTHON_ABI "0_29_32"
+#define CYTHON_HEX_VERSION 0x001D20F0
#define CYTHON_FUTURE_DIVISION 0
#include <stddef.h>
#ifndef offsetof
@@ -62,6 +62,7 @@ END: Cython Metadata */
#define CYTHON_COMPILING_IN_PYPY 1
#define CYTHON_COMPILING_IN_PYSTON 0
#define CYTHON_COMPILING_IN_CPYTHON 0
+ #define CYTHON_COMPILING_IN_NOGIL 0
#undef CYTHON_USE_TYPE_SLOTS
#define CYTHON_USE_TYPE_SLOTS 0
#undef CYTHON_USE_PYTYPE_LOOKUP
@@ -98,10 +99,14 @@ END: Cython Metadata */
#define CYTHON_USE_DICT_VERSIONS 0
#undef CYTHON_USE_EXC_INFO_STACK
#define CYTHON_USE_EXC_INFO_STACK 0
+ #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
+ #define CYTHON_UPDATE_DESCRIPTOR_DOC (PYPY_VERSION_HEX >= 0x07030900)
+ #endif
#elif defined(PYSTON_VERSION)
#define CYTHON_COMPILING_IN_PYPY 0
#define CYTHON_COMPILING_IN_PYSTON 1
#define CYTHON_COMPILING_IN_CPYTHON 0
+ #define CYTHON_COMPILING_IN_NOGIL 0
#ifndef CYTHON_USE_TYPE_SLOTS
#define CYTHON_USE_TYPE_SLOTS 1
#endif
@@ -139,10 +144,59 @@ END: Cython Metadata */
#define CYTHON_USE_DICT_VERSIONS 0
#undef CYTHON_USE_EXC_INFO_STACK
#define CYTHON_USE_EXC_INFO_STACK 0
+ #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
+ #define CYTHON_UPDATE_DESCRIPTOR_DOC 0
+ #endif
+#elif defined(PY_NOGIL)
+ #define CYTHON_COMPILING_IN_PYPY 0
+ #define CYTHON_COMPILING_IN_PYSTON 0
+ #define CYTHON_COMPILING_IN_CPYTHON 0
+ #define CYTHON_COMPILING_IN_NOGIL 1
+ #ifndef CYTHON_USE_TYPE_SLOTS
+ #define CYTHON_USE_TYPE_SLOTS 1
+ #endif
+ #undef CYTHON_USE_PYTYPE_LOOKUP
+ #define CYTHON_USE_PYTYPE_LOOKUP 0
+ #ifndef CYTHON_USE_ASYNC_SLOTS
+ #define CYTHON_USE_ASYNC_SLOTS 1
+ #endif
+ #undef CYTHON_USE_PYLIST_INTERNALS
+ #define CYTHON_USE_PYLIST_INTERNALS 0
+ #ifndef CYTHON_USE_UNICODE_INTERNALS
+ #define CYTHON_USE_UNICODE_INTERNALS 1
+ #endif
+ #undef CYTHON_USE_UNICODE_WRITER
+ #define CYTHON_USE_UNICODE_WRITER 0
+ #undef CYTHON_USE_PYLONG_INTERNALS
+ #define CYTHON_USE_PYLONG_INTERNALS 0
+ #ifndef CYTHON_AVOID_BORROWED_REFS
+ #define CYTHON_AVOID_BORROWED_REFS 0
+ #endif
+ #ifndef CYTHON_ASSUME_SAFE_MACROS
+ #define CYTHON_ASSUME_SAFE_MACROS 1
+ #endif
+ #ifndef CYTHON_UNPACK_METHODS
+ #define CYTHON_UNPACK_METHODS 1
+ #endif
+ #undef CYTHON_FAST_THREAD_STATE
+ #define CYTHON_FAST_THREAD_STATE 0
+ #undef CYTHON_FAST_PYCALL
+ #define CYTHON_FAST_PYCALL 0
+ #ifndef CYTHON_PEP489_MULTI_PHASE_INIT
+ #define CYTHON_PEP489_MULTI_PHASE_INIT 1
+ #endif
+ #ifndef CYTHON_USE_TP_FINALIZE
+ #define CYTHON_USE_TP_FINALIZE 1
+ #endif
+ #undef CYTHON_USE_DICT_VERSIONS
+ #define CYTHON_USE_DICT_VERSIONS 0
+ #undef CYTHON_USE_EXC_INFO_STACK
+ #define CYTHON_USE_EXC_INFO_STACK 0
#else
#define CYTHON_COMPILING_IN_PYPY 0
#define CYTHON_COMPILING_IN_PYSTON 0
#define CYTHON_COMPILING_IN_CPYTHON 1
+ #define CYTHON_COMPILING_IN_NOGIL 0
#ifndef CYTHON_USE_TYPE_SLOTS
#define CYTHON_USE_TYPE_SLOTS 1
#endif
@@ -170,7 +224,7 @@ END: Cython Metadata */
#ifndef CYTHON_USE_UNICODE_INTERNALS
#define CYTHON_USE_UNICODE_INTERNALS 1
#endif
- #if PY_VERSION_HEX < 0x030300F0
+ #if PY_VERSION_HEX < 0x030300F0 || PY_VERSION_HEX >= 0x030B00A2
#undef CYTHON_USE_UNICODE_WRITER
#define CYTHON_USE_UNICODE_WRITER 0
#elif !defined(CYTHON_USE_UNICODE_WRITER)
@@ -185,11 +239,14 @@ END: Cython Metadata */
#ifndef CYTHON_UNPACK_METHODS
#define CYTHON_UNPACK_METHODS 1
#endif
- #ifndef CYTHON_FAST_THREAD_STATE
+ #if PY_VERSION_HEX >= 0x030B00A4
+ #undef CYTHON_FAST_THREAD_STATE
+ #define CYTHON_FAST_THREAD_STATE 0
+ #elif !defined(CYTHON_FAST_THREAD_STATE)
#define CYTHON_FAST_THREAD_STATE 1
#endif
#ifndef CYTHON_FAST_PYCALL
- #define CYTHON_FAST_PYCALL 1
+ #define CYTHON_FAST_PYCALL (PY_VERSION_HEX < 0x030A0000)
#endif
#ifndef CYTHON_PEP489_MULTI_PHASE_INIT
#define CYTHON_PEP489_MULTI_PHASE_INIT (PY_VERSION_HEX >= 0x03050000)
@@ -200,15 +257,23 @@ END: Cython Metadata */
#ifndef CYTHON_USE_DICT_VERSIONS
#define CYTHON_USE_DICT_VERSIONS (PY_VERSION_HEX >= 0x030600B1)
#endif
- #ifndef CYTHON_USE_EXC_INFO_STACK
+ #if PY_VERSION_HEX >= 0x030B00A4
+ #undef CYTHON_USE_EXC_INFO_STACK
+ #define CYTHON_USE_EXC_INFO_STACK 0
+ #elif !defined(CYTHON_USE_EXC_INFO_STACK)
#define CYTHON_USE_EXC_INFO_STACK (PY_VERSION_HEX >= 0x030700A3)
#endif
+ #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
+ #define CYTHON_UPDATE_DESCRIPTOR_DOC 1
+ #endif
#endif
#if !defined(CYTHON_FAST_PYCCALL)
#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1)
#endif
#if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
+ #if PY_MAJOR_VERSION < 3
+ #include "longintrepr.h"
+ #endif
#undef SHIFT
#undef BASE
#undef MASK
@@ -325,9 +390,68 @@ END: Cython Metadata */
#define __Pyx_DefaultClassType PyClass_Type
#else
#define __Pyx_BUILTIN_MODULE_NAME "builtins"
-#if PY_VERSION_HEX >= 0x030800A4 && PY_VERSION_HEX < 0x030800B2
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
- PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
+ #define __Pyx_DefaultClassType PyType_Type
+#if PY_VERSION_HEX >= 0x030B00A1
+ static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, int k, int l, int s, int f,
+ PyObject *code, PyObject *c, PyObject* n, PyObject *v,
+ PyObject *fv, PyObject *cell, PyObject* fn,
+ PyObject *name, int fline, PyObject *lnos) {
+ PyObject *kwds=NULL, *argcount=NULL, *posonlyargcount=NULL, *kwonlyargcount=NULL;
+ PyObject *nlocals=NULL, *stacksize=NULL, *flags=NULL, *replace=NULL, *call_result=NULL, *empty=NULL;
+ const char *fn_cstr=NULL;
+ const char *name_cstr=NULL;
+ PyCodeObject* co=NULL;
+ PyObject *type, *value, *traceback;
+ PyErr_Fetch(&type, &value, &traceback);
+ if (!(kwds=PyDict_New())) goto end;
+ if (!(argcount=PyLong_FromLong(a))) goto end;
+ if (PyDict_SetItemString(kwds, "co_argcount", argcount) != 0) goto end;
+ if (!(posonlyargcount=PyLong_FromLong(0))) goto end;
+ if (PyDict_SetItemString(kwds, "co_posonlyargcount", posonlyargcount) != 0) goto end;
+ if (!(kwonlyargcount=PyLong_FromLong(k))) goto end;
+ if (PyDict_SetItemString(kwds, "co_kwonlyargcount", kwonlyargcount) != 0) goto end;
+ if (!(nlocals=PyLong_FromLong(l))) goto end;
+ if (PyDict_SetItemString(kwds, "co_nlocals", nlocals) != 0) goto end;
+ if (!(stacksize=PyLong_FromLong(s))) goto end;
+ if (PyDict_SetItemString(kwds, "co_stacksize", stacksize) != 0) goto end;
+ if (!(flags=PyLong_FromLong(f))) goto end;
+ if (PyDict_SetItemString(kwds, "co_flags", flags) != 0) goto end;
+ if (PyDict_SetItemString(kwds, "co_code", code) != 0) goto end;
+ if (PyDict_SetItemString(kwds, "co_consts", c) != 0) goto end;
+ if (PyDict_SetItemString(kwds, "co_names", n) != 0) goto end;
+ if (PyDict_SetItemString(kwds, "co_varnames", v) != 0) goto end;
+ if (PyDict_SetItemString(kwds, "co_freevars", fv) != 0) goto end;
+ if (PyDict_SetItemString(kwds, "co_cellvars", cell) != 0) goto end;
+ if (PyDict_SetItemString(kwds, "co_linetable", lnos) != 0) goto end;
+ if (!(fn_cstr=PyUnicode_AsUTF8AndSize(fn, NULL))) goto end;
+ if (!(name_cstr=PyUnicode_AsUTF8AndSize(name, NULL))) goto end;
+ if (!(co = PyCode_NewEmpty(fn_cstr, name_cstr, fline))) goto end;
+ if (!(replace = PyObject_GetAttrString((PyObject*)co, "replace"))) goto cleanup_code_too;
+ if (!(empty = PyTuple_New(0))) goto cleanup_code_too; // unfortunately __pyx_empty_tuple isn't available here
+ if (!(call_result = PyObject_Call(replace, empty, kwds))) goto cleanup_code_too;
+ Py_XDECREF((PyObject*)co);
+ co = (PyCodeObject*)call_result;
+ call_result = NULL;
+ if (0) {
+ cleanup_code_too:
+ Py_XDECREF((PyObject*)co);
+ co = NULL;
+ }
+ end:
+ Py_XDECREF(kwds);
+ Py_XDECREF(argcount);
+ Py_XDECREF(posonlyargcount);
+ Py_XDECREF(kwonlyargcount);
+ Py_XDECREF(nlocals);
+ Py_XDECREF(stacksize);
+ Py_XDECREF(replace);
+ Py_XDECREF(call_result);
+ Py_XDECREF(empty);
+ if (type) {
+ PyErr_Restore(type, value, traceback);
+ }
+ return co;
+ }
#else
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
@@ -565,10 +689,10 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) {
#if PY_VERSION_HEX < 0x030200A4
typedef long Py_hash_t;
#define __Pyx_PyInt_FromHash_t PyInt_FromLong
- #define __Pyx_PyInt_AsHash_t PyInt_AsLong
+ #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsHash_t
#else
#define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
- #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
+ #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsSsize_t
#endif
#if PY_MAJOR_VERSION >= 3
#define __Pyx_PyMethod_New(func, self, klass) ((self) ? ((void)(klass), PyMethod_New(func, self)) : __Pyx_NewRef(func))
@@ -593,8 +717,10 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) {
} __Pyx_PyAsyncMethodsStruct;
#endif
-#if defined(WIN32) || defined(MS_WINDOWS)
- #define _USE_MATH_DEFINES
+#if defined(_WIN32) || defined(WIN32) || defined(MS_WINDOWS)
+ #if !defined(_USE_MATH_DEFINES)
+ #define _USE_MATH_DEFINES
+ #endif
#endif
#include <math.h>
#ifdef NAN
@@ -625,8 +751,8 @@ static CYTHON_INLINE float __PYX_NAN() {
#endif
#endif
-#define __PYX_HAVE__src__screening__gap_test_p_1
-#define __PYX_HAVE_API__src__screening__gap_test_p_1
+#define __PYX_HAVE__slopescreening__screening__gap_test_p_1
+#define __PYX_HAVE_API__slopescreening__screening__gap_test_p_1
/* Early includes */
#include <string.h>
#include <stdio.h>
@@ -734,6 +860,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x);
(likely(PyTuple_CheckExact(obj)) ? __Pyx_NewRef(obj) : PySequence_Tuple(obj))
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
+static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject*);
#if CYTHON_ASSUME_SAFE_MACROS
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
#else
@@ -868,10 +995,10 @@ static const char *__pyx_filename;
static const char *__pyx_f[] = {
- "src/screening/gap_test_p_1.pyx",
+ "slopescreening/screening/gap_test_p_1.pyx",
"stringsource",
- "venv/lib/python3.8/site-packages/numpy/__init__.pxd",
- "venv/lib/python3.8/site-packages/Cython/Includes/cpython/type.pxd",
+ "venv/lib/python3.10/site-packages/numpy/__init__.pxd",
+ "venv/lib/python3.10/site-packages/Cython/Includes/cpython/type.pxd",
};
/* BufferFormatStructs.proto */
#define IS_UNSIGNED(type) (((type) -1) > 0)
@@ -910,7 +1037,7 @@ typedef struct {
} __Pyx_BufFmt_Context;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":690
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":689
* # in Cython to enable them only on the right systems.
*
* ctypedef npy_int8 int8_t # <<<<<<<<<<<<<<
@@ -919,7 +1046,7 @@ typedef struct {
*/
typedef npy_int8 __pyx_t_5numpy_int8_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":691
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":690
*
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t # <<<<<<<<<<<<<<
@@ -928,7 +1055,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t;
*/
typedef npy_int16 __pyx_t_5numpy_int16_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":692
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":691
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t # <<<<<<<<<<<<<<
@@ -937,7 +1064,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t;
*/
typedef npy_int32 __pyx_t_5numpy_int32_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":693
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":692
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t
* ctypedef npy_int64 int64_t # <<<<<<<<<<<<<<
@@ -946,7 +1073,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t;
*/
typedef npy_int64 __pyx_t_5numpy_int64_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":697
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":696
* #ctypedef npy_int128 int128_t
*
* ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<<
@@ -955,7 +1082,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t;
*/
typedef npy_uint8 __pyx_t_5numpy_uint8_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":698
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":697
*
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<<
@@ -964,7 +1091,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t;
*/
typedef npy_uint16 __pyx_t_5numpy_uint16_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":699
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":698
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<<
@@ -973,7 +1100,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t;
*/
typedef npy_uint32 __pyx_t_5numpy_uint32_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":700
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":699
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t
* ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<<
@@ -982,7 +1109,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t;
*/
typedef npy_uint64 __pyx_t_5numpy_uint64_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":704
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":703
* #ctypedef npy_uint128 uint128_t
*
* ctypedef npy_float32 float32_t # <<<<<<<<<<<<<<
@@ -991,7 +1118,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t;
*/
typedef npy_float32 __pyx_t_5numpy_float32_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":705
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":704
*
* ctypedef npy_float32 float32_t
* ctypedef npy_float64 float64_t # <<<<<<<<<<<<<<
@@ -1000,7 +1127,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t;
*/
typedef npy_float64 __pyx_t_5numpy_float64_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":714
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":713
* # The int types are mapped a bit surprising --
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t # <<<<<<<<<<<<<<
@@ -1009,7 +1136,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t;
*/
typedef npy_long __pyx_t_5numpy_int_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":715
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":714
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t # <<<<<<<<<<<<<<
@@ -1018,7 +1145,7 @@ typedef npy_long __pyx_t_5numpy_int_t;
*/
typedef npy_longlong __pyx_t_5numpy_long_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":716
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":715
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t
* ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<<
@@ -1027,7 +1154,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t;
*/
typedef npy_longlong __pyx_t_5numpy_longlong_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":718
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":717
* ctypedef npy_longlong longlong_t
*
* ctypedef npy_ulong uint_t # <<<<<<<<<<<<<<
@@ -1036,7 +1163,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t;
*/
typedef npy_ulong __pyx_t_5numpy_uint_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":719
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":718
*
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<<
@@ -1045,7 +1172,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t;
*/
typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":720
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":719
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t
* ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<<
@@ -1054,7 +1181,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
*/
typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":722
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":721
* ctypedef npy_ulonglong ulonglong_t
*
* ctypedef npy_intp intp_t # <<<<<<<<<<<<<<
@@ -1063,7 +1190,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
*/
typedef npy_intp __pyx_t_5numpy_intp_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":723
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":722
*
* ctypedef npy_intp intp_t
* ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<<
@@ -1072,7 +1199,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t;
*/
typedef npy_uintp __pyx_t_5numpy_uintp_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":725
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":724
* ctypedef npy_uintp uintp_t
*
* ctypedef npy_double float_t # <<<<<<<<<<<<<<
@@ -1081,7 +1208,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t;
*/
typedef npy_double __pyx_t_5numpy_float_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":726
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":725
*
* ctypedef npy_double float_t
* ctypedef npy_double double_t # <<<<<<<<<<<<<<
@@ -1090,7 +1217,7 @@ typedef npy_double __pyx_t_5numpy_float_t;
*/
typedef npy_double __pyx_t_5numpy_double_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":727
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":726
* ctypedef npy_double float_t
* ctypedef npy_double double_t
* ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<<
@@ -1099,14 +1226,14 @@ typedef npy_double __pyx_t_5numpy_double_t;
*/
typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
-/* "src/screening/gap_test_p_1.pyx":16
+/* "slopescreening/screening/gap_test_p_1.pyx":16
* cimport cython
*
* ctypedef np.npy_bool bool_t # <<<<<<<<<<<<<<
*
* from cpython.mem cimport PyMem_Malloc, PyMem_Realloc, PyMem_Free
*/
-typedef npy_bool __pyx_t_3src_9screening_12gap_test_p_1_bool_t;
+typedef npy_bool __pyx_t_14slopescreening_9screening_12gap_test_p_1_bool_t;
/* Declarations.proto */
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
@@ -1133,9 +1260,9 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do
/*--- Type declarations ---*/
-struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne;
+struct __pyx_obj_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":729
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":728
* ctypedef npy_longdouble longdouble_t
*
* ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<<
@@ -1144,7 +1271,7 @@ struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne;
*/
typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":730
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":729
*
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<<
@@ -1153,7 +1280,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
*/
typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":731
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":730
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t
* ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<<
@@ -1162,7 +1289,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
*/
typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":733
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":732
* ctypedef npy_clongdouble clongdouble_t
*
* ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<<
@@ -1171,14 +1298,14 @@ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
*/
typedef npy_cdouble __pyx_t_5numpy_complex_t;
-/* "src/screening/gap_test_p_1.pyx":23
+/* "slopescreening/screening/gap_test_p_1.pyx":23
* #(AbstractGapScreening)
*
* cdef class GapTestPequalOne: # <<<<<<<<<<<<<<
* """ Generalized test
* """
*/
-struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne {
+struct __pyx_obj_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne {
PyObject_HEAD
double *vec_cumsum_gammas;
double *vec_kappa_q;
@@ -1368,13 +1495,21 @@ static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args,
#ifndef Py_MEMBER_SIZE
#define Py_MEMBER_SIZE(type, member) sizeof(((type *)0)->member)
#endif
+#if CYTHON_FAST_PYCALL
static size_t __pyx_pyframe_localsplus_offset = 0;
#include "frameobject.h"
+#if PY_VERSION_HEX >= 0x030b00a6
+ #ifndef Py_BUILD_CORE
+ #define Py_BUILD_CORE 1
+ #endif
+ #include "internal/pycore_frame.h"
+#endif
#define __Pxy_PyFrame_Initialize_Offsets()\
((void)__Pyx_BUILD_ASSERT_EXPR(sizeof(PyFrameObject) == offsetof(PyFrameObject, f_localsplus) + Py_MEMBER_SIZE(PyFrameObject, f_localsplus)),\
(void)(__pyx_pyframe_localsplus_offset = ((size_t)PyFrame_Type.tp_basicsize) - Py_MEMBER_SIZE(PyFrameObject, f_localsplus)))
#define __Pyx_PyFrame_GetLocalsplus(frame)\
(assert(__pyx_pyframe_localsplus_offset), (PyObject **)(((char *)(frame)) + __pyx_pyframe_localsplus_offset))
+#endif // CYTHON_FAST_PYCALL
#endif
/* PyObjectCall.proto */
@@ -1762,16 +1897,16 @@ static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0;
/* Module declarations from 'cython' */
-/* Module declarations from 'src.screening.gap_test_p_1' */
-static PyTypeObject *__pyx_ptype_3src_9screening_12gap_test_p_1_GapTestPequalOne = 0;
+/* Module declarations from 'slopescreening.screening.gap_test_p_1' */
+static PyTypeObject *__pyx_ptype_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne = 0;
static __Pyx_TypeInfo __Pyx_TypeInfo_nn_npy_double = { "npy_double", NULL, sizeof(npy_double), { 0 }, 0, 'R', 0, 0 };
static __Pyx_TypeInfo __Pyx_TypeInfo_long = { "long", NULL, sizeof(long), { 0 }, 0, IS_UNSIGNED(long) ? 'U' : 'I', IS_UNSIGNED(long), 0 };
static __Pyx_TypeInfo __Pyx_TypeInfo_nn_npy_bool = { "npy_bool", NULL, sizeof(npy_bool), { 0 }, 0, IS_UNSIGNED(npy_bool) ? 'U' : 'I', IS_UNSIGNED(npy_bool), 0 };
-#define __Pyx_MODULE_NAME "src.screening.gap_test_p_1"
-extern int __pyx_module_is_main_src__screening__gap_test_p_1;
-int __pyx_module_is_main_src__screening__gap_test_p_1 = 0;
+#define __Pyx_MODULE_NAME "slopescreening.screening.gap_test_p_1"
+extern int __pyx_module_is_main_slopescreening__screening__gap_test_p_1;
+int __pyx_module_is_main_slopescreening__screening__gap_test_p_1 = 0;
-/* Implementation of 'src.screening.gap_test_p_1' */
+/* Implementation of 'slopescreening.screening.gap_test_p_1' */
static PyObject *__pyx_builtin_range;
static PyObject *__pyx_builtin_TypeError;
static PyObject *__pyx_builtin_ImportError;
@@ -1807,10 +1942,10 @@ static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback";
static const char __pyx_k_coeff_dual_scaling[] = "coeff_dual_scaling";
static const char __pyx_k_AbstractGapScreening[] = "AbstractGapScreening";
static const char __pyx_k_vec_coherence_function[] = "vec_coherence_function";
-static const char __pyx_k_src_screening_ascreening[] = "src.screening.ascreening";
static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import";
static const char __pyx_k_self_vec_cumsum_gammas_self_vec[] = "self.vec_cumsum_gammas,self.vec_kappa_q cannot be converted to a Python object for pickling";
static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import";
+static const char __pyx_k_slopescreening_screening_ascreen[] = "slopescreening.screening.ascreening";
static PyObject *__pyx_n_s_AbstractGapScreening;
static PyObject *__pyx_n_s_Atcabs;
static PyObject *__pyx_n_s_GapTestPequalOne;
@@ -1841,18 +1976,18 @@ static PyObject *__pyx_n_s_reduce_ex;
static PyObject *__pyx_kp_s_self_vec_cumsum_gammas_self_vec;
static PyObject *__pyx_n_s_setstate;
static PyObject *__pyx_n_s_setstate_cython;
+static PyObject *__pyx_n_s_slopescreening_screening_ascreen;
static PyObject *__pyx_n_s_sqrt;
-static PyObject *__pyx_n_s_src_screening_ascreening;
static PyObject *__pyx_n_s_test;
static PyObject *__pyx_n_s_vec_coherence_function;
static PyObject *__pyx_n_s_vec_gammas;
static PyObject *__pyx_n_s_zeros;
-static int __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self, PyArrayObject *__pyx_v_vec_gammas, PyArrayObject *__pyx_v_vec_coherence_function); /* proto */
-static void __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_2__dealloc__(struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4apply_test(struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_gap, double __pyx_v_lbd, CYTHON_UNUSED PyArrayObject *__pyx_v_vec_gammas, double __pyx_v_coeff_dual_scaling, double __pyx_v_offset_radius, PyArrayObject *__pyx_v_index); /* proto */
-static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_6__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_8__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
-static PyObject *__pyx_tp_new_3src_9screening_12gap_test_p_1_GapTestPequalOne(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
+static int __pyx_pf_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne___init__(struct __pyx_obj_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self, PyArrayObject *__pyx_v_vec_gammas, PyArrayObject *__pyx_v_vec_coherence_function); /* proto */
+static void __pyx_pf_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_2__dealloc__(struct __pyx_obj_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_4apply_test(struct __pyx_obj_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_gap, double __pyx_v_lbd, CYTHON_UNUSED PyArrayObject *__pyx_v_vec_gammas, double __pyx_v_coeff_dual_scaling, double __pyx_v_offset_radius, PyArrayObject *__pyx_v_index); /* proto */
+static PyObject *__pyx_pf_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_6__reduce_cython__(CYTHON_UNUSED struct __pyx_obj_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_8__setstate_cython__(CYTHON_UNUSED struct __pyx_obj_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v___pyx_state); /* proto */
+static PyObject *__pyx_tp_new_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
static PyObject *__pyx_int_1;
static PyObject *__pyx_int_neg_1;
static PyObject *__pyx_slice_;
@@ -1863,7 +1998,7 @@ static PyObject *__pyx_tuple__5;
static PyObject *__pyx_tuple__6;
/* Late includes */
-/* "src/screening/gap_test_p_1.pyx":39
+/* "slopescreening/screening/gap_test_p_1.pyx":39
* @cython.boundscheck(False) # turn off bounds-checking for entire function
* @cython.wraparound(False) # turn off negative index wrapping for entire function
* def __init__( # <<<<<<<<<<<<<<
@@ -1872,8 +2007,8 @@ static PyObject *__pyx_tuple__6;
*/
/* Python wrapper */
-static int __pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static int __pyx_pw_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyArrayObject *__pyx_v_vec_gammas = 0;
PyArrayObject *__pyx_v_vec_coherence_function = 0;
int __pyx_lineno = 0;
@@ -1924,13 +2059,13 @@ static int __pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_1__init__(
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("__init__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 39, __pyx_L3_error)
__pyx_L3_error:;
- __Pyx_AddTraceback("src.screening.gap_test_p_1.GapTestPequalOne.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("slopescreening.screening.gap_test_p_1.GapTestPequalOne.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_vec_gammas), __pyx_ptype_5numpy_ndarray, 1, "vec_gammas", 0))) __PYX_ERR(0, 41, __pyx_L1_error)
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_vec_coherence_function), __pyx_ptype_5numpy_ndarray, 1, "vec_coherence_function", 0))) __PYX_ERR(0, 42, __pyx_L1_error)
- __pyx_r = __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(((struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *)__pyx_v_self), __pyx_v_vec_gammas, __pyx_v_vec_coherence_function);
+ __pyx_r = __pyx_pf_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne___init__(((struct __pyx_obj_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne *)__pyx_v_self), __pyx_v_vec_gammas, __pyx_v_vec_coherence_function);
/* function exit code */
goto __pyx_L0;
@@ -1941,7 +2076,7 @@ static int __pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_1__init__(
return __pyx_r;
}
-static int __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self, PyArrayObject *__pyx_v_vec_gammas, PyArrayObject *__pyx_v_vec_coherence_function) {
+static int __pyx_pf_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne___init__(struct __pyx_obj_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self, PyArrayObject *__pyx_v_vec_gammas, PyArrayObject *__pyx_v_vec_coherence_function) {
int __pyx_v_n;
int __pyx_v_i;
__Pyx_LocalBuf_ND __pyx_pybuffernd_vec_coherence_function;
@@ -1982,7 +2117,7 @@ static int __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(s
}
__pyx_pybuffernd_vec_coherence_function.diminfo[0].strides = __pyx_pybuffernd_vec_coherence_function.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_vec_coherence_function.diminfo[0].shape = __pyx_pybuffernd_vec_coherence_function.rcbuffer->pybuffer.shape[0];
- /* "src/screening/gap_test_p_1.pyx":45
+ /* "slopescreening/screening/gap_test_p_1.pyx":45
* ):
*
* cdef int n = vec_gammas.shape[0] # <<<<<<<<<<<<<<
@@ -1991,7 +2126,7 @@ static int __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(s
*/
__pyx_v_n = (__pyx_v_vec_gammas->dimensions[0]);
- /* "src/screening/gap_test_p_1.pyx":57
+ /* "slopescreening/screening/gap_test_p_1.pyx":57
* # self.vec_kappa_q = &buf2[0]
*
* self.vec_cumsum_gammas = <double*> PyMem_Malloc(n * sizeof(double)) # <<<<<<<<<<<<<<
@@ -2000,7 +2135,7 @@ static int __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(s
*/
__pyx_v_self->vec_cumsum_gammas = ((double *)PyMem_Malloc((__pyx_v_n * (sizeof(double)))));
- /* "src/screening/gap_test_p_1.pyx":58
+ /* "slopescreening/screening/gap_test_p_1.pyx":58
*
* self.vec_cumsum_gammas = <double*> PyMem_Malloc(n * sizeof(double))
* self.vec_cumsum_gammas[0] = vec_gammas[0] # <<<<<<<<<<<<<<
@@ -2010,7 +2145,7 @@ static int __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(s
__pyx_t_1 = 0;
(__pyx_v_self->vec_cumsum_gammas[0]) = (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_gammas.rcbuffer->pybuffer.buf, __pyx_t_1, __pyx_pybuffernd_vec_gammas.diminfo[0].strides));
- /* "src/screening/gap_test_p_1.pyx":60
+ /* "slopescreening/screening/gap_test_p_1.pyx":60
* self.vec_cumsum_gammas[0] = vec_gammas[0]
*
* self.vec_kappa_q = <double*> PyMem_Malloc(n * sizeof(double)) # <<<<<<<<<<<<<<
@@ -2019,7 +2154,7 @@ static int __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(s
*/
__pyx_v_self->vec_kappa_q = ((double *)PyMem_Malloc((__pyx_v_n * (sizeof(double)))));
- /* "src/screening/gap_test_p_1.pyx":62
+ /* "slopescreening/screening/gap_test_p_1.pyx":62
* self.vec_kappa_q = <double*> PyMem_Malloc(n * sizeof(double))
*
* cdef int i = 0 # <<<<<<<<<<<<<<
@@ -2028,7 +2163,7 @@ static int __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(s
*/
__pyx_v_i = 0;
- /* "src/screening/gap_test_p_1.pyx":63
+ /* "slopescreening/screening/gap_test_p_1.pyx":63
*
* cdef int i = 0
* for i in range(1, n): # <<<<<<<<<<<<<<
@@ -2040,7 +2175,7 @@ static int __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(s
for (__pyx_t_4 = 1; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
__pyx_v_i = __pyx_t_4;
- /* "src/screening/gap_test_p_1.pyx":64
+ /* "slopescreening/screening/gap_test_p_1.pyx":64
* cdef int i = 0
* for i in range(1, n):
* self.vec_cumsum_gammas[i] = self.vec_cumsum_gammas[i-1] + vec_gammas[i] # <<<<<<<<<<<<<<
@@ -2051,7 +2186,7 @@ static int __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(s
(__pyx_v_self->vec_cumsum_gammas[__pyx_v_i]) = ((__pyx_v_self->vec_cumsum_gammas[(__pyx_v_i - 1)]) + (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_gammas.rcbuffer->pybuffer.buf, __pyx_t_1, __pyx_pybuffernd_vec_gammas.diminfo[0].strides)));
}
- /* "src/screening/gap_test_p_1.pyx":66
+ /* "slopescreening/screening/gap_test_p_1.pyx":66
* self.vec_cumsum_gammas[i] = self.vec_cumsum_gammas[i-1] + vec_gammas[i]
*
* for i in range(n): # <<<<<<<<<<<<<<
@@ -2063,7 +2198,7 @@ static int __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(s
for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
__pyx_v_i = __pyx_t_4;
- /* "src/screening/gap_test_p_1.pyx":67
+ /* "slopescreening/screening/gap_test_p_1.pyx":67
*
* for i in range(n):
* self.vec_kappa_q[i] = np.sqrt( # <<<<<<<<<<<<<<
@@ -2076,7 +2211,7 @@ static int __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(s
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "src/screening/gap_test_p_1.pyx":68
+ /* "slopescreening/screening/gap_test_p_1.pyx":68
* for i in range(n):
* self.vec_kappa_q[i] = np.sqrt(
* (1. + vec_coherence_function[i]) * (i + 1.) # <<<<<<<<<<<<<<
@@ -2103,7 +2238,7 @@ static int __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(s
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- /* "src/screening/gap_test_p_1.pyx":67
+ /* "slopescreening/screening/gap_test_p_1.pyx":67
*
* for i in range(n):
* self.vec_kappa_q[i] = np.sqrt( # <<<<<<<<<<<<<<
@@ -2115,7 +2250,7 @@ static int __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(s
(__pyx_v_self->vec_kappa_q[__pyx_v_i]) = __pyx_t_9;
}
- /* "src/screening/gap_test_p_1.pyx":76
+ /* "slopescreening/screening/gap_test_p_1.pyx":76
* # ).copy()
*
* self.name = "Gap test p=1 (cython)" # <<<<<<<<<<<<<<
@@ -2124,7 +2259,7 @@ static int __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(s
*/
__pyx_v_self->name = ((char *)"Gap test p=1 (cython)");
- /* "src/screening/gap_test_p_1.pyx":39
+ /* "slopescreening/screening/gap_test_p_1.pyx":39
* @cython.boundscheck(False) # turn off bounds-checking for entire function
* @cython.wraparound(False) # turn off negative index wrapping for entire function
* def __init__( # <<<<<<<<<<<<<<
@@ -2147,7 +2282,7 @@ static int __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(s
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_vec_coherence_function.rcbuffer->pybuffer);
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_vec_gammas.rcbuffer->pybuffer);
__Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);}
- __Pyx_AddTraceback("src.screening.gap_test_p_1.GapTestPequalOne.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("slopescreening.screening.gap_test_p_1.GapTestPequalOne.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
goto __pyx_L2;
__pyx_L0:;
@@ -2158,7 +2293,7 @@ static int __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(s
return __pyx_r;
}
-/* "src/screening/gap_test_p_1.pyx":79
+/* "slopescreening/screening/gap_test_p_1.pyx":79
*
*
* def __dealloc__(self): # <<<<<<<<<<<<<<
@@ -2167,21 +2302,21 @@ static int __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne___init__(s
*/
/* Python wrapper */
-static void __pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_3__dealloc__(PyObject *__pyx_v_self) {
+static void __pyx_pw_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_3__dealloc__(PyObject *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
- __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_2__dealloc__(((struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *)__pyx_v_self));
+ __pyx_pf_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_2__dealloc__(((struct __pyx_obj_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne *)__pyx_v_self));
/* function exit code */
__Pyx_RefNannyFinishContext();
}
-static void __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_2__dealloc__(struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self) {
+static void __pyx_pf_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_2__dealloc__(struct __pyx_obj_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__dealloc__", 0);
- /* "src/screening/gap_test_p_1.pyx":80
+ /* "slopescreening/screening/gap_test_p_1.pyx":80
*
* def __dealloc__(self):
* PyMem_Free(self.vec_cumsum_gammas) # no-op if self.data is NULL # <<<<<<<<<<<<<<
@@ -2190,7 +2325,7 @@ static void __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_2__deallo
*/
PyMem_Free(__pyx_v_self->vec_cumsum_gammas);
- /* "src/screening/gap_test_p_1.pyx":81
+ /* "slopescreening/screening/gap_test_p_1.pyx":81
* def __dealloc__(self):
* PyMem_Free(self.vec_cumsum_gammas) # no-op if self.data is NULL
* PyMem_Free(self.vec_kappa_q) # no-op if self.data is NULL # <<<<<<<<<<<<<<
@@ -2199,7 +2334,7 @@ static void __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_2__deallo
*/
PyMem_Free(__pyx_v_self->vec_kappa_q);
- /* "src/screening/gap_test_p_1.pyx":79
+ /* "slopescreening/screening/gap_test_p_1.pyx":79
*
*
* def __dealloc__(self): # <<<<<<<<<<<<<<
@@ -2211,7 +2346,7 @@ static void __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_2__deallo
__Pyx_RefNannyFinishContext();
}
-/* "src/screening/gap_test_p_1.pyx":86
+/* "slopescreening/screening/gap_test_p_1.pyx":86
* @cython.boundscheck(False) # turn off bounds-checking for entire function
* @cython.wraparound(False) # turn off negative index wrapping for entire function
* def apply_test(self, # <<<<<<<<<<<<<<
@@ -2220,9 +2355,9 @@ static void __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_2__deallo
*/
/* Python wrapper */
-static PyObject *__pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_5apply_test(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4apply_test[] = " Apply the Gap safe sphere screening test\n\n Implementation of the safe screening test\n \n Parameters\n ----------\n Atcabs : np.ndarray\n vector matA.T @ vecc where vec is dual admissible in absolute value\n size [n]\n gap : positive float\n duality gap\n lbd : positive float\n regularization parameters\n vec_gammas : np.ndarray\n slope parameters\n size [n,]\n vec_gammas : np.ndarray\n slope parameters\n size [n,]\n coeff_dual_scaling : positif float\n If coeff_dual_scaling is not feasible, dual scaling factor\n such taht vecu / coeff_dual_scaling os dual feasible\n Here for code optimization purposes\n Default value is 1. (vecu is feasible)\n offset_radius : float\n additive term added to the redius\n default is 0\n index : np.ndarray\n Array of indices that sort Atu in absolute value\n default is None\n \n Returns\n -------\n calI_screen : np.ndarray\n vector of boolean\n True if screening test passes and False otherwise\n size [n,]\n ";
-static PyObject *__pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_5apply_test(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pw_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_5apply_test(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_4apply_test[] = " Apply the Gap safe sphere screening test\n\n Implementation of the safe screening test\n \n Parameters\n ----------\n Atcabs : np.ndarray\n vector matA.T @ vecc where vec is dual admissible in absolute value\n size [n]\n gap : positive float\n duality gap\n lbd : positive float\n regularization parameters\n vec_gammas : np.ndarray\n slope parameters\n size [n,]\n vec_gammas : np.ndarray\n slope parameters\n size [n,]\n coeff_dual_scaling : positif float\n If coeff_dual_scaling is not feasible, dual scaling factor\n such taht vecu / coeff_dual_scaling os dual feasible\n Here for code optimization purposes\n Default value is 1. (vecu is feasible)\n offset_radius : float\n additive term added to the redius\n default is 0\n index : np.ndarray\n Array of indices that sort Atu in absolute value\n default is None\n \n Returns\n -------\n calI_screen : np.ndarray\n vector of boolean\n True if screening test passes and False otherwise\n size [n,]\n ";
+static PyObject *__pyx_pw_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_5apply_test(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyArrayObject *__pyx_v_Atcabs = 0;
double __pyx_v_gap;
double __pyx_v_lbd;
@@ -2240,7 +2375,7 @@ static PyObject *__pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_5app
static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_Atcabs,&__pyx_n_s_gap,&__pyx_n_s_lbd,&__pyx_n_s_vec_gammas,&__pyx_n_s_coeff_dual_scaling,&__pyx_n_s_offset_radius,&__pyx_n_s_index,0};
PyObject* values[7] = {0,0,0,0,0,0,0};
- /* "src/screening/gap_test_p_1.pyx":93
+ /* "slopescreening/screening/gap_test_p_1.pyx":93
* double coeff_dual_scaling = 1.,
* double offset_radius=0.,
* np.ndarray[long, ndim=1] index=None # <<<<<<<<<<<<<<
@@ -2350,16 +2485,16 @@ static PyObject *__pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_5app
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("apply_test", 0, 4, 7, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 86, __pyx_L3_error)
__pyx_L3_error:;
- __Pyx_AddTraceback("src.screening.gap_test_p_1.GapTestPequalOne.apply_test", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("slopescreening.screening.gap_test_p_1.GapTestPequalOne.apply_test", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_Atcabs), __pyx_ptype_5numpy_ndarray, 1, "Atcabs", 0))) __PYX_ERR(0, 87, __pyx_L1_error)
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_vec_gammas), __pyx_ptype_5numpy_ndarray, 1, "vec_gammas", 0))) __PYX_ERR(0, 90, __pyx_L1_error)
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_index), __pyx_ptype_5numpy_ndarray, 1, "index", 0))) __PYX_ERR(0, 93, __pyx_L1_error)
- __pyx_r = __pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4apply_test(((struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *)__pyx_v_self), __pyx_v_Atcabs, __pyx_v_gap, __pyx_v_lbd, __pyx_v_vec_gammas, __pyx_v_coeff_dual_scaling, __pyx_v_offset_radius, __pyx_v_index);
+ __pyx_r = __pyx_pf_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_4apply_test(((struct __pyx_obj_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne *)__pyx_v_self), __pyx_v_Atcabs, __pyx_v_gap, __pyx_v_lbd, __pyx_v_vec_gammas, __pyx_v_coeff_dual_scaling, __pyx_v_offset_radius, __pyx_v_index);
- /* "src/screening/gap_test_p_1.pyx":86
+ /* "slopescreening/screening/gap_test_p_1.pyx":86
* @cython.boundscheck(False) # turn off bounds-checking for entire function
* @cython.wraparound(False) # turn off negative index wrapping for entire function
* def apply_test(self, # <<<<<<<<<<<<<<
@@ -2376,7 +2511,7 @@ static PyObject *__pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_5app
return __pyx_r;
}
-static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4apply_test(struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_gap, double __pyx_v_lbd, CYTHON_UNUSED PyArrayObject *__pyx_v_vec_gammas, double __pyx_v_coeff_dual_scaling, double __pyx_v_offset_radius, PyArrayObject *__pyx_v_index) {
+static PyObject *__pyx_pf_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_4apply_test(struct __pyx_obj_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne *__pyx_v_self, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_gap, double __pyx_v_lbd, CYTHON_UNUSED PyArrayObject *__pyx_v_vec_gammas, double __pyx_v_coeff_dual_scaling, double __pyx_v_offset_radius, PyArrayObject *__pyx_v_index) {
int __pyx_v_n;
int __pyx_v_q;
int __pyx_v_l_q;
@@ -2460,7 +2595,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
}
__pyx_pybuffernd_index.diminfo[0].strides = __pyx_pybuffernd_index.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_index.diminfo[0].shape = __pyx_pybuffernd_index.rcbuffer->pybuffer.shape[0];
- /* "src/screening/gap_test_p_1.pyx":134
+ /* "slopescreening/screening/gap_test_p_1.pyx":134
* """
*
* cdef int n = Atcabs.shape[0] # <<<<<<<<<<<<<<
@@ -2469,7 +2604,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
*/
__pyx_v_n = (__pyx_v_Atcabs->dimensions[0]);
- /* "src/screening/gap_test_p_1.pyx":136
+ /* "slopescreening/screening/gap_test_p_1.pyx":136
* cdef int n = Atcabs.shape[0]
* cdef int q, l_q
* cdef int l_min = 0 # <<<<<<<<<<<<<<
@@ -2478,7 +2613,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
*/
__pyx_v_l_min = 0;
- /* "src/screening/gap_test_p_1.pyx":139
+ /* "slopescreening/screening/gap_test_p_1.pyx":139
*
* cdef double bound
* cdef double radius = coeff_dual_scaling * np.sqrt(2 * gap) + offset_radius # <<<<<<<<<<<<<<
@@ -2524,7 +2659,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_radius = __pyx_t_6;
- /* "src/screening/gap_test_p_1.pyx":140
+ /* "slopescreening/screening/gap_test_p_1.pyx":140
* cdef double bound
* cdef double radius = coeff_dual_scaling * np.sqrt(2 * gap) + offset_radius
* cdef double coeff_lbd = coeff_dual_scaling * lbd # <<<<<<<<<<<<<<
@@ -2533,7 +2668,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
*/
__pyx_v_coeff_lbd = (__pyx_v_coeff_dual_scaling * __pyx_v_lbd);
- /* "src/screening/gap_test_p_1.pyx":142
+ /* "slopescreening/screening/gap_test_p_1.pyx":142
* cdef double coeff_lbd = coeff_dual_scaling * lbd
*
* cdef np.ndarray[np.npy_double, ndim=1] sigmas = np.zeros(n+1) # <<<<<<<<<<<<<<
@@ -2577,7 +2712,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
__pyx_v_sigmas = ((PyArrayObject *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "src/screening/gap_test_p_1.pyx":145
+ /* "slopescreening/screening/gap_test_p_1.pyx":145
*
* # output
* cdef np.ndarray[np.npy_bool, ndim=1] calI_screen = np.zeros(n, dtype=bool) # <<<<<<<<<<<<<<
@@ -2618,7 +2753,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
__pyx_v_calI_screen = ((PyArrayObject *)__pyx_t_3);
__pyx_t_3 = 0;
- /* "src/screening/gap_test_p_1.pyx":148
+ /* "slopescreening/screening/gap_test_p_1.pyx":148
*
* # 1. Sort in descending order
* if index is None: # <<<<<<<<<<<<<<
@@ -2629,7 +2764,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
__pyx_t_10 = (__pyx_t_9 != 0);
if (__pyx_t_10) {
- /* "src/screening/gap_test_p_1.pyx":149
+ /* "slopescreening/screening/gap_test_p_1.pyx":149
* # 1. Sort in descending order
* if index is None:
* index = np.argsort(Atcabs)[::-1] # <<<<<<<<<<<<<<
@@ -2682,7 +2817,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
__Pyx_DECREF_SET(__pyx_v_index, ((PyArrayObject *)__pyx_t_2));
__pyx_t_2 = 0;
- /* "src/screening/gap_test_p_1.pyx":148
+ /* "slopescreening/screening/gap_test_p_1.pyx":148
*
* # 1. Sort in descending order
* if index is None: # <<<<<<<<<<<<<<
@@ -2691,7 +2826,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
*/
}
- /* "src/screening/gap_test_p_1.pyx":152
+ /* "slopescreening/screening/gap_test_p_1.pyx":152
*
* # Cdric' notations compliant
* sigmas[1:] = np.cumsum(Atcabs[index]) # <<<<<<<<<<<<<<
@@ -2724,7 +2859,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
if (unlikely(PyObject_SetItem(((PyObject *)__pyx_v_sigmas), __pyx_slice__2, __pyx_t_2) < 0)) __PYX_ERR(0, 152, __pyx_L1_error)
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "src/screening/gap_test_p_1.pyx":154
+ /* "slopescreening/screening/gap_test_p_1.pyx":154
* sigmas[1:] = np.cumsum(Atcabs[index])
*
* for q in range(n-1, -1, -1): # <<<<<<<<<<<<<<
@@ -2734,7 +2869,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
for (__pyx_t_12 = (__pyx_v_n - 1); __pyx_t_12 > -1; __pyx_t_12-=1) {
__pyx_v_q = __pyx_t_12;
- /* "src/screening/gap_test_p_1.pyx":155
+ /* "slopescreening/screening/gap_test_p_1.pyx":155
*
* for q in range(n-1, -1, -1):
* bound = coeff_lbd * self.vec_cumsum_gammas[q] - self.vec_kappa_q[q] * radius - sigmas[q] # <<<<<<<<<<<<<<
@@ -2744,7 +2879,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
__pyx_t_16 = __pyx_v_q;
__pyx_v_bound = (((__pyx_v_coeff_lbd * (__pyx_v_self->vec_cumsum_gammas[__pyx_v_q])) - ((__pyx_v_self->vec_kappa_q[__pyx_v_q]) * __pyx_v_radius)) - (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_sigmas.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_sigmas.diminfo[0].strides)));
- /* "src/screening/gap_test_p_1.pyx":157
+ /* "slopescreening/screening/gap_test_p_1.pyx":157
* bound = coeff_lbd * self.vec_cumsum_gammas[q] - self.vec_kappa_q[q] * radius - sigmas[q]
*
* if Atcabs[index[q]] < bound: # <<<<<<<<<<<<<<
@@ -2756,7 +2891,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
__pyx_t_10 = (((*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_Atcabs.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_Atcabs.diminfo[0].strides)) < __pyx_v_bound) != 0);
if (__pyx_t_10) {
- /* "src/screening/gap_test_p_1.pyx":158
+ /* "slopescreening/screening/gap_test_p_1.pyx":158
*
* if Atcabs[index[q]] < bound:
* l_q = 0 # <<<<<<<<<<<<<<
@@ -2765,7 +2900,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
*/
__pyx_v_l_q = 0;
- /* "src/screening/gap_test_p_1.pyx":157
+ /* "slopescreening/screening/gap_test_p_1.pyx":157
* bound = coeff_lbd * self.vec_cumsum_gammas[q] - self.vec_kappa_q[q] * radius - sigmas[q]
*
* if Atcabs[index[q]] < bound: # <<<<<<<<<<<<<<
@@ -2775,7 +2910,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
goto __pyx_L6;
}
- /* "src/screening/gap_test_p_1.pyx":160
+ /* "slopescreening/screening/gap_test_p_1.pyx":160
* l_q = 0
*
* elif Atcabs[index[n-1]] >= bound: # <<<<<<<<<<<<<<
@@ -2787,7 +2922,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
__pyx_t_10 = (((*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_Atcabs.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_Atcabs.diminfo[0].strides)) >= __pyx_v_bound) != 0);
if (__pyx_t_10) {
- /* "src/screening/gap_test_p_1.pyx":161
+ /* "slopescreening/screening/gap_test_p_1.pyx":161
*
* elif Atcabs[index[n-1]] >= bound:
* return calI_screen # <<<<<<<<<<<<<<
@@ -2799,7 +2934,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
__pyx_r = ((PyObject *)__pyx_v_calI_screen);
goto __pyx_L0;
- /* "src/screening/gap_test_p_1.pyx":160
+ /* "slopescreening/screening/gap_test_p_1.pyx":160
* l_q = 0
*
* elif Atcabs[index[n-1]] >= bound: # <<<<<<<<<<<<<<
@@ -2808,7 +2943,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
*/
}
- /* "src/screening/gap_test_p_1.pyx":164
+ /* "slopescreening/screening/gap_test_p_1.pyx":164
*
* else:
* l_q = q + np.argmax(Atcabs[index[q:]] < bound) # <<<<<<<<<<<<<<
@@ -2865,7 +3000,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
}
__pyx_L6:;
- /* "src/screening/gap_test_p_1.pyx":166
+ /* "slopescreening/screening/gap_test_p_1.pyx":166
* l_q = q + np.argmax(Atcabs[index[q:]] < bound)
*
* l_min = max(l_min, l_q) # <<<<<<<<<<<<<<
@@ -2882,7 +3017,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
__pyx_v_l_min = __pyx_t_21;
}
- /* "src/screening/gap_test_p_1.pyx":168
+ /* "slopescreening/screening/gap_test_p_1.pyx":168
* l_min = max(l_min, l_q)
*
* calI_screen[index[l_min:]] = True # <<<<<<<<<<<<<<
@@ -2899,7 +3034,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
if (unlikely(PyObject_SetItem(((PyObject *)__pyx_v_calI_screen), __pyx_t_4, Py_True) < 0)) __PYX_ERR(0, 168, __pyx_L1_error)
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "src/screening/gap_test_p_1.pyx":169
+ /* "slopescreening/screening/gap_test_p_1.pyx":169
*
* calI_screen[index[l_min:]] = True
* return calI_screen # <<<<<<<<<<<<<<
@@ -2909,7 +3044,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
__pyx_r = ((PyObject *)__pyx_v_calI_screen);
goto __pyx_L0;
- /* "src/screening/gap_test_p_1.pyx":86
+ /* "slopescreening/screening/gap_test_p_1.pyx":86
* @cython.boundscheck(False) # turn off bounds-checking for entire function
* @cython.wraparound(False) # turn off negative index wrapping for entire function
* def apply_test(self, # <<<<<<<<<<<<<<
@@ -2935,7 +3070,7 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_sigmas.rcbuffer->pybuffer);
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_vec_gammas.rcbuffer->pybuffer);
__Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);}
- __Pyx_AddTraceback("src.screening.gap_test_p_1.GapTestPequalOne.apply_test", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("slopescreening.screening.gap_test_p_1.GapTestPequalOne.apply_test", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
goto __pyx_L2;
__pyx_L0:;
@@ -2960,19 +3095,19 @@ static PyObject *__pyx_pf_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4app
*/
/* Python wrapper */
-static PyObject *__pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_7__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static PyObject *__pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_7__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pw_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_7__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static PyObject *__pyx_pw_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_7__reduce_cython__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
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if (__pyx_t_1) {
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__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":935
+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":934
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- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":937
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__pyx_r = ((PyObject *)__pyx_v_base);
goto __pyx_L0;
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":933
+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":932
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return __pyx_r;
}
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* cdef inline int import_array() except -1: # <<<<<<<<<<<<<<
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* # Cython code.
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__Pyx_XGOTREF(__pyx_t_3);
/*try:*/ {
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":943
+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":942
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- __pyx_t_4 = _import_array(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(2, 943, __pyx_L3_error)
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- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":942
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* # Cython code.
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goto __pyx_L8_try_end;
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* # Cython code.
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__pyx_L8_try_end:;
}
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":941
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* # Versions of the import_* functions which are more suitable for
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return __pyx_r;
}
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* raise ImportError("numpy.core.multiarray failed to import")
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int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("import_umath", 0);
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*
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__Pyx_XGOTREF(__pyx_t_3);
/*try:*/ {
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":949
+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":948
* cdef inline int import_umath() except -1:
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*/
- __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(2, 949, __pyx_L3_error)
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- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":948
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*
* cdef inline int import_umath() except -1:
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goto __pyx_L8_try_end;
__pyx_L3_error:;
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":950
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if (__pyx_t_4) {
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*
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__pyx_L8_try_end:;
}
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+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":946
* raise ImportError("numpy.core.multiarray failed to import")
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return __pyx_r;
}
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+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":952
* raise ImportError("numpy.core.umath failed to import")
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*
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__Pyx_XGOTREF(__pyx_t_3);
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+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":954
* cdef inline int import_ufunc() except -1:
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*/
- __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(2, 955, __pyx_L3_error)
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*
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goto __pyx_L8_try_end;
__pyx_L3_error:;
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":956
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if (__pyx_t_4) {
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- if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_6, &__pyx_t_7) < 0) __PYX_ERR(2, 956, __pyx_L5_except_error)
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goto __pyx_L5_except_error;
__pyx_L5_except_error:;
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":954
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*
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__pyx_L8_try_end:;
}
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":953
+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":952
* raise ImportError("numpy.core.umath failed to import")
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* cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<<
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return __pyx_r;
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- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":979
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goto __pyx_L0;
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":967
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*
*
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return __pyx_r;
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*
*
* cdef inline bint is_datetime64_object(object obj): # <<<<<<<<<<<<<<
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return __pyx_r;
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goto __pyx_L0;
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*
*
* cdef inline npy_datetime get_datetime64_value(object obj) nogil: # <<<<<<<<<<<<<<
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return __pyx_r;
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*
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* cdef inline npy_timedelta get_timedelta64_value(object obj) nogil: # <<<<<<<<<<<<<<
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__pyx_r = ((PyTimedeltaScalarObject *)__pyx_v_obj)->obval;
goto __pyx_L0;
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":1007
+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":1006
*
*
* cdef inline npy_timedelta get_timedelta64_value(object obj) nogil: # <<<<<<<<<<<<<<
@@ -4051,7 +4186,7 @@ static CYTHON_INLINE npy_timedelta __pyx_f_5numpy_get_timedelta64_value(PyObject
return __pyx_r;
}
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":1014
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":1013
*
*
* cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) nogil: # <<<<<<<<<<<<<<
@@ -4062,7 +4197,7 @@ 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;
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":1018
+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":1017
* returns the unit part of the dtype for a numpy datetime64 object.
* """
* return <NPY_DATETIMEUNIT>(<PyDatetimeScalarObject*>obj).obmeta.base # <<<<<<<<<<<<<<
@@ -4070,7 +4205,7 @@ 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;
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":1014
+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":1013
*
*
* cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) nogil: # <<<<<<<<<<<<<<
@@ -4083,7 +4218,7 @@ static CYTHON_INLINE NPY_DATETIMEUNIT __pyx_f_5numpy_get_datetime64_unit(PyObjec
return __pyx_r;
}
-static PyObject *__pyx_tp_new_3src_9screening_12gap_test_p_1_GapTestPequalOne(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+static PyObject *__pyx_tp_new_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
PyObject *o;
if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
o = (*t->tp_alloc)(t, 0);
@@ -4094,7 +4229,7 @@ static PyObject *__pyx_tp_new_3src_9screening_12gap_test_p_1_GapTestPequalOne(Py
return o;
}
-static void __pyx_tp_dealloc_3src_9screening_12gap_test_p_1_GapTestPequalOne(PyObject *o) {
+static void __pyx_tp_dealloc_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne(PyObject *o) {
#if CYTHON_USE_TP_FINALIZE
if (unlikely(PyType_HasFeature(Py_TYPE(o), Py_TPFLAGS_HAVE_FINALIZE) && Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) {
if (PyObject_CallFinalizerFromDealloc(o)) return;
@@ -4104,26 +4239,26 @@ static void __pyx_tp_dealloc_3src_9screening_12gap_test_p_1_GapTestPequalOne(PyO
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
__Pyx_SET_REFCNT(o, Py_REFCNT(o) + 1);
- __pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_3__dealloc__(o);
+ __pyx_pw_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_3__dealloc__(o);
__Pyx_SET_REFCNT(o, Py_REFCNT(o) - 1);
PyErr_Restore(etype, eval, etb);
}
(*Py_TYPE(o)->tp_free)(o);
}
-static PyMethodDef __pyx_methods_3src_9screening_12gap_test_p_1_GapTestPequalOne[] = {
- {"apply_test", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_5apply_test, METH_VARARGS|METH_KEYWORDS, __pyx_doc_3src_9screening_12gap_test_p_1_16GapTestPequalOne_4apply_test},
- {"__reduce_cython__", (PyCFunction)__pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_7__reduce_cython__, METH_NOARGS, 0},
- {"__setstate_cython__", (PyCFunction)__pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_9__setstate_cython__, METH_O, 0},
+static PyMethodDef __pyx_methods_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne[] = {
+ {"apply_test", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_5apply_test, METH_VARARGS|METH_KEYWORDS, __pyx_doc_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_4apply_test},
+ {"__reduce_cython__", (PyCFunction)__pyx_pw_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_7__reduce_cython__, METH_NOARGS, 0},
+ {"__setstate_cython__", (PyCFunction)__pyx_pw_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_9__setstate_cython__, METH_O, 0},
{0, 0, 0, 0}
};
-static PyTypeObject __pyx_type_3src_9screening_12gap_test_p_1_GapTestPequalOne = {
+static PyTypeObject __pyx_type_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne = {
PyVarObject_HEAD_INIT(0, 0)
- "src.screening.gap_test_p_1.GapTestPequalOne", /*tp_name*/
- sizeof(struct __pyx_obj_3src_9screening_12gap_test_p_1_GapTestPequalOne), /*tp_basicsize*/
+ "slopescreening.screening.gap_test_p_1.GapTestPequalOne", /*tp_name*/
+ sizeof(struct __pyx_obj_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_3src_9screening_12gap_test_p_1_GapTestPequalOne, /*tp_dealloc*/
+ __pyx_tp_dealloc_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne, /*tp_dealloc*/
#if PY_VERSION_HEX < 0x030800b4
0, /*tp_print*/
#endif
@@ -4156,7 +4291,7 @@ static PyTypeObject __pyx_type_3src_9screening_12gap_test_p_1_GapTestPequalOne =
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_3src_9screening_12gap_test_p_1_GapTestPequalOne, /*tp_methods*/
+ __pyx_methods_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -4164,9 +4299,9 @@ static PyTypeObject __pyx_type_3src_9screening_12gap_test_p_1_GapTestPequalOne =
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pw_3src_9screening_12gap_test_p_1_16GapTestPequalOne_1__init__, /*tp_init*/
+ __pyx_pw_14slopescreening_9screening_12gap_test_p_1_16GapTestPequalOne_1__init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_3src_9screening_12gap_test_p_1_GapTestPequalOne, /*tp_new*/
+ __pyx_tp_new_14slopescreening_9screening_12gap_test_p_1_GapTestPequalOne, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -4179,12 +4314,15 @@ static PyTypeObject __pyx_type_3src_9screening_12gap_test_p_1_GapTestPequalOne =
#if PY_VERSION_HEX >= 0x030400a1
0, /*tp_finalize*/
#endif
- #if PY_VERSION_HEX >= 0x030800b1
+ #if PY_VERSION_HEX >= 0x030800b1 && (!CYTHON_COMPILING_IN_PYPY || PYPY_VERSION_NUM >= 0x07030800)
0, /*tp_vectorcall*/
#endif
#if PY_VERSION_HEX >= 0x030800b4 && PY_VERSION_HEX < 0x03090000
0, /*tp_print*/
#endif
+ #if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX >= 0x03090000
+ 0, /*tp_pypy_flags*/
+ #endif
};
static PyMethodDef __pyx_methods[] = {
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{&__pyx_n_s_setstate, __pyx_k_setstate, sizeof(__pyx_k_setstate), 0, 0, 1, 1},
{&__pyx_n_s_setstate_cython, __pyx_k_setstate_cython, sizeof(__pyx_k_setstate_cython), 0, 0, 1, 1},
+ {&__pyx_n_s_slopescreening_screening_ascreen, __pyx_k_slopescreening_screening_ascreen, sizeof(__pyx_k_slopescreening_screening_ascreen), 0, 0, 1, 1},
{&__pyx_n_s_sqrt, __pyx_k_sqrt, sizeof(__pyx_k_sqrt), 0, 0, 1, 1},
- {&__pyx_n_s_src_screening_ascreening, __pyx_k_src_screening_ascreening, sizeof(__pyx_k_src_screening_ascreening), 0, 0, 1, 1},
{&__pyx_n_s_test, __pyx_k_test, sizeof(__pyx_k_test), 0, 0, 1, 1},
{&__pyx_n_s_vec_coherence_function, __pyx_k_vec_coherence_function, sizeof(__pyx_k_vec_coherence_function), 0, 0, 1, 1},
{&__pyx_n_s_vec_gammas, __pyx_k_vec_gammas, sizeof(__pyx_k_vec_gammas), 0, 0, 1, 1},
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__pyx_builtin_TypeError = __Pyx_GetBuiltinName(__pyx_n_s_TypeError); if (!__pyx_builtin_TypeError) __PYX_ERR(1, 2, __pyx_L1_error)
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+ __pyx_builtin_ImportError = __Pyx_GetBuiltinName(__pyx_n_s_ImportError); if (!__pyx_builtin_ImportError) __PYX_ERR(2, 944, __pyx_L1_error)
return 0;
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__Pyx_RefNannyDeclarations
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__Pyx_GOTREF(__pyx_slice_);
__Pyx_GIVEREF(__pyx_slice_);
- /* "src/screening/gap_test_p_1.pyx":152
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__Pyx_GIVEREF(__pyx_tuple__4);
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":945
+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":944
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* cdef inline int import_umath() except -1:
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__Pyx_GIVEREF(__pyx_tuple__5);
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":951
+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":950
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- __pyx_type_3src_9screening_12gap_test_p_1_GapTestPequalOne.tp_print = 0;
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__pyx_ptype_5numpy_ufunc = __Pyx_ImportType(__pyx_t_1, "numpy", "ufunc", sizeof(PyUFuncObject), __Pyx_ImportType_CheckSize_Ignore);
- if (!__pyx_ptype_5numpy_ufunc) __PYX_ERR(2, 827, __pyx_L1_error)
+ if (!__pyx_ptype_5numpy_ufunc) __PYX_ERR(2, 826, __pyx_L1_error)
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_RefNannyFinishContext();
return 0;
@@ -4667,14 +4805,14 @@ if (!__Pyx_RefNanny) {
#if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT)
if (__Pyx_init_sys_getdefaultencoding_params() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
#endif
- if (__pyx_module_is_main_src__screening__gap_test_p_1) {
+ if (__pyx_module_is_main_slopescreening__screening__gap_test_p_1) {
if (PyObject_SetAttr(__pyx_m, __pyx_n_s_name, __pyx_n_s_main) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
}
#if PY_MAJOR_VERSION >= 3
{
PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) __PYX_ERR(0, 1, __pyx_L1_error)
- if (!PyDict_GetItemString(modules, "src.screening.gap_test_p_1")) {
- if (unlikely(PyDict_SetItemString(modules, "src.screening.gap_test_p_1", __pyx_m) < 0)) __PYX_ERR(0, 1, __pyx_L1_error)
+ if (!PyDict_GetItemString(modules, "slopescreening.screening.gap_test_p_1")) {
+ if (unlikely(PyDict_SetItemString(modules, "slopescreening.screening.gap_test_p_1", __pyx_m) < 0)) __PYX_ERR(0, 1, __pyx_L1_error)
}
}
#endif
@@ -4695,22 +4833,22 @@ if (!__Pyx_RefNanny) {
if (__Pyx_patch_abc() < 0) __PYX_ERR(0, 1, __pyx_L1_error)
#endif
- /* "src/screening/gap_test_p_1.pyx":3
+ /* "slopescreening/screening/gap_test_p_1.pyx":3
* # -*- coding: utf-8 -*-
* # Based on https://cython.readthedocs.io/en/latest/src/tutorial/numpy.html
* import numpy as np # <<<<<<<<<<<<<<
*
- * from src.screening.ascreening import AbstractGapScreening
+ * from slopescreening.screening.ascreening import AbstractGapScreening
*/
__pyx_t_1 = __Pyx_Import(__pyx_n_s_numpy, 0, -1); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 3, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_1);
if (PyDict_SetItem(__pyx_d, __pyx_n_s_np, __pyx_t_1) < 0) __PYX_ERR(0, 3, __pyx_L1_error)
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "src/screening/gap_test_p_1.pyx":5
+ /* "slopescreening/screening/gap_test_p_1.pyx":5
* import numpy as np
*
- * from src.screening.ascreening import AbstractGapScreening # <<<<<<<<<<<<<<
+ * from slopescreening.screening.ascreening import AbstractGapScreening # <<<<<<<<<<<<<<
*
*
*/
@@ -4719,7 +4857,7 @@ if (!__Pyx_RefNanny) {
__Pyx_INCREF(__pyx_n_s_AbstractGapScreening);
__Pyx_GIVEREF(__pyx_n_s_AbstractGapScreening);
PyList_SET_ITEM(__pyx_t_1, 0, __pyx_n_s_AbstractGapScreening);
- __pyx_t_2 = __Pyx_Import(__pyx_n_s_src_screening_ascreening, __pyx_t_1, -1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 5, __pyx_L1_error)
+ __pyx_t_2 = __Pyx_Import(__pyx_n_s_slopescreening_screening_ascreen, __pyx_t_1, -1); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 5, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_1 = __Pyx_ImportFrom(__pyx_t_2, __pyx_n_s_AbstractGapScreening); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 5, __pyx_L1_error)
@@ -4728,7 +4866,7 @@ if (!__Pyx_RefNanny) {
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "src/screening/gap_test_p_1.pyx":1
+ /* "slopescreening/screening/gap_test_p_1.pyx":1
* # -*- coding: utf-8 -*- # <<<<<<<<<<<<<<
* # Based on https://cython.readthedocs.io/en/latest/src/tutorial/numpy.html
* import numpy as np
@@ -4738,7 +4876,7 @@ if (!__Pyx_RefNanny) {
if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_2) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":1014
+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":1013
*
*
* cdef inline NPY_DATETIMEUNIT get_datetime64_unit(object obj) nogil: # <<<<<<<<<<<<<<
@@ -4754,11 +4892,11 @@ if (!__Pyx_RefNanny) {
__Pyx_XDECREF(__pyx_t_2);
if (__pyx_m) {
if (__pyx_d) {
- __Pyx_AddTraceback("init src.screening.gap_test_p_1", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("init slopescreening.screening.gap_test_p_1", __pyx_clineno, __pyx_lineno, __pyx_filename);
}
Py_CLEAR(__pyx_m);
} else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_ImportError, "init src.screening.gap_test_p_1");
+ PyErr_SetString(PyExc_ImportError, "init slopescreening.screening.gap_test_p_1");
}
__pyx_L0:;
__Pyx_RefNannyFinishContext();
@@ -6417,17 +6555,35 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStrNoError(PyObject* obj, P
static int __Pyx_setup_reduce(PyObject* type_obj) {
int ret = 0;
PyObject *object_reduce = NULL;
+ PyObject *object_getstate = NULL;
PyObject *object_reduce_ex = NULL;
PyObject *reduce = NULL;
PyObject *reduce_ex = NULL;
PyObject *reduce_cython = NULL;
PyObject *setstate = NULL;
PyObject *setstate_cython = NULL;
+ PyObject *getstate = NULL;
#if CYTHON_USE_PYTYPE_LOOKUP
- if (_PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate)) goto __PYX_GOOD;
+ getstate = _PyType_Lookup((PyTypeObject*)type_obj, __pyx_n_s_getstate);
#else
- if (PyObject_HasAttr(type_obj, __pyx_n_s_getstate)) goto __PYX_GOOD;
+ getstate = __Pyx_PyObject_GetAttrStrNoError(type_obj, __pyx_n_s_getstate);
+ if (!getstate && PyErr_Occurred()) {
+ goto __PYX_BAD;
+ }
#endif
+ if (getstate) {
+#if CYTHON_USE_PYTYPE_LOOKUP
+ object_getstate = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_getstate);
+#else
+ object_getstate = __Pyx_PyObject_GetAttrStrNoError((PyObject*)&PyBaseObject_Type, __pyx_n_s_getstate);
+ if (!object_getstate && PyErr_Occurred()) {
+ goto __PYX_BAD;
+ }
+#endif
+ if (object_getstate != getstate) {
+ goto __PYX_GOOD;
+ }
+ }
#if CYTHON_USE_PYTYPE_LOOKUP
object_reduce_ex = _PyType_Lookup(&PyBaseObject_Type, __pyx_n_s_reduce_ex); if (!object_reduce_ex) goto __PYX_BAD;
#else
@@ -6472,6 +6628,8 @@ __PYX_GOOD:
#if !CYTHON_USE_PYTYPE_LOOKUP
Py_XDECREF(object_reduce);
Py_XDECREF(object_reduce_ex);
+ Py_XDECREF(object_getstate);
+ Py_XDECREF(getstate);
#endif
Py_XDECREF(reduce);
Py_XDECREF(reduce_ex);
@@ -6653,7 +6811,7 @@ static int __Pyx_CLineForTraceback(CYTHON_NCP_UNUSED PyThreadState *tstate, int
}
if (!use_cline) {
c_line = 0;
- PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False);
+ (void) PyObject_SetAttr(__pyx_cython_runtime, __pyx_n_s_cline_in_traceback, Py_False);
}
else if (use_cline == Py_False || (use_cline != Py_True && PyObject_Not(use_cline) != 0)) {
c_line = 0;
@@ -6747,33 +6905,40 @@ static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
#include "compile.h"
#include "frameobject.h"
#include "traceback.h"
+#if PY_VERSION_HEX >= 0x030b00a6
+ #ifndef Py_BUILD_CORE
+ #define Py_BUILD_CORE 1
+ #endif
+ #include "internal/pycore_frame.h"
+#endif
static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
const char *funcname, int c_line,
int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
+ PyCodeObject *py_code = NULL;
+ PyObject *py_funcname = NULL;
#if PY_MAJOR_VERSION < 3
+ PyObject *py_srcfile = NULL;
py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
if (!py_srcfile) goto bad;
+ #endif
if (c_line) {
#if PY_MAJOR_VERSION < 3
py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
+ if (!py_funcname) goto bad;
#else
py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
+ if (!py_funcname) goto bad;
+ funcname = PyUnicode_AsUTF8(py_funcname);
+ if (!funcname) goto bad;
#endif
}
else {
#if PY_MAJOR_VERSION < 3
py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
+ if (!py_funcname) goto bad;
#endif
}
- if (!py_funcname) goto bad;
+ #if PY_MAJOR_VERSION < 3
py_code = __Pyx_PyCode_New(
0,
0,
@@ -6792,11 +6957,16 @@ static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
__pyx_empty_bytes /*PyObject *lnotab*/
);
Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
+ #else
+ py_code = PyCode_NewEmpty(filename, funcname, py_line);
+ #endif
+ Py_XDECREF(py_funcname); // XDECREF since it's only set on Py3 if cline
return py_code;
bad:
- Py_XDECREF(py_srcfile);
Py_XDECREF(py_funcname);
+ #if PY_MAJOR_VERSION < 3
+ Py_XDECREF(py_srcfile);
+ #endif
return NULL;
}
static void __Pyx_AddTraceback(const char *funcname, int c_line,
@@ -6804,14 +6974,24 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line,
PyCodeObject *py_code = 0;
PyFrameObject *py_frame = 0;
PyThreadState *tstate = __Pyx_PyThreadState_Current;
+ PyObject *ptype, *pvalue, *ptraceback;
if (c_line) {
c_line = __Pyx_CLineForTraceback(tstate, c_line);
}
py_code = __pyx_find_code_object(c_line ? -c_line : py_line);
if (!py_code) {
+ __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback);
py_code = __Pyx_CreateCodeObjectForTraceback(
funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
+ if (!py_code) {
+ /* If the code object creation fails, then we should clear the
+ fetched exception references and propagate the new exception */
+ Py_XDECREF(ptype);
+ Py_XDECREF(pvalue);
+ Py_XDECREF(ptraceback);
+ goto bad;
+ }
+ __Pyx_ErrRestoreInState(tstate, ptype, pvalue, ptraceback);
__pyx_insert_code_object(c_line ? -c_line : py_line, py_code);
}
py_frame = PyFrame_New(
@@ -7748,11 +7928,33 @@ static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObj
/* CheckBinaryVersion */
static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
+ char ctversion[5];
+ int same=1, i, found_dot;
+ const char* rt_from_call = Py_GetVersion();
+ PyOS_snprintf(ctversion, 5, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
+ found_dot = 0;
+ for (i = 0; i < 4; i++) {
+ if (!ctversion[i]) {
+ same = (rt_from_call[i] < '0' || rt_from_call[i] > '9');
+ break;
+ }
+ if (rt_from_call[i] != ctversion[i]) {
+ same = 0;
+ break;
+ }
+ }
+ if (!same) {
+ char rtversion[5] = {'\0'};
char message[200];
+ for (i=0; i<4; ++i) {
+ if (rt_from_call[i] == '.') {
+ if (found_dot) break;
+ found_dot = 1;
+ } else if (rt_from_call[i] < '0' || rt_from_call[i] > '9') {
+ break;
+ }
+ rtversion[i] = rt_from_call[i];
+ }
PyOS_snprintf(message, sizeof(message),
"compiletime version %s of module '%.100s' "
"does not match runtime version %s",
@@ -8010,6 +8212,23 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
Py_DECREF(x);
return ival;
}
+static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject* o) {
+ if (sizeof(Py_hash_t) == sizeof(Py_ssize_t)) {
+ return (Py_hash_t) __Pyx_PyIndex_AsSsize_t(o);
+#if PY_MAJOR_VERSION < 3
+ } else if (likely(PyInt_CheckExact(o))) {
+ return PyInt_AS_LONG(o);
+#endif
+ } else {
+ Py_ssize_t ival;
+ PyObject *x;
+ x = PyNumber_Index(o);
+ if (!x) return -1;
+ ival = PyInt_AsLong(x);
+ Py_DECREF(x);
+ return ival;
+ }
+}
static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b) {
return b ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False);
}
diff --git a/src/screening/gap_test_p_1.pyx b/slopescreening/screening/gap_test_p_1.pyx
similarity index 98%
rename from src/screening/gap_test_p_1.pyx
rename to slopescreening/screening/gap_test_p_1.pyx
index 9fc4aa1..d01208d 100644
--- a/src/screening/gap_test_p_1.pyx
+++ b/slopescreening/screening/gap_test_p_1.pyx
@@ -2,7 +2,7 @@
# Based on https://cython.readthedocs.io/en/latest/src/tutorial/numpy.html
import numpy as np
-from src.screening.ascreening import AbstractGapScreening
+from slopescreening.screening.ascreening import AbstractGapScreening
# "cimport" is used to import special compile-time information
diff --git a/src/screening/gap_test_p_q.py b/slopescreening/screening/gap_test_p_q.py
similarity index 95%
rename from src/screening/gap_test_p_q.py
rename to slopescreening/screening/gap_test_p_q.py
index 6520ba0..1923359 100644
--- a/src/screening/gap_test_p_q.py
+++ b/slopescreening/screening/gap_test_p_q.py
@@ -1,7 +1,7 @@
# -*- coding: utf-8 -*-
import numpy as np
-from src.screening.ascreening import AbstractGapScreening
+from slopescreening.screening.ascreening import AbstractGapScreening
class GapTestPequalQ(AbstractGapScreening):
diff --git a/src/screening/utils.c b/slopescreening/screening/utils.c
similarity index 91%
rename from src/screening/utils.c
rename to slopescreening/screening/utils.c
index f9e32a5..254c0ea 100644
--- a/src/screening/utils.c
+++ b/slopescreening/screening/utils.c
@@ -1,15 +1,15 @@
-/* Generated by Cython 0.29.24 */
+/* Generated by Cython 0.29.32 */
/* BEGIN: Cython Metadata
{
"distutils": {
"depends": [],
- "name": "src.screening.utils",
+ "name": "slopescreening.screening.utils",
"sources": [
- "src/screening/utils.pyx"
+ "slopescreening/screening/utils.pyx"
]
},
- "module_name": "src.screening.utils"
+ "module_name": "slopescreening.screening.utils"
}
END: Cython Metadata */
@@ -22,8 +22,8 @@ END: Cython Metadata */
#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000)
#error Cython requires Python 2.6+ or Python 3.3+.
#else
-#define CYTHON_ABI "0_29_24"
-#define CYTHON_HEX_VERSION 0x001D18F0
+#define CYTHON_ABI "0_29_32"
+#define CYTHON_HEX_VERSION 0x001D20F0
#define CYTHON_FUTURE_DIVISION 0
#include <stddef.h>
#ifndef offsetof
@@ -62,6 +62,7 @@ END: Cython Metadata */
#define CYTHON_COMPILING_IN_PYPY 1
#define CYTHON_COMPILING_IN_PYSTON 0
#define CYTHON_COMPILING_IN_CPYTHON 0
+ #define CYTHON_COMPILING_IN_NOGIL 0
#undef CYTHON_USE_TYPE_SLOTS
#define CYTHON_USE_TYPE_SLOTS 0
#undef CYTHON_USE_PYTYPE_LOOKUP
@@ -98,10 +99,14 @@ END: Cython Metadata */
#define CYTHON_USE_DICT_VERSIONS 0
#undef CYTHON_USE_EXC_INFO_STACK
#define CYTHON_USE_EXC_INFO_STACK 0
+ #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
+ #define CYTHON_UPDATE_DESCRIPTOR_DOC (PYPY_VERSION_HEX >= 0x07030900)
+ #endif
#elif defined(PYSTON_VERSION)
#define CYTHON_COMPILING_IN_PYPY 0
#define CYTHON_COMPILING_IN_PYSTON 1
#define CYTHON_COMPILING_IN_CPYTHON 0
+ #define CYTHON_COMPILING_IN_NOGIL 0
#ifndef CYTHON_USE_TYPE_SLOTS
#define CYTHON_USE_TYPE_SLOTS 1
#endif
@@ -139,10 +144,59 @@ END: Cython Metadata */
#define CYTHON_USE_DICT_VERSIONS 0
#undef CYTHON_USE_EXC_INFO_STACK
#define CYTHON_USE_EXC_INFO_STACK 0
+ #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
+ #define CYTHON_UPDATE_DESCRIPTOR_DOC 0
+ #endif
+#elif defined(PY_NOGIL)
+ #define CYTHON_COMPILING_IN_PYPY 0
+ #define CYTHON_COMPILING_IN_PYSTON 0
+ #define CYTHON_COMPILING_IN_CPYTHON 0
+ #define CYTHON_COMPILING_IN_NOGIL 1
+ #ifndef CYTHON_USE_TYPE_SLOTS
+ #define CYTHON_USE_TYPE_SLOTS 1
+ #endif
+ #undef CYTHON_USE_PYTYPE_LOOKUP
+ #define CYTHON_USE_PYTYPE_LOOKUP 0
+ #ifndef CYTHON_USE_ASYNC_SLOTS
+ #define CYTHON_USE_ASYNC_SLOTS 1
+ #endif
+ #undef CYTHON_USE_PYLIST_INTERNALS
+ #define CYTHON_USE_PYLIST_INTERNALS 0
+ #ifndef CYTHON_USE_UNICODE_INTERNALS
+ #define CYTHON_USE_UNICODE_INTERNALS 1
+ #endif
+ #undef CYTHON_USE_UNICODE_WRITER
+ #define CYTHON_USE_UNICODE_WRITER 0
+ #undef CYTHON_USE_PYLONG_INTERNALS
+ #define CYTHON_USE_PYLONG_INTERNALS 0
+ #ifndef CYTHON_AVOID_BORROWED_REFS
+ #define CYTHON_AVOID_BORROWED_REFS 0
+ #endif
+ #ifndef CYTHON_ASSUME_SAFE_MACROS
+ #define CYTHON_ASSUME_SAFE_MACROS 1
+ #endif
+ #ifndef CYTHON_UNPACK_METHODS
+ #define CYTHON_UNPACK_METHODS 1
+ #endif
+ #undef CYTHON_FAST_THREAD_STATE
+ #define CYTHON_FAST_THREAD_STATE 0
+ #undef CYTHON_FAST_PYCALL
+ #define CYTHON_FAST_PYCALL 0
+ #ifndef CYTHON_PEP489_MULTI_PHASE_INIT
+ #define CYTHON_PEP489_MULTI_PHASE_INIT 1
+ #endif
+ #ifndef CYTHON_USE_TP_FINALIZE
+ #define CYTHON_USE_TP_FINALIZE 1
+ #endif
+ #undef CYTHON_USE_DICT_VERSIONS
+ #define CYTHON_USE_DICT_VERSIONS 0
+ #undef CYTHON_USE_EXC_INFO_STACK
+ #define CYTHON_USE_EXC_INFO_STACK 0
#else
#define CYTHON_COMPILING_IN_PYPY 0
#define CYTHON_COMPILING_IN_PYSTON 0
#define CYTHON_COMPILING_IN_CPYTHON 1
+ #define CYTHON_COMPILING_IN_NOGIL 0
#ifndef CYTHON_USE_TYPE_SLOTS
#define CYTHON_USE_TYPE_SLOTS 1
#endif
@@ -170,7 +224,7 @@ END: Cython Metadata */
#ifndef CYTHON_USE_UNICODE_INTERNALS
#define CYTHON_USE_UNICODE_INTERNALS 1
#endif
- #if PY_VERSION_HEX < 0x030300F0
+ #if PY_VERSION_HEX < 0x030300F0 || PY_VERSION_HEX >= 0x030B00A2
#undef CYTHON_USE_UNICODE_WRITER
#define CYTHON_USE_UNICODE_WRITER 0
#elif !defined(CYTHON_USE_UNICODE_WRITER)
@@ -185,11 +239,14 @@ END: Cython Metadata */
#ifndef CYTHON_UNPACK_METHODS
#define CYTHON_UNPACK_METHODS 1
#endif
- #ifndef CYTHON_FAST_THREAD_STATE
+ #if PY_VERSION_HEX >= 0x030B00A4
+ #undef CYTHON_FAST_THREAD_STATE
+ #define CYTHON_FAST_THREAD_STATE 0
+ #elif !defined(CYTHON_FAST_THREAD_STATE)
#define CYTHON_FAST_THREAD_STATE 1
#endif
#ifndef CYTHON_FAST_PYCALL
- #define CYTHON_FAST_PYCALL 1
+ #define CYTHON_FAST_PYCALL (PY_VERSION_HEX < 0x030A0000)
#endif
#ifndef CYTHON_PEP489_MULTI_PHASE_INIT
#define CYTHON_PEP489_MULTI_PHASE_INIT (PY_VERSION_HEX >= 0x03050000)
@@ -200,15 +257,23 @@ END: Cython Metadata */
#ifndef CYTHON_USE_DICT_VERSIONS
#define CYTHON_USE_DICT_VERSIONS (PY_VERSION_HEX >= 0x030600B1)
#endif
- #ifndef CYTHON_USE_EXC_INFO_STACK
+ #if PY_VERSION_HEX >= 0x030B00A4
+ #undef CYTHON_USE_EXC_INFO_STACK
+ #define CYTHON_USE_EXC_INFO_STACK 0
+ #elif !defined(CYTHON_USE_EXC_INFO_STACK)
#define CYTHON_USE_EXC_INFO_STACK (PY_VERSION_HEX >= 0x030700A3)
#endif
+ #ifndef CYTHON_UPDATE_DESCRIPTOR_DOC
+ #define CYTHON_UPDATE_DESCRIPTOR_DOC 1
+ #endif
#endif
#if !defined(CYTHON_FAST_PYCCALL)
#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1)
#endif
#if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
+ #if PY_MAJOR_VERSION < 3
+ #include "longintrepr.h"
+ #endif
#undef SHIFT
#undef BASE
#undef MASK
@@ -325,9 +390,68 @@ END: Cython Metadata */
#define __Pyx_DefaultClassType PyClass_Type
#else
#define __Pyx_BUILTIN_MODULE_NAME "builtins"
-#if PY_VERSION_HEX >= 0x030800A4 && PY_VERSION_HEX < 0x030800B2
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
- PyCode_New(a, 0, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
+ #define __Pyx_DefaultClassType PyType_Type
+#if PY_VERSION_HEX >= 0x030B00A1
+ static CYTHON_INLINE PyCodeObject* __Pyx_PyCode_New(int a, int k, int l, int s, int f,
+ PyObject *code, PyObject *c, PyObject* n, PyObject *v,
+ PyObject *fv, PyObject *cell, PyObject* fn,
+ PyObject *name, int fline, PyObject *lnos) {
+ PyObject *kwds=NULL, *argcount=NULL, *posonlyargcount=NULL, *kwonlyargcount=NULL;
+ PyObject *nlocals=NULL, *stacksize=NULL, *flags=NULL, *replace=NULL, *call_result=NULL, *empty=NULL;
+ const char *fn_cstr=NULL;
+ const char *name_cstr=NULL;
+ PyCodeObject* co=NULL;
+ PyObject *type, *value, *traceback;
+ PyErr_Fetch(&type, &value, &traceback);
+ if (!(kwds=PyDict_New())) goto end;
+ if (!(argcount=PyLong_FromLong(a))) goto end;
+ if (PyDict_SetItemString(kwds, "co_argcount", argcount) != 0) goto end;
+ if (!(posonlyargcount=PyLong_FromLong(0))) goto end;
+ if (PyDict_SetItemString(kwds, "co_posonlyargcount", posonlyargcount) != 0) goto end;
+ if (!(kwonlyargcount=PyLong_FromLong(k))) goto end;
+ if (PyDict_SetItemString(kwds, "co_kwonlyargcount", kwonlyargcount) != 0) goto end;
+ if (!(nlocals=PyLong_FromLong(l))) goto end;
+ if (PyDict_SetItemString(kwds, "co_nlocals", nlocals) != 0) goto end;
+ if (!(stacksize=PyLong_FromLong(s))) goto end;
+ if (PyDict_SetItemString(kwds, "co_stacksize", stacksize) != 0) goto end;
+ if (!(flags=PyLong_FromLong(f))) goto end;
+ if (PyDict_SetItemString(kwds, "co_flags", flags) != 0) goto end;
+ if (PyDict_SetItemString(kwds, "co_code", code) != 0) goto end;
+ if (PyDict_SetItemString(kwds, "co_consts", c) != 0) goto end;
+ if (PyDict_SetItemString(kwds, "co_names", n) != 0) goto end;
+ if (PyDict_SetItemString(kwds, "co_varnames", v) != 0) goto end;
+ if (PyDict_SetItemString(kwds, "co_freevars", fv) != 0) goto end;
+ if (PyDict_SetItemString(kwds, "co_cellvars", cell) != 0) goto end;
+ if (PyDict_SetItemString(kwds, "co_linetable", lnos) != 0) goto end;
+ if (!(fn_cstr=PyUnicode_AsUTF8AndSize(fn, NULL))) goto end;
+ if (!(name_cstr=PyUnicode_AsUTF8AndSize(name, NULL))) goto end;
+ if (!(co = PyCode_NewEmpty(fn_cstr, name_cstr, fline))) goto end;
+ if (!(replace = PyObject_GetAttrString((PyObject*)co, "replace"))) goto cleanup_code_too;
+ if (!(empty = PyTuple_New(0))) goto cleanup_code_too; // unfortunately __pyx_empty_tuple isn't available here
+ if (!(call_result = PyObject_Call(replace, empty, kwds))) goto cleanup_code_too;
+ Py_XDECREF((PyObject*)co);
+ co = (PyCodeObject*)call_result;
+ call_result = NULL;
+ if (0) {
+ cleanup_code_too:
+ Py_XDECREF((PyObject*)co);
+ co = NULL;
+ }
+ end:
+ Py_XDECREF(kwds);
+ Py_XDECREF(argcount);
+ Py_XDECREF(posonlyargcount);
+ Py_XDECREF(kwonlyargcount);
+ Py_XDECREF(nlocals);
+ Py_XDECREF(stacksize);
+ Py_XDECREF(replace);
+ Py_XDECREF(call_result);
+ Py_XDECREF(empty);
+ if (type) {
+ PyErr_Restore(type, value, traceback);
+ }
+ return co;
+ }
#else
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\
PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
@@ -565,10 +689,10 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) {
#if PY_VERSION_HEX < 0x030200A4
typedef long Py_hash_t;
#define __Pyx_PyInt_FromHash_t PyInt_FromLong
- #define __Pyx_PyInt_AsHash_t PyInt_AsLong
+ #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsHash_t
#else
#define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
- #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
+ #define __Pyx_PyInt_AsHash_t __Pyx_PyIndex_AsSsize_t
#endif
#if PY_MAJOR_VERSION >= 3
#define __Pyx_PyMethod_New(func, self, klass) ((self) ? ((void)(klass), PyMethod_New(func, self)) : __Pyx_NewRef(func))
@@ -593,8 +717,10 @@ static CYTHON_INLINE void * PyThread_tss_get(Py_tss_t *key) {
} __Pyx_PyAsyncMethodsStruct;
#endif
-#if defined(WIN32) || defined(MS_WINDOWS)
- #define _USE_MATH_DEFINES
+#if defined(_WIN32) || defined(WIN32) || defined(MS_WINDOWS)
+ #if !defined(_USE_MATH_DEFINES)
+ #define _USE_MATH_DEFINES
+ #endif
#endif
#include <math.h>
#ifdef NAN
@@ -625,8 +751,8 @@ static CYTHON_INLINE float __PYX_NAN() {
#endif
#endif
-#define __PYX_HAVE__src__screening__utils
-#define __PYX_HAVE_API__src__screening__utils
+#define __PYX_HAVE__slopescreening__screening__utils
+#define __PYX_HAVE_API__slopescreening__screening__utils
/* Early includes */
#include <string.h>
#include <stdio.h>
@@ -734,6 +860,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x);
(likely(PyTuple_CheckExact(obj)) ? __Pyx_NewRef(obj) : PySequence_Tuple(obj))
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
+static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject*);
#if CYTHON_ASSUME_SAFE_MACROS
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
#else
@@ -868,9 +995,9 @@ static const char *__pyx_filename;
static const char *__pyx_f[] = {
- "src/screening/utils.pyx",
- "venv/lib/python3.8/site-packages/numpy/__init__.pxd",
- "venv/lib/python3.8/site-packages/Cython/Includes/cpython/type.pxd",
+ "slopescreening/screening/utils.pyx",
+ "venv/lib/python3.10/site-packages/numpy/__init__.pxd",
+ "venv/lib/python3.10/site-packages/Cython/Includes/cpython/type.pxd",
};
/* BufferFormatStructs.proto */
#define IS_UNSIGNED(type) (((type) -1) > 0)
@@ -909,7 +1036,7 @@ typedef struct {
} __Pyx_BufFmt_Context;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":690
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":689
* # in Cython to enable them only on the right systems.
*
* ctypedef npy_int8 int8_t # <<<<<<<<<<<<<<
@@ -918,7 +1045,7 @@ typedef struct {
*/
typedef npy_int8 __pyx_t_5numpy_int8_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":691
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":690
*
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t # <<<<<<<<<<<<<<
@@ -927,7 +1054,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t;
*/
typedef npy_int16 __pyx_t_5numpy_int16_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":692
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":691
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t # <<<<<<<<<<<<<<
@@ -936,7 +1063,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t;
*/
typedef npy_int32 __pyx_t_5numpy_int32_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":693
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":692
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t
* ctypedef npy_int64 int64_t # <<<<<<<<<<<<<<
@@ -945,7 +1072,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t;
*/
typedef npy_int64 __pyx_t_5numpy_int64_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":697
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":696
* #ctypedef npy_int128 int128_t
*
* ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<<
@@ -954,7 +1081,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t;
*/
typedef npy_uint8 __pyx_t_5numpy_uint8_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":698
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":697
*
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<<
@@ -963,7 +1090,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t;
*/
typedef npy_uint16 __pyx_t_5numpy_uint16_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":699
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":698
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<<
@@ -972,7 +1099,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t;
*/
typedef npy_uint32 __pyx_t_5numpy_uint32_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":700
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":699
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t
* ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<<
@@ -981,7 +1108,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t;
*/
typedef npy_uint64 __pyx_t_5numpy_uint64_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":704
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":703
* #ctypedef npy_uint128 uint128_t
*
* ctypedef npy_float32 float32_t # <<<<<<<<<<<<<<
@@ -990,7 +1117,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t;
*/
typedef npy_float32 __pyx_t_5numpy_float32_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":705
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":704
*
* ctypedef npy_float32 float32_t
* ctypedef npy_float64 float64_t # <<<<<<<<<<<<<<
@@ -999,7 +1126,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t;
*/
typedef npy_float64 __pyx_t_5numpy_float64_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":714
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":713
* # The int types are mapped a bit surprising --
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t # <<<<<<<<<<<<<<
@@ -1008,7 +1135,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t;
*/
typedef npy_long __pyx_t_5numpy_int_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":715
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":714
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t # <<<<<<<<<<<<<<
@@ -1017,7 +1144,7 @@ typedef npy_long __pyx_t_5numpy_int_t;
*/
typedef npy_longlong __pyx_t_5numpy_long_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":716
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":715
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t
* ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<<
@@ -1026,7 +1153,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t;
*/
typedef npy_longlong __pyx_t_5numpy_longlong_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":718
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":717
* ctypedef npy_longlong longlong_t
*
* ctypedef npy_ulong uint_t # <<<<<<<<<<<<<<
@@ -1035,7 +1162,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t;
*/
typedef npy_ulong __pyx_t_5numpy_uint_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":719
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":718
*
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<<
@@ -1044,7 +1171,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t;
*/
typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":720
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":719
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t
* ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<<
@@ -1053,7 +1180,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
*/
typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":722
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":721
* ctypedef npy_ulonglong ulonglong_t
*
* ctypedef npy_intp intp_t # <<<<<<<<<<<<<<
@@ -1062,7 +1189,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
*/
typedef npy_intp __pyx_t_5numpy_intp_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":723
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":722
*
* ctypedef npy_intp intp_t
* ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<<
@@ -1071,7 +1198,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t;
*/
typedef npy_uintp __pyx_t_5numpy_uintp_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":725
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":724
* ctypedef npy_uintp uintp_t
*
* ctypedef npy_double float_t # <<<<<<<<<<<<<<
@@ -1080,7 +1207,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t;
*/
typedef npy_double __pyx_t_5numpy_float_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":726
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":725
*
* ctypedef npy_double float_t
* ctypedef npy_double double_t # <<<<<<<<<<<<<<
@@ -1089,7 +1216,7 @@ typedef npy_double __pyx_t_5numpy_float_t;
*/
typedef npy_double __pyx_t_5numpy_double_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":727
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":726
* ctypedef npy_double float_t
* ctypedef npy_double double_t
* ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<<
@@ -1098,14 +1225,14 @@ typedef npy_double __pyx_t_5numpy_double_t;
*/
typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
-/* "src/screening/utils.pyx":13
+/* "slopescreening/screening/utils.pyx":13
* cimport cython
*
* ctypedef np.npy_bool bool_t # <<<<<<<<<<<<<<
*
*
*/
-typedef npy_bool __pyx_t_3src_9screening_5utils_bool_t;
+typedef npy_bool __pyx_t_14slopescreening_9screening_5utils_bool_t;
/* Declarations.proto */
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
@@ -1133,7 +1260,7 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do
/*--- Type declarations ---*/
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":729
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":728
* ctypedef npy_longdouble longdouble_t
*
* ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<<
@@ -1142,7 +1269,7 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do
*/
typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":730
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":729
*
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<<
@@ -1151,7 +1278,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
*/
typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":731
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":730
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t
* ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<<
@@ -1160,7 +1287,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
*/
typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":733
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":732
* ctypedef npy_clongdouble clongdouble_t
*
* ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<<
@@ -1389,13 +1516,21 @@ static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args,
#ifndef Py_MEMBER_SIZE
#define Py_MEMBER_SIZE(type, member) sizeof(((type *)0)->member)
#endif
+#if CYTHON_FAST_PYCALL
static size_t __pyx_pyframe_localsplus_offset = 0;
#include "frameobject.h"
+#if PY_VERSION_HEX >= 0x030b00a6
+ #ifndef Py_BUILD_CORE
+ #define Py_BUILD_CORE 1
+ #endif
+ #include "internal/pycore_frame.h"
+#endif
#define __Pxy_PyFrame_Initialize_Offsets()\
((void)__Pyx_BUILD_ASSERT_EXPR(sizeof(PyFrameObject) == offsetof(PyFrameObject, f_localsplus) + Py_MEMBER_SIZE(PyFrameObject, f_localsplus)),\
(void)(__pyx_pyframe_localsplus_offset = ((size_t)PyFrame_Type.tp_basicsize) - Py_MEMBER_SIZE(PyFrameObject, f_localsplus)))
#define __Pyx_PyFrame_GetLocalsplus(frame)\
(assert(__pyx_pyframe_localsplus_offset), (PyObject **)(((char *)(frame)) + __pyx_pyframe_localsplus_offset))
+#endif // CYTHON_FAST_PYCALL
#endif
/* PyObjectCall2Args.proto */
@@ -1719,15 +1854,15 @@ static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0;
/* Module declarations from 'cython' */
-/* Module declarations from 'src.screening.utils' */
+/* Module declarations from 'slopescreening.screening.utils' */
static __Pyx_TypeInfo __Pyx_TypeInfo_nn_npy_double = { "npy_double", NULL, sizeof(npy_double), { 0 }, 0, 'R', 0, 0 };
static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_int_t = { "int_t", NULL, sizeof(__pyx_t_5numpy_int_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_5numpy_int_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_5numpy_int_t), 0 };
static __Pyx_TypeInfo __Pyx_TypeInfo_nn_npy_bool = { "npy_bool", NULL, sizeof(npy_bool), { 0 }, 0, IS_UNSIGNED(npy_bool) ? 'U' : 'I', IS_UNSIGNED(npy_bool), 0 };
-#define __Pyx_MODULE_NAME "src.screening.utils"
-extern int __pyx_module_is_main_src__screening__utils;
-int __pyx_module_is_main_src__screening__utils = 0;
+#define __Pyx_MODULE_NAME "slopescreening.screening.utils"
+extern int __pyx_module_is_main_slopescreening__screening__utils;
+int __pyx_module_is_main_slopescreening__screening__utils = 0;
-/* Implementation of 'src.screening.utils' */
+/* Implementation of 'slopescreening.screening.utils' */
static PyObject *__pyx_builtin_range;
static PyObject *__pyx_builtin_ImportError;
static const char __pyx_k_k[] = "k";
@@ -1768,11 +1903,11 @@ static const char __pyx_k_vec_kappa_q[] = "vec_kappa_q";
static const char __pyx_k_gap_kappa_test[] = "gap_kappa_test";
static const char __pyx_k_vec_cumsum_gammas[] = "vec_cumsum_gammas";
static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback";
-static const char __pyx_k_src_screening_utils[] = "src.screening.utils";
static const char __pyx_k_GAP_Ptest_mixed_impl[] = "GAP_Ptest_mixed_impl";
-static const char __pyx_k_src_screening_utils_pyx[] = "src/screening/utils.pyx";
+static const char __pyx_k_slopescreening_screening_utils[] = "slopescreening.screening.utils";
static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import";
static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import";
+static const char __pyx_k_slopescreening_screening_utils_p[] = "slopescreening/screening/utils.pyx";
static PyObject *__pyx_n_s_Atcabs;
static PyObject *__pyx_n_s_GAP_Ptest_mixed_impl;
static PyObject *__pyx_n_s_ImportError;
@@ -1805,8 +1940,8 @@ static PyObject *__pyx_n_s_r;
static PyObject *__pyx_n_s_radius;
static PyObject *__pyx_n_s_range;
static PyObject *__pyx_n_s_sigmas;
-static PyObject *__pyx_n_s_src_screening_utils;
-static PyObject *__pyx_kp_s_src_screening_utils_pyx;
+static PyObject *__pyx_n_s_slopescreening_screening_utils;
+static PyObject *__pyx_kp_s_slopescreening_screening_utils_p;
static PyObject *__pyx_n_s_tau;
static PyObject *__pyx_n_s_test;
static PyObject *__pyx_n_s_vec_cumsum_gammas;
@@ -1816,8 +1951,8 @@ static PyObject *__pyx_n_s_vec_kappa_q;
static PyObject *__pyx_n_s_vec_q_star;
static PyObject *__pyx_n_s_vec_r_star;
static PyObject *__pyx_n_s_zeros;
-static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_vec_gammas, double __pyx_v_lbd, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_radius, PyArrayObject *__pyx_v_index); /* proto */
-static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_vec_cumsum_gammas, PyArrayObject *__pyx_v_vec_kappa_q, double __pyx_v_lbd, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_radius, PyArrayObject *__pyx_v_index); /* proto */
+static PyObject *__pyx_pf_14slopescreening_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_vec_gammas, double __pyx_v_lbd, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_radius, PyArrayObject *__pyx_v_index); /* proto */
+static PyObject *__pyx_pf_14slopescreening_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_vec_cumsum_gammas, PyArrayObject *__pyx_v_vec_kappa_q, double __pyx_v_lbd, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_radius, PyArrayObject *__pyx_v_index); /* proto */
static PyObject *__pyx_int_1;
static PyObject *__pyx_int_neg_1;
static PyObject *__pyx_slice_;
@@ -1831,7 +1966,7 @@ static PyObject *__pyx_codeobj__7;
static PyObject *__pyx_codeobj__9;
/* Late includes */
-/* "src/screening/utils.pyx":18
+/* "slopescreening/screening/utils.pyx":18
* @cython.boundscheck(False) # turn off bounds-checking for entire function
* @cython.wraparound(False) # turn off negative index wrapping for entire function
* def GAP_Ptest_mixed_impl( # <<<<<<<<<<<<<<
@@ -1840,9 +1975,9 @@ static PyObject *__pyx_codeobj__9;
*/
/* Python wrapper */
-static PyObject *__pyx_pw_3src_9screening_5utils_1GAP_Ptest_mixed_impl(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static PyMethodDef __pyx_mdef_3src_9screening_5utils_1GAP_Ptest_mixed_impl = {"GAP_Ptest_mixed_impl", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_3src_9screening_5utils_1GAP_Ptest_mixed_impl, METH_VARARGS|METH_KEYWORDS, 0};
-static PyObject *__pyx_pw_3src_9screening_5utils_1GAP_Ptest_mixed_impl(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pw_14slopescreening_9screening_5utils_1GAP_Ptest_mixed_impl(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static PyMethodDef __pyx_mdef_14slopescreening_9screening_5utils_1GAP_Ptest_mixed_impl = {"GAP_Ptest_mixed_impl", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_14slopescreening_9screening_5utils_1GAP_Ptest_mixed_impl, METH_VARARGS|METH_KEYWORDS, 0};
+static PyObject *__pyx_pw_14slopescreening_9screening_5utils_1GAP_Ptest_mixed_impl(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyArrayObject *__pyx_v_vec_gammas = 0;
double __pyx_v_lbd;
PyArrayObject *__pyx_v_Atcabs = 0;
@@ -1926,14 +2061,14 @@ static PyObject *__pyx_pw_3src_9screening_5utils_1GAP_Ptest_mixed_impl(PyObject
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("GAP_Ptest_mixed_impl", 1, 5, 5, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 18, __pyx_L3_error)
__pyx_L3_error:;
- __Pyx_AddTraceback("src.screening.utils.GAP_Ptest_mixed_impl", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("slopescreening.screening.utils.GAP_Ptest_mixed_impl", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_vec_gammas), __pyx_ptype_5numpy_ndarray, 1, "vec_gammas", 0))) __PYX_ERR(0, 20, __pyx_L1_error)
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_Atcabs), __pyx_ptype_5numpy_ndarray, 1, "Atcabs", 0))) __PYX_ERR(0, 22, __pyx_L1_error)
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_index), __pyx_ptype_5numpy_ndarray, 1, "index", 0))) __PYX_ERR(0, 24, __pyx_L1_error)
- __pyx_r = __pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(__pyx_self, __pyx_v_vec_gammas, __pyx_v_lbd, __pyx_v_Atcabs, __pyx_v_radius, __pyx_v_index);
+ __pyx_r = __pyx_pf_14slopescreening_9screening_5utils_GAP_Ptest_mixed_impl(__pyx_self, __pyx_v_vec_gammas, __pyx_v_lbd, __pyx_v_Atcabs, __pyx_v_radius, __pyx_v_index);
/* function exit code */
goto __pyx_L0;
@@ -1944,12 +2079,12 @@ static PyObject *__pyx_pw_3src_9screening_5utils_1GAP_Ptest_mixed_impl(PyObject
return __pyx_r;
}
-static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_vec_gammas, double __pyx_v_lbd, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_radius, PyArrayObject *__pyx_v_index) {
+static PyObject *__pyx_pf_14slopescreening_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_vec_gammas, double __pyx_v_lbd, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_radius, PyArrayObject *__pyx_v_index) {
int __pyx_v_n;
int __pyx_v_k;
int __pyx_v_q;
int __pyx_v_r;
- __pyx_t_3src_9screening_5utils_bool_t __pyx_v_bool_exit;
+ __pyx_t_14slopescreening_9screening_5utils_bool_t __pyx_v_bool_exit;
double __pyx_v_tau;
PyArrayObject *__pyx_v_vec_q_star = 0;
PyArrayObject *__pyx_v_vec_r_star = 0;
@@ -2038,7 +2173,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
}
__pyx_pybuffernd_index.diminfo[0].strides = __pyx_pybuffernd_index.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_index.diminfo[0].shape = __pyx_pybuffernd_index.rcbuffer->pybuffer.shape[0];
- /* "src/screening/utils.pyx":27
+ /* "slopescreening/screening/utils.pyx":27
* ):
*
* cdef int n = Atcabs.shape[0] # <<<<<<<<<<<<<<
@@ -2047,7 +2182,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
*/
__pyx_v_n = (__pyx_v_Atcabs->dimensions[0]);
- /* "src/screening/utils.pyx":29
+ /* "slopescreening/screening/utils.pyx":29
* cdef int n = Atcabs.shape[0]
* cdef int k, q, r
* cdef bool_t bool_exit = False # <<<<<<<<<<<<<<
@@ -2056,7 +2191,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
*/
__pyx_v_bool_exit = 0;
- /* "src/screening/utils.pyx":30
+ /* "slopescreening/screening/utils.pyx":30
* cdef int k, q, r
* cdef bool_t bool_exit = False
* cdef double tau = 0 # <<<<<<<<<<<<<<
@@ -2065,7 +2200,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
*/
__pyx_v_tau = 0.0;
- /* "src/screening/utils.pyx":33
+ /* "slopescreening/screening/utils.pyx":33
*
* # arange because I want entries 0, 1 being 0 and 1!
* cdef np.ndarray[np.int_t, ndim=1] vec_q_star = np.arange(n+1, dtype=np.int) # <<<<<<<<<<<<<<
@@ -2112,7 +2247,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
__pyx_v_vec_q_star = ((PyArrayObject *)__pyx_t_5);
__pyx_t_5 = 0;
- /* "src/screening/utils.pyx":34
+ /* "slopescreening/screening/utils.pyx":34
* # arange because I want entries 0, 1 being 0 and 1!
* cdef np.ndarray[np.int_t, ndim=1] vec_q_star = np.arange(n+1, dtype=np.int)
* cdef np.ndarray[np.int_t, ndim=1] vec_r_star = np.arange(n+1, dtype=np.int) # <<<<<<<<<<<<<<
@@ -2159,7 +2294,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
__pyx_v_vec_r_star = ((PyArrayObject *)__pyx_t_4);
__pyx_t_4 = 0;
- /* "src/screening/utils.pyx":37
+ /* "slopescreening/screening/utils.pyx":37
*
* # Sortie
* cdef np.ndarray[np.npy_bool, ndim=1] calI_screen = np.zeros(n, dtype=np.bool) # <<<<<<<<<<<<<<
@@ -2206,7 +2341,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
__pyx_v_calI_screen = ((PyArrayObject *)__pyx_t_2);
__pyx_t_2 = 0;
- /* "src/screening/utils.pyx":40
+ /* "slopescreening/screening/utils.pyx":40
*
* # 2. Precomputing quantities
* cdef np.ndarray[np.npy_double, ndim=1] vec_f = np.cumsum( # <<<<<<<<<<<<<<
@@ -2219,7 +2354,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "src/screening/utils.pyx":41
+ /* "slopescreening/screening/utils.pyx":41
* # 2. Precomputing quantities
* cdef np.ndarray[np.npy_double, ndim=1] vec_f = np.cumsum(
* lbd * vec_gammas[::-1] - Atcabs[index[::-1]] - radius # <<<<<<<<<<<<<<
@@ -2266,7 +2401,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "src/screening/utils.pyx":42
+ /* "slopescreening/screening/utils.pyx":42
* cdef np.ndarray[np.npy_double, ndim=1] vec_f = np.cumsum(
* lbd * vec_gammas[::-1] - Atcabs[index[::-1]] - radius
* )[::-1] # <<<<<<<<<<<<<<
@@ -2290,7 +2425,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
__pyx_v_vec_f = ((PyArrayObject *)__pyx_t_3);
__pyx_t_3 = 0;
- /* "src/screening/utils.pyx":44
+ /* "slopescreening/screening/utils.pyx":44
* )[::-1]
*
* for k in range(2, n+1): # <<<<<<<<<<<<<<
@@ -2302,7 +2437,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
for (__pyx_t_12 = 2; __pyx_t_12 < __pyx_t_11; __pyx_t_12+=1) {
__pyx_v_k = __pyx_t_12;
- /* "src/screening/utils.pyx":47
+ /* "slopescreening/screening/utils.pyx":47
* #+1 is to match paper index
* vec_q_star[k] = k \
* if vec_f[k-1] - vec_f[k-2] > lbd * (vec_gammas[k-1] - vec_gammas[k-2]) \ # <<<<<<<<<<<<<<
@@ -2315,7 +2450,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
__pyx_t_17 = (__pyx_v_k - 2);
if (((((*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_f.rcbuffer->pybuffer.buf, __pyx_t_14, __pyx_pybuffernd_vec_f.diminfo[0].strides)) - (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_f.rcbuffer->pybuffer.buf, __pyx_t_15, __pyx_pybuffernd_vec_f.diminfo[0].strides))) > (__pyx_v_lbd * ((*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_gammas.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_vec_gammas.diminfo[0].strides)) - (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_gammas.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_vec_gammas.diminfo[0].strides))))) != 0)) {
- /* "src/screening/utils.pyx":46
+ /* "slopescreening/screening/utils.pyx":46
* for k in range(2, n+1):
* #+1 is to match paper index
* vec_q_star[k] = k \ # <<<<<<<<<<<<<<
@@ -2325,7 +2460,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
__pyx_t_13 = __pyx_v_k;
} else {
- /* "src/screening/utils.pyx":48
+ /* "slopescreening/screening/utils.pyx":48
* vec_q_star[k] = k \
* if vec_f[k-1] - vec_f[k-2] > lbd * (vec_gammas[k-1] - vec_gammas[k-2]) \
* else vec_q_star[k-1] # <<<<<<<<<<<<<<
@@ -2336,7 +2471,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
__pyx_t_13 = (*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int_t *, __pyx_pybuffernd_vec_q_star.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_vec_q_star.diminfo[0].strides));
}
- /* "src/screening/utils.pyx":46
+ /* "slopescreening/screening/utils.pyx":46
* for k in range(2, n+1):
* #+1 is to match paper index
* vec_q_star[k] = k \ # <<<<<<<<<<<<<<
@@ -2346,7 +2481,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
__pyx_t_17 = __pyx_v_k;
*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int_t *, __pyx_pybuffernd_vec_q_star.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_vec_q_star.diminfo[0].strides) = __pyx_t_13;
- /* "src/screening/utils.pyx":51
+ /* "slopescreening/screening/utils.pyx":51
*
* vec_r_star[k] = k \
* if vec_f[k-1] > vec_f[k-2] \ # <<<<<<<<<<<<<<
@@ -2357,7 +2492,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
__pyx_t_16 = (__pyx_v_k - 2);
if ((((*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_f.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_vec_f.diminfo[0].strides)) > (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_f.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_vec_f.diminfo[0].strides))) != 0)) {
- /* "src/screening/utils.pyx":50
+ /* "slopescreening/screening/utils.pyx":50
* else vec_q_star[k-1]
*
* vec_r_star[k] = k \ # <<<<<<<<<<<<<<
@@ -2367,7 +2502,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
__pyx_t_13 = __pyx_v_k;
} else {
- /* "src/screening/utils.pyx":52
+ /* "slopescreening/screening/utils.pyx":52
* vec_r_star[k] = k \
* if vec_f[k-1] > vec_f[k-2] \
* else vec_r_star[k-1] # <<<<<<<<<<<<<<
@@ -2378,7 +2513,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
__pyx_t_13 = (*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int_t *, __pyx_pybuffernd_vec_r_star.rcbuffer->pybuffer.buf, __pyx_t_15, __pyx_pybuffernd_vec_r_star.diminfo[0].strides));
}
- /* "src/screening/utils.pyx":50
+ /* "slopescreening/screening/utils.pyx":50
* else vec_q_star[k-1]
*
* vec_r_star[k] = k \ # <<<<<<<<<<<<<<
@@ -2389,7 +2524,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int_t *, __pyx_pybuffernd_vec_r_star.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_vec_r_star.diminfo[0].strides) = __pyx_t_13;
}
- /* "src/screening/utils.pyx":55
+ /* "slopescreening/screening/utils.pyx":55
*
* # 3. Tests
* for k in range(n, 0, -1): # <<<<<<<<<<<<<<
@@ -2399,7 +2534,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
for (__pyx_t_12 = __pyx_v_n; __pyx_t_12 > 0; __pyx_t_12-=1) {
__pyx_v_k = __pyx_t_12;
- /* "src/screening/utils.pyx":56
+ /* "slopescreening/screening/utils.pyx":56
* # 3. Tests
* for k in range(n, 0, -1):
* q = vec_q_star[k] # <<<<<<<<<<<<<<
@@ -2409,7 +2544,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
__pyx_t_16 = __pyx_v_k;
__pyx_v_q = (*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int_t *, __pyx_pybuffernd_vec_q_star.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_vec_q_star.diminfo[0].strides));
- /* "src/screening/utils.pyx":57
+ /* "slopescreening/screening/utils.pyx":57
* for k in range(n, 0, -1):
* q = vec_q_star[k]
* while q >= 1: # <<<<<<<<<<<<<<
@@ -2420,7 +2555,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
__pyx_t_19 = ((__pyx_v_q >= 1) != 0);
if (!__pyx_t_19) break;
- /* "src/screening/utils.pyx":59
+ /* "slopescreening/screening/utils.pyx":59
* while q >= 1:
* # Implicit definition of the best value of p given q
* r = vec_r_star[q] # <<<<<<<<<<<<<<
@@ -2430,7 +2565,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
__pyx_t_16 = __pyx_v_q;
__pyx_v_r = (*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_int_t *, __pyx_pybuffernd_vec_r_star.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_vec_r_star.diminfo[0].strides));
- /* "src/screening/utils.pyx":62
+ /* "slopescreening/screening/utils.pyx":62
*
* # Evaluation of the threshold
* tau = vec_f[r-1] - vec_f[q-1] + (lbd * vec_gammas[q-1] - radius) # <<<<<<<<<<<<<<
@@ -2442,7 +2577,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
__pyx_t_15 = (__pyx_v_q - 1);
__pyx_v_tau = (((*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_f.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_vec_f.diminfo[0].strides)) - (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_f.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_vec_f.diminfo[0].strides))) + ((__pyx_v_lbd * (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_gammas.rcbuffer->pybuffer.buf, __pyx_t_15, __pyx_pybuffernd_vec_gammas.diminfo[0].strides))) - __pyx_v_radius));
- /* "src/screening/utils.pyx":65
+ /* "slopescreening/screening/utils.pyx":65
*
* # Test
* if Atcabs[index[k-1]] >= tau: # <<<<<<<<<<<<<<
@@ -2454,7 +2589,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
__pyx_t_19 = (((*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_Atcabs.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_Atcabs.diminfo[0].strides)) >= __pyx_v_tau) != 0);
if (__pyx_t_19) {
- /* "src/screening/utils.pyx":66
+ /* "slopescreening/screening/utils.pyx":66
* # Test
* if Atcabs[index[k-1]] >= tau:
* bool_exit = True # <<<<<<<<<<<<<<
@@ -2463,7 +2598,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
*/
__pyx_v_bool_exit = 1;
- /* "src/screening/utils.pyx":67
+ /* "slopescreening/screening/utils.pyx":67
* if Atcabs[index[k-1]] >= tau:
* bool_exit = True
* break # <<<<<<<<<<<<<<
@@ -2472,7 +2607,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
*/
goto __pyx_L8_break;
- /* "src/screening/utils.pyx":65
+ /* "slopescreening/screening/utils.pyx":65
*
* # Test
* if Atcabs[index[k-1]] >= tau: # <<<<<<<<<<<<<<
@@ -2481,7 +2616,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
*/
}
- /* "src/screening/utils.pyx":70
+ /* "slopescreening/screening/utils.pyx":70
*
* # Next critical point
* q = vec_q_star[r-1] # <<<<<<<<<<<<<<
@@ -2493,7 +2628,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
}
__pyx_L8_break:;
- /* "src/screening/utils.pyx":72
+ /* "slopescreening/screening/utils.pyx":72
* q = vec_q_star[r-1]
*
* if bool_exit: # <<<<<<<<<<<<<<
@@ -2503,7 +2638,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
__pyx_t_19 = (__pyx_v_bool_exit != 0);
if (__pyx_t_19) {
- /* "src/screening/utils.pyx":73
+ /* "slopescreening/screening/utils.pyx":73
*
* if bool_exit:
* break # <<<<<<<<<<<<<<
@@ -2512,7 +2647,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
*/
goto __pyx_L6_break;
- /* "src/screening/utils.pyx":72
+ /* "slopescreening/screening/utils.pyx":72
* q = vec_q_star[r-1]
*
* if bool_exit: # <<<<<<<<<<<<<<
@@ -2523,7 +2658,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
}
__pyx_L6_break:;
- /* "src/screening/utils.pyx":75
+ /* "slopescreening/screening/utils.pyx":75
* break
*
* calI_screen[index[k:]] = True # <<<<<<<<<<<<<<
@@ -2541,7 +2676,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
if (unlikely(PyObject_SetItem(((PyObject *)__pyx_v_calI_screen), __pyx_t_3, Py_True) < 0)) __PYX_ERR(0, 75, __pyx_L1_error)
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "src/screening/utils.pyx":76
+ /* "slopescreening/screening/utils.pyx":76
*
* calI_screen[index[k:]] = True
* return calI_screen # <<<<<<<<<<<<<<
@@ -2553,7 +2688,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
__pyx_r = ((PyObject *)__pyx_v_calI_screen);
goto __pyx_L0;
- /* "src/screening/utils.pyx":18
+ /* "slopescreening/screening/utils.pyx":18
* @cython.boundscheck(False) # turn off bounds-checking for entire function
* @cython.wraparound(False) # turn off negative index wrapping for entire function
* def GAP_Ptest_mixed_impl( # <<<<<<<<<<<<<<
@@ -2580,7 +2715,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_vec_q_star.rcbuffer->pybuffer);
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_vec_r_star.rcbuffer->pybuffer);
__Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);}
- __Pyx_AddTraceback("src.screening.utils.GAP_Ptest_mixed_impl", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("slopescreening.screening.utils.GAP_Ptest_mixed_impl", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
goto __pyx_L2;
__pyx_L0:;
@@ -2601,7 +2736,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
return __pyx_r;
}
-/* "src/screening/utils.pyx":81
+/* "slopescreening/screening/utils.pyx":81
* @cython.boundscheck(False) # turn off bounds-checking for entire function
* @cython.wraparound(False) # turn off negative index wrapping for entire function
* def gap_kappa_test( # <<<<<<<<<<<<<<
@@ -2610,9 +2745,9 @@ static PyObject *__pyx_pf_3src_9screening_5utils_GAP_Ptest_mixed_impl(CYTHON_UNU
*/
/* Python wrapper */
-static PyObject *__pyx_pw_3src_9screening_5utils_3gap_kappa_test(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static PyMethodDef __pyx_mdef_3src_9screening_5utils_3gap_kappa_test = {"gap_kappa_test", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_3src_9screening_5utils_3gap_kappa_test, METH_VARARGS|METH_KEYWORDS, 0};
-static PyObject *__pyx_pw_3src_9screening_5utils_3gap_kappa_test(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pw_14slopescreening_9screening_5utils_3gap_kappa_test(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static PyMethodDef __pyx_mdef_14slopescreening_9screening_5utils_3gap_kappa_test = {"gap_kappa_test", (PyCFunction)(void*)(PyCFunctionWithKeywords)__pyx_pw_14slopescreening_9screening_5utils_3gap_kappa_test, METH_VARARGS|METH_KEYWORDS, 0};
+static PyObject *__pyx_pw_14slopescreening_9screening_5utils_3gap_kappa_test(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyArrayObject *__pyx_v_vec_cumsum_gammas = 0;
PyArrayObject *__pyx_v_vec_kappa_q = 0;
double __pyx_v_lbd;
@@ -2707,7 +2842,7 @@ static PyObject *__pyx_pw_3src_9screening_5utils_3gap_kappa_test(PyObject *__pyx
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("gap_kappa_test", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 81, __pyx_L3_error)
__pyx_L3_error:;
- __Pyx_AddTraceback("src.screening.utils.gap_kappa_test", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("slopescreening.screening.utils.gap_kappa_test", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
@@ -2715,7 +2850,7 @@ static PyObject *__pyx_pw_3src_9screening_5utils_3gap_kappa_test(PyObject *__pyx
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_vec_kappa_q), __pyx_ptype_5numpy_ndarray, 1, "vec_kappa_q", 0))) __PYX_ERR(0, 83, __pyx_L1_error)
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_Atcabs), __pyx_ptype_5numpy_ndarray, 1, "Atcabs", 0))) __PYX_ERR(0, 85, __pyx_L1_error)
if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_index), __pyx_ptype_5numpy_ndarray, 1, "index", 0))) __PYX_ERR(0, 87, __pyx_L1_error)
- __pyx_r = __pyx_pf_3src_9screening_5utils_2gap_kappa_test(__pyx_self, __pyx_v_vec_cumsum_gammas, __pyx_v_vec_kappa_q, __pyx_v_lbd, __pyx_v_Atcabs, __pyx_v_radius, __pyx_v_index);
+ __pyx_r = __pyx_pf_14slopescreening_9screening_5utils_2gap_kappa_test(__pyx_self, __pyx_v_vec_cumsum_gammas, __pyx_v_vec_kappa_q, __pyx_v_lbd, __pyx_v_Atcabs, __pyx_v_radius, __pyx_v_index);
/* function exit code */
goto __pyx_L0;
@@ -2726,7 +2861,7 @@ static PyObject *__pyx_pw_3src_9screening_5utils_3gap_kappa_test(PyObject *__pyx
return __pyx_r;
}
-static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_vec_cumsum_gammas, PyArrayObject *__pyx_v_vec_kappa_q, double __pyx_v_lbd, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_radius, PyArrayObject *__pyx_v_index) {
+static PyObject *__pyx_pf_14slopescreening_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_vec_cumsum_gammas, PyArrayObject *__pyx_v_vec_kappa_q, double __pyx_v_lbd, PyArrayObject *__pyx_v_Atcabs, double __pyx_v_radius, PyArrayObject *__pyx_v_index) {
int __pyx_v_n;
int __pyx_v_q;
int __pyx_v_l_q;
@@ -2813,7 +2948,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED P
}
__pyx_pybuffernd_index.diminfo[0].strides = __pyx_pybuffernd_index.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_index.diminfo[0].shape = __pyx_pybuffernd_index.rcbuffer->pybuffer.shape[0];
- /* "src/screening/utils.pyx":90
+ /* "slopescreening/screening/utils.pyx":90
* ):
*
* cdef int n = Atcabs.shape[0] # <<<<<<<<<<<<<<
@@ -2822,7 +2957,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED P
*/
__pyx_v_n = (__pyx_v_Atcabs->dimensions[0]);
- /* "src/screening/utils.pyx":92
+ /* "slopescreening/screening/utils.pyx":92
* cdef int n = Atcabs.shape[0]
* cdef int q, l_q
* cdef int l_min = 0 # <<<<<<<<<<<<<<
@@ -2831,7 +2966,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED P
*/
__pyx_v_l_min = 0;
- /* "src/screening/utils.pyx":96
+ /* "slopescreening/screening/utils.pyx":96
*
* # Sortie
* cdef np.ndarray[np.npy_bool, ndim=1] calI_screen = np.zeros(n, dtype=np.bool) # <<<<<<<<<<<<<<
@@ -2878,7 +3013,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED P
__pyx_v_calI_screen = ((PyArrayObject *)__pyx_t_5);
__pyx_t_5 = 0;
- /* "src/screening/utils.pyx":99
+ /* "slopescreening/screening/utils.pyx":99
*
* # Cdric' notations compliant
* cdef np.ndarray[np.npy_double, ndim=1] sigmas = np.zeros(n) # <<<<<<<<<<<<<<
@@ -2922,7 +3057,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED P
__pyx_v_sigmas = ((PyArrayObject *)__pyx_t_5);
__pyx_t_5 = 0;
- /* "src/screening/utils.pyx":100
+ /* "slopescreening/screening/utils.pyx":100
* # Cdric' notations compliant
* cdef np.ndarray[np.npy_double, ndim=1] sigmas = np.zeros(n)
* sigmas[1:] = np.cumsum(Atcabs[index[:-1]]) # <<<<<<<<<<<<<<
@@ -2958,7 +3093,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED P
if (unlikely(PyObject_SetItem(((PyObject *)__pyx_v_sigmas), __pyx_slice__3, __pyx_t_5) < 0)) __PYX_ERR(0, 100, __pyx_L1_error)
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "src/screening/utils.pyx":102
+ /* "slopescreening/screening/utils.pyx":102
* sigmas[1:] = np.cumsum(Atcabs[index[:-1]])
*
* for q in range(n-1, -1, -1): # <<<<<<<<<<<<<<
@@ -2968,7 +3103,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED P
for (__pyx_t_8 = (__pyx_v_n - 1); __pyx_t_8 > -1; __pyx_t_8-=1) {
__pyx_v_q = __pyx_t_8;
- /* "src/screening/utils.pyx":103
+ /* "slopescreening/screening/utils.pyx":103
*
* for q in range(n-1, -1, -1):
* bound = lbd * vec_cumsum_gammas[q] - vec_kappa_q[q] * radius - sigmas[q] # <<<<<<<<<<<<<<
@@ -2980,7 +3115,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED P
__pyx_t_11 = __pyx_v_q;
__pyx_v_bound = (((__pyx_v_lbd * (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_cumsum_gammas.rcbuffer->pybuffer.buf, __pyx_t_9, __pyx_pybuffernd_vec_cumsum_gammas.diminfo[0].strides))) - ((*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_vec_kappa_q.rcbuffer->pybuffer.buf, __pyx_t_10, __pyx_pybuffernd_vec_kappa_q.diminfo[0].strides)) * __pyx_v_radius)) - (*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_sigmas.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_sigmas.diminfo[0].strides)));
- /* "src/screening/utils.pyx":105
+ /* "slopescreening/screening/utils.pyx":105
* bound = lbd * vec_cumsum_gammas[q] - vec_kappa_q[q] * radius - sigmas[q]
*
* if Atcabs[index[q]] < bound: # <<<<<<<<<<<<<<
@@ -2992,7 +3127,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED P
__pyx_t_12 = (((*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_Atcabs.rcbuffer->pybuffer.buf, __pyx_t_10, __pyx_pybuffernd_Atcabs.diminfo[0].strides)) < __pyx_v_bound) != 0);
if (__pyx_t_12) {
- /* "src/screening/utils.pyx":106
+ /* "slopescreening/screening/utils.pyx":106
*
* if Atcabs[index[q]] < bound:
* l_q = 0 # <<<<<<<<<<<<<<
@@ -3001,7 +3136,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED P
*/
__pyx_v_l_q = 0;
- /* "src/screening/utils.pyx":105
+ /* "slopescreening/screening/utils.pyx":105
* bound = lbd * vec_cumsum_gammas[q] - vec_kappa_q[q] * radius - sigmas[q]
*
* if Atcabs[index[q]] < bound: # <<<<<<<<<<<<<<
@@ -3011,7 +3146,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED P
goto __pyx_L5;
}
- /* "src/screening/utils.pyx":107
+ /* "slopescreening/screening/utils.pyx":107
* if Atcabs[index[q]] < bound:
* l_q = 0
* elif Atcabs[index[n-1]] >= bound: # <<<<<<<<<<<<<<
@@ -3023,7 +3158,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED P
__pyx_t_12 = (((*__Pyx_BufPtrStrided1d(npy_double *, __pyx_pybuffernd_Atcabs.rcbuffer->pybuffer.buf, __pyx_t_10, __pyx_pybuffernd_Atcabs.diminfo[0].strides)) >= __pyx_v_bound) != 0);
if (__pyx_t_12) {
- /* "src/screening/utils.pyx":108
+ /* "slopescreening/screening/utils.pyx":108
* l_q = 0
* elif Atcabs[index[n-1]] >= bound:
* return calI_screen # <<<<<<<<<<<<<<
@@ -3035,7 +3170,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED P
__pyx_r = ((PyObject *)__pyx_v_calI_screen);
goto __pyx_L0;
- /* "src/screening/utils.pyx":107
+ /* "slopescreening/screening/utils.pyx":107
* if Atcabs[index[q]] < bound:
* l_q = 0
* elif Atcabs[index[n-1]] >= bound: # <<<<<<<<<<<<<<
@@ -3044,7 +3179,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED P
*/
}
- /* "src/screening/utils.pyx":110
+ /* "slopescreening/screening/utils.pyx":110
* return calI_screen
* else:
* l_q = q + np.argmax(Atcabs[index[q:]] < bound) # <<<<<<<<<<<<<<
@@ -3101,7 +3236,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED P
}
__pyx_L5:;
- /* "src/screening/utils.pyx":112
+ /* "slopescreening/screening/utils.pyx":112
* l_q = q + np.argmax(Atcabs[index[q:]] < bound)
*
* l_min = max(l_min, l_q) # <<<<<<<<<<<<<<
@@ -3118,7 +3253,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED P
__pyx_v_l_min = __pyx_t_16;
}
- /* "src/screening/utils.pyx":114
+ /* "slopescreening/screening/utils.pyx":114
* l_min = max(l_min, l_q)
*
* calI_screen[index[l_min:]] = True # <<<<<<<<<<<<<<
@@ -3135,7 +3270,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED P
if (unlikely(PyObject_SetItem(((PyObject *)__pyx_v_calI_screen), __pyx_t_3, Py_True) < 0)) __PYX_ERR(0, 114, __pyx_L1_error)
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "src/screening/utils.pyx":115
+ /* "slopescreening/screening/utils.pyx":115
*
* calI_screen[index[l_min:]] = True
* return calI_screen # <<<<<<<<<<<<<<
@@ -3145,7 +3280,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED P
__pyx_r = ((PyObject *)__pyx_v_calI_screen);
goto __pyx_L0;
- /* "src/screening/utils.pyx":81
+ /* "slopescreening/screening/utils.pyx":81
* @cython.boundscheck(False) # turn off bounds-checking for entire function
* @cython.wraparound(False) # turn off negative index wrapping for entire function
* def gap_kappa_test( # <<<<<<<<<<<<<<
@@ -3172,7 +3307,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED P
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_vec_cumsum_gammas.rcbuffer->pybuffer);
__Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_vec_kappa_q.rcbuffer->pybuffer);
__Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);}
- __Pyx_AddTraceback("src.screening.utils.gap_kappa_test", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("slopescreening.screening.utils.gap_kappa_test", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
goto __pyx_L2;
__pyx_L0:;
@@ -3190,7 +3325,7 @@ static PyObject *__pyx_pf_3src_9screening_5utils_2gap_kappa_test(CYTHON_UNUSED P
return __pyx_r;
}
-/* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":735
+/* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":734
* ctypedef npy_cdouble complex_t
*
* cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<<
@@ -3207,7 +3342,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("PyArray_MultiIterNew1", 0);
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":736
+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":735
*
* cdef inline object PyArray_MultiIterNew1(a):
* return PyArray_MultiIterNew(1, <void*>a) # <<<<<<<<<<<<<<
@@ -3215,13 +3350,13 @@ 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(1, 736, __pyx_L1_error)
+ __pyx_t_1 = PyArray_MultiIterNew(1, ((void *)__pyx_v_a)); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 735, __pyx_L1_error)
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":735
+ /* "venv/lib/python3.10/site-packages/numpy/__init__.pxd":734
* ctypedef npy_cdouble complex_t
*
* cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<<
@@ -3240,7 +3375,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__
return __pyx_r;
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__Pyx_XGOTREF(__pyx_t_3);
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__Pyx_XGOTREF(__pyx_t_3);
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- __pyx_t_4 = _import_umath(); if (unlikely(__pyx_t_4 == ((int)-1))) __PYX_ERR(1, 955, __pyx_L3_error)
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__pyx_L8_try_end:;
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goto __pyx_L0;
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npy_timedelta __pyx_r;
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goto __pyx_L0;
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NPY_DATETIMEUNIT __pyx_r;
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__Pyx_GIVEREF(__pyx_slice__3);
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* @cython.wraparound(False) # turn off negative index wrapping for entire function
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- __pyx_t_1 = PyImport_ImportModule("numpy"); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 200, __pyx_L1_error)
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- if (!__pyx_ptype_5numpy_dtype) __PYX_ERR(1, 200, __pyx_L1_error)
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- if (!__pyx_ptype_5numpy_broadcast) __PYX_ERR(1, 227, __pyx_L1_error)
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- if (!__pyx_ptype_5numpy_ndarray) __PYX_ERR(1, 239, __pyx_L1_error)
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- if (!__pyx_ptype_5numpy_unsignedinteger) __PYX_ERR(1, 779, __pyx_L1_error)
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__pyx_ptype_5numpy_inexact = __Pyx_ImportType(__pyx_t_1, "numpy", "inexact", sizeof(PyObject), __Pyx_ImportType_CheckSize_Warn);
- if (!__pyx_ptype_5numpy_inexact) __PYX_ERR(1, 781, __pyx_L1_error)
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- if (!__pyx_ptype_5numpy_floating) __PYX_ERR(1, 783, __pyx_L1_error)
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__pyx_ptype_5numpy_complexfloating = __Pyx_ImportType(__pyx_t_1, "numpy", "complexfloating", sizeof(PyObject), __Pyx_ImportType_CheckSize_Warn);
- if (!__pyx_ptype_5numpy_complexfloating) __PYX_ERR(1, 785, __pyx_L1_error)
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- if (!__pyx_ptype_5numpy_flexible) __PYX_ERR(1, 787, __pyx_L1_error)
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- if (!__pyx_ptype_5numpy_character) __PYX_ERR(1, 789, __pyx_L1_error)
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- if (!__pyx_ptype_5numpy_ufunc) __PYX_ERR(1, 827, __pyx_L1_error)
+ if (!__pyx_ptype_5numpy_ufunc) __PYX_ERR(1, 826, __pyx_L1_error)
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if (PyObject_SetAttr(__pyx_m, __pyx_n_s_name, __pyx_n_s_main) < 0) __PYX_ERR(0, 1, __pyx_L1_error)
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PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) __PYX_ERR(0, 1, __pyx_L1_error)
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- if (unlikely(PyDict_SetItemString(modules, "src.screening.utils", __pyx_m) < 0)) __PYX_ERR(0, 1, __pyx_L1_error)
+ if (!PyDict_GetItemString(modules, "slopescreening.screening.utils")) {
+ if (unlikely(PyDict_SetItemString(modules, "slopescreening.screening.utils", __pyx_m) < 0)) __PYX_ERR(0, 1, __pyx_L1_error)
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "src/screening/utils.pyx":18
+ /* "slopescreening/screening/utils.pyx":18
* @cython.boundscheck(False) # turn off bounds-checking for entire function
* @cython.wraparound(False) # turn off negative index wrapping for entire function
* def GAP_Ptest_mixed_impl( # <<<<<<<<<<<<<<
* # np.ndarray[np.npy_double, ndim=1] vec_f,
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- __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_3src_9screening_5utils_1GAP_Ptest_mixed_impl, NULL, __pyx_n_s_src_screening_utils); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 18, __pyx_L1_error)
+ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_14slopescreening_9screening_5utils_1GAP_Ptest_mixed_impl, NULL, __pyx_n_s_slopescreening_screening_utils); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 18, __pyx_L1_error)
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- /* "src/screening/utils.pyx":81
+ /* "slopescreening/screening/utils.pyx":81
* @cython.boundscheck(False) # turn off bounds-checking for entire function
* @cython.wraparound(False) # turn off negative index wrapping for entire function
* def gap_kappa_test( # <<<<<<<<<<<<<<
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*/
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+ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_14slopescreening_9screening_5utils_3gap_kappa_test, NULL, __pyx_n_s_slopescreening_screening_utils); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 81, __pyx_L1_error)
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- /* "src/screening/utils.pyx":1
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- /* "venv/lib/python3.8/site-packages/numpy/__init__.pxd":1014
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Py_CLEAR(__pyx_m);
} else if (!PyErr_Occurred()) {
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#include "compile.h"
#include "frameobject.h"
#include "traceback.h"
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+ #define Py_BUILD_CORE 1
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+#endif
static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
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int py_line, const char *filename) {
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- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
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+ PyObject *py_srcfile = NULL;
py_srcfile = PyString_FromString(filename);
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if (!py_srcfile) goto bad;
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#if PY_MAJOR_VERSION < 3
py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
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py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
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}
else {
#if PY_MAJOR_VERSION < 3
py_funcname = PyString_FromString(funcname);
- #else
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}
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py_code = __Pyx_PyCode_New(
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);
Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
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return py_code;
bad:
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Py_XDECREF(py_funcname);
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return NULL;
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PyCodeObject *py_code = 0;
PyFrameObject *py_frame = 0;
PyThreadState *tstate = __Pyx_PyThreadState_Current;
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if (c_line) {
c_line = __Pyx_CLineForTraceback(tstate, c_line);
}
py_code = __pyx_find_code_object(c_line ? -c_line : py_line);
if (!py_code) {
+ __Pyx_ErrFetchInState(tstate, &ptype, &pvalue, &ptraceback);
py_code = __Pyx_CreateCodeObjectForTraceback(
funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
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+ goto bad;
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}
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- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
+ char ctversion[5];
+ int same=1, i, found_dot;
+ const char* rt_from_call = Py_GetVersion();
+ PyOS_snprintf(ctversion, 5, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
+ found_dot = 0;
+ for (i = 0; i < 4; i++) {
+ if (!ctversion[i]) {
+ same = (rt_from_call[i] < '0' || rt_from_call[i] > '9');
+ break;
+ }
+ if (rt_from_call[i] != ctversion[i]) {
+ same = 0;
+ break;
+ }
+ }
+ if (!same) {
+ char rtversion[5] = {'\0'};
char message[200];
+ for (i=0; i<4; ++i) {
+ if (rt_from_call[i] == '.') {
+ if (found_dot) break;
+ found_dot = 1;
+ } else if (rt_from_call[i] < '0' || rt_from_call[i] > '9') {
+ break;
+ }
+ rtversion[i] = rt_from_call[i];
+ }
PyOS_snprintf(message, sizeof(message),
"compiletime version %s of module '%.100s' "
"does not match runtime version %s",
@@ -7853,6 +8032,23 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
Py_DECREF(x);
return ival;
}
+static CYTHON_INLINE Py_hash_t __Pyx_PyIndex_AsHash_t(PyObject* o) {
+ if (sizeof(Py_hash_t) == sizeof(Py_ssize_t)) {
+ return (Py_hash_t) __Pyx_PyIndex_AsSsize_t(o);
+#if PY_MAJOR_VERSION < 3
+ } else if (likely(PyInt_CheckExact(o))) {
+ return PyInt_AS_LONG(o);
+#endif
+ } else {
+ Py_ssize_t ival;
+ PyObject *x;
+ x = PyNumber_Index(o);
+ if (!x) return -1;
+ ival = PyInt_AsLong(x);
+ Py_DECREF(x);
+ return ival;
+ }
+}
static CYTHON_INLINE PyObject * __Pyx_PyBool_FromLong(long b) {
return b ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False);
}
diff --git a/src/screening/utils.pyx b/slopescreening/screening/utils.pyx
similarity index 100%
rename from src/screening/utils.pyx
rename to slopescreening/screening/utils.pyx
diff --git a/src/solver/parameters.py b/slopescreening/solver/parameters.py
similarity index 94%
rename from src/solver/parameters.py
rename to slopescreening/solver/parameters.py
index 2e24c76..6722fb3 100755
--- a/src/solver/parameters.py
+++ b/slopescreening/solver/parameters.py
@@ -4,7 +4,7 @@ import enum
import numpy as np
-from src.screening.ascreening import AbstractGapScreening
+from slopescreening.screening.ascreening import AbstractGapScreening
class EnumLipchitzOptions(enum.Enum):
diff --git a/src/solver/prox.py b/slopescreening/solver/prox.py
similarity index 100%
rename from src/solver/prox.py
rename to slopescreening/solver/prox.py
diff --git a/src/solver/slope.py b/slopescreening/solver/slope.py
similarity index 98%
rename from src/solver/slope.py
rename to slopescreening/solver/slope.py
index 0d5449f..c84bd71 100755
--- a/src/solver/slope.py
+++ b/slopescreening/solver/slope.py
@@ -3,8 +3,8 @@ import time
import numpy as np
-from src.solver.parameters import SlopeParameters, EnumLipchitzOptions, DualScalingOptions
-from src.solver.prox import prox_owl
+from slopescreening.solver.parameters import SlopeParameters, EnumLipchitzOptions, DualScalingOptions
+from slopescreening.solver.prox import prox_owl
def primal_func(vecy, Ax, x, lbd, vec_gammas) -> float:
diff --git a/src/utils.py b/slopescreening/utils.py
similarity index 100%
rename from src/utils.py
rename to slopescreening/utils.py
diff --git a/src/__init__.py b/src/__init__.py
deleted file mode 100755
index 9e77438..0000000
--- a/src/__init__.py
+++ /dev/null
@@ -1,3 +0,0 @@
-# -*- coding: utf-8 -*-
-
-from src.__version import __version__
\ No newline at end of file
diff --git a/tests/test_solver.py b/tests/test_solver.py
index 6cfdba4..a05c248 100644
--- a/tests/test_solver.py
+++ b/tests/test_solver.py
@@ -2,10 +2,10 @@
import unittest
import numpy as np
-import src.utils as utils
-from src.dictionaries import generate_dic
-from src.solver.slope import slope_gp
-from src.solver.parameters import SlopeParameters
+import slopescreening.utils as utils
+from slopescreening.dictionaries import generate_dic
+from slopescreening.solver.slope import slope_gp
+from slopescreening.solver.parameters import SlopeParameters
class TestSolver(unittest.TestCase):
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 4017a3c..678e1b8 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -2,9 +2,9 @@
import unittest
import numpy as np
-import src.utils as utils
-from src.dictionaries import generate_dic
-from src.solver.slope import slope_gp
+import slopescreening.utils as utils
+from slopescreening.dictionaries import generate_dic
+from slopescreening.solver.slope import slope_gp
class TestUtilsModule(unittest.TestCase):
--
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