BUG: add missing c_distributions.pxd to enable cython use of random C…

…-API
numpy · seberg · Mar 16, 2020 · Jan 29, 2020 · Jan 30, 2020 · Jan 31, 2020
commit 5094692e2735b743e9a819cfca873825b0e9a746
diff --git a/numpy/random/_generator.pyx b/numpy/random/_generator.pyx
@@ -11,6 +11,7 @@ import numpy as np
 cimport numpy as np
 from numpy.core.multiarray import normalize_axis_index
 
+from .c_distributions cimport *
 from libc cimport string
 from libc.stdint cimport (uint8_t, uint16_t, uint32_t, uint64_t,
                           int32_t, int64_t, INT64_MAX, SIZE_MAX)
@@ -27,117 +28,8 @@ from ._common cimport (POISSON_LAM_MAX, CONS_POSITIVE, CONS_NONE,
             check_array_constraint, check_constraint, disc, discrete_broadcast_iii,
         )
 
-
-cdef extern from "numpy/random/distributions.h":
-
-    struct s_binomial_t:
-        int has_binomial
-        double psave
-        int64_t nsave
-        double r
-        double q
-        double fm
-        int64_t m
-        double p1
-        double xm
-        double xl
-        double xr
-        double c
-        double laml
-        double lamr
-        double p2
-        double p3
-        double p4
-
-    ctypedef s_binomial_t binomial_t
-
-    double random_standard_uniform(bitgen_t *bitgen_state) nogil
-    void random_standard_uniform_fill(bitgen_t* bitgen_state, np.npy_intp cnt, double *out) nogil
-    double random_standard_exponential(bitgen_t *bitgen_state) nogil
-    double random_standard_exponential_f(bitgen_t *bitgen_state) nogil
-    void random_standard_exponential_fill(bitgen_t *bitgen_state, np.npy_intp cnt, double *out) nogil
-    void random_standard_exponential_fill_f(bitgen_t *bitgen_state, np.npy_intp cnt, double *out) nogil
-    void random_standard_exponential_inv_fill(bitgen_t *bitgen_state, np.npy_intp cnt, double *out) nogil
-    void random_standard_exponential_inv_fill_f(bitgen_t *bitgen_state, np.npy_intp cnt, double *out) nogil
-    double random_standard_normal(bitgen_t* bitgen_state) nogil
-    void random_standard_normal_fill(bitgen_t *bitgen_state, np.npy_intp count, double *out) nogil
-    void random_standard_normal_fill_f(bitgen_t *bitgen_state, np.npy_intp count, float *out) nogil
-    double random_standard_gamma(bitgen_t *bitgen_state, double shape) nogil
-
-    float random_standard_uniform_f(bitgen_t *bitgen_state) nogil
-    void random_standard_uniform_fill_f(bitgen_t* bitgen_state, np.npy_intp cnt, float *out) nogil
-    float random_standard_normal_f(bitgen_t* bitgen_state) nogil
-    float random_standard_gamma_f(bitgen_t *bitgen_state, float shape) nogil
-
-    int64_t random_positive_int64(bitgen_t *bitgen_state) nogil
-    int32_t random_positive_int32(bitgen_t *bitgen_state) nogil
-    int64_t random_positive_int(bitgen_t *bitgen_state) nogil
-    uint64_t random_uint(bitgen_t *bitgen_state) nogil
-
-    double random_normal(bitgen_t *bitgen_state, double loc, double scale) nogil
-
-    double random_gamma(bitgen_t *bitgen_state, double shape, double scale) nogil
-    float random_gamma_f(bitgen_t *bitgen_state, float shape, float scale) nogil
-
-    double random_exponential(bitgen_t *bitgen_state, double scale) nogil
-    double random_uniform(bitgen_t *bitgen_state, double lower, double range) nogil
-    double random_beta(bitgen_t *bitgen_state, double a, double b) nogil
-    double random_chisquare(bitgen_t *bitgen_state, double df) nogil
-    double random_f(bitgen_t *bitgen_state, double dfnum, double dfden) nogil
-    double random_standard_cauchy(bitgen_t *bitgen_state) nogil
-    double random_pareto(bitgen_t *bitgen_state, double a) nogil
-    double random_weibull(bitgen_t *bitgen_state, double a) nogil
-    double random_power(bitgen_t *bitgen_state, double a) nogil
-    double random_laplace(bitgen_t *bitgen_state, double loc, double scale) nogil
-    double random_gumbel(bitgen_t *bitgen_state, double loc, double scale) nogil
-    double random_logistic(bitgen_t *bitgen_state, double loc, double scale) nogil
-    double random_lognormal(bitgen_t *bitgen_state, double mean, double sigma) nogil
-    double random_rayleigh(bitgen_t *bitgen_state, double mode) nogil
-    double random_standard_t(bitgen_t *bitgen_state, double df) nogil
-    double random_noncentral_chisquare(bitgen_t *bitgen_state, double df,
-                                       double nonc) nogil
-    double random_noncentral_f(bitgen_t *bitgen_state, double dfnum,
-                               double dfden, double nonc) nogil
-    double random_wald(bitgen_t *bitgen_state, double mean, double scale) nogil
-    double random_vonmises(bitgen_t *bitgen_state, double mu, double kappa) nogil
-    double random_triangular(bitgen_t *bitgen_state, double left, double mode,
-                             double right) nogil
-
-    int64_t random_poisson(bitgen_t *bitgen_state, double lam) nogil
-    int64_t random_negative_binomial(bitgen_t *bitgen_state, double n, double p) nogil
-    int64_t random_binomial(bitgen_t *bitgen_state, double p, int64_t n, binomial_t *binomial) nogil
-    int64_t random_logseries(bitgen_t *bitgen_state, double p) nogil
-    int64_t random_geometric_search(bitgen_t *bitgen_state, double p) nogil
-    int64_t random_geometric_inversion(bitgen_t *bitgen_state, double p) nogil
-    int64_t random_geometric(bitgen_t *bitgen_state, double p) nogil
-    int64_t random_zipf(bitgen_t *bitgen_state, double a) nogil
-    int64_t random_hypergeometric(bitgen_t *bitgen_state, int64_t good, int64_t bad,
-                                    int64_t sample) nogil
-
-    uint64_t random_interval(bitgen_t *bitgen_state, uint64_t max) nogil
-
-    # Generate random uint64 numbers in closed interval [off, off + rng].
-    uint64_t random_bounded_uint64(bitgen_t *bitgen_state,
-                                   uint64_t off, uint64_t rng,
-                                   uint64_t mask, bint use_masked) nogil
-
-    void random_multinomial(bitgen_t *bitgen_state, int64_t n, int64_t *mnix,
-                            double *pix, np.npy_intp d, binomial_t *binomial) nogil
-
-    int random_multivariate_hypergeometric_count(bitgen_t *bitgen_state,
-                          int64_t total,
-                          size_t num_colors, int64_t *colors,
-                          int64_t nsample,
-                          size_t num_variates, int64_t *variates) nogil
-    void random_multivariate_hypergeometric_marginals(bitgen_t *bitgen_state,
-                               int64_t total,
-                               size_t num_colors, int64_t *colors,
-                               int64_t nsample,
-                               size_t num_variates, int64_t *variates) nogil
-
 np.import_array()
 
-
 cdef int64_t _safe_sum_nonneg_int64(size_t num_colors, int64_t *colors):
     """
     Sum the values in the array `colors`.

diff --git a/numpy/random/c_distributions.pxd b/numpy/random/c_distributions.pxd
@@ -0,0 +1,114 @@
+#!python
+#cython: wraparound=False, nonecheck=False, boundscheck=False, cdivision=True, language_level=3
+from numpy cimport npy_intp
+
+from libc.stdint cimport (uint64_t, int32_t, int64_t)
+from numpy.random cimport bitgen_t
+
+cdef extern from "numpy/random/distributions.h":
+
+    struct s_binomial_t:
+        int has_binomial
+        double psave
+        int64_t nsave
+        double r
+        double q
+        double fm
+        int64_t m
+        double p1
+        double xm
+        double xl
+        double xr
+        double c
+        double laml
+        double lamr
+        double p2
+        double p3
+        double p4
+
+    ctypedef s_binomial_t binomial_t
+
+    double random_standard_uniform(bitgen_t *bitgen_state) nogil
+    void random_standard_uniform_fill(bitgen_t* bitgen_state, npy_intp cnt, double *out) nogil
+    double random_standard_exponential(bitgen_t *bitgen_state) nogil
+    double random_standard_exponential_f(bitgen_t *bitgen_state) nogil
+    void random_standard_exponential_fill(bitgen_t *bitgen_state, npy_intp cnt, double *out) nogil
+    void random_standard_exponential_fill_f(bitgen_t *bitgen_state, npy_intp cnt, double *out) nogil
+    void random_standard_exponential_inv_fill(bitgen_t *bitgen_state, npy_intp cnt, double *out) nogil
+    void random_standard_exponential_inv_fill_f(bitgen_t *bitgen_state, npy_intp cnt, double *out) nogil
+    double random_standard_normal(bitgen_t* bitgen_state) nogil
+    void random_standard_normal_fill(bitgen_t *bitgen_state, npy_intp count, double *out) nogil
+    void random_standard_normal_fill_f(bitgen_t *bitgen_state, npy_intp count, float *out) nogil
+    double random_standard_gamma(bitgen_t *bitgen_state, double shape) nogil
+
+    float random_standard_uniform_f(bitgen_t *bitgen_state) nogil
+    void random_standard_uniform_fill_f(bitgen_t* bitgen_state, npy_intp cnt, float *out) nogil
+    float random_standard_normal_f(bitgen_t* bitgen_state) nogil
+    float random_standard_gamma_f(bitgen_t *bitgen_state, float shape) nogil
+
+    int64_t random_positive_int64(bitgen_t *bitgen_state) nogil
+    int32_t random_positive_int32(bitgen_t *bitgen_state) nogil
+    int64_t random_positive_int(bitgen_t *bitgen_state) nogil
+    uint64_t random_uint(bitgen_t *bitgen_state) nogil
+
+    double random_normal(bitgen_t *bitgen_state, double loc, double scale) nogil
+
+    double random_gamma(bitgen_t *bitgen_state, double shape, double scale) nogil
+    float random_gamma_f(bitgen_t *bitgen_state, float shape, float scale) nogil
+
+    double random_exponential(bitgen_t *bitgen_state, double scale) nogil
+    double random_uniform(bitgen_t *bitgen_state, double lower, double range) nogil
+    double random_beta(bitgen_t *bitgen_state, double a, double b) nogil
+    double random_chisquare(bitgen_t *bitgen_state, double df) nogil
+    double random_f(bitgen_t *bitgen_state, double dfnum, double dfden) nogil
+    double random_standard_cauchy(bitgen_t *bitgen_state) nogil
+    double random_pareto(bitgen_t *bitgen_state, double a) nogil
+    double random_weibull(bitgen_t *bitgen_state, double a) nogil
+    double random_power(bitgen_t *bitgen_state, double a) nogil
+    double random_laplace(bitgen_t *bitgen_state, double loc, double scale) nogil
+    double random_gumbel(bitgen_t *bitgen_state, double loc, double scale) nogil
+    double random_logistic(bitgen_t *bitgen_state, double loc, double scale) nogil
+    double random_lognormal(bitgen_t *bitgen_state, double mean, double sigma) nogil
+    double random_rayleigh(bitgen_t *bitgen_state, double mode) nogil
+    double random_standard_t(bitgen_t *bitgen_state, double df) nogil
+    double random_noncentral_chisquare(bitgen_t *bitgen_state, double df,
+                                       double nonc) nogil
+    double random_noncentral_f(bitgen_t *bitgen_state, double dfnum,
+                               double dfden, double nonc) nogil
+    double random_wald(bitgen_t *bitgen_state, double mean, double scale) nogil
+    double random_vonmises(bitgen_t *bitgen_state, double mu, double kappa) nogil
+    double random_triangular(bitgen_t *bitgen_state, double left, double mode,
+                             double right) nogil
+
+    int64_t random_poisson(bitgen_t *bitgen_state, double lam) nogil
+    int64_t random_negative_binomial(bitgen_t *bitgen_state, double n, double p) nogil
+    int64_t random_binomial(bitgen_t *bitgen_state, double p, int64_t n, binomial_t *binomial) nogil
+    int64_t random_logseries(bitgen_t *bitgen_state, double p) nogil
+    int64_t random_geometric_search(bitgen_t *bitgen_state, double p) nogil
+    int64_t random_geometric_inversion(bitgen_t *bitgen_state, double p) nogil
+    int64_t random_geometric(bitgen_t *bitgen_state, double p) nogil
+    int64_t random_zipf(bitgen_t *bitgen_state, double a) nogil
+    int64_t random_hypergeometric(bitgen_t *bitgen_state, int64_t good, int64_t bad,
+                                    int64_t sample) nogil
+
+    uint64_t random_interval(bitgen_t *bitgen_state, uint64_t max) nogil
+
+    # Generate random uint64 numbers in closed interval [off, off + rng].
+    uint64_t random_bounded_uint64(bitgen_t *bitgen_state,
+                                   uint64_t off, uint64_t rng,
+                                   uint64_t mask, bint use_masked) nogil
+
+    void random_multinomial(bitgen_t *bitgen_state, int64_t n, int64_t *mnix,
+                            double *pix, npy_intp d, binomial_t *binomial) nogil
+
+    int random_multivariate_hypergeometric_count(bitgen_t *bitgen_state,
+                          int64_t total,
+                          size_t num_colors, int64_t *colors,
+                          int64_t nsample,
+                          size_t num_variates, int64_t *variates) nogil
+    void random_multivariate_hypergeometric_marginals(bitgen_t *bitgen_state,
+                               int64_t total,
+                               size_t num_colors, int64_t *colors,
+                               int64_t nsample,
+                               size_t num_variates, int64_t *variates) nogil
+
diff --git a/numpy/random/setup.py b/numpy/random/setup.py
@@ -52,6 +52,7 @@ def generate_libraries(ext, build_dir):
     PCG64_DEFS = []
     # One can force emulated 128-bit arithmetic if one wants.
     #PCG64_DEFS += [('PCG_FORCE_EMULATED_128BIT_MATH', '1')]
+    depends = ['__init__.pxd', 'c_distributions.pxd']
 
     for gen in ['mt19937']:
         # gen.pyx, src/gen/gen.c, src/gen/gen-jump.c
@@ -63,7 +64,7 @@ def generate_libraries(ext, build_dir):
                              libraries=EXTRA_LIBRARIES,
                              extra_compile_args=EXTRA_COMPILE_ARGS,
                              extra_link_args=EXTRA_LINK_ARGS,
-                             depends=['_%s.pyx' % gen],
+                             depends=depends + ['_%s.pyx' % gen],
                              define_macros=defs,
                              )
     for gen in ['philox', 'pcg64', 'sfc64']:
@@ -76,8 +77,8 @@ def generate_libraries(ext, build_dir):
                              libraries=EXTRA_LIBRARIES,
                              extra_compile_args=EXTRA_COMPILE_ARGS,
                              extra_link_args=EXTRA_LINK_ARGS,
-                             depends=['_%s.pyx' % gen, '_bit_generator.pyx',
-                                      '_bit_generator.pxd'],
+                             depends=depends + ['_%s.pyx' % gen,
+                                   '_bit_generator.pyx', '_bit_generator.pxd'],
                              define_macros=_defs,
                              )
     for gen in ['_common', '_bit_generator']:
@@ -88,7 +89,7 @@ def generate_libraries(ext, build_dir):
                             extra_compile_args=EXTRA_COMPILE_ARGS,
                              extra_link_args=EXTRA_LINK_ARGS,
                              include_dirs=['.', 'src'],
-                             depends=['%s.pyx' % gen, '%s.pxd' % gen,],
+                             depends=depends + ['%s.pyx' % gen, '%s.pxd' % gen,],
                              define_macros=defs,
                              )
         config.add_data_files('{0}.pxd'.format(gen))
@@ -107,7 +108,7 @@ def generate_libraries(ext, build_dir):
                              extra_compile_args=EXTRA_COMPILE_ARGS,
                              include_dirs=['.', 'src'],
                              extra_link_args=EXTRA_LINK_ARGS,
-                             depends=['%s.pyx' % gen],
+                             depends=depends + ['%s.pyx' % gen],
                              define_macros=defs,
                              )
     config.add_data_files('_bounded_integers.pxd')
@@ -120,10 +121,10 @@ def generate_libraries(ext, build_dir):
                          libraries=EXTRA_LIBRARIES,
                          extra_compile_args=EXTRA_COMPILE_ARGS,
                          extra_link_args=EXTRA_LINK_ARGS,
-                         depends=['mtrand.pyx'],
+                         depends=depends + ['mtrand.pyx'],
                          define_macros=defs + LEGACY_DEFS,
                          )
-    config.add_data_files('__init__.pxd')
+    config.add_data_files(*depends)
     return config