From d7a9c90fa204b138a60c054db4b08b0c5d6a0b16 Mon Sep 17 00:00:00 2001
From: zoj <44142765+zoj613@users.noreply.github.com>
Date: Sun, 4 Apr 2021 20:57:46 +0200
Subject: [PATCH 1/5] MAINT: clean python module and use strings as arguments
 for structured_precision_mvnorm's matrix_type arguments

---
 README.md              |  2 +-
 pyhtnorm/__init__.pxd  |  1 -
 pyhtnorm/_htnorm.pyx   | 83 +++++++++++++++++++++++++++++++++---------
 pyhtnorm/c_htnorm.pxd  | 55 ----------------------------
 tests/test_pyhtnorm.py |  4 +-
 5 files changed, 68 insertions(+), 77 deletions(-)
 delete mode 100644 pyhtnorm/__init__.pxd
 delete mode 100644 pyhtnorm/c_htnorm.pxd

diff --git a/README.md b/README.md
index 556974a..5b59039 100644
--- a/README.md
+++ b/README.md
@@ -109,7 +109,7 @@ interface is such that the code can be easily integrated into other existing lib
 Since `v1.0.0`, it supports passing a `numpy.random.Generator` instance as a parameter to aid reproducibility.
 
 ```python
-from pyhtnorm import hyperplane_truncated_mvnorm
+from pyhtnorm import hyperplane_truncated_mvnorm, structured_precision_mvnorm
 import numpy as np
 
 rng = np.random.default_rng()
diff --git a/pyhtnorm/__init__.pxd b/pyhtnorm/__init__.pxd
deleted file mode 100644
index e31493a..0000000
--- a/pyhtnorm/__init__.pxd
+++ /dev/null
@@ -1 +0,0 @@
-from pyhtnorm.c_htnorm cimport *
diff --git a/pyhtnorm/_htnorm.pyx b/pyhtnorm/_htnorm.pyx
index cc0143e..8325a5f 100644
--- a/pyhtnorm/_htnorm.pyx
+++ b/pyhtnorm/_htnorm.pyx
@@ -34,12 +34,12 @@ References
 
 """
 from cpython.pycapsule cimport PyCapsule_GetPointer
+from libc.stdint cimport uint64_t
 
-import numpy as np
 cimport numpy as np
 from numpy.random cimport BitGenerator, bitgen_t
 
-from pyhtnorm.c_htnorm cimport *
+from numpy.random import default_rng
 
 
 np.import_array()
@@ -48,7 +48,54 @@ cdef extern from "../src/dist.h":
     int HTNORM_ALLOC_ERROR
 
 
-cdef inline void validate_return_info(info):
+cdef extern from "../include/rng.h" nogil:
+    ctypedef struct rng_t:
+        void* base
+        uint64_t (*next_uint64)(void* state)
+        double (*next_double)(void* state)
+
+
+cdef extern from "../include/htnorm.h" nogil:
+    ctypedef enum mat_type "type_t":
+        NORMAL
+        DIAGONAL
+        IDENTITY
+
+    ctypedef struct ht_config_t:
+        size_t gnrow
+        size_t gncol
+        const double* mean
+        const double* cov
+        const double* g
+        const double* r
+        bint diag
+
+    ctypedef struct sp_config_t:
+        mat_type a_id
+        mat_type o_id
+        size_t pnrow
+        size_t pncol
+        const double* mean
+        const double* a
+        const double* phi
+        const double* omega
+        bint struct_mean
+
+    void init_ht_config(ht_config_t* conf, size_t gnrow, size_t gncol,
+                        const double* mean, const double* cov, const double* g,
+                        const double* r, bint diag)
+
+    void init_sp_config(sp_config_t* conf, size_t pnrow, size_t pncol,
+                        const double* mean, const double* a, const double* phi,
+                        const double* omega, bint struct_mean, mat_type a_id,
+                        mat_type o_id)
+
+    int htn_hyperplane_truncated_mvn(rng_t* rng, const ht_config_t* conf, double* out)
+
+    int htn_structured_precision_mvn(rng_t* rng, const sp_config_t* conf, double* out)
+
+
+cdef inline void validate_return_info(int info):
     if info == HTNORM_ALLOC_ERROR:
         raise MemoryError("Not enough memory to allocate resources.")
     elif info < 0:
@@ -62,13 +109,14 @@ cdef inline void validate_return_info(info):
         )
 
 
-cdef set _VALID_MATRIX_TYPES = {NORMAL, DIAGONAL, IDENTITY}
+cdef dict MAT_TYPE = {"regular": NORMAL, "diagonal": DIAGONAL, "identity": IDENTITY}
+cdef const char* BITGEN_NAME = "BitGenerator"
 
 
-cdef inline void initialize_rng(BitGenerator bitgenerator, rng_t* htnorm_rng):
+cdef inline void initialize_rng(object bitgenerator, rng_t* htnorm_rng):
     cdef bitgen_t* bitgen
 
-    bitgen = <bitgen_t*>PyCapsule_GetPointer(bitgenerator.capsule, "BitGenerator")
+    bitgen = <bitgen_t*>PyCapsule_GetPointer(bitgenerator.capsule, BITGEN_NAME)
     htnorm_rng.base = bitgen.state
     htnorm_rng.next_uint64 = bitgen.next_uint64
     htnorm_rng.next_double = bitgen.next_double
@@ -135,7 +183,6 @@ def hyperplane_truncated_mvnorm(
         the algorithm could not successfully generate the samples.
 
     """
-    cdef BitGenerator bitgenerator
     cdef rng_t rng
     cdef ht_config_t config
     cdef int info
@@ -152,7 +199,7 @@ def hyperplane_truncated_mvnorm(
     init_ht_config(&config, g.shape[0], g.shape[1], &mean[0],
                    &cov[0, 0], &g[0, 0], &r[0], diag)
 
-    bitgenerator = np.random.default_rng(random_state)._bit_generator
+    bitgenerator = default_rng(random_state)._bit_generator
     initialize_rng(bitgenerator, &rng)
 
     with bitgenerator.lock, nogil:
@@ -169,14 +216,15 @@ def structured_precision_mvnorm(
     double[:,::1] phi,
     double[:,::1] omega,
     bint mean_structured=False,
-    int a_type=0,
-    int o_type=0,
+    str a_type="regular",
+    str o_type="regular",
     double[:] out=None,
     random_state=None
 ):
     """
     structured_precision_mvnorm(mean, a, phi, omega, mean_structured=False,
-                                a_type=0, o_type=0, out=None, random_state=None)
+                                a_type="regular", o_type="regular",
+                                out=None, random_state=None)
 
     Sample from a MVN with a structured precision matrix :math:`\Lambda`
     .. math::
@@ -197,9 +245,9 @@ def structured_precision_mvnorm(
         such than ``mean = (precision)^-1 * phi^T * omega * t``. If this
         is set to True, then the `mean` parameter is assumed to contain the
         array ``t``.
-    a_type : {0, 1, 2}, optional, default=0
+    a_type : {"regular", "diagonal", "identity"}, optional, default="regular"
         Whether `a` ia a normal, diagonal or identity matrix.
-    o_type : {0, 1, 2}, optional, default=0
+    o_type : {"regular", "diagonal", "identity"}, optional, default="regular"
         Whether `omega` ia a normal, diagonal or identity matrix.
     out : 1d array, optional, default=None
         An array of the same shape as `mean` to store the samples. If not
@@ -228,7 +276,6 @@ def structured_precision_mvnorm(
         the algorithm could not successfully generate the samples.
 
     """
-    cdef BitGenerator bitgenerator
     cdef rng_t rng
     cdef sp_config_t config
     cdef int info
@@ -238,8 +285,8 @@ def structured_precision_mvnorm(
         raise ValueError('`omega` and `a` both need to be square matrices')
     elif (phi.shape[0] != omega.shape[0]) or (phi.shape[1] != a.shape[0]):
         raise ValueError('Shapes of `phi`, `omega` and `a` are not consistent')
-    elif not {a_type, o_type}.issubset(_VALID_MATRIX_TYPES):
-        raise ValueError(f"`a_type` & `o_type` must be one of {_VALID_MATRIX_TYPES}")
+    elif not {a_type, o_type}.issubset(MAT_TYPE):
+        raise ValueError(f"`a_type` & `o_type` must be one of {set(MAT_TYPE)}")
     elif has_out and out.shape[0] != mean.shape[0]:
         raise ValueError("`out` must have the same size as the mean array.")
     elif not has_out:
@@ -248,9 +295,9 @@ def structured_precision_mvnorm(
 
     init_sp_config(&config, phi.shape[0], phi.shape[1], &mean[0], &a[0, 0],
                    &phi[0, 0], &omega[0, 0], mean_structured,
-                   <mat_type>a_type, <mat_type>o_type)
+                   MAT_TYPE[a_type], MAT_TYPE[o_type])
 
-    bitgenerator = np.random.default_rng(random_state)._bit_generator
+    bitgenerator = default_rng(random_state)._bit_generator
     initialize_rng(bitgenerator, &rng)
 
     with bitgenerator.lock, nogil:
diff --git a/pyhtnorm/c_htnorm.pxd b/pyhtnorm/c_htnorm.pxd
deleted file mode 100644
index 815cce4..0000000
--- a/pyhtnorm/c_htnorm.pxd
+++ /dev/null
@@ -1,55 +0,0 @@
-# cython: language_level=3
-"""
-Copyright (c) 2020-2021, Zolisa Bleki
-
-SPDX-License-Identifier: BSD-3-Clause */
-"""
-from libc.stdint cimport uint64_t
-
-
-cdef extern from "../include/rng.h":
-    ctypedef struct rng_t:
-        void* base
-        uint64_t (*next_uint64)(void* state) nogil
-        double (*next_double)(void* state) nogil
-
-
-cdef extern from "../include/htnorm.h":
-
-    ctypedef enum mat_type "type_t":
-        NORMAL
-        DIAGONAL
-        IDENTITY
-
-    ctypedef struct ht_config_t:
-        size_t gnrow
-        size_t gncol
-        const double* mean
-        const double* cov
-        const double* g
-        const double* r
-        bint is_diag "diag"
-
-    ctypedef struct sp_config_t:
-        mat_type a_id
-        mat_type o_id
-        size_t pnrow
-        size_t pncol
-        const double* mean
-        const double* a
-        const double* phi
-        const double* omega
-        bint struct_mean
-
-    void init_ht_config(ht_config_t* conf, size_t gnrow, size_t gncol,
-                        const double* mean, const double* cov, const double* g,
-                        const double* r, bint diag) nogil
-
-    void init_sp_config(sp_config_t* conf, size_t pnrow, size_t pncol,
-                        const double* mean, const double* a, const double* phi,
-                        const double* omega, bint struct_mean, mat_type a_id,
-                        mat_type o_id) nogil
-
-    int htn_hyperplane_truncated_mvn(rng_t* rng, const ht_config_t* conf, double* out) nogil
-
-    int htn_structured_precision_mvn(rng_t* rng, const sp_config_t* conf, double* out) nogil
diff --git a/tests/test_pyhtnorm.py b/tests/test_pyhtnorm.py
index 602096d..a5029d1 100644
--- a/tests/test_pyhtnorm.py
+++ b/tests/test_pyhtnorm.py
@@ -82,7 +82,7 @@ def test_structured_mvn(structured_mvn_data):
         structured_precision_mvnorm(mean, a2, phi, omega2)
     # raise error if invalid matrix structure is specified
     with pytest.raises(ValueError):
-        structured_precision_mvnorm(mean, a, phi, omega, a_type=-1000)
+        structured_precision_mvnorm(mean, a, phi, omega, a_type="wrong type")
     # rest for non-numerical values
     a2 = a.copy()
     a2[0] = np.nan
@@ -94,7 +94,7 @@ def test_structured_mvn(structured_mvn_data):
     arr1 = structured_precision_mvnorm(mean, a, phi, omega, random_state=rng)
     rng = np.random.default_rng(10)
     arr2 = structured_precision_mvnorm(
-        mean, a, phi, omega, o_type=1, a_type=1, random_state=rng
+        mean, a, phi, omega, o_type="diagonal", a_type="diagonal", random_state=rng
     )
     assert np.allclose(arr1, arr2)
     # test results of passing output array through the `out` parameter

From f8ad760f790496b4245cce4621e0dcae992e02bc Mon Sep 17 00:00:00 2001
From: zoj <44142765+zoj613@users.noreply.github.com>
Date: Sun, 4 Apr 2021 21:36:29 +0200
Subject: [PATCH 2/5] MAINT: clean python module and use strings as arguments
 for structured_precision_mvnorm's matrix_type arguments

---
 R/htnorm.r                    | 22 ++++++++++++++++------
 README.md                     |  7 +++++++
 man/HTNGenerator.Rd           |  2 +-
 tests/testthat/test_rhtnorm.r |  2 +-
 4 files changed, 25 insertions(+), 8 deletions(-)

diff --git a/R/htnorm.r b/R/htnorm.r
index 2f7c53f..558fa2d 100644
--- a/R/htnorm.r
+++ b/R/htnorm.r
@@ -1,7 +1,7 @@
 # Copyright (c) 2020, Zolisa Bleki
 # SPDX-License-Identifier: BSD-3-Clause
 
-matrix_type <- c(0, 1, 2)
+matrix_type <- c("regular", "diagonal", "identity")
 
 
 validate_output <- function(res) {
@@ -60,10 +60,20 @@ strprec_mvn <- function(rng, mean, a, phi, omega, str_mean, a_id, o_id, out) {
     )
 
     if (!is.element(a_id, matrix_type) || !is.element(o_id, matrix_type))
-        stop("`a_type` and `o_type` need to be one of {0, 1, 2}")
+        stop("`a_type` and `o_type` need to be one of {'regular', 'diagonal', 'identity'}")
 
-    a_id <- as.integer(a_id)
-    o_id <- as.integer(o_id)
+    a_id <- switch(
+        a_id,
+        "regular" = as.integer(0),
+        "diagonal" = as.integer(1),
+        "identity" = as.integer(2)
+    )
+    o_id <- switch(
+        o_id,
+        "regular" = as.integer(0),
+        "diagonal" = as.integer(1),
+        "identity" = as.integer(2)
+    )
 
     if (is.null(out))
         out <- rep(0, length(mean))
@@ -118,7 +128,7 @@ strprec_mvn <- function(rng, mean, a, phi, omega, str_mean, a_id, o_id, out) {
 #' phi <- eig$vectors
 #' omega <- diag(eig$values)
 #' a <- diag(runif(length(mean)))
-#' rng$structured_precision_mvnorm(mean, a, phi, omega, a_type = 1, out = out)
+#' rng$structured_precision_mvnorm(mean, a, phi, omega, a_type = "diagonal", out = out)
 HTNGenerator <- function(seed = NULL, gen = "xrs128p") {
 
     if (is.numeric(seed)) {
@@ -151,7 +161,7 @@ HTNGenerator <- function(seed = NULL, gen = "xrs128p") {
     }
 
     res$structured_precision_mvnorm <- function(
-        mean, a, phi, omega, str_mean = FALSE, a_type = 0, o_type = 0, out= NULL
+        mean, a, phi, omega, str_mean = FALSE, a_type = "regular", o_type = "regular", out= NULL
     ) {
         if (is.null(out)) {
             strprec_mvn(
diff --git a/README.md b/README.md
index 5b59039..b0e5b2c 100644
--- a/README.md
+++ b/README.md
@@ -166,6 +166,13 @@ sum(samples)
 out <- rep(0, 1000)
 rng$hyperplane_truncated_mvnorm(mean, cov, G, r, out = out)
 sum(out)  #verify
+
+out <- rep(0, 1000)
+eig <- eigen(cov)
+phi <- eig$vectors
+omega <- diag(eig$values)
+a <- diag(runif(length(mean)))
+rng$structured_precision_mvnorm(mean, a, phi, omega, a_type = "diagonal", out = out)
 ```
 
 ## Licensing
diff --git a/man/HTNGenerator.Rd b/man/HTNGenerator.Rd
index 0e11fdb..7c36337 100644
--- a/man/HTNGenerator.Rd
+++ b/man/HTNGenerator.Rd
@@ -41,7 +41,7 @@ eig <- eigen(cov)
 phi <- eig$vectors
 omega <- diag(eig$values)
 a <- diag(runif(length(mean)))
-rng$structured_precision_mvnorm(mean, a, phi, omega, a_type = 1, out = out)
+rng$structured_precision_mvnorm(mean, a, phi, omega, a_type = "diagonal", out = out)
 }
 \references{
 Cong, Yulai; Chen, Bo; Zhou, Mingyuan. Fast Simulation of 
diff --git a/tests/testthat/test_rhtnorm.r b/tests/testthat/test_rhtnorm.r
index 32d12ec..aefe6a5 100644
--- a/tests/testthat/test_rhtnorm.r
+++ b/tests/testthat/test_rhtnorm.r
@@ -86,7 +86,7 @@ test_that("structured precision normal", {
     # test consistency of output when `a_type` or `o_type` is given
     gen1 <- HTNGenerator(10)$structured_precision_mvnorm(mean, a, phi, omega)
     gen2 <- HTNGenerator(10)$structured_precision_mvnorm(
-        mean, a, phi, omega, a_type = 1, o_type = 1
+        mean, a, phi, omega, a_type = "diagonal", o_type = "diagonal"
     )
     expect_equal(gen1, gen2)
     # test results of passing output array through the `out` parameter

From 36909881c4036839469f1d8487d356165cf0e24c Mon Sep 17 00:00:00 2001
From: zoj <44142765+zoj613@users.noreply.github.com>
Date: Sun, 4 Apr 2021 22:47:51 +0200
Subject: [PATCH 3/5] MAINT: rename some files and tidy up

---
 Makefile                                      |   4 +-
 README.md                                     |   2 +-
 build.py                                      |   6 +-
 include/htnorm.h                              |   2 +-
 include/{rng.h => htnorm_rng.h}               |   0
 pyhtnorm/_htnorm.pyx                          |   6 +-
 src/LICENSE-PCG32.txt                         | 202 ------------------
 src/LICENSE-ZIGGURAT.txt                      |  58 -----
 src/Makevars                                  |   8 +-
 src/htnorm.c                                  |   9 +-
 ...always_inline.h => htnorm_always_inline.h} |   7 +
 src/{blas.h => htnorm_blas.h}                 |   0
 src/{dist.c => htnorm_distributions.c}        |   9 +-
 src/{dist.h => htnorm_distributions.h}        |   5 +-
 ...pcg32_minimal.h => htnorm_pcg32_minimal.h} |   2 +-
 src/{pcg64.h => htnorm_pcg64.h}               |   4 +-
 src/{r_wrapper.c => htnorm_r_wrapper.c}       |   2 +-
 src/{rng.c => htnorm_rng.c}                   |   7 +-
 src/{splitmax64.h => htnorm_splitmix64.h}     |   2 +-
 ...xoroshiro128p.h => htnorm_xoroshiro128p.h} |   2 +-
 ...onstants.h => htnorm_ziggurat_constants.h} |   0
 21 files changed, 41 insertions(+), 296 deletions(-)
 rename include/{rng.h => htnorm_rng.h} (100%)
 delete mode 100644 src/LICENSE-PCG32.txt
 delete mode 100644 src/LICENSE-ZIGGURAT.txt
 rename src/{always_inline.h => htnorm_always_inline.h} (76%)
 rename src/{blas.h => htnorm_blas.h} (100%)
 rename src/{dist.c => htnorm_distributions.c} (96%)
 rename src/{dist.h => htnorm_distributions.h} (97%)
 rename src/{pcg32_minimal.h => htnorm_pcg32_minimal.h} (96%)
 rename src/{pcg64.h => htnorm_pcg64.h} (94%)
 rename src/{r_wrapper.c => htnorm_r_wrapper.c} (99%)
 rename src/{rng.c => htnorm_rng.c} (93%)
 rename src/{splitmax64.h => htnorm_splitmix64.h} (95%)
 rename src/{xoroshiro128p.h => htnorm_xoroshiro128p.h} (96%)
 rename src/{zig_constants.h => htnorm_ziggurat_constants.h} (100%)

diff --git a/Makefile b/Makefile
index a2d8517..ff544d9 100644
--- a/Makefile
+++ b/Makefile
@@ -16,9 +16,9 @@ LIBS_DIR ?= /usr/lib
 override LIBS_DIR := -L$(LIBS_DIR)
 LIBS := -lm -lblas -llapack
 
-SRCFILES = src/dist.c src/htnorm.c src/rng.c
+SRCFILES = src/htnorm_distributions.c src/htnorm.c src/htnorm_rng.c
 
-OBJ = src/dist.o src/htnorm.o src/rng.o
+OBJ = src/htnorm_distributions.o src/htnorm.o src/htnorm_rng.o
 
 
 %.o: %.c
diff --git a/README.md b/README.md
index b0e5b2c..8588b20 100644
--- a/README.md
+++ b/README.md
@@ -194,7 +194,7 @@ see the [LICENSE][6] file.
 [2]: https://www.pcg-random.org/
 [3]: https://en.wikipedia.org/wiki/Xoroshiro128%2B
 [4]: ./include/htnorm.h 
-[5]: ./include/rng.h
+[5]: ./include/htnorm_rng.h
 [6]: ./LICENSE
 [7]: https://python-poetry.org/docs/pyproject/
 [8]: https://www.sciencedirect.com/science/article/abs/pii/S2211675317301574 
diff --git a/build.py b/build.py
index 7263e61..e6bfd64 100644
--- a/build.py
+++ b/build.py
@@ -6,8 +6,8 @@
 
 source_files = [
     "pyhtnorm/_htnorm.c",
-    "src/rng.c",
-    "src/dist.c",
+    "src/htnorm_rng.c",
+    "src/htnorm_distributions.c",
     "src/htnorm.c"
 ]
 
@@ -32,7 +32,7 @@
     Extension(
         "_htnorm",
         source_files,
-        include_dirs=[np.get_include(), './include'],
+        include_dirs=[np.get_include(), './include', 'src'],
         library_dirs=library_dirs,
         libraries=libraries,
         define_macros=[('NPY_NO_DEPRECATED_API', 0)],
diff --git a/include/htnorm.h b/include/htnorm.h
index 11f0cd6..f9d7f37 100644
--- a/include/htnorm.h
+++ b/include/htnorm.h
@@ -28,7 +28,7 @@
 #include <stdbool.h>
 #include <stddef.h>
 
-#include "rng.h"
+#include "htnorm_rng.h"
 
 
 typedef enum {NORMAL, DIAGONAL, IDENTITY} type_t;
diff --git a/include/rng.h b/include/htnorm_rng.h
similarity index 100%
rename from include/rng.h
rename to include/htnorm_rng.h
diff --git a/pyhtnorm/_htnorm.pyx b/pyhtnorm/_htnorm.pyx
index 8325a5f..822043e 100644
--- a/pyhtnorm/_htnorm.pyx
+++ b/pyhtnorm/_htnorm.pyx
@@ -44,18 +44,18 @@ from numpy.random import default_rng
 
 np.import_array()
 
-cdef extern from "../src/dist.h":
+cdef extern from "htnorm_distributions.h":
     int HTNORM_ALLOC_ERROR
 
 
-cdef extern from "../include/rng.h" nogil:
+cdef extern from "htnorm_rng.h" nogil:
     ctypedef struct rng_t:
         void* base
         uint64_t (*next_uint64)(void* state)
         double (*next_double)(void* state)
 
 
-cdef extern from "../include/htnorm.h" nogil:
+cdef extern from "htnorm.h" nogil:
     ctypedef enum mat_type "type_t":
         NORMAL
         DIAGONAL
diff --git a/src/LICENSE-PCG32.txt b/src/LICENSE-PCG32.txt
deleted file mode 100644
index 8f71f43..0000000
--- a/src/LICENSE-PCG32.txt
+++ /dev/null
@@ -1,202 +0,0 @@
-                                 Apache License
-                           Version 2.0, January 2004
-                        http://www.apache.org/licenses/
-
-   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
-
-   1. Definitions.
-
-      "License" shall mean the terms and conditions for use, reproduction,
-      and distribution as defined by Sections 1 through 9 of this document.
-
-      "Licensor" shall mean the copyright owner or entity authorized by
-      the copyright owner that is granting the License.
-
-      "Legal Entity" shall mean the union of the acting entity and all
-      other entities that control, are controlled by, or are under common
-      control with that entity. For the purposes of this definition,
-      "control" means (i) the power, direct or indirect, to cause the
-      direction or management of such entity, whether by contract or
-      otherwise, or (ii) ownership of fifty percent (50%) or more of the
-      outstanding shares, or (iii) beneficial ownership of such entity.
-
-      "You" (or "Your") shall mean an individual or Legal Entity
-      exercising permissions granted by this License.
-
-      "Source" form shall mean the preferred form for making modifications,
-      including but not limited to software source code, documentation
-      source, and configuration files.
-
-      "Object" form shall mean any form resulting from mechanical
-      transformation or translation of a Source form, including but
-      not limited to compiled object code, generated documentation,
-      and conversions to other media types.
-
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diff --git a/src/LICENSE-ZIGGURAT.txt b/src/LICENSE-ZIGGURAT.txt
deleted file mode 100644
index 43a7928..0000000
--- a/src/LICENSE-ZIGGURAT.txt
+++ /dev/null
@@ -1,58 +0,0 @@
-Copyright (c) 2005-2017, NumPy Developers.
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are
-met:
-
-* Redistributions of source code must retain the above copyright
-   notice, this list of conditions and the following disclaimer.
-
-* Redistributions in binary form must reproduce the above
-   copyright notice, this list of conditions and the following
-   disclaimer in the documentation and/or other materials provided
-   with the distribution.
-
-* Neither the name of the NumPy Developers nor the names of any
-   contributors may be used to endorse or promote products derived
-   from this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
-THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
-
-The ziggurat methods were derived from Julia.
-
-Copyright (c) 2009-2019: Jeff Bezanson, Stefan Karpinski, Viral B. Shah,
-and other contributors:
-
-https://github.com/JuliaLang/julia/contributors
-
-Permission is hereby granted, free of charge, to any person obtaining
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-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/src/Makevars b/src/Makevars
index 50f8b58..0304eb9 100644
--- a/src/Makevars
+++ b/src/Makevars
@@ -1,16 +1,16 @@
 PKG_CPPFLAGS = -I../include -DHTNORM_COLMAJOR
 PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) 
 
-OBJS = htnorm.o rng.o dist.o
+OBJS = htnorm_distributions.o htnorm.o htnorm_rng.o
 
 all:
 	@$(MAKE) $(SHLIB)
 	@rm -f *.mod src/*.o *.o
 
-$(SHLIB): r_wrapper.o
+$(SHLIB): htnorm_r_wrapper.o
 
-r_wrapper.o: $(OBJS)
-htnorm.o: dist.o
+htnorm_r_wrapper.o: $(OBJS)
+htnorm.o: htnorm_distributions.o
 
 clean:
 	@rm -rf *.o *.mod *.d *.rc *.so *.dylib *.dll *.a *.lib $(SHLIB) $(OBJECTS)
diff --git a/src/htnorm.c b/src/htnorm.c
index 78417db..19b0f0f 100644
--- a/src/htnorm.c
+++ b/src/htnorm.c
@@ -8,14 +8,13 @@
  * macro for several lines per function because matrix manipulation with BLAS
  * / LAPACK in C heavily depends on the memory layout of the input.
  * */
-#include <stddef.h>
 #include <string.h>
 
-#include "blas.h"
-#include "dist.h"
+#include "htnorm_blas.h"
+#include "htnorm_distributions.h"
 
 
-inline void
+ALWAYS_INLINE(void)
 init_ht_config(ht_config_t* conf, size_t gnrow, size_t gncol, const double* mean,
                const double* cov, const double* g, const double* r, bool diag)
 {
@@ -29,7 +28,7 @@ init_ht_config(ht_config_t* conf, size_t gnrow, size_t gncol, const double* mean
 }
 
 
-inline void
+ALWAYS_INLINE(void)
 init_sp_config(sp_config_t* conf, size_t pnrow, size_t pncol, const double* mean,
                const double* a, const double* phi, const double* omega,
                bool struct_mean, type_t a_id, type_t o_id)
diff --git a/src/always_inline.h b/src/htnorm_always_inline.h
similarity index 76%
rename from src/always_inline.h
rename to src/htnorm_always_inline.h
index f156b96..5d05797 100644
--- a/src/always_inline.h
+++ b/src/htnorm_always_inline.h
@@ -1,3 +1,10 @@
+/* Copyright (c) 2020, Zolisa Bleki
+ *
+ * SPDX-License-Identifier: BSD-3-Clause 
+ *
+ * This file is derived from an example in the documentation of clang.
+ */
+#pragma once
 #ifndef HTNORM_ALWAYS_INLINE_H
 #define HTNORM_ALWAYS_INLINE_H
 
diff --git a/src/blas.h b/src/htnorm_blas.h
similarity index 100%
rename from src/blas.h
rename to src/htnorm_blas.h
diff --git a/src/dist.c b/src/htnorm_distributions.c
similarity index 96%
rename from src/dist.c
rename to src/htnorm_distributions.c
index 5c05934..44782ae 100644
--- a/src/dist.c
+++ b/src/htnorm_distributions.c
@@ -5,9 +5,9 @@
 #include <stddef.h>
 #include <string.h>
 
-#include "blas.h"
-#include "dist.h"
-#include "zig_constants.h"
+#include "htnorm_blas.h"
+#include "htnorm_distributions.h"
+#include "htnorm_ziggurat_constants.h"
 
 #define std_normal_rand_fill(rng, arr_size, arr) \
     for (int ii = (arr_size); ii--;) (arr)[ii] = std_normal_rand((rng))
@@ -69,16 +69,17 @@ mvn_rand_cov(rng_t* rng, const double* mean, const double* cov, int nrow,
     if (factor == NULL)
         return HTNORM_ALLOC_ERROR;
 
-    // do cholesky factorization.
     int info;
     static const int incx = 1;
     static const double one = 1;
     memcpy(factor, cov, nrow * nrow * sizeof(*factor));
+    // do cholesky factorization.
     POTRF(nrow, factor, nrow, info);
     if (!info) {
         std_normal_rand_fill(rng, nrow, out);
         // triangular matrix-vector product. L * z.
         TRMV(nrow, factor, nrow, out, incx);
+        // mean + L * z
         AXPY(nrow, one, mean, out);
     }
 
diff --git a/src/dist.h b/src/htnorm_distributions.h
similarity index 97%
rename from src/dist.h
rename to src/htnorm_distributions.h
index f8b4e56..f731b3f 100644
--- a/src/dist.h
+++ b/src/htnorm_distributions.h
@@ -9,12 +9,11 @@
 #ifndef HTNORM_DIST_H
 #define HTNORM_DIST_H
 
-#include <stdbool.h>
 #include <stdlib.h>
 
-#include "../include/rng.h"
+#include "../include/htnorm_rng.h"
 #include "../include/htnorm.h"
-#include "always_inline.h"
+#include "htnorm_always_inline.h"
 
 // error number for failed memory allocation throughout the library
 #define HTNORM_ALLOC_ERROR -100
diff --git a/src/pcg32_minimal.h b/src/htnorm_pcg32_minimal.h
similarity index 96%
rename from src/pcg32_minimal.h
rename to src/htnorm_pcg32_minimal.h
index aba4634..e3a2f46 100644
--- a/src/pcg32_minimal.h
+++ b/src/htnorm_pcg32_minimal.h
@@ -8,7 +8,7 @@
 
 #include <stdint.h>
 
-#include "always_inline.h"
+#include "htnorm_always_inline.h"
 
 typedef struct pcg32_rand {
     uint64_t state;
diff --git a/src/pcg64.h b/src/htnorm_pcg64.h
similarity index 94%
rename from src/pcg64.h
rename to src/htnorm_pcg64.h
index e53900e..1c4323b 100644
--- a/src/pcg64.h
+++ b/src/htnorm_pcg64.h
@@ -4,8 +4,8 @@
 #ifndef HTNORM_PCG64_H
 #define HTNORM_PCG64_H
 
-#include "pcg32_minimal.h"
-#include "splitmax64.h"
+#include "htnorm_pcg32_minimal.h"
+#include "htnorm_splitmix64.h"
 
 typedef struct {pcg32_random_t gen[2];} pcg64_random_t;
 
diff --git a/src/r_wrapper.c b/src/htnorm_r_wrapper.c
similarity index 99%
rename from src/r_wrapper.c
rename to src/htnorm_r_wrapper.c
index 129c107..2f72a0c 100644
--- a/src/r_wrapper.c
+++ b/src/htnorm_r_wrapper.c
@@ -4,7 +4,7 @@
 #include <R.h>
 #include <Rinternals.h>
 
-#include "../include/htnorm.h"
+#include "htnorm.h"
 
 enum RNG_TYPE {Xoroshiro128p, PCG64}; 
 
diff --git a/src/rng.c b/src/htnorm_rng.c
similarity index 93%
rename from src/rng.c
rename to src/htnorm_rng.c
index 9794371..f55cb46 100644
--- a/src/rng.c
+++ b/src/htnorm_rng.c
@@ -4,10 +4,9 @@
 #include <stdlib.h>
 #include <time.h>
 
-#include "pcg64.h"
-#include "xoroshiro128p.h"
-
-#include "../include/rng.h"
+#include "htnorm_pcg64.h"
+#include "htnorm_xoroshiro128p.h"
+#include "../include/htnorm_rng.h"
 
 
 ALWAYS_INLINE(void)
diff --git a/src/splitmax64.h b/src/htnorm_splitmix64.h
similarity index 95%
rename from src/splitmax64.h
rename to src/htnorm_splitmix64.h
index 430a8ab..f6875d1 100644
--- a/src/splitmax64.h
+++ b/src/htnorm_splitmix64.h
@@ -11,7 +11,7 @@ See <http://creativecommons.org/publicdomain/zero/1.0/>. */
 
 #include <stdint.h>
 
-#include "always_inline.h"
+#include "htnorm_always_inline.h"
 
 // generate a postive integer using the splitmix64 bit generator
 static ALWAYS_INLINE(uint64_t)
diff --git a/src/xoroshiro128p.h b/src/htnorm_xoroshiro128p.h
similarity index 96%
rename from src/xoroshiro128p.h
rename to src/htnorm_xoroshiro128p.h
index 89929f2..3adcf3d 100644
--- a/src/xoroshiro128p.h
+++ b/src/htnorm_xoroshiro128p.h
@@ -9,7 +9,7 @@
 
 #include <stdint.h>
 
-#include "always_inline.h"
+#include "htnorm_always_inline.h"
 
 typedef struct {uint64_t s[2];} xrs128p_random_t;
 
diff --git a/src/zig_constants.h b/src/htnorm_ziggurat_constants.h
similarity index 100%
rename from src/zig_constants.h
rename to src/htnorm_ziggurat_constants.h

From f967c518690cdd18a2ad23a891e4c3b6ff7754f6 Mon Sep 17 00:00:00 2001
From: zoj <44142765+zoj613@users.noreply.github.com>
Date: Sun, 4 Apr 2021 22:48:25 +0200
Subject: [PATCH 4/5] DOC: Add third_party_licenses directory

---
 third_party_licenses/LICENSE-OPENBLAS.txt |  32 ++++
 third_party_licenses/LICENSE-PCG32.txt    | 206 ++++++++++++++++++++++
 third_party_licenses/LICENSE-ZIGGURAT.txt |  63 +++++++
 3 files changed, 301 insertions(+)
 create mode 100644 third_party_licenses/LICENSE-OPENBLAS.txt
 create mode 100644 third_party_licenses/LICENSE-PCG32.txt
 create mode 100644 third_party_licenses/LICENSE-ZIGGURAT.txt

diff --git a/third_party_licenses/LICENSE-OPENBLAS.txt b/third_party_licenses/LICENSE-OPENBLAS.txt
new file mode 100644
index 0000000..d8a6db2
--- /dev/null
+++ b/third_party_licenses/LICENSE-OPENBLAS.txt
@@ -0,0 +1,32 @@
+The wheel distribution of pyhtnorm contains OpenBLAS binaries.
+
+
+Copyright (c) 2011-2014, The OpenBLAS Project
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   1. Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer in
+      the documentation and/or other materials provided with the
+      distribution.
+   3. Neither the name of the OpenBLAS project nor the names of 
+      its contributors may be used to endorse or promote products 
+      derived from this software without specific prior written 
+      permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
+USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/third_party_licenses/LICENSE-PCG32.txt b/third_party_licenses/LICENSE-PCG32.txt
new file mode 100644
index 0000000..04619f9
--- /dev/null
+++ b/third_party_licenses/LICENSE-PCG32.txt
@@ -0,0 +1,206 @@
+The code for the PCG32 bitgenerator at src/htnorm_pcg32_minimal.h was obtained
+from M. E. O'Neill's pcg-random package. Website of original code: pcg-random.org
+ 
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
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+      direction or management of such entity, whether by contract or
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+
+      "You" (or "Your") shall mean an individual or Legal Entity
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+
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+
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diff --git a/third_party_licenses/LICENSE-ZIGGURAT.txt b/third_party_licenses/LICENSE-ZIGGURAT.txt
new file mode 100644
index 0000000..5dc0667
--- /dev/null
+++ b/third_party_licenses/LICENSE-ZIGGURAT.txt
@@ -0,0 +1,63 @@
+The ziggurat constants at src/htnorm_ziggurat_constants.h and well as the
+standard normal distribution random number generator implementation where
+obtained from the numpy package.
+
+
+Copyright (c) 2005-2017, NumPy Developers.
+All rights reserved.
+
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+modification, are permitted provided that the following conditions are
+met:
+
+* Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above
+   copyright notice, this list of conditions and the following
+   disclaimer in the documentation and/or other materials provided
+   with the distribution.
+
+* Neither the name of the NumPy Developers nor the names of any
+   contributors may be used to endorse or promote products derived
+   from this software without specific prior written permission.
+
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+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+
+The ziggurat methods were derived from Julia.
+
+Copyright (c) 2009-2019: Jeff Bezanson, Stefan Karpinski, Viral B. Shah,
+and other contributors:
+
+https://github.com/JuliaLang/julia/contributors
+
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+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

From 41d8369aae745e530d8103e6b52c188ab5f2caa8 Mon Sep 17 00:00:00 2001
From: zoj <44142765+zoj613@users.noreply.github.com>
Date: Mon, 5 Apr 2021 00:52:53 +0200
Subject: [PATCH 5/5] Update build files and version number

---
 DESCRIPTION     |  2 +-
 build-wheels.sh | 29 ++++++++++++++++-------------
 pyproject.toml  | 12 +++++-------
 3 files changed, 22 insertions(+), 21 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index bc760fc..e830028 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: htnorm
-Version: 0.2.0
+Version: 1.0.0
 Title: Fast Simulation of Hyperplane-Truncated Multivariate Normal Distributions
 Author: Zolisa Bleki
 Maintainer: Zolisa Bleki <zolisa.bleki@gmail.com>
diff --git a/build-wheels.sh b/build-wheels.sh
index 74110e4..463e722 100755
--- a/build-wheels.sh
+++ b/build-wheels.sh
@@ -7,35 +7,38 @@ set -e -u -x
 cd $(dirname $0)
 
 bin_arr=(
-    /opt/python/cp36-cp36m/bin
-    /opt/python/cp37-cp37m/bin
+    #/opt/python/cp37-cp37m/bin
     /opt/python/cp38-cp38/bin
-    /opt/python/cp39-cp39/bin
+    #/opt/python/cp39-cp39/bin
 )
 
 # add  python to image's path
-export PATH=/opt/python/cp38-cp38/bin/:$PATH
+export PATH=/opt/python/cp37-cp37m/bin/:$PATH
 # download install script
 curl -#sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py > get-poetry.py
 # install using local archive
-python get-poetry.py -y --file poetry-1.1.4-linux.tar.gz
+python get-poetry.py -y --file poetry-1.1.5-linux.tar.gz
 # install openblas
 yum install -y openblas-devel
 
 function build_poetry_wheels
 {
-    # build wheels for 3.6-3.9 with poetry 
+    # build wheels for 3.7-3.9 with poetry 
     for BIN in "${bin_arr[@]}"; do
         rm -Rf build/*
         # install build deps
-        "${BIN}/python" ${HOME}/.poetry/bin/poetry run pip install numpy
+        "${BIN}/python" ${HOME}/.poetry/bin/poetry run pip install numpy==1.18.1
         BUILD_WHEELS=1 "${BIN}/python" ${HOME}/.poetry/bin/poetry build -f wheel
-        auditwheel repair dist/*.whl --plat $1
-        whl="$(basename dist/*.whl)"
-        "${BIN}/python" -m pip install wheelhouse/"$whl"
-        # test if installed wheel imports correctly
-        "${BIN}/python" -c "from pyhtnorm import *"
-        rm dist/*.whl
+        mkdir -p ./tmp
+        for whl in dist/*.whl; do
+            auditwheel repair "$whl" --plat $1 -w "./tmp" 
+            whlname="$(basename "$(echo ./tmp/*.whl)")"
+            "${BIN}/python" -m pip install ./tmp/"$whlname"
+            # test if installed wheel imports correctly
+            "${BIN}/python" -c "from pyhtnorm import *"
+            mv ./tmp/*.whl wheelhouse/
+            rm "$whl"
+        done
     done
 }
 
diff --git a/pyproject.toml b/pyproject.toml
index 1992f50..617070d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyhtnorm"
-version = "1.0.0"
+version = "2.0.0"
 description = "Fast Simulation of Hyperplane-Truncated Multivatiate Normal Distributions" 
 authors = ["Zolisa Bleki"]
 license = "BSD-3-Clause"
@@ -20,17 +20,15 @@ include = [
     {path = "include", format = "sdist"},
     {path = "src/*.c", format = "sdist"},
     {path = "src/*.h", format = "sdist"},
-    {path = "src/*.txt", format = "sdist"},
-
-    {path = "pyhtnorm/*.pxd"}
+    {path = "third_party_licenses"},
 ]
 
 [tool.poetry.build]
 script = "build.py"
 
 [tool.poetry.dependencies]
-python = "^3.6.1"
-numpy = "^1.17.0"
+python = "^3.7.0"
+numpy = "^1.18.1"
 
 [tool.poetry.dev-dependencies]
 Cython = "^0.29.20"
@@ -38,5 +36,5 @@ pytest = "*"
 toml = "^0.10.2"
 
 [build-system]
-requires = ["poetry-core>=1.0.0a9", "wheel", "setuptools", "numpy>=1.17"]
+requires = ["poetry-core>=1.0.0a9", "wheel", "setuptools", "numpy==1.18.1"]
 build-backend = "poetry.core.masonry.api"