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-rw-r--r--new_python/Makefile88
-rw-r--r--new_python/SyncRNG/__init__.py49
-rw-r--r--new_python/SyncRNG/__version__.py5
-rw-r--r--new_python/setup.py103
-rw-r--r--new_python/src/_syncrng.c407
-rw-r--r--new_python/tests/first_1000_seed_0.txt1000
-rw-r--r--new_python/tests/test_syncrng.py53
7 files changed, 0 insertions, 1705 deletions
diff --git a/new_python/Makefile b/new_python/Makefile
deleted file mode 100644
index 940a07b..0000000
--- a/new_python/Makefile
+++ /dev/null
@@ -1,88 +0,0 @@
-#
-# Makefile for easier installation and cleanup
-#
-# Uses self-documenting macros from here:
-# http://marmelab.com/blog/2016/02/29/auto-documented-makefile.html
-#
-
-SHELL := bash
-.SHELLFLAGS := -eu -o pipefail -c
-MAKEFLAGS += --no-builtin-rules
-
-PACKAGE=SyncRNG
-VENV_DIR=/tmp/sync_venv/
-
-.PHONY: help
-
-.DEFAULT_GOAL := help
-
-help:
- @grep -E '^[0-9a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) |\
- awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-15s\033[0m\
- %s\n", $$1, $$2}'
-
-################
-# Installation #
-################
-
-.PHONY: inplace install
-
-inplace:
- python setup.py build_ext --inplace
-
-install: ## Install for the current user using the default python command
- python setup.py build_ext --inplace && \
- python setup.py install --user
-
-################
-# Distribution #
-################
-
-.PHONY: release dist
-
-release: ## Make a release
- python make_release.py
-
-dist: ## Make Python source distribution
- python setup.py sdist
-
-
-###########
-# Testing #
-###########
-
-.PHONY: test
-
-test: venv ## Run nosetests using the default nosetests command
- source $(VENV_DIR)/bin/activate && green -a -vv ./tests
-
-#######################
-# Virtual environment #
-#######################
-
-.PHONY: venv
-
-venv: $(VENV_DIR)/bin/activate
-
-$(VENV_DIR)/bin/activate:
- test -d $(VENV_DIR) || python -m venv $(VENV_DIR)
- source $(VENV_DIR)/bin/activate && pip install -e .[dev]
- touch $(VENV_DIR)/bin/activate
-
-
-############
-# Clean up #
-############
-
-.PHONY: clean
-
-clean: ## Clean build dist and egg directories left after install
- rm -rf $(VENV_DIR)
- rm -rf ./dist ./build ./$(PACKAGE).egg-info
- rm -rf ./build
- rm -rf ./$(PACKAGE).egg-info
- rm -rf *.so
- rm -f MANIFEST
- rm -f .coverage
- find . -type f -iname '*.pyc' -delete
- find . -type d -name '__pycache__' -empty -delete
diff --git a/new_python/SyncRNG/__init__.py b/new_python/SyncRNG/__init__.py
deleted file mode 100644
index 6d67746..0000000
--- a/new_python/SyncRNG/__init__.py
+++ /dev/null
@@ -1,49 +0,0 @@
-"""
-Simple interface to SyncRNG. This file defines a SyncRNG object which can be
-used to seed and pull numbers from the RNG.
-
-"""
-
-from copy import deepcopy
-from warnings import warn
-
-from _syncrng import seed as _seed
-from _syncrng import rand as _rand
-
-
-class SyncRNG(object):
- def __init__(self, seed=0):
- self.BPF = 32
- self.seed = seed
- self.state = _seed(self.seed)
-
- def randi(self):
- tmp = _rand(self.state)
- self.state = tmp[:-1]
- return int(tmp[-1])
-
- def rand(self):
- return self.randi() * 2.3283064365387e-10
-
- def randbelow(self, n):
- maxsize = 1 << self.BPF
- if n >= maxsize:
- warn(
- "Underlying random generator does not supply \n"
- "enough bits to choose from a population range this "
- "large.\n"
- )
- return int(self.rand() * n)
- rem = maxsize % n
- limit = (maxsize - rem) / maxsize
- r = self.rand()
- while r >= limit:
- r = self.rand()
- return int(r * maxsize) % n
-
- def shuffle(self, x):
- y = deepcopy(x)
- for i in reversed(range(1, len(y))):
- j = self.randbelow(i + 1)
- y[i], y[j] = y[j], y[i]
- return y
diff --git a/new_python/SyncRNG/__version__.py b/new_python/SyncRNG/__version__.py
deleted file mode 100644
index cfd0ff9..0000000
--- a/new_python/SyncRNG/__version__.py
+++ /dev/null
@@ -1,5 +0,0 @@
-# -*- coding: utf-8 -*-
-
-VERSION = (1, 3 ,0)
-
-__version__ = '.'.join(map(str, VERSION))
diff --git a/new_python/setup.py b/new_python/setup.py
deleted file mode 100644
index 4c37187..0000000
--- a/new_python/setup.py
+++ /dev/null
@@ -1,103 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-"""
-Setup file for SyncRNG
-
-Author: Gertjan van den Burg
-Date: Oct. 12, 2016
-"""
-
-import io
-import os
-
-from setuptools import find_packages, setup
-from distutils.extension import Extension
-
-# Package meta-data.
-AUTHOR = "Gertjan van den Burg"
-DESCRIPTION = "Generate the same random numbers in R and Python"
-EMAIL = "gertjanvandenburg@gmail.com"
-LICENSE = "GPLv2"
-LICENSE_TROVE = "License :: OSI Approved :: GNU General Public License v2 (GPLv2)"
-NAME = "SyncRNG"
-REQUIRES_PYTHON = ">=3.6.0"
-URL = "https://github.com/GjjvdBurg/SyncRNG"
-VERSION = None
-
-# What packages are required for this module to be executed?
-REQUIRED = []
-
-docs_require = []
-test_require = []
-dev_require = ["green"]
-
-# What packages are optional?
-EXTRAS = {
- "docs": docs_require,
- "test": test_require,
- "dev": docs_require + test_require + dev_require,
-}
-
-# The rest you shouldn't have to touch too much :)
-# ------------------------------------------------
-# Except, perhaps the License and Trove Classifiers!
-# If you do change the License, remember to change the Trove Classifier for that!
-
-here = os.path.abspath(os.path.dirname(__file__))
-
-# Import the README and use it as the long-description.
-# Note: this will only work if 'README.md' is present in your MANIFEST.in file!
-try:
- with io.open(os.path.join(here, "README.md"), encoding="utf-8") as f:
- long_description = "\n" + f.read()
-except FileNotFoundError:
- long_description = DESCRIPTION
-
-# Load the package's __version__.py module as a dictionary.
-about = {}
-if not VERSION:
- project_slug = NAME.replace("-", "_").replace(" ", "_")
- with open(os.path.join(here, project_slug, "__version__.py")) as f:
- exec(f.read(), about)
-else:
- about["__version__"] = VERSION
-
-# Where the magic happens:
-setup(
- name=NAME,
- version=about["__version__"],
- description=DESCRIPTION,
- long_description=long_description,
- long_description_content_type="text/markdown",
- author=AUTHOR,
- author_email=EMAIL,
- python_requires=REQUIRES_PYTHON,
- url=URL,
- packages=find_packages(
- exclude=["tests", "*.tests", "*.tests.*", "tests.*"]
- ),
- install_requires=REQUIRED,
- extras_require=EXTRAS,
- include_package_data=True,
- license=LICENSE,
- ext_modules=[
- Extension(
- "_syncrng",
- define_macros=[('TARGETPYTHON', '1')],
- sources=["src/_syncrng.c"],
- extra_compile_args=['-g']
- )
- ],
- classifiers=[
- # Trove classifiers
- # Full list: https://pypi.python.org/pypi?%3Aaction=list_classifiers
- LICENSE_TROVE,
- 'Intended Audience :: Developers',
- 'Intended Audience :: Science/Research',
- 'License :: OSI Approved :: GNU General Public License v2 (GPLv2)',
- 'Programming Language :: Python :: 2.7',
- 'Programming Language :: Python :: 3',
- 'Topic :: Scientific/Engineering :: Mathematics'
- ],
-)
diff --git a/new_python/src/_syncrng.c b/new_python/src/_syncrng.c
deleted file mode 100644
index 3a8cf68..0000000
--- a/new_python/src/_syncrng.c
+++ /dev/null
@@ -1,407 +0,0 @@
-#ifdef TARGETPYTHON
-#include "Python.h"
-#include <stdint.h>
-#endif
-
-#ifndef TARGETPYTHON
-#define STRICT_R_HEADERS
-#include <stdint.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <R.h>
-#include <Rinternals.h>
-#include <R_ext/Random.h>
-#include <R_ext/Rdynload.h>
-#endif
-
-/**
- * @brief Generate a single random number using the capped Tausworthe RNG
- *
- * @details
- * This generates random numbers according to the process described in [1]. As
- * an additional step, the resulting random number is capped to 0xFFFFFFFF
- * using a bitwise and. This is done to yield the range [0, 2^32-1]. On
- * return, the state variables are updated.
- *
- * [1]: @article{l1996maximally,
- * title={Maximally equidistributed combined Tausworthe generators},
- * author={L’ecuyer, Pierre},
- * journal={Mathematics of Computation of the American Mathematical
- * Society},
- * volume={65},
- * number={213},
- * pages={203--213},
- * year={1996}
- * }
- *
- * @param[in,out] state pointer to current state array
- *
- * @return a generated random number
- */
-uint32_t lfsr113(uint64_t **state)
-{
- uint64_t z1, z2, z3, z4;
- uint64_t b;
-
- z1 = (*state)[0];
- z2 = (*state)[1];
- z3 = (*state)[2];
- z4 = (*state)[3];
-
- b = (((z1 << 6) ^ z1) >> 13);
- z1 = (((z1 & 4294967294) << 18) ^ b);
-
- b = (((z2 << 2) ^ z2) >> 27);
- z2 = (((z2 & 4294967288) << 2) ^ b);
-
- b = (((z3 << 13) ^ z3) >> 21);
- z3 = (((z3 & 4294967280) << 7) ^ b);
-
- b = (((z4 << 3) ^ z4) >> 12);
- z4 = (((z4 & 4294967168) << 13) ^ b);
-
- b = (z1 ^ z2 ^ z3 ^ z4);
-
- (*state)[0] = z1;
- (*state)[1] = z2;
- (*state)[2] = z3;
- (*state)[3] = z4;
-
- b = b & 0xFFFFFFFF;
-
- return((uint32_t) b);
-}
-
-/**
- * @brief Seed the Tausworthe RNG using a seed value
- *
- * @details
- * This function seeds the state array using a supplied seed value. As noted
- * in [1] (see lfsr113()), the values of z1, z2, z3, and z4 should be larger
- * than 1, 7, 15, and 127 respectively.
- *
- * @param[in] seed user supplied seed value for the RNG
- * @param[out] state state of the RNG
- */
-void lfsr113_seed(uint32_t seed, uint64_t **state)
-{
- uint64_t z1 = 2,
- z2 = 8,
- z3 = 16,
- z4 = 128;
-
- z1 = (z1 * (seed + 1));
- z2 = (z2 * (seed + 1));
- z3 = (z3 * (seed + 1));
- z4 = (z4 * (seed + 1));
-
- z1 = (z1 > 1) ? z1 : z1 + 1;
- z2 = (z2 > 7) ? z2 : z2 + 7;
- z3 = (z3 > 15) ? z3 : z3 + 15;
- z4 = (z4 > 127) ? z4 : z4 + 127;
-
- if (*state == NULL) {
- (*state) = malloc(sizeof(uint64_t)*4);
- }
-
- (*state)[0] = z1;
- (*state)[1] = z2;
- (*state)[2] = z3;
- (*state)[3] = z4;
-}
-
-#ifdef TARGETPYTHON
-/*
- *
- * Start of Python code
- *
- */
-
-static PyObject *_syncrng_seed(PyObject *self, PyObject *args)
-{
- uint32_t seed;
- uint64_t *state = NULL;
-<<<<<<< HEAD:new_R/src/syncrng.c
-=======
-
- PyObject *dblObj;
->>>>>>> python:new_python/src/_syncrng.c
-
- if (!PyArg_ParseTuple(args, "O", &dblObj))
- return NULL;
-
- seed = (uint32_t) PyLong_AsLong(dblObj);
- lfsr113_seed(seed, &state);
-
- PyObject *pystate = Py_BuildValue("[d, d, d, d, d]",
- (double) state[0],
- (double) state[1],
- (double) state[2],
- (double) state[3],
- -1.0);
- free(state);
- return pystate;
-}
-
-static PyObject *_syncrng_rand(PyObject *self, PyObject *args)
-{
-<<<<<<< HEAD:new_R/src/syncrng.c
- uint32_t i, value, numints;
- uint64_t *localstate;
-=======
- int i;
- uint32_t rand;
- uint64_t *localstate = malloc(sizeof(uint64_t) * 4);
->>>>>>> python:new_python/src/_syncrng.c
-
- PyObject *listObj;
- PyObject *dblObj;
-
- if (!PyArg_ParseTuple(args, "O!", &PyList_Type, &listObj))
- return NULL;
-
-<<<<<<< HEAD:new_R/src/syncrng.c
- // we're just assuming you would never pass more than 4 values
- localstate = malloc(sizeof(uint32_t)*5);
- numints = PyList_Size(listObj);
- for (i=0; i<numints; i++) {
- intObj = PyList_GetItem(listObj, i);
- value = (uint32_t) PyLong_AsLong(intObj);
- localstate[i] = value;
- }
-
- uint32_t rand = lfsr113(&localstate);
- localstate[4] = rand;
-=======
- for (i=0; i<4; i++) {
- dblObj = PyList_GetItem(listObj, i);
- localstate[i] = (uint64_t) PyFloat_AS_DOUBLE(dblObj);
- }
-
- rand = lfsr113(&localstate);
->>>>>>> python:new_python/src/_syncrng.c
-
- PyObject *pystate = Py_BuildValue("[d, d, d, d, d]",
- (double) localstate[0],
- (double) localstate[1],
- (double) localstate[2],
- (double) localstate[3],
- (double) rand);
- free(localstate);
- return pystate;
-}
-
-static PyMethodDef SyncRNGMethods[] = {
- {"seed", _syncrng_seed, METH_VARARGS,
- "Seed the RNG."},
- {"rand", _syncrng_rand, METH_VARARGS,
- "Generate a single random integer using SyncRNG."},
- {NULL, NULL, 0, NULL}
-};
-
-#if PY_MAJOR_VERSION >= 3
- static struct PyModuleDef moduledef = {
- PyModuleDef_HEAD_INIT,
- "_syncrng",
- "Python interface to SyncRNG",
- -1,
- SyncRNGMethods,
- NULL,
- NULL,
- NULL,
- NULL
- };
-#endif
-
-
-static PyObject *
-moduleinit(void)
-{
- PyObject *m;
-
- #if PY_MAJOR_VERSION >= 3
- m = PyModule_Create(&moduledef);
- #else
- m = Py_InitModule3("_syncrng", SyncRNGMethods,
- "Python interface to SyncRNG");
- #endif
-
- return m;
-}
-
-#if PY_MAJOR_VERSION >= 3
-PyMODINIT_FUNC
-PyInit__syncrng(void)
-{
- return moduleinit();
-}
-#else
-PyMODINIT_FUNC
-init_syncrng(void)
-{
- moduleinit();
-}
-#endif
-#endif
-
-#ifndef TARGETPYTHON
-
-/*
- *
- * Start of R code
- *
- */
-
-SEXP R_syncrng_seed(SEXP seed);
-SEXP R_syncrng_rand(SEXP state);
-
-R_CallMethodDef callMethods[] = {
- {"R_syncrng_seed", (DL_FUNC) &R_syncrng_seed, 1},
- {"R_syncrng_rand", (DL_FUNC) &R_syncrng_seed, 1},
- {NULL, NULL, 0}
-};
-R_CMethodDef cMethods[] = {
- {NULL, NULL, 0}
-};
-
-void R_init_myLib(DllInfo *info)
-{
- R_registerRoutines(info, cMethods, callMethods, NULL, NULL);
- R_useDynamicSymbols(info, TRUE);
-}
-
-// Set the seed for the generator from the reference class
-SEXP R_syncrng_seed(SEXP seed)
-{
- int i;
- double *pseed = REAL(seed),
- *pstate = NULL;
- uint32_t useed = (uint32_t) *pseed;
- uint64_t *state = NULL;
-
- lfsr113_seed(useed, &state);
-
- SEXP Rstate = PROTECT(allocVector(REALSXP, 5));
- pstate = REAL(Rstate);
- for (i=0; i<4; i++) {
- pstate[i] = (double) state[i];
- }
- pstate[4] = -1.0;
- free(state);
-
- UNPROTECT(1);
- return Rstate;
-}
-
-// get a random number from the reference class
-SEXP R_syncrng_rand(SEXP state)
-{
- uint64_t *localstate = malloc(sizeof(uint64_t)*4);
- double *pstate = REAL(state);
- int i;
- for (i=0; i<4; i++) {
- localstate[i] = (uint64_t) pstate[i];
- }
-
- uint32_t rand = lfsr113(&localstate);
-
- SEXP Rstate = PROTECT(allocVector(REALSXP, 5));
- pstate = REAL(Rstate);
-
- for (i=0; i<4; i++) {
- pstate[i] = (double) localstate[i];
- }
- pstate[4] = (double) rand;
- UNPROTECT(1);
-
- free(localstate);
-
- return Rstate;
-}
-
-/*
- * The following code is used to make SyncRNG a real "user-defined" RNG
- * follwing .Random.user documentation.
- *
- */
-
-static uint32_t global_R_seed;
-<<<<<<< HEAD:new_R/src/syncrng.c
-static int global_R_nseed = 1;
-=======
-static uint32_t global_R_nseed = 1;
->>>>>>> python:new_python/src/_syncrng.c
-static double global_R_result_uniform;
-static double global_R_result_normal;
-static uint64_t *global_R_state = NULL;
-
-double *user_unif_rand()
-{
- if (global_R_state == NULL) {
- // if it's not seeded yet we seed it with 0
- global_R_seed = 0;
- lfsr113_seed(global_R_seed, &global_R_state);
- }
-
- uint32_t rand = lfsr113(&global_R_state);
- global_R_result_uniform = rand * 2.3283064365387e-10;
- return &global_R_result_uniform;
-}
-
-// see: https://stackoverflow.com/q/47824450/1154005
-Int32 _unscramble(Int32 scram)
-{
- int j;
- for (j=0; j<50; j++) {
- scram = ((scram - 1) * 2783094533);
- }
- return scram;
-}
-
-// note that Int32 is "unsigned int" which is not necessarily 32 bit
-void user_unif_init(Int32 seed_in)
-{
- global_R_seed = seed_in;
- uint32_t useed = _unscramble(seed_in);
-
- // destroy the previous state, we're reseeding the RNG
- if (global_R_state != NULL) {
- free(global_R_state);
- global_R_state = NULL;
- }
- lfsr113_seed(useed, &global_R_state);
-}
-
-int *user_unif_nseed()
-{
- return &global_R_nseed;
-}
-
-int *user_unif_seedloc()
-{
- return (int *) &global_R_seed;
-}
-
-double *user_norm_rand()
-{
- double u, v, z, x;
- do {
- u = *user_unif_rand();
- v = 0.857764 * (2. * (*user_unif_rand()) - 1);
- x = v/u;
- z = 0.25 * x * x;
- if (z < 1. - u)
- break;
- if (z > 0.259/u + 0.35)
- continue;
- } while (z > -log(u));
- global_R_result_normal = x;
- return &global_R_result_normal;
-}
-
-/*
- *
- * End of R code
- *
- */
-#endif
diff --git a/new_python/tests/first_1000_seed_0.txt b/new_python/tests/first_1000_seed_0.txt
deleted file mode 100644
index 50aef45..0000000
--- a/new_python/tests/first_1000_seed_0.txt
+++ /dev/null
@@ -1,1000 +0,0 @@
-1574944
-268744
-33556004
-8390676
-16851968
-2147582472
-134350084
-1074315269
-2097666
-2693283843
-50598144
-402792448
-536872117
-2281705500
-2097216
-67127296
-1192
-4097
-413712
-68096
-537198610
-9502976
-1077936653
-23069188
-256
-271065282
-1375735819
-1075056808
-137344
-537396752
-71370760
-134520872
-3196164
-24836
-2164785857
-2183397387
-269344
-41977872
-943785105
-2195975
-2283815708
-3170454
-68182051
-2281710785
-34344960
-1074024480
-460824
-839122944
-7438364
-155238412
-2166440334
-67126401
-3489693830
-1124336267
-537284650
-8392144
-805381657
-2165408
-29452
-2146516
-33704323
-2148282537
-19138624
-1619267616
-33754640
-671155715
-549519625
-3422584857
-7889684
-12289
-3223323809
-302387200
-1334448
-12654616
-940410368
-69321472
-205808168
-2167956679
-422150
-3506449091
-3263561808
-1350900792
-6425240
-809550976
-543263112
-203481359
-2146694
-1196512
-3355967617
-61734977
-8853552
-46403088
-704741917
-540082961
-2365612954
-2149671132
-117458370
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-59121344
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-5308846
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-20730196
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-1241543311
-3229405863
-84162883
-2687116417
-308610137
-1217697952
-34756884
-940057617
-2757853260
-2281750584
-2117046
-8536213
-2432762497
-2200211979
-143004704
-9555090
-541402267
-2688090691
-140792396
-18901124
-34619827
-2281975939
-1126991882
-1611028540
-1510426
-570433665
-4261976
-201367560
-2151409932
-159745
-2416476396
-36078209
-545545526
-47188314
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diff --git a/new_python/tests/test_syncrng.py b/new_python/tests/test_syncrng.py
deleted file mode 100644
index 58b504d..0000000
--- a/new_python/tests/test_syncrng.py
+++ /dev/null
@@ -1,53 +0,0 @@
-# -*- coding: utf-8 -*-
-
-import os
-import unittest
-
-from SyncRNG import SyncRNG
-
-
-class SyncRNGTestCase(unittest.TestCase):
- def test_randi(self):
- s = SyncRNG(seed=123456)
- self.assertEqual(s.randi(), 959852049)
- self.assertEqual(s.randi(), 2314333085)
- self.assertEqual(s.randi(), 2255782734)
- self.assertEqual(s.randi(), 2921461239)
- self.assertEqual(s.randi(), 1024197102)
-
- def test_rand(self):
- s = SyncRNG(seed=123456)
- self.assertAlmostEqual(s.rand(), 959852049 / pow(2, 32))
- self.assertAlmostEqual(s.rand(), 2314333085 / pow(2, 32))
- self.assertAlmostEqual(s.rand(), 2255782734 / pow(2, 32))
- self.assertAlmostEqual(s.rand(), 2921461239 / pow(2, 32))
- self.assertAlmostEqual(s.rand(), 1024197102 / pow(2, 32))
-
- def test_randbelow(self):
- s = SyncRNG(seed=123456)
- self.assertEqual(s.randbelow(5), 4)
- self.assertEqual(s.randbelow(5), 0)
- self.assertEqual(s.randbelow(5), 4)
- self.assertEqual(s.randbelow(5), 4)
- self.assertEqual(s.randbelow(5), 2)
-
- def test_shuffle(self):
- s = SyncRNG(seed=123456)
- x = [1, 2, 3, 4, 5]
- y = s.shuffle(x)
- self.assertEqual(y, [3, 4, 1, 2, 5])
-
- def test_first_1000(self):
- s = SyncRNG(seed=0)
-
- here = os.path.dirname(__file__)
- test_file = os.path.join(here, "first_1000_seed_0.txt")
-
- with open(test_file, "r") as fid:
- for line in fid:
- exp = int(line.strip())
- self.assertTrue(exp == s.randi())
-
-
-if __name__ == "__main__":
- unittest.main()
generated by cgit v1.2.3 (git 2.25.1) at 2026-01-12 07:46:35 +0000