Rename directories, remove extra test dir

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 @@
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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()