Merge pull request #9 from ELIFE-ASU/dev

Update to version 0.0.3

.gitignore

@@ -31,4 +31,11 @@
 build
 
 # Visual Studio Code
-.vscode
+.vscode
+
+# temporary directories
+tmp
+temp
+
+# distribution directories and files
+dist/inform-*

CMakeLists.txt

@@ -2,14 +2,16 @@ cmake_minimum_required(VERSION 2.8)
 project(inform C)
 
 set(${PROJECT_NAME}_VERSION_MAJOR 0)
-set(${PROJECT_NAME}_VERSION_MINOR 0.2)
+set(${PROJECT_NAME}_VERSION_MINOR 0.3)
 set(${PROJECT_NAME}_VERSION ${${PROJECT_NAME}_VERSION_MAJOR}.${${PROJECT_NAME}_VERSION_MINOR})
 
+message(STATUS "inform version: ${${PROJECT_NAME}_VERSION}")
+
 if (UNIX)
     add_definitions("-Wall -Wextra -Werror -Wno-unused-parameter -std=gnu1x")
     set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -ggdb -pg")
 elseif(MSVC)
-    add_definitions("/Wall")
+    add_definitions("/DLIBRARY_EXPORTS")
 endif()
 
 if (APPLE)
@@ -19,16 +21,20 @@ endif()
 include_directories(include)
 add_subdirectory(src)
 add_library(${PROJECT_NAME} SHARED ${${PROJECT_NAME}_SOURCES})
-add_library(${PROJECT_NAME}_STATIC ${${PROJECT_NAME}_SOURCES})
+add_library(${PROJECT_NAME}_static ${${PROJECT_NAME}_SOURCES})
 set_target_properties(${PROJECT_NAME} PROPERTIES OUTPUT_NAME ${PROJECT_NAME} VERSION ${${PROJECT_NAME}_VERSION})
-set_target_properties(${PROJECT_NAME}_STATIC PROPERTIES OUTPUT_NAME ${PROJECT_NAME} VERSION ${${PROJECT_NAME}_VERSION})
+if (MSVC)
+    set_target_properties(${PROJECT_NAME}_static PROPERTIES VERSION ${${PROJECT_NAME}_VERSION})
+else()
+    set_target_properties(${PROJECT_NAME}_static PROPERTIES OUTPUT_NAME ${PROJECT_NAME} VERSION ${${PROJECT_NAME}_VERSION})
+endif()
 
 if (UNIX)
     target_link_libraries(${PROJECT_NAME} m)
 endif()
 
 install(TARGETS ${PROJECT_NAME} EXPORT ${PROJECT_NAME} DESTINATION lib)
-install(TARGETS ${PROJECT_NAME}_STATIC EXPORT ${PROJECT_NAME} DESTINATION lib)
+install(TARGETS ${PROJECT_NAME}_static EXPORT ${PROJECT_NAME} DESTINATION lib)
 install(DIRECTORY include/ DESTINATION include)
 
 enable_testing()

README.md

@@ -40,5 +40,5 @@ Inform is still under heavy development. As such, the API and the feature set ar
 
 ## Build Status
 - Linux/OSX: [![Build Status](https://travis-ci.org/ELIFE-ASU/Inform.svg?branch=master)](https://travis-ci.org/ELIFE-ASU/Inform)
-- Windows: **Appveyor Support Pending**
+- Windows: [![Build Status](https://ci.appveyor.com/api/projects/status/7y015h6p7n0q7097/branch/master?svg=true)](https://ci.appveyor.com/project/dglmoore/inform-vx977)
 - Code Coverage: **Coming Soon**

appveyor.yml

@@ -0,0 +1,15 @@
+version: 0.0.3.{build}
+configuration:
+- Debug
+- Release
+platform:
+- x64
+- x86
+- Any CPU
+before_build:
+- ps: cmake .
+build:
+  project: ALL_BUILD.vcxproj
+  verbosity: normal
+test_script:
+- cmd: test\%CONFIGURATION%\inform_unittest.exe

dist/install.sh

@@ -0,0 +1,24 @@
+#!/usr/bin/env bash
+
+function usage {
+    echo "Usage: ${0##*/} [--prefix=<prefix>]"
+    exit 1
+}
+
+if [[ $# -eq 0 ]]; then
+    prefix=/usr/local
+elif [[ $# -eq 1 ]]; then
+    prefix=${1#"--prefix="}
+    if [[ $prefix == $1 ]]; then
+        prefix=${1#"--PREFIX="}
+        if [[ $prefix == $1 ]]; then
+            usage
+        fi
+    fi
+else
+    usage
+fi
+
+mkdir -p $prefix
+cp -R include $prefix
+cp -R lib $prefix

dist/package.ps1

@@ -0,0 +1,20 @@
+$version = (cmake . -Bbuild/production -DCMAKE_BUILD_TYPE=Release -G "NMake Makefiles" | Select-String '-- inform version: ')
+$version = $version.ToString().Split(' ')[3]
+
+$prefix = "inform-$version"
+$target = "dist/$prefix"
+$archive = "$($target)_win-amd64.zip"
+
+cmake . -Bbuild/production -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX="$target" | Out-Null
+cd build/production
+nmake
+test/inform_unittest.exe
+nmake install
+cd ../..
+Copy-Item LICENSE $target
+Copy-Item README.md $target
+
+Remove-Item -force $archive
+Add-Type -Assembly System.IO.Compression.FileSystem
+$compressionLevel = [System.IO.Compression.CompressionLevel]::Optimal
+[System.IO.Compression.ZipFile]::CreateFromDirectory($target, $archive, $compressionLevel, $true)

dist/package.sh

@@ -0,0 +1,19 @@
+#!/usr/bin/env bash
+
+version=$(cmake -H. -Bbuild/production -DCMAKE_BUILD_TYPE=Release | grep "\-\- inform version:")
+version=${version#"-- inform version: "}
+
+target=inform-$version
+prefix=dist/$target
+tarball=$target"_linux-x86_64.tar.gz"
+
+cmake -H. -Bbuild/production -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$prefix > /dev/null
+make -C build/production all test
+make -C build/production install > /dev/null
+cp dist/install.sh $prefix > /dev/null
+cp LICENSE $prefix > /dev/null
+cp README.md $prefix > /dev/null
+
+cd dist
+echo "Creating tarball: dist/$tarball"
+tar czf $tarball $target

include/inform/active_info.h

@@ -3,7 +3,7 @@
 // license that can be found in the LICENSE file.
 #pragma once
 
-#include <inform/shannon.h>
+#include <inform/error.h>
 
 #ifdef __cplusplus
 extern "C"
@@ -18,9 +18,11 @@ extern "C"
  * @param[in] m      the number of time steps in each time series
  * @param[in] b      the base or number of distinct states at each time step
  * @param[in] k      the history length used to calculate the active information
+ * @param[out] err   an error structure
  * @return the active information for the ensemble
  */
-double inform_active_info(uint64_t const *series, size_t n, size_t m, uint64_t b, uint64_t k);
+EXPORT double inform_active_info(int const *series, size_t n, size_t m, int b,
+    size_t k, inform_error *err);
 
 /**
  * Compute the local active information of a ensemble of time series
@@ -31,10 +33,11 @@ double inform_active_info(uint64_t const *series, size_t n, size_t m, uint64_t b
  * @param[in] b      the base or number of distinct states at each time step
  * @param[in] k      the history length used to calculate the active information
  * @param[out] ai    the local active information
- * @return an error code
+ * @param[out] err   an error structure
+ * @return a pointer to the local active information array
  */
-int inform_local_active_info(uint64_t const *series, size_t n, size_t m,
-    uint64_t b, uint64_t k, double *ai);
+EXPORT double *inform_local_active_info(int const *series, size_t n, size_t m, int b,
+    size_t k, double *ai, inform_error *err);
 
 #ifdef __cplusplus
 }

include/inform/block_entropy.h

@@ -0,0 +1,44 @@
+// Copyright 2016 ELIFE. All rights reserved.
+// Use of this source code is governed by a MIT
+// license that can be found in the LICENSE file.
+#pragma once
+
+#include <inform/error.h>
+
+#ifdef __cplusplus
+extern "C"
+{
+#endif
+
+/**
+ * Compute the block entropy of an ensemble of time series
+ *
+ * @param[in] series the ensemble of time series
+ * @param[in] n      the number of initial conditions
+ * @param[in] m      the number of time steps in each time series
+ * @param[in] b      the base or number of distinct states at each time step
+ * @param[in] k      the history length used to calculate the active information
+ * @param[out] err   an error structure
+ * @return the block entropy for the ensemble
+ */
+EXPORT double inform_block_entropy(int const *series, size_t n, size_t m, int b,
+    size_t k, inform_error *err);
+
+/**
+ * Compute the local block entropy of a ensemble of time series
+ *
+ * @param[in] series the ensemble of time series
+ * @param[in] n      the number of initial conditions
+ * @param[in] m      the number of time steps in each time series
+ * @param[in] b      the base or number of distinct states at each time step
+ * @param[in] k      the history length used to calculate the active information
+ * @param[out] ent   the local entropy
+ * @param[out] err   an error structure
+ * @return a pointer to the local block entropy array
+ */
+EXPORT double *inform_local_block_entropy(int const *series, size_t n, size_t m,
+    int b, size_t k, double *ent, inform_error *err);
+
+#ifdef __cplusplus
+}
+#endif

include/inform/dist.h

@@ -3,6 +3,7 @@
 // license that can be found in the LICENSE file.
 #pragma once
 
+#include <inform/export.h>
 #include <stdint.h>
 #include <stdlib.h>
 #include <stdbool.h>
@@ -46,7 +47,7 @@ extern "C"
 typedef struct inform_distribution
 {
     /// the histogram or array of observation frequencies
-    uint64_t *histogram;
+    uint32_t *histogram;
     /// the size of the support
     size_t size;
     /// the number of observations made so far
@@ -64,7 +65,7 @@ typedef struct inform_distribution
  * @param[in] n the number of distinct events that could be observed
  * @return the distribution
  */
-inform_dist* inform_dist_alloc(size_t n);
+EXPORT inform_dist* inform_dist_alloc(size_t n);
 /**
  * Resize the distribution to have new support.
  *
@@ -88,7 +89,7 @@ inform_dist* inform_dist_alloc(size_t n);
  * @param[in] n        the desired support size
  * @return the reallocated distribution
  */
-inform_dist* inform_dist_realloc(inform_dist *dist, size_t n);
+EXPORT inform_dist* inform_dist_realloc(inform_dist *dist, size_t n);
 /**
  * Copy a distribution to a destination.
  *
@@ -103,7 +104,7 @@ inform_dist* inform_dist_realloc(inform_dist *dist, size_t n);
  * @param[in,out] the destination distribution
  * @return a pointer to the copied distribution
  */
-inform_dist* inform_dist_copy(inform_dist const *src, inform_dist *dest);
+EXPORT inform_dist* inform_dist_copy(inform_dist const *src, inform_dist *dest);
 /**
  * Duplicate a distribution.
  *
@@ -117,21 +118,21 @@ inform_dist* inform_dist_copy(inform_dist const *src, inform_dist *dest);
  * @param[in] dist the source distribution
  * @return the new distribution
  */
-inform_dist* inform_dist_dup(inform_dist const *dist);
+EXPORT inform_dist* inform_dist_dup(inform_dist const *dist);
 /**
  * Create a distribution from an underlying histogram.
  *
  * @param[in] data the underlying histogram data
  * @param[in] n    the number of events in the histogram
  * @return the new distribution
  */
-inform_dist* inform_dist_create(uint64_t const *data, size_t n);
+EXPORT inform_dist* inform_dist_create(uint32_t const *data, size_t n);
 /**
  * Free all dynamically allocated memory associated with a distribution.
  *
  * @param[in] dist the distribution to free
  */
-void inform_dist_free(inform_dist *dist);
+EXPORT void inform_dist_free(inform_dist *dist);
 
 /**
  * Get the size of the distribution's support.
@@ -141,7 +142,7 @@ void inform_dist_free(inform_dist *dist);
  * @param[in] dist the distribution
  * @return the size of the distribution's support
  */
-size_t inform_dist_size(inform_dist const *dist);
+EXPORT size_t inform_dist_size(inform_dist const *dist);
 /**
  * Get the total number of observations so far made.
  *
@@ -150,7 +151,7 @@ size_t inform_dist_size(inform_dist const *dist);
  * @param[in] dist the distribution
  * @return the number of observations thus far made
  */
-uint64_t inform_dist_counts(inform_dist const *dist);
+EXPORT uint64_t inform_dist_counts(inform_dist const *dist);
 /**
  * Determine whether or not the distribution is valid.
  *
@@ -162,7 +163,7 @@ uint64_t inform_dist_counts(inform_dist const *dist);
  * @param[in] dist the distribution
  * @return the validity of the distribution
  */
-bool inform_dist_is_valid(inform_dist const *dist);
+EXPORT bool inform_dist_is_valid(inform_dist const *dist);
 
 /**
  * Get the number of occurances of a given event.
@@ -176,7 +177,7 @@ bool inform_dist_is_valid(inform_dist const *dist);
  *
  * @see inform_dist_set
  */
-uint64_t inform_dist_get(inform_dist const *dist, uint64_t event);
+EXPORT uint32_t inform_dist_get(inform_dist const *dist, size_t event);
 /**
  * Set the number of occurances of a given event.
  *
@@ -195,7 +196,7 @@ uint64_t inform_dist_get(inform_dist const *dist, uint64_t event);
  * @see inform_dist_get
  * @see inform_dist_tick
  */
-uint64_t inform_dist_set(inform_dist *dist, uint64_t event, uint64_t x);
+EXPORT uint32_t inform_dist_set(inform_dist *dist, size_t event, uint32_t x);
 
 /**
  * Increment the number of observations of a given event.
@@ -213,7 +214,7 @@ uint64_t inform_dist_set(inform_dist *dist, uint64_t event, uint64_t x);
  *
  * @see inform_dist_set
  */
-uint64_t inform_dist_tick(inform_dist *dist, uint64_t event);
+EXPORT uint32_t inform_dist_tick(inform_dist *dist, size_t event);
 
 /**
  * Extact the probability of an event.
@@ -231,7 +232,7 @@ uint64_t inform_dist_tick(inform_dist *dist, uint64_t event);
  * @see inform_dist_get
  * @see inform_dist_dump
  */
-double inform_dist_prob(inform_dist const *dist, uint64_t event);
+EXPORT double inform_dist_prob(inform_dist const *dist, size_t event);
 /**
  * Dump the probabilities of all events to an array.
  *
@@ -248,7 +249,7 @@ double inform_dist_prob(inform_dist const *dist, uint64_t event);
  * @param[in] probs the size of the preallocated array
  * @return the number of probabilities written to the array
  */
-size_t inform_dist_dump(inform_dist const *dist, double *probs, size_t n);
+EXPORT size_t inform_dist_dump(inform_dist const *dist, double *probs, size_t n);
 
 #ifdef __cplusplus
 }