Statistics

.github/workflows/test.yml

@@ -14,21 +14,24 @@ jobs:
     name: 'Tests'
     strategy:
       matrix:
-        php: ['8.1.12']
+        php: ['8.1.13']
 
     runs-on: 'ubuntu-20.04'
     env:
       PHP_VERSION: ${{ matrix.php }}
     steps:
       - name: 'Check out repository'
-        uses: 'actions/checkout@v2'
+        uses: 'actions/checkout@v3'
         with:
           path: 'php-ext-gsl'
 
-      - uses: actions/cache@v2
+      - uses: actions/cache@v3
+        if: ${{ always() }}
         with:
           path: ~/build-cache/php
           key: ${{ runner.os }}-${{ matrix.php }}
+          restore-keys: |
+            ${{ runner.os }}-${{ matrix.php }}
 
       - name: 'Build PHP'
         run: './php-ext-gsl/.github/workflows/test/build-php.sh'
@@ -37,4 +40,15 @@ jobs:
         run: './php-ext-gsl/.github/workflows/test/build-php-ext-gsl.sh'
 
       - name: 'Run tests'
-        run: './php-ext-gsl/.github/workflows/test/tests.sh'
+        run: './php-ext-gsl/.github/workflows/test/tests.sh'
+
+      - name: Archive test errors
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v3
+        with:
+          name: test-errors
+          path: php-ext-gsl/tests/*.diff
+          retention-days: 5
+      - name: Download all workflow run artifacts
+        if: ${{ failure() }}
+        uses: actions/download-artifact@v3

.github/workflows/test/build-php-ext-gsl.sh

@@ -8,7 +8,7 @@ php --version
 cd php-ext-gsl
 
 phpize
-./configure
+./configure --with-gsl CFLAGS="$CFLAGS -Wno-implicit-function-declaration"
 php -dmemory_limit=-1 build/gen_stub.php --force-regeneration
 sed -i 's/$user_input = fgets($fp, 10);/$user_input = "s";/g' run-tests.php
 make

CMakeList.txt

@@ -0,0 +1,25 @@
+cmake_minimum_required(VERSION 3.8)
+project(gslext C)
+
+set(SOURCE_FILES gslext gslext.c)
+
+execute_process (
+        COMMAND php-config --include-dir
+        OUTPUT_VARIABLE PHP_SOURCE
+)
+string(REGEX REPLACE "\n$" "" PHP_SOURCE "${PHP_SOURCE}")
+
+message("Using source directory: ${PHP_SOURCE}")
+
+include_directories(${PHP_SOURCE})
+include_directories(${PHP_SOURCE}/main)
+include_directories(${PHP_SOURCE}/Zend)
+include_directories(${PHP_SOURCE}/TSRM)
+include_directories(${PROJECT_SOURCE_DIR})
+
+add_custom_target(configure
+        COMMAND phpize && ./configure
+        DEPENDS ${SOURCE_FILES}
+        WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})
+
+add_library(___ EXCLUDE_FROM_ALL ${SOURCE_FILES})

README.md

@@ -1 +1,25 @@
 # PHP Extension for GNU Scientific Library (GSL)
+
+## TODO
+* refactor all functions from GSL_ to gsl_
+* refactor to use helper instead converting in each function
+
+## GSL coverage
+* [Mathematical Constants](https://www.gnu.org/software/gsl/doc/html/math.html#mathematical-constants)
+* [Elementary Functions](https://www.gnu.org/software/gsl/doc/html/math.html#elementary-functions)
+* [Small integer powers](https://www.gnu.org/software/gsl/doc/html/math.html#small-integer-powers)
+* [Testing for Odd and Even Numbers](https://www.gnu.org/software/gsl/doc/html/math.html#testing-for-odd-and-even-numbers)
+* [Maximum and Minimum functions](https://www.gnu.org/software/gsl/doc/html/math.html#maximum-and-minimum-functions)
+* [Approximate Comparison of Floating Point Numbers](https://www.gnu.org/software/gsl/doc/html/math.html#approximate-comparison-of-floating-point-numbers)
+* []()
+* []()
+* []()
+* []()
+* []()
+* [Statistics](https://www.gnu.org/software/gsl/doc/html/statistics.html)
+* [Running Statistics](https://www.gnu.org/software/gsl/doc/html/rstat.html)
+
+Full list of functions in [PHP stub file](gslext.stub.php)
+
+## Tests
+* tests in this extension are only to check if functions are working. Correctness of calculations relays on library

build.sh

@@ -1,6 +1,6 @@
 make distclean
 phpize
-./configure --with-gsl
+./configure --with-gsl CFLAGS="$CFLAGS -Wno-implicit-function-declaration"
 php -dmemory_limit=-1 build/gen_stub.php --force-regeneration
 sed -i 's/$user_input = fgets($fp, 10);/$user_input = "s";/g' run-tests.php
 make && make test

gslext.c

@@ -7,10 +7,14 @@
 #endif
 
 #include "php.h"
+#include "php_ini.h"
+#include "zend_exceptions.h"
 #include "ext/standard/info.h"
 #include "php_gslext.h"
 #include "gslext_arginfo.h"
 
+#include "gslext_helpers.c"
+
 #include "inc/_functions.inc"
 
 /* For compatibility with older PHP versions */

gslext.stub.php

@@ -38,3 +38,71 @@ function GSL_max_float(float $a, float $b): float {}
 
 // fcmp
 function GSL_fcmp(float $x, float $y, float $epsilon): int {}
+
+// Statistics
+function gsl_stats_mean(array $data, int $stride): float {}
+function gsl_stats_variance(array $data, int $stride): float {}
+function gsl_stats_variance_m(array $data, int $stride, float $mean): float {}
+function gsl_stats_sd(array $data, int $stride): float {}
+function gsl_stats_tss(array $data, int $stride): float {}
+function gsl_stats_tss_m(array $data, int $stride, float $mean): float {}
+function gsl_stats_variance_with_fixed_mean(array $data, int $stride, float $mean): float {}
+function gsl_stats_sd_with_fixed_mean(array $data, int $stride, float $mean): float {}
+function gsl_stats_absdev(array $data, int $stride): float {}
+function gsl_stats_absdev_m(array $data, int $stride, float $mean): float {}
+function gsl_stats_skew(array $data, int $stride): float {}
+function gsl_stats_skew_m_sd(array $data, int $stride, float $mean, float $sd): float {}
+function gsl_stats_kurtosis(array $data, int $stride): float {}
+function gsl_stats_kurtosis_m_sd(array $data, int $stride, float $mean, float $sd): float {}
+function gsl_stats_lag1_autocorrelation(array $data, int $stride): float {}
+function gsl_stats_lag1_autocorrelation_m(array $data, int $stride, float $mean): float {}
+function gsl_stats_covariance(array $data1, int $stride1, array $data2, int $stride2): float {}
+function gsl_stats_covariance_m(array $data1, int $stride1, array $data2, int $stride2, float $mean1, float $mean2): float {}
+function gsl_stats_correlation(array $data1, int $stride1, array $data2, int $stride2): float {}
+function gsl_stats_spearman(array $data1, int $stride1, array $data2, int $stride2, array $work): float {}
+function gsl_stats_wmean(array $w, int $wstride, array $data, int $stride): float {}
+function gsl_stats_wvariance(array $w, int $wstride, array $data, int $stride): float {}
+function gsl_stats_wvariance_m(array $w, int $wstride, array $data, int $stride, float $wmean): float {}
+function gsl_stats_wsd(array $w, int $wstride, array $data, int $stride): float {}
+function gsl_stats_wsd_m(array $w, int $wstride, array $data, int $stride, float $wmean): float {}
+function gsl_stats_wvariance_with_fixed_mean(array $w, int $wstride, array $data, int $stride, float $mean): float {}
+function gsl_stats_wsd_with_fixed_mean(array $w, int $wstride, array $data, int $stride, float $mean): float {}
+function gsl_stats_wtss(array $w, int $wstride, array $data, int $stride): float {}
+function gsl_stats_wtss_m(array $w, int $wstride, array $data, int $stride, float $mean): float {}
+function gsl_stats_wabsdev(array $w, int $wstride, array $data, int $stride): float {}
+function gsl_stats_wabsdev_m(array $w, int $wstride, array $data, int $stride, float $mean): float {}
+function gsl_stats_wskew(array $w, int $wstride, array $data, int $stride): float {}
+function gsl_stats_wskew_m_sd(array $w, int $wstride, array $data, int $stride, float $wmean, float $wds): float {}
+function gsl_stats_wkurtosis(array $w, int $wstride, array $data, int $stride): float {}
+function gsl_stats_wkurtosis_m_sd(array $w, int $wstride, array $data, int $stride, float $wmean, float $wds): float {}
+function gsl_stats_max(array $data, int $stride): float {}
+function gsl_stats_min(array $data, int $stride): float {}
+function gsl_stats_minmax(float &$min, float &$max, array $data, int $stride): void {}
+function gsl_stats_min_index(array $data, int $stride): int {}
+function gsl_stats_max_index(array $data, int $stride): int {}
+function gsl_stats_minmax_index(int &$min_index, int &$max_index, array $data, int $stride): void {}
+function gsl_stats_median_from_sorted_data(array $sorted_data, int $stride): float {}
+function gsl_stats_median(array $data, int $stride): float {}
+function gsl_stats_quantile_from_sorted_data(array $sorted_data, int $stride, float $f): float {}
+function gsl_stats_select(array $data, int $stride, int $k): float {}
+function gsl_stats_trmean_from_sorted_data(float $alpha, array $sorted_data, int $stride): float {}
+function gsl_stats_gastwirth_from_sorted_data(array $sorted_data, int $stride): float {}
+function gsl_stats_mad0(array $data, int $stride): float {}
+function gsl_stats_mad(array $data, int $stride): float {}
+function gsl_stats_Sn0_from_sorted_data(array $sorted_data, int $stride): float {}
+function gsl_stats_Sn_from_sorted_data(array $sorted_data, int $stride): float {}
+function gsl_stats_Qn0_from_sorted_data(array $sorted_data, int $stride): float {}
+function gsl_stats_Qn_from_sorted_data(array $sorted_data, int $stride): float {}
+
+// Running Statistics
+function gsl_rstat_min(array $data): float {}
+function gsl_rstat_max(array $data): float {}
+function gsl_rstat_mean(array $data): float {}
+function gsl_rstat_variance(array $data): float {}
+function gsl_rstat_sd(array $data): float {}
+function gsl_rstat_sd_mean(array $data): float {}
+function gsl_rstat_rms(array $data): float {}
+function gsl_rstat_skew(array $data): float {}
+function gsl_rstat_kurtosis(array $data): float {}
+function gsl_rstat_median(array $data): float {}
+function gsl_rstat_quantile_get(array $data, float $factor): float {}