Squashed 'externals/coda-oss/' changes from df07c512d..26de66952

26de66952 Merge branch 'main' into cpp17
605d24898 duplicate existing HDF5 unittests using HighFive (#657)
134233279 add 'override'; fix ASAN-detected memory leaks (#656)

git-subtree-dir: externals/coda-oss
git-subtree-split: 26de66952d92ee80c1e76232dc9819d062454109

CMakeLists.txt

@@ -24,8 +24,18 @@ if (${CMAKE_PROJECT_NAME} STREQUAL coda-oss)
     if (MSVC)
        add_compile_options(/WX) # warnings as errors
        add_compile_options(/MP) # multi-processor compile
+
+       if (ENABLE_ASAN)
+            # https://docs.microsoft.com/en-us/cpp/sanitizers/asan?view=msvc-160
+            add_compile_options(/fsanitize=address)
+       endif()
     elseif (UNIX)
        add_compile_options(-Werror) # warnings as errors
+       if (ENABLE_ASAN)
+            # https://gcc.gnu.org/onlinedocs/gcc/Instrumentation-Options.html
+            add_compile_options(-fsanitize=address)
+            add_link_options(-fsanitize=address)
+       endif()
     endif()
 
     list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")

ReleaseNotes.md

@@ -11,8 +11,15 @@
  ```
 # coda-oss Release Notes
 
+## [Release 2023-??-??](https://github.com/mdaus/coda-oss/releases/tag/2023-??-??)
+* *zlib* updated to [1.2.13](https://github.com/madler/zlib/releases/tag/v1.2.13).
+* new `mem::ComplexView` class to make it easier to process complex data stored in parallel. 
+* adjust compiler flags for clean *CMake* builds.
+* wrap common "file open" routines (e.g., `fopen()`) to support `sys::expandEnvironmentVariables()`.
+* add header-only [HighFive](https://github.com/BlueBrain/HighFive) HDF5-wrapper library.
+
 ## [Release 2022-12-14](https://github.com/mdaus/coda-oss/releases/tag/2022-12-14)
-* removed remaining vestigates of `std::auto_ptr`, provide `mem::AutoPtr` for the tiny handful of
+* removed remaining vestiges of `std::auto_ptr`, provide `mem::AutoPtr` for the tiny handful of
   places (e.g., SWIG bindings) that still need copying.
 * `xml::lite::Element` overloads to make creting new XML documents easier; see unittests for examples.
 * try even harder to find unittest files in various scenarios.
@@ -30,7 +37,7 @@
 * Utilitiy routines for finding various files when unit-testing.
 * Removed C++14 work-arounds needed in C++11. Legacy C++ exception specificatons removed.
 * Rebuild `waf` for FIPS error; added more debug options.
-
+ 
 ## [Release 2022-08-30](https://github.com/mdaus/coda-oss/releases/tag/2022-08-30)
 * XML is now always written as UTF-8; the code will still try to read Windows-1252.
 * `Uri`s are no longer validated by default.

UnitTest/UnitTest.vcxproj

@@ -25,6 +25,7 @@
     <PlatformToolset>v143</PlatformToolset>
     <UseOfMfc>false</UseOfMfc>
     <CharacterSet>Unicode</CharacterSet>
+    <EnableASAN>true</EnableASAN>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
     <ConfigurationType>DynamicLibrary</ConfigurationType>
@@ -33,6 +34,7 @@
     <WholeProgramOptimization>true</WholeProgramOptimization>
     <UseOfMfc>false</UseOfMfc>
     <CharacterSet>Unicode</CharacterSet>
+    <EnableASAN>true</EnableASAN>
   </PropertyGroup>
   <Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
   <ImportGroup Label="ExtensionSettings">

modules/c++/CMakeLists.txt

@@ -18,8 +18,8 @@ elseif (UNIX)
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wzero-as-null-pointer-constant")
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Woverloaded-virtual")
     #set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wold-style-cast")
-    #set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wsuggest-final-types -Wsuggest-final-methods")
-    #set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wsuggest-override")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wsuggest-final-types -Wsuggest-final-methods")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wsuggest-override")
 endif()
 
 # add an interface library for unittests

modules/c++/cli/unittests/test_cli.cpp

@@ -171,10 +171,10 @@ TEST_CASE(testRequired)
     parser.addArgument("-v --verbose", "Toggle verbose", cli::STORE_TRUE);
     parser.addArgument("-c --config", "Specify a config file", cli::STORE)->setRequired(true);
 
-    std::unique_ptr<cli::Results> results;
-    TEST_EXCEPTION(results.reset(parser.parse(str::split(""))));
-    TEST_EXCEPTION(results.reset(parser.parse(str::split("-c"))));
-    results.reset(parser.parse(str::split("-c configFile")));
+    const std::string program(testName);
+    TEST_EXCEPTION(parser.parse(program, str::split("")));
+    TEST_EXCEPTION(parser.parse(program, str::split("-c")));
+    const auto results = parser.parse(program, str::split("-c configFile"));
     TEST_ASSERT_EQ(results->get<std::string>("config"), "configFile");
 }
 

modules/c++/coda-oss-lite.vcxproj

@@ -421,12 +421,14 @@
     <ConfigurationType>DynamicLibrary</ConfigurationType>
     <UseDebugLibraries>true</UseDebugLibraries>
     <PlatformToolset>v143</PlatformToolset>
+    <EnableASAN>true</EnableASAN>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
     <ConfigurationType>DynamicLibrary</ConfigurationType>
     <UseDebugLibraries>false</UseDebugLibraries>
     <PlatformToolset>v143</PlatformToolset>
     <WholeProgramOptimization>true</WholeProgramOptimization>
+    <EnableASAN>true</EnableASAN>
   </PropertyGroup>
   <Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
   <ImportGroup Label="ExtensionSettings">

modules/c++/except/source/Backtrace.cpp

@@ -57,6 +57,10 @@ struct BacktraceHelper final
     BacktraceHelper(char** stackSymbols)
         : mStackSymbols(stackSymbols)
     {}
+    BacktraceHelper(const BacktraceHelper&) = delete;
+    BacktraceHelper& operator=(const BacktraceHelper&) = delete;
+    BacktraceHelper(BacktraceHelper&&) = default;
+    BacktraceHelper& operator=(BacktraceHelper&&) = default;
 
     ~BacktraceHelper()
     {

modules/c++/hdf5.lite/CMakeLists.txt

@@ -1,8 +1,8 @@
 set(MODULE_NAME hdf5.lite)
 
 if(CODA_ENABLE_HDF5)
-    set(MODULE_DEPS except-c++ types-c++ io-c++ coda_oss-c++)
-    list(APPEND MODULE_DEPS hdf5-c++)
+    set(MODULE_DEPS highfive-c++ hdf5-c++)
+    list(APPEND MODULE_DEPS except-c++ types-c++ io-c++ coda_oss-c++)
 
     coda_add_module(
         ${MODULE_NAME}

modules/c++/hdf5.lite/include/hdf5/lite/Write.h

@@ -25,8 +25,8 @@
 #pragma once
 
 /*!
- * \file  Read.h
- * \brief HDF File-reading API
+ * \file  Write.h
+ * \brief HDF File-writing API
  *
  * These are simple routines to write HDF5 files; they're loosely modeled after the MATLab API
  * https://www.mathworks.com/help/matlab/ref/h5create.html
@@ -51,20 +51,20 @@ CODA_OSS_API void createFile(const coda_oss::filesystem::path&, const std::strin
 CODA_OSS_API void createFile(const coda_oss::filesystem::path&, const std::string& ds, SpanRC<const double>);
 inline void createFile(const coda_oss::filesystem::path& path, const std::string& ds, SpanRC<double> data_)
 {
-	SpanRC<const double> data(data_.data(), data_.dims());
-	createFile(path, ds, data);
+    SpanRC<const double> data(data_.data(), data_.dims());
+    createFile(path, ds, data);
 }
 CODA_OSS_API void createFile(const coda_oss::filesystem::path&, const std::string& ds, SpanRC<const float>);
 inline void createFile(const coda_oss::filesystem::path& path, const std::string& ds, SpanRC<float> data_)
 {
     SpanRC<const float> data(data_.data(), data_.dims());
-	createFile(path, ds, data);
+    createFile(path, ds, data);
 }
 
 CODA_OSS_API void writeFile(const coda_oss::filesystem::path&, const std::string& loc, SpanRC<const double>);
 inline void writeFile(const coda_oss::filesystem::path& path, const std::string& ds, SpanRC<double> data_)
 {
-	SpanRC<const double> data(data_.data(), data_.dims());
+    SpanRC<const double> data(data_.data(), data_.dims());
     writeFile(path, ds, data);
 }
 CODA_OSS_API void writeFile(const coda_oss::filesystem::path&, const std::string& loc, SpanRC<const float>);

modules/c++/hdf5.lite/include/hdf5/lite/highfive.h

@@ -0,0 +1,75 @@
+/* =========================================================================
+ * This file is part of hdf5.lite-c++ 
+ * =========================================================================
+ * 
+ * (C) Copyright 2022, Maxar Technologies, Inc.
+ *
+ * hdf5.lite-c++ is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public 
+ * License along with this program; If not, 
+ * see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifndef CODA_OSS_hdf5_lite_highfive_h_INCLUDED_
+#define CODA_OSS_hdf5_lite_highfive_h_INCLUDED_
+#pragma once
+
+/*!
+ * \file  highfive.h
+ * \brief Utility routines for using HighFive
+ */
+
+#include <string>
+
+#include "highfive/H5Easy.hpp"
+#include "highfive/H5DataSet.hpp"
+
+#include "SpanRC.h"
+
+namespace hdf5
+{
+namespace lite
+{
+template <typename T>
+inline HighFive::DataSet writeDataSet(H5Easy::File& file, SpanRC<T> data, const std::string& dataset_name /*, TODO ...*/)
+{
+    const std::vector<size_t> dims{data.dims().row, data.dims().col};
+    const HighFive::DataSpace dataspace{dims};
+    auto retval = file.createDataSet<T>(dataset_name, dataspace);
+    retval.write_raw(data.data());
+    return retval;
+}
+
+template <typename T>
+inline SpanRC<T> readDataSet(HighFive::DataSet& dataSet, std::vector<T>& result /*, TODO ...*/)
+{
+    const auto dimensions = dataSet.getSpace().getDimensions();
+    const types::RowCol<size_t> dims(dimensions[0], dimensions[1]);
+
+    result.resize(dims.area());
+    dataSet.read(result.data());
+
+    return SpanRC<T>(result.data(), dims);
+}
+
+template <typename T>
+inline SpanRC<T> load(H5Easy::File& file, const std::string& dataset_name, std::vector<T>& result /*, TODO ...*/)
+{
+    auto dataSet = file.getDataSet(dataset_name);
+    return readDataSet(dataSet, result);
+}
+
+}
+}
+
+#endif // CODA_OSS_hdf5_lite_highfive_h_INCLUDED_

modules/c++/hdf5.lite/unittests/test_hdf5write.cpp

@@ -85,7 +85,7 @@ TEST_CASE(test_hdf5Write)
     for (size_t i = 0; i < result.size(); i++)
     {
         const auto expected = static_cast<double>(i);
-        TEST_ASSERT_ALMOST_EQ(result[i], expected);
+        TEST_ASSERT_EQ(result[i], expected);
     }
 }