Merge pull request #224 from sameeul/drop_boost_req

Drop boost requirement

.github/workflows/environment.yaml

@@ -8,7 +8,6 @@ dependencies:
   - lz4-c
   - xz
   - zlib
-  - boost-cpp>=1.63
   - xtensor >=0.24,<0.25
   - xtensor-python >=0.26,<0.27
   - xsimd >=8,<9

CMakeLists.txt

@@ -27,17 +27,7 @@ message(STATUS "Building z5 v${${PROJECT_NAME}_VERSION}")
 # C++ Standard
 ##############################
 
-# check whether we have c++ 17
-
-message(STATUS "CXX_FLAGS: ${CMAKE_CXX_FLAGS}")
-set(CPP17 "${CMAKE_CXX_FLAGS}" MATCHES "-std=c\\+\\+17" CACHE INTERNAL "")
-if (CPP17)
-    message(STATUS "Using c++ 17")
-    set(CMAKE_CXX_STANDARD 17)
-else()
-    message(STATUS "Using c++ 14")
-    set(CMAKE_CXX_STANDARD 14)
-endif()
+set(CMAKE_CXX_STANDARD 17)
 
 # make sure the compiler supports the requested c++ standard
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
@@ -53,14 +43,6 @@ if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
 endif()
 string(TOUPPER "${CMAKE_BUILD_TYPE}" U_CMAKE_BUILD_TYPE)
 
-# NOTE whether we need to enable the old ABI depends
-# on which ABI boost is compiled with.
-# If you get boost linker errors try to enable / disable the old ABI
-option(USE_OLD_ABI "Use the old GCC ABI to be compatible with old GLIBC versions" OFF)
-if(USE_OLD_ABI)
-    message(STATUS "Using old GCC ABI")
-    add_definitions(-D_GLIBCXX_USE_CXX11_ABI=0)
-endif()
 
 if(MSVC)
     add_definitions(/DNOMINMAX)
@@ -155,53 +137,11 @@ endif()
 # find libraries - pthread
 find_package(Threads)
 
-
-###############################
-# Boost
-###############################
-
-# If WITH_BOOST_FS is set, we always use the boost filesystem library
-# otherwise, we check if we have c++17 support. If so, we use std::filesystem,
-# otherwise we fall back to boost filesystem.
-if(CPP17)
-    SET(WITH_BOOST_FS FALSE CACHE BOOL "")
-else()
-    SET(WITH_BOOST_FS TRUE CACHE BOOL "")
+# add C++ filesystem
+if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+    SET(FILESYSTEM_LIBRARIES "stdc++fs")
 endif()
 
-if (MSVC)
-    SET(BOOST_ROOT "${CMAKE_PREFIX_PATH}/Library")
-    SET(BOOST_LIBRARYDIR "${CMAKE_PREFIX_PATH}/Library/lib")
-else()
-    SET(BOOST_ROOT "${CMAKE_PREFIX_PATH}")
-    SET(BOOST_LIBRARYDIR "${CMAKE_PREFIX_PATH}/lib")
-endif()
-SET(Boost_NO_SYSTEM_PATHS ON)
-
-if(WITH_BOOST_FS)
-    message(STATUS "With boost filesystem")
-    find_package(Boost 1.63.0 COMPONENTS system filesystem REQUIRED)
-    add_definitions(-DWITH_BOOST_FS)
-    SET(FILESYSTEM_LIBRARIES "${Boost_FILESYSTEM_LIBRARY};${Boost_SYSTEM_LIBRARY}")
-else()
-    message(STATUS "With std filesystem")
-    find_package(Boost 1.63.0 REQUIRED)
-
-    # see this issue for discussions about the filesystem lib in CMake
-    # https://gitlab.kitware.com/cmake/cmake/issues/17834
-    if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
-        SET(FILESYSTEM_LIBRARIES "stdc++fs")
-    endif()
-
-    # on clang, we need to enable libc++experimental, see
-    # https://stackoverflow.com/a/45332844
-    if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
-        SET(FILESYSTEM_LIBRARIES "c++experimental")
-    endif()
-endif()
-include_directories(${Boost_INCLUDE_DIR})
-
-
 ###################
 # xtensor libraries
 ###################
@@ -318,22 +258,6 @@ if(BUILD_Z5PY)
     # find pybind11, which is required to build the python bindings
     # the find package command will find python and set the python variables
     find_package(pybind11 REQUIRED)
-    if (CPP17)
-        message(STATUS "Using c++ 17 for pybind")
-        if(MSVC)
-            set(PYBIND11_CPP_STANDARD /std:c++17)
-        else()
-            set(PYBIND11_CPP_STANDARD -std=c++17)
-        endif()
-    else()
-        message(STATUS "Using c++ 14 for pybind")
-        if(MSVC)
-            set(PYBIND11_CPP_STANDARD /std:c++14)
-        else()
-            set(PYBIND11_CPP_STANDARD -std=c++14)
-        endif()
-    endif()
-
     # pybind11 does not include numpy, so we must search for it in addition here
     find_package(NumPy REQUIRED)
     include_directories(${NUMPY_INCLUDE_DIRS})

include/z5/common.hxx

@@ -1,93 +1,13 @@
 #pragma once
 
 #include <fstream>
+#include <filesystem>
+namespace fs = std::filesystem;
+
+inline fs::path relativeImpl(const fs::path & from, const fs::path & to){
+    return fs::relative(to, from);
+}
 
-// helpful summary of compiler versions
-// https://blog.kowalczyk.info/article/j/guide-to-predefined-macros-in-c-compilers-gcc-clang-msvc-etc..html
-
-// include boost::filesystem or std::filesystem header
-// and define the namespace fs
-#ifdef WITH_BOOST_FS
-    #ifndef BOOST_FILESYSTEM_NO_DEPRECATED
-        #define BOOST_FILESYSTEM_NO_DEPRECATED
-    #endif
-    #include <boost/filesystem.hpp>
-    #include <boost/filesystem/fstream.hpp>
-    namespace fs = boost::filesystem;
-
-    // relative path in boost filesystem behaves unexpectedly, so we use the
-    // same implementation as below
-	inline fs::path relativeImpl(const fs::path & from, const fs::path & to) {
-	   fs::path::const_iterator fromIter = from.begin();
-	   fs::path::const_iterator toIter = to.begin();
-
-	   while (fromIter != from.end() && toIter != to.end() && (*toIter) == (*fromIter)){
-	      ++toIter;
-	      ++fromIter;
-	   }
-
-	   fs::path finalPath;
-	   while (fromIter != from.end()){
-	      finalPath /= "..";
-	      ++fromIter;
-	   }
-
-	   while (toIter != to.end()){
-	      finalPath /= *toIter;
-	      ++toIter;
-	   }
-
-	   return finalPath;
-	}
-#else
-    // macos behaves very weird here, I can't get it to build on
-    // osx < 10.15 right now. For now the workaround is to use boost filesystem ...
-    // TODO MSVC check ?
-    #if (defined(__GNUC__) && (__GNUC__ > 7)) || defined(__clang__) || (defined(_MSC_VER) && _MSC_VER > 1900)
-        #include <filesystem>
-        namespace fs = std::filesystem;
-
-        // need to be consistent with the other implementations
-        inline fs::path relativeImpl(const fs::path & from, const fs::path & to){
-            return fs::relative(to, from);
-        }
-
-    #else
-        #include <experimental/filesystem>
-        namespace fs = std::experimental::filesystem;
-
-        // experimental::filesystem does not have relative yet, so
-        // we re-implement it following:
-        // https://stackoverflow.com/questions/10167382/boostfilesystem-get-relative-path/37715252#37715252
-		inline fs::path relativeImpl(const fs::path & from, const fs::path & to){
-		   // Start at the root path and while they are the same then do nothing then when they first
-		   // diverge take the entire from path, swap it with '..' segments, and then append the remainder of the to path.
-		   fs::path::const_iterator fromIter = from.begin();
-		   fs::path::const_iterator toIter = to.begin();
-
-		   // Loop through both while they are the same to find nearest common directory
-		   while (fromIter != from.end() && toIter != to.end() && (*toIter) == (*fromIter)){
-		      ++toIter;
-		      ++fromIter;
-		   }
-
-		   // Replace from path segments with '..' (from => nearest common directory)
-		   fs::path finalPath;
-		   while (fromIter != from.end()){
-		      finalPath /= "..";
-		      ++fromIter;
-		   }
-
-		   // Append the remainder of the to path (nearest common directory => to)
-		   while (toIter != to.end()){
-		      finalPath /= *toIter;
-		      ++toIter;
-		   }
-
-		   return finalPath;
-		}
-    #endif
-#endif
 
 namespace z5 {
 

include/z5/factory.hxx

@@ -19,12 +19,7 @@ namespace z5 {
                 return;
             }
             nlohmann::json j;
-
-            #ifdef WITH_BOOST_FS
-            fs::ifstream file(path);
-            #else
             std::ifstream file(path);
-            #endif
             file >> j;
             file.close();
 

include/z5/filesystem/attributes.hxx

@@ -14,11 +14,7 @@ namespace attrs_detail {
         if(!fs::exists(path)) {
             return;
         }
-        #ifdef WITH_BOOST_FS
-        fs::ifstream file(path);
-        #else
         std::ifstream file(path);
-        #endif
         file >> j;
         file.close();
     }
@@ -27,22 +23,14 @@ namespace attrs_detail {
         nlohmann::json jOut;
         // if we already have attributes, read them
         if(fs::exists(path)) {
-            #ifdef WITH_BOOST_FS
-            fs::ifstream file(path);
-            #else
             std::ifstream file(path);
-            #endif
             file >> jOut;
             file.close();
         }
         for(auto jIt = j.begin(); jIt != j.end(); ++jIt) {
             jOut[jIt.key()] = jIt.value();
         }
-        #ifdef WITH_BOOST_FS
-        fs::ofstream file(path);
-        #else
         std::ofstream file(path);
-        #endif
         file << jOut;
         file.close();
     }
@@ -51,23 +39,15 @@ namespace attrs_detail {
         nlohmann::json jOut;
         // if we already have attributes, read them
         if(fs::exists(path)) {
-            #ifdef WITH_BOOST_FS
-            fs::ifstream file(path);
-            #else
             std::ifstream file(path);
-            #endif
             file >> jOut;
             file.close();
         }
         else {
             return;
         }
         jOut.erase(key);
-        #ifdef WITH_BOOST_FS
-        fs::ofstream file(path);
-        #else
         std::ofstream file(path);
-        #endif
         file << jOut;
         file.close();
     }

include/z5/filesystem/dataset.hxx

@@ -209,22 +209,14 @@ namespace filesystem {
     private:
 
         inline void write(const fs::path & path, const std::vector<char> & buffer) const {
-            #ifdef WITH_BOOST_FS
-            fs::ofstream file(path, std::ios::binary);
-            #else
             std::ofstream file(path, std::ios::binary);
-            #endif
             file.write(&buffer[0], buffer.size());
             file.close();
         }
 
         inline void read(const fs::path & path, std::vector<char> & buffer) const {
             // open input stream and read the filesize
-            #ifdef WITH_BOOST_FS
-            fs::ifstream file(path, std::ios::binary);
-            #else
             std::ifstream file(path, std::ios::binary);
-            #endif
 
             file.seekg(0, std::ios::end);
             const std::size_t file_size = file.tellg();
@@ -256,11 +248,7 @@ namespace filesystem {
 
         inline bool read_varlen_from_n5_header(const fs::path & path,
                                                std::size_t & chunkSize) const {
-            #ifdef WITH_BOOST_FS
-            fs::ifstream file(path, std::ios::binary);
-            #else
             std::ifstream file(path, std::ios::binary);
-            #endif
 
             // read the mode
             uint16_t mode;
@@ -291,11 +279,7 @@ namespace filesystem {
 
         inline void read_shape_from_n5_header(const fs::path & path,
                                               types::ShapeType & chunkShape) const {
-            #ifdef WITH_BOOST_FS
-            fs::ifstream file(path, std::ios::binary);
-            #else
             std::ifstream file(path, std::ios::binary);
-            #endif
 
             // advance the file by 2 to skip the mode
             file.seekg(2);

include/z5/filesystem/handle.hxx

@@ -310,7 +310,7 @@ namespace handle {
     // get z5::filesystem::handle::File from char pointer corresponding
     // to the file on filesystem
     inline File getFileHandle(const char * path) {
-        fs::path path_(std::string(path));
+        fs::path path_{std::string(path)};
         File ret(path);
         return ret;
     }

include/z5/filesystem/metadata.hxx

@@ -9,21 +9,13 @@ namespace filesystem {
 namespace metadata_detail {
 
     inline void writeMetadata(const fs::path & path, const nlohmann::json & j) {
-        #ifdef WITH_BOOST_FS
-        fs::ofstream file(path);
-        #else
         std::ofstream file(path);
-        #endif
         file << std::setw(4) << j << std::endl;
         file.close();
     }
 
     inline void readMetadata(const fs::path & path, nlohmann::json & j) {
-        #ifdef WITH_BOOST_FS
-        fs::ifstream file(path);
-        #else
         std::ifstream file(path);
-        #endif
         file >> j;
         file.close();
     }