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Use CPP 17 standard instead of cpp11 #841

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Use CPP 17 standard instead of cpp11 #841

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f2e4a49
[cmake] bump cpp standard to c++17 ...
jgrewe Feb 11, 2023
fcb1757
[c++17] use std::optional instead of boost
jgrewe Feb 11, 2023
a2dd0f3
[filesystem] use std::filesystem instead of boost
jgrewe Feb 11, 2023
5aabc52
[Dimnension] fix rebase errors
jgrewe Feb 11, 2023
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10 changes: 5 additions & 5 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ option(BUILD_COVERAGE "Build with coverage information" OFF)
set(HAVE_COVERAGE OFF)

if(NOT WIN32)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS_INIT} -std=c++11") ## Optimize
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS_INIT} -std=c++17") ## Optimize
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -pedantic -Wunreachable-code")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unused-local-typedef") # boost + clang

Expand Down Expand Up @@ -104,8 +104,8 @@ include_directories("${PROJECT_BINARY_DIR}/include")

### scan files
include_directories(BEFORE include)
file(GLOB_RECURSE nix_SOURCES src/*.cpp)
file(GLOB_RECURSE nix_INCLUDES include/*.hpp)
file(GLOB_RECURSE nix_SOURCES "src/[!.#]*.cpp")
file(GLOB_RECURSE nix_INCLUDES "include/[!.#]*.hpp")
list(APPEND nix_INCLUDES "${PROJECT_BINARY_DIR}/include/nix/nixversion.hpp")

### BACKENDS
Expand All @@ -115,8 +115,8 @@ set(backends "hdf5")
include_directories(${CMAKE_SOURCE_DIR}/backend)

foreach(backend ${backends})
file(GLOB_RECURSE backend_SOURCES "backend/${backend}/*.cpp")
file(GLOB_RECURSE backend_INCLUDES "backend/${backend}/*.hpp")
file(GLOB_RECURSE backend_SOURCES "backend/${backend}/[!.#]*.cpp")
file(GLOB_RECURSE backend_INCLUDES "backend/${backend}/[!.#]*.hpp")

list(APPEND nix_SOURCES ${backend_SOURCES})
list(APPEND nix_INCLUDES ${backend_INCLUDES})
Expand Down
24 changes: 12 additions & 12 deletions backend/hdf5/BaseTagHDF5.cpp
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Expand Up @@ -53,14 +53,14 @@ bool BaseTagHDF5::hasReference(const std::string &name_or_id) const {


ndsize_t BaseTagHDF5::referenceCount() const {
boost::optional<H5Group> g = refs_group(false);
std::optional<H5Group> g = refs_group(false);
return g ? g->objectCount() : size_t(0);
}


std::shared_ptr<IDataArray> BaseTagHDF5::getReference(const std::string &name_or_id) const {
std::shared_ptr<IDataArray> da;
boost::optional<H5Group> g = refs_group(false);
std::optional<H5Group> g = refs_group(false);

std::string id = block()->resolveEntityId({name_or_id, ObjectType::DataArray});
if (g && hasReference(id)) {
Expand All @@ -72,13 +72,13 @@ std::shared_ptr<IDataArray> BaseTagHDF5::getReference(const std::string &name_o
}

std::shared_ptr<IDataArray> BaseTagHDF5::getReference(ndsize_t index) const {
boost::optional<H5Group> g = refs_group(false);
std::optional<H5Group> g = refs_group(false);
std::string id = g ? g->objectName(index) : "";
return getReference(id);
}

void BaseTagHDF5::addReference(const std::string &name_or_id) {
boost::optional<H5Group> g = refs_group(true);
std::optional<H5Group> g = refs_group(true);

if (!block()->hasEntity({name_or_id, ObjectType::DataArray}))
throw std::runtime_error("BaseTagHDF5::addReference: DataArray not found in block!");
Expand All @@ -90,7 +90,7 @@ void BaseTagHDF5::addReference(const std::string &name_or_id) {


bool BaseTagHDF5::removeReference(const std::string &name_or_id) {
boost::optional<H5Group> g = refs_group(false);
std::optional<H5Group> g = refs_group(false);
bool removed = false;

if (g && hasReference(name_or_id)) {
Expand Down Expand Up @@ -124,19 +124,19 @@ bool BaseTagHDF5::hasFeature(const std::string &name_or_id) const {


ndsize_t BaseTagHDF5::featureCount() const {
boost::optional<H5Group> g = feature_group(false);
std::optional<H5Group> g = feature_group(false);
return g ? g->objectCount() : size_t(0);
}


std::shared_ptr<IFeature> BaseTagHDF5::getFeature(const std::string &name_or_id) const {
std::shared_ptr<FeatureHDF5> feature;
boost::optional<H5Group> g = feature_group(false);
std::optional<H5Group> g = feature_group(false);

if (g) {
boost::optional<H5Group> group = g->findGroupByNameOrAttribute("name", name_or_id);
std::optional<H5Group> group = g->findGroupByNameOrAttribute("name", name_or_id);
if (group)
feature = std::make_shared<FeatureHDF5>(file(), block(), group.get());
feature = std::make_shared<FeatureHDF5>(file(), block(), group.value());
else {
for (ndsize_t i = 0; i < g->objectCount(); i++) {
H5Group gr = g->openGroup(g->objectName(i), false);
Expand All @@ -154,7 +154,7 @@ std::shared_ptr<IFeature> BaseTagHDF5::getFeature(const std::string &name_or_id)


std::shared_ptr<IFeature> BaseTagHDF5::getFeature(ndsize_t index) const {
boost::optional<H5Group> g = feature_group(false);
std::optional<H5Group> g = feature_group(false);
std::string id = g->objectName(index);
return getFeature(id);
}
Expand All @@ -165,7 +165,7 @@ std::shared_ptr<IFeature> BaseTagHDF5::createFeature(const std::string &name_or
throw std::runtime_error("DataArray not found in Block!");
}
std::string rep_id = util::createId();
boost::optional<H5Group> g = feature_group(true);
std::optional<H5Group> g = feature_group(true);

H5Group group = g->openGroup(rep_id, true);
DataArray data = std::dynamic_pointer_cast<IDataArray>(block()->getEntity({name_or_id, ObjectType::DataArray}));
Expand All @@ -174,7 +174,7 @@ std::shared_ptr<IFeature> BaseTagHDF5::createFeature(const std::string &name_or


bool BaseTagHDF5::deleteFeature(const std::string &name_or_id) {
boost::optional<H5Group> g = feature_group(false);
std::optional<H5Group> g = feature_group(false);
bool deleted = false;

if (g && hasFeature(name_or_id)) {
Expand Down
44 changes: 22 additions & 22 deletions backend/hdf5/BlockHDF5.cpp
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Expand Up @@ -58,8 +58,8 @@ BlockHDF5::BlockHDF5(const shared_ptr<IFile> &file, const H5Group &group, const
// Generic access methods
//--------------------------------------------------

boost::optional<H5Group> BlockHDF5::groupForObjectType(ObjectType type, bool create) const {
boost::optional<H5Group> p;
std::optional<H5Group> BlockHDF5::groupForObjectType(ObjectType type, bool create) const {
std::optional<H5Group> p;

switch (type) {
case ObjectType::DataArray:
Expand Down Expand Up @@ -87,20 +87,20 @@ boost::optional<H5Group> BlockHDF5::groupForObjectType(ObjectType type, bool cre
break;

default:
p = boost::optional<H5Group>(create);
p = std::optional<H5Group>(create);
}

return p;
}

boost::optional<H5Group> BlockHDF5::findEntityGroup(const nix::Identity &ident) const {
boost::optional<H5Group> p = groupForObjectType(ident.type());
std::optional<H5Group> BlockHDF5::findEntityGroup(const nix::Identity &ident) const {
std::optional<H5Group> p = groupForObjectType(ident.type());

if (!p) {
return p;
}

boost::optional<H5Group> g;
std::optional<H5Group> g;
const std::string &iname = ident.name();
const std::string &iid = ident.id();

Expand All @@ -115,7 +115,7 @@ boost::optional<H5Group> BlockHDF5::findEntityGroup(const nix::Identity &ident)
bool foundNeedle = p->hasObject(needle);

if (foundNeedle) {
g = boost::make_optional(p->openGroup(needle, false));
g = std::make_optional(p->openGroup(needle, false));
} else if (haveId) {
g = p->findGroupByAttribute("entity_id", iid);
}
Expand All @@ -125,7 +125,7 @@ boost::optional<H5Group> BlockHDF5::findEntityGroup(const nix::Identity &ident)
g->getAttr("entity_id", eid);

if (eid != iid) {
return boost::optional<H5Group>();
return std::optional<H5Group>();
}
}

Expand All @@ -137,7 +137,7 @@ std::string BlockHDF5::resolveEntityId(const nix::Identity &ident) const {
return ident.id();
}

boost::optional<H5Group> g = findEntityGroup(ident);
std::optional<H5Group> g = findEntityGroup(ident);
if (!g) {
return "";
}
Expand All @@ -149,12 +149,12 @@ std::string BlockHDF5::resolveEntityId(const nix::Identity &ident) const {
}

bool BlockHDF5::hasEntity(const nix::Identity &ident) const {
boost::optional<H5Group> p = findEntityGroup(ident);
std::optional<H5Group> p = findEntityGroup(ident);
return !!p;
}

std::shared_ptr<base::IEntity> BlockHDF5::getEntity(const nix::Identity &ident) const {
boost::optional<H5Group> eg = findEntityGroup(ident);
std::optional<H5Group> eg = findEntityGroup(ident);

switch (ident.type()) {
case ObjectType::DataArray: {
Expand Down Expand Up @@ -213,19 +213,19 @@ std::shared_ptr<base::IEntity> BlockHDF5::getEntity(const nix::Identity &ident)
}

std::shared_ptr<base::IEntity>BlockHDF5::getEntity(ObjectType type, ndsize_t index) const {
boost::optional<H5Group> eg = groupForObjectType(type);
std::optional<H5Group> eg = groupForObjectType(type);
string name = eg ? eg->objectName(index) : "";
return getEntity({name, "", type});
}

ndsize_t BlockHDF5::entityCount(ObjectType type) const {
boost::optional<H5Group> g = groupForObjectType(type);
std::optional<H5Group> g = groupForObjectType(type);
return g ? g->objectCount() : ndsize_t(0);
}

bool BlockHDF5::removeEntity(const nix::Identity &ident) {
boost::optional<H5Group> p = groupForObjectType(ident.type());
boost::optional<H5Group> eg = findEntityGroup(ident);
std::optional<H5Group> p = groupForObjectType(ident.type());
std::optional<H5Group> eg = findEntityGroup(ident);

if (!p || !eg) {
return false;
Expand Down Expand Up @@ -255,15 +255,15 @@ bool BlockHDF5::removeEntity(const nix::Identity &ident) {

shared_ptr<ISource> BlockHDF5::createSource(const string &name, const string &type) {
string id = util::createId();
boost::optional<H5Group> g = source_group(true);
std::optional<H5Group> g = source_group(true);

H5Group group = g->openGroup(name, true);
return make_shared<SourceHDF5>(file(), block(), group, id, type, name);
}


bool BlockHDF5::deleteSource(const string &name_or_id) {
boost::optional<H5Group> g = source_group();
std::optional<H5Group> g = source_group();
bool deleted = false;

if (g) {
Expand Down Expand Up @@ -293,7 +293,7 @@ bool BlockHDF5::deleteSource(const string &name_or_id) {
shared_ptr<ITag> BlockHDF5::createTag(const std::string &name, const std::string &type,
const std::vector<double> &position) {
string id = util::createId();
boost::optional<H5Group> g = tag_group(true);
std::optional<H5Group> g = tag_group(true);

H5Group group = g->openGroup(name);
return make_shared<TagHDF5>(file(), block(), group, id, type, name, position);
Expand All @@ -310,7 +310,7 @@ shared_ptr<IDataArray> BlockHDF5::createDataArray(const std::string &name,
const NDSize &shape,
const Compression &compression) {
string id = util::createId();
boost::optional<H5Group> g = data_array_group(true);
std::optional<H5Group> g = data_array_group(true);

H5Group group = g->openGroup(name, true);
auto da = make_shared<DataArrayHDF5>(file(), block(), group, id, type, name);
Expand All @@ -330,7 +330,7 @@ std::shared_ptr<IDataFrame> BlockHDF5::createDataFrame(const std::string &name,
const Compression &compression) {

string id = util::createId();
boost::optional<H5Group> g = data_frame_group(true);
std::optional<H5Group> g = data_frame_group(true);
H5Group group = g->openGroup(name, true);

auto df = make_shared<DataFrameHDF5>(file(), block(), group, id, type, name);
Expand All @@ -346,7 +346,7 @@ std::shared_ptr<IDataFrame> BlockHDF5::createDataFrame(const std::string &name,
shared_ptr<IMultiTag> BlockHDF5::createMultiTag(const std::string &name, const std::string &type,
const DataArray &positions) {
string id = util::createId();
boost::optional<H5Group> g = multi_tag_group(true);
std::optional<H5Group> g = multi_tag_group(true);

H5Group group = g->openGroup(name);
return make_shared<MultiTagHDF5>(file(), block(), group, id, type, name, positions);
Expand All @@ -358,7 +358,7 @@ shared_ptr<IMultiTag> BlockHDF5::createMultiTag(const std::string &name, const s

shared_ptr<IGroup> BlockHDF5::createGroup(const std::string &name, const std::string &type) {
string id = util::createId();
boost::optional<H5Group> g = groups_group(true);
std::optional<H5Group> g = groups_group(true);

H5Group group = g->openGroup(name);
return make_shared<GroupHDF5>(file(), block(), group, id, type, name);
Expand Down
6 changes: 3 additions & 3 deletions backend/hdf5/BlockHDF5.hpp
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Expand Up @@ -14,7 +14,7 @@

#include <vector>
#include <string>
#include <boost/optional.hpp>
#include <optional>

namespace nix {
namespace hdf5 {
Expand Down Expand Up @@ -67,9 +67,9 @@ class BlockHDF5 : virtual public base::IBlock, public EntityWithMetadataHDF5,

private:
// Helper methods for generic entity related methods below
boost::optional<H5Group> groupForObjectType(ObjectType ot, bool create = false) const;
std::optional<H5Group> groupForObjectType(ObjectType ot, bool create = false) const;

boost::optional<H5Group> findEntityGroup(const nix::Identity &ident) const;
std::optional<H5Group> findEntityGroup(const nix::Identity &ident) const;

public:
//--------------------------------------------------
Expand Down
20 changes: 10 additions & 10 deletions backend/hdf5/DataArrayHDF5.cpp
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Expand Up @@ -41,8 +41,8 @@ DataArrayHDF5::DataArrayHDF5(const shared_ptr<IFile> &file, const shared_ptr<IBl
// Element getters and setters
//--------------------------------------------------

boost::optional<std::string> DataArrayHDF5::label() const {
boost::optional<std::string> ret;
std::optional<std::string> DataArrayHDF5::label() const {
std::optional<std::string> ret;
string value;
bool have_attr = group().getAttr("label", value);

Expand All @@ -68,8 +68,8 @@ void DataArrayHDF5::label(const none_t t) {
}


boost::optional<std::string> DataArrayHDF5::unit() const {
boost::optional<std::string> ret;
std::optional<std::string> DataArrayHDF5::unit() const {
std::optional<std::string> ret;
string value;
bool have_attr = group().getAttr("unit", value);
if (have_attr) {
Expand All @@ -94,8 +94,8 @@ void DataArrayHDF5::unit(const none_t t) {


// TODO use defaults
boost::optional<double> DataArrayHDF5::expansionOrigin() const {
boost::optional<double> ret;
std::optional<double> DataArrayHDF5::expansionOrigin() const {
std::optional<double> ret;
double expansion_origin;
bool have_attr = group().getAttr("expansion_origin", expansion_origin);
if (have_attr) {
Expand Down Expand Up @@ -157,7 +157,7 @@ void DataArrayHDF5::polynomCoefficients(const none_t t) {


ndsize_t DataArrayHDF5::dimensionCount() const {
boost::optional<H5Group> g = dimension_group();
std::optional<H5Group> g = dimension_group();
ndsize_t count = 0;
if (g) {
count = g->objectCount();
Expand All @@ -168,7 +168,7 @@ ndsize_t DataArrayHDF5::dimensionCount() const {

shared_ptr<IDimension> DataArrayHDF5::getDimension(ndsize_t index) const {
shared_ptr<IDimension> dim;
boost::optional<H5Group> g = dimension_group();
std::optional<H5Group> g = dimension_group();

if (g) {
string str_id = util::numToStr(index);
Expand Down Expand Up @@ -219,7 +219,7 @@ std::shared_ptr<base::IDataFrameDimension> DataArrayHDF5::createDataFrameDimensi


H5Group DataArrayHDF5::createDimensionGroup(ndsize_t index) {
boost::optional<H5Group> g = dimension_group(true);
std::optional<H5Group> g = dimension_group(true);

ndsize_t dim_max = dimensionCount() + 1;
if (index > dim_max || index <= 0)
Expand All @@ -236,7 +236,7 @@ H5Group DataArrayHDF5::createDimensionGroup(ndsize_t index) {

bool DataArrayHDF5::deleteDimensions() {
string dim_id;
boost::optional<H5Group> g = dimension_group();
std::optional<H5Group> g = dimension_group();
for (ndsize_t i = dimensionCount(); i > 0; --i) {
dim_id = util::numToStr(i);
if (g->hasGroup(dim_id)) {
Expand Down
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