Squashed 'modules/rmf/dependency/RMF/' changes from b2caa73f34..7ca61…

…270d2 7ca61270d2 Replace typedef with 'using' 20f87aa7e5 Use equals keyword for empty special methods 9251ccaf34 Use range-based for loops 0b6c0470d7 Replace NULL with nullptr cad4f2b59b Remove deprecated C++ headers 1b2ab66f4b Simplify by using emplace_back git-subtree-dir: modules/rmf/dependency/RMF git-subtree-split: 7ca61270d20076ccd838b4e6444020edc69a6b03
salilab · Oct 16, 2023 · 0311700 · 0311700
1 parent 2970ec3
commit 0311700
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Showing 21 changed files with 51 additions and 50 deletions.
diff --git a/modules/rmf/dependency/RMF/bin/rmf3_dump.cpp b/modules/rmf/dependency/RMF/bin/rmf3_dump.cpp
@@ -3,7 +3,7 @@
  */
 
 #include <memory>
-#include <stddef.h>
+#include <cstddef>
 #include <exception>
 #include <iostream>
 #include <string>

diff --git a/modules/rmf/dependency/RMF/bin/rmf_cat.cpp b/modules/rmf/dependency/RMF/bin/rmf_cat.cpp
@@ -25,7 +25,7 @@ int main(int argc, char** argv) {
         "input-files,i",
         boost::program_options::value<std::vector<std::string> >(&inputs),
         "input rmf file");
-    positional_names.push_back("input_1.rmf input_2.rmf ... output.rmf");
+    positional_names.emplace_back("input_1.rmf input_2.rmf ... output.rmf");
     positional_options_description.add("input-files", -1);
     process_options(argc, argv);
     if (inputs.size() < 3) {

diff --git a/modules/rmf/dependency/RMF/bin/rmf_interpolate.cpp b/modules/rmf/dependency/RMF/bin/rmf_interpolate.cpp
@@ -118,7 +118,7 @@ void interpolate_frames(int num, double noise, double angle_noise,
   // boost::random_device seed_gen;
   boost::mt19937 rng;
   // rng.seed(seed_gen());
-  rng.seed(static_cast<boost::uint64_t>(std::time(NULL)));
+  rng.seed(static_cast<boost::uint64_t>(std::time(nullptr)));
   boost::normal_distribution<> nd(0.0, noise);
   boost::variate_generator<boost::mt19937&, boost::normal_distribution<> >
       normal_random(rng, nd);

diff --git a/modules/rmf/dependency/RMF/bin/rmf_pdb.cpp b/modules/rmf/dependency/RMF/bin/rmf_pdb.cpp
@@ -148,8 +148,8 @@ RMF_ENABLE_WARNINGS namespace {
       out << str;
     }
     RMF::NodeConstHandles ch = nh.get_children();
-    for (unsigned int i = 0; i < ch.size(); ++i) {
-      current_index = write_atoms(out, current_index, ch[i], ipf, af, cf, rf,
+    for (const auto &c : ch) {
+      current_index = write_atoms(out, current_index, c, ipf, af, cf, rf,
                                   chain, residue_index, residue_type);
     }
     return current_index;

diff --git a/modules/rmf/dependency/RMF/bin/rmf_transform.cpp b/modules/rmf/dependency/RMF/bin/rmf_transform.cpp
@@ -67,8 +67,8 @@ void transform(RMF::NodeHandle nh,
   RMF_TRANSFORM_LIST(cf, Cylinder, coordinates_list);
   RMF_TRANSFORM_LIST(sf, Segment, coordinates_list);
   RMF::NodeHandles children = nh.get_children();
-  for (unsigned int i = 0; i < children.size(); ++i) {
-    transform(children[i], ipf, rpf, rff, bf, cf, sf, scale, translation);
+  for (const auto &child: children) {
+    transform(child, ipf, rpf, rff, bf, cf, sf, scale, translation);
   }
 }
 }

diff --git a/modules/rmf/dependency/RMF/bin/rmf_xml.cpp b/modules/rmf/dependency/RMF/bin/rmf_xml.cpp
@@ -74,14 +74,14 @@ void show_hierarchy(RMF::NodeConstHandle nh, const RMF::Categories& cs,
       << "type=\"" << nh.get_type() << "\">\n";
   if (seen.find(nh) == seen.end()) {
     if (variables_map.count("verbose")) {
-      for (unsigned int i = 0; i < cs.size(); ++i) {
-        show_data_xml(nh, cs[i], out);
+      for (const auto &c : cs) {
+        show_data_xml(nh, c, out);
       }
     }
     RMF::NodeConstHandles children = nh.get_children();
-    for (unsigned int i = 0; i < children.size(); ++i) {
+    for (const auto &child : children) {
       out << "<child>\n";
-      show_hierarchy(children[i], cs, seen, out);
+      show_hierarchy(child, cs, seen, out);
       out << "</child>\n";
     }
     seen.insert(nh);

diff --git a/modules/rmf/dependency/RMF/src/backend/BackwardsIO.cpp b/modules/rmf/dependency/RMF/src/backend/BackwardsIO.cpp
@@ -26,7 +26,7 @@ std::array<std::string, 4> make_array(std::string a, std::string b,
   return ret;
 }
 }
-typedef std::pair<std::string, std::array<std::string, 3> > P3;
+using P3 = std::pair<std::string, std::array<std::string, 3> >;
 const P3 vector_3_names[] = {
     P3("coordinates", make_array("cartesian x", "cartesian y", "cartesian z")),
     P3("translation",
@@ -44,7 +44,7 @@ const int vector_3_names_size =
 
 V3N vector_3_names_map(vector_3_names, vector_3_names + vector_3_names_size);
 
-typedef std::pair<std::string, std::array<std::string, 4> > P4;
+using P4 = std::pair<std::string, std::array<std::string, 4> >;
 
 const P4 vector_4_names[] = {
     P4("orientation", make_array("orientation r", "orientation i",

diff --git a/modules/rmf/dependency/RMF/src/backend/avro/traits.cpp b/modules/rmf/dependency/RMF/src/backend/avro/traits.cpp
@@ -398,7 +398,7 @@ struct BackwardsTypeDatas {
 };
 
 struct BackwardsFrame {
-  typedef rmf_raw_avro2::_Frame_json_Union__0__ info_t;
+  using info_t = rmf_raw_avro2::_Frame_json_Union__0__;
   info_t info;
   std::vector<rmf_raw_avro2::Node> nodes;
   std::vector<rmf_raw_avro2::KeyInfo> keys;

diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_avro/create.cpp b/modules/rmf/dependency/RMF/src/backend/deprecated_avro/create.cpp
@@ -36,12 +36,12 @@ namespace RMF {
 namespace avro_backend {
 namespace {
 
-typedef backends::BackwardsIO<avro_backend::AvroSharedData<
-    avro_backend::SingleAvroFile> > SingleAvroShareData;
-typedef backends::BackwardsIO<avro_backend::AvroSharedData<
-    avro_backend::MultipleAvroFileWriter> > AvroWriterShareData;
-typedef backends::BackwardsIO<avro_backend::AvroSharedData<
-    avro_backend::MultipleAvroFileReader> > AvroReaderShareData;
+using SingleAvroShareData = backends::BackwardsIO<avro_backend::AvroSharedData<
+    avro_backend::SingleAvroFile> >;
+using AvroWriterShareData = backends::BackwardsIO<avro_backend::AvroSharedData<
+    avro_backend::MultipleAvroFileWriter> >;
+using AvroReaderShareData = backends::BackwardsIO<avro_backend::AvroSharedData<
+    avro_backend::MultipleAvroFileReader> >;
 
 struct SingleTextAvroFactory : public RMF::backends::IOFactory {
   virtual std::string get_file_extension() const override {
@@ -55,7 +55,7 @@ struct SingleTextAvroFactory : public RMF::backends::IOFactory {
       const std::string& name) const override {
     return std::make_shared<SingleAvroShareData>(name, true, false);
   }
-  virtual ~SingleTextAvroFactory() {}
+  virtual ~SingleTextAvroFactory() = default;
 };
 
 struct SingleAvroFactory : public SingleTextAvroFactory {
@@ -76,7 +76,7 @@ struct SingleAvroFactory : public SingleTextAvroFactory {
       return std::shared_ptr<RMF::backends::IO>();
     }
   }
-  virtual ~SingleAvroFactory() {}
+  virtual ~SingleAvroFactory() = default;
 };
 
 struct MultipleAvroFactory : public RMF::backends::IOFactory {
@@ -91,7 +91,7 @@ struct MultipleAvroFactory : public RMF::backends::IOFactory {
       const std::string& name) const override {
     return std::make_shared<AvroWriterShareData>(name, true, false);
   }
-  virtual ~MultipleAvroFactory() {}
+  virtual ~MultipleAvroFactory() = default;
 };
 }  // namespace
 std::vector<std::shared_ptr<backends::IOFactory> > get_factories() {

diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5SharedData.cpp b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5SharedData.cpp
@@ -278,10 +278,9 @@ unsigned int HDF5SharedData::add_category_impl(std::string name) {
 
 Categories HDF5SharedData::get_categories() const {
   Categories ret;
-  for (CategoryDataMap::const_iterator it = category_data_map_.begin();
-       it != category_data_map_.end(); ++it) {
-    if (it->second.name == "link") continue;
-    ret.push_back(it->first);
+  for (const auto &it : category_data_map_) {
+    if (it.second.name == "link") continue;
+    ret.push_back(it.first);
   }
   return ret;
 }

diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5SharedData.h b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/HDF5SharedData.h
@@ -13,7 +13,7 @@
 #include <array>
 #include <boost/ptr_container/ptr_vector.hpp>
 #include <hdf5.h>
-#include <stddef.h>
+#include <cstddef>
 #include <algorithm>
 #include <functional>
 #include <string>

diff --git a/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/create.cpp b/modules/rmf/dependency/RMF/src/backend/deprecated_hdf5/create.cpp
@@ -29,7 +29,7 @@ namespace RMF {
 namespace hdf5_backend {
 namespace {
 
-typedef backends::BackwardsIO<HDF5SharedData> MIO;
+using MIO = backends::BackwardsIO<HDF5SharedData>;
 
 struct HDF5Factory : public RMF::backends::IOFactory {
   virtual std::string get_file_extension() const override {
@@ -43,7 +43,7 @@ struct HDF5Factory : public RMF::backends::IOFactory {
       const std::string& name) const override {
     return std::make_shared<MIO>(name, true, false);
   }
-  virtual ~HDF5Factory() {}
+  virtual ~HDF5Factory() = default;
 };
 
 }  // namespace

diff --git a/modules/rmf/dependency/RMF/src/exceptions.cpp b/modules/rmf/dependency/RMF/src/exceptions.cpp
@@ -17,7 +17,7 @@
 RMF_ENABLE_WARNINGS
 
 namespace RMF {
-Exception::Exception() {}
+Exception::Exception() = default;
 
 const char* Exception::what() const noexcept {
   try {
@@ -30,7 +30,8 @@ const char* Exception::what() const noexcept {
   return message_.c_str();
 }
 
-Exception::~Exception() noexcept {}
+Exception::~Exception() noexcept = default;
+
 std::string get_message(const Exception& e) {
   using namespace RMF::internal::ErrorInfo;
   try {
@@ -95,16 +96,16 @@ std::string get_message(const Exception& e) {
   }
 }
 UsageException::UsageException() : Exception() {}
-UsageException::~UsageException() noexcept {}
+UsageException::~UsageException() noexcept = default;
 
 IOException::IOException() : Exception() {}
-IOException::~IOException() noexcept {}
+IOException::~IOException() noexcept = default;
 
 IndexException::IndexException() : Exception() {}
-IndexException::~IndexException() noexcept {}
+IndexException::~IndexException() noexcept = default;
 
 InternalException::InternalException() : Exception() {}
-InternalException::~InternalException() noexcept {}
+InternalException::~InternalException() noexcept = default;
 
 } /* namespace RMF */
 

diff --git a/modules/rmf/dependency/RMF/src/hdf5_wrapper.cpp b/modules/rmf/dependency/RMF/src/hdf5_wrapper.cpp
@@ -223,8 +223,8 @@ std::string File::get_name() const {
   return std::string(buf.get());
 }
 
-File::~File() {}
-ConstFile::~ConstFile() {}
+File::~File() = default;
+ConstFile::~ConstFile() = default;
 
 int get_number_of_open_handles(ConstFile f) {
   H5garbage_collect();

diff --git a/modules/rmf/dependency/RMF/test/test_associations.cpp b/modules/rmf/dependency/RMF/test/test_associations.cpp
@@ -5,7 +5,7 @@
  *  Copyright 2007-2022 IMP Inventors. All rights reserved.
  *
  */
-#include <assert.h>
+#include <cassert>
 #include <memory>
 #include <stdio.h>
 #include <exception>

diff --git a/modules/rmf/dependency/RMF/test/test_avro2_low_level.cpp b/modules/rmf/dependency/RMF/test/test_avro2_low_level.cpp
@@ -1,4 +1,4 @@
-#include <assert.h>
+#include <cassert>
 #include <avrocpp/api/Compiler.hh>
 #include <avrocpp/api/DataFile.hh>
 #include <backend/avro/raw_frame.h>

diff --git a/modules/rmf/dependency/RMF/test/test_avro2_validate.cpp b/modules/rmf/dependency/RMF/test/test_avro2_validate.cpp
@@ -107,10 +107,10 @@ void validate() {
   fr.id = FrameID(1);
   validate_one(fr, Frame());
   FileDataChanges changes;
-  changes.categories.push_back(std::make_pair(Category(0), "hi"));
-  changes.node_types.push_back(std::make_pair(ROOT, "root"));
-  changes.frame_types.push_back(std::make_pair(STATIC, "static"));
-  changes.node_sets.push_back(std::make_pair(1, NodeIDs(2, NodeID(10))));
+  changes.categories.emplace_back(Category(0), "hi");
+  changes.node_types.emplace_back(ROOT, "root");
+  changes.frame_types.emplace_back(STATIC, "static");
+  changes.node_sets.emplace_back(1, NodeIDs(2, NodeID(10)));
   FileData data;
   validate_one(changes, data);
   validate_raw(fr);

diff --git a/modules/rmf/dependency/RMF/test/test_buffer.cpp b/modules/rmf/dependency/RMF/test/test_buffer.cpp
@@ -5,7 +5,7 @@
  *  Copyright 2007-2022 IMP Inventors. All rights reserved.
  *
  */
-#include <assert.h>
+#include <cassert>
 
 #include "RMF/BufferHandle.h"
 #include "RMF/FileConstHandle.h"

diff --git a/modules/rmf/dependency/RMF/test/test_fill.cpp b/modules/rmf/dependency/RMF/test/test_fill.cpp
@@ -15,7 +15,7 @@
 #include <H5Spublic.h>
 #include <H5Tpublic.h>
 #include <H5public.h>
-#include <stddef.h>
+#include <cstddef>
 #include <iostream>
 
 #define HDF5_CALL(x)                                             \
@@ -48,12 +48,13 @@ void set_value(hid_t ds, int i, int j, double v) {
   ij[0] = i;
   ij[1] = j;
   hsize_t one = 1;
-  HDF5_HANDLE(ids, H5Screate_simple(1, &one, NULL), &H5Sclose);
+  HDF5_HANDLE(ids, H5Screate_simple(1, &one, nullptr), &H5Sclose);
   hsize_t ones[2];
   ones[0] = 1;
   ones[1] = 1;
   HDF5_HANDLE(space, H5Dget_space(ds), &H5Sclose);
-  HDF5_CALL(H5Sselect_hyperslab(space, H5S_SELECT_SET, ij, ones, ones, NULL));
+  HDF5_CALL(H5Sselect_hyperslab(space, H5S_SELECT_SET, ij, ones, ones,
+                                nullptr));
   HDF5_CALL(H5Dwrite(ds, H5T_NATIVE_DOUBLE, ids, space, H5P_DEFAULT, &v));
 }
 }

diff --git a/modules/rmf/dependency/RMF/test/test_json_encode_decode.cpp b/modules/rmf/dependency/RMF/test/test_json_encode_decode.cpp
@@ -1,4 +1,4 @@
-#include <assert.h>
+#include <cassert>
 #include <avrocpp/api/Compiler.hh>
 #include <avrocpp/api/Decoder.hh>
 #include <avrocpp/api/Encoder.hh>

diff --git a/modules/rmf/dependency/RMF/test/test_ranges.cpp b/modules/rmf/dependency/RMF/test/test_ranges.cpp
@@ -1,4 +1,4 @@
-#include <assert.h>
+#include <cassert>
 #include <boost/iterator/iterator_facade.hpp>
 #include <boost/range/distance.hpp>
 #include <string>