Merge for 1.5.0 release

.github/workflows/build.yml

@@ -65,7 +65,6 @@ jobs:
         ../tools/coverage/setup.py
         PYTHONPATH=`pwd`/coverage cmake .. -DCMAKE_BUILD_TYPE="${{ matrix.build }}" -DCMAKE_CXX_FLAGS="${{ matrix.flags }}" -DCMAKE_EXE_LINKER_FLAGS="${{ matrix.flags }}" -DCMAKE_MODULE_LINKER_FLAGS="${{ matrix.flags }}" -DCMAKE_SHARED_LINKER_FLAGS="${{ matrix.flags }}"
         make -j 2
-        export LD_PRELOAD=/lib/x86_64-linux-gnu/libSegFault.so
         ctest -j 2 --output-on-failure -L ${{ matrix.tests }}
     - name: Combine coverage
       run: |

CMakeLists.txt

@@ -119,6 +119,11 @@ else()
   link_directories(${Log4CXX_LIBRARY_DIR})
 endif()
 
+if(${PYTHON_NUMPY_FOUND})
+  set(RMF_HAS_NUMPY "1" CACHE BOOL "Whether to include numpy support" FORCE)
+else()
+  set(RMF_HAS_NUMPY "0" CACHE BOOL "Whether to include numpy support" FORCE)
+endif()
 
 include(GNUInstallDirs)
 
@@ -134,7 +139,8 @@ set(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR}/lib)
 
 # Version information
 set (RMF_VERSION_MAJOR 1)
-set (RMF_VERSION_MINOR 4)
+set (RMF_VERSION_MINOR 5)
+set (RMF_VERSION_MICRO 0)
 
 set(RMF_SOVERSION "${RMF_VERSION_MAJOR}.${RMF_VERSION_MINOR}" CACHE INTERNAL "" FORCE)
 set(RMF_HAS_DEBUG_VECTOR 0 CACHE BOOL "Whether to use a bounds checked vector")

ChangeLog.md

@@ -1,6 +1,18 @@
 Change Log {#changelog}
 ==========
 
+# 1.5.0 - 2023-03-22 # {#changelog_1_5_0}
+- Windows builds now require MS Visual Studio 2015 or later (for full C++11
+  support). The following macros for pre-C++11 environments are no longer
+  needed and are deprecated: `RMF_NOEXCEPT`, `RMF_CANEXCEPT`.
+- All RMF binaries now report the full version (including micro version)
+  when the --version flag is used (e.g. "1.4.1", not "1.4").
+- If built with NumPy, some Python-specific functions are now provided to
+  allow direct access to RMF data via NumPy arrays.
+- File handles can now be explicitly closed (via a `close` method). Most IO
+  operations on a closed handle will now raise an error. In Python file handles
+  now support the context manager protocol so can be used in 'with' blocks.
+
 # 1.4.1 - 2022-11-21 # {#changelog_1_4_1}
 - Build fixes to work with SWIG 4.1.
 - Various internal build scripts now use 'python3' rather than

README.md

@@ -14,7 +14,7 @@ and score data.
 The main documentation is found on the
 [web site](http://integrativemodeling.org/rmf/nightly/doc/).
 
-Copyright 2007-2022 IMP Inventors.
+Copyright 2007-2023 IMP Inventors.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

benchmark/benchmark_rmf.cpp

@@ -7,9 +7,9 @@
 
 #include <boost/iterator/iterator_facade.hpp>
 #include <boost/filesystem/operations.hpp>
-#include <boost/timer.hpp>
 #include <exception>
 #include <iostream>
+#include <chrono>
 #include <string>
 #include <vector>
 
@@ -45,6 +45,21 @@ std::string show_size(unsigned int sz) {
   return oss.str();
 }
 
+class Timer {
+  std::chrono::steady_clock::time_point start_time_;
+public:
+  Timer() {
+    start_time_ = std::chrono::steady_clock::now();
+  }
+
+  double elapsed() const {
+    auto end_time = std::chrono::steady_clock::now();
+    auto time_span = std::chrono::duration_cast<
+                      std::chrono::duration<double> >(end_time - start_time_);
+    return time_span.count();
+  }
+};
+
 void benchmark_size(std::string path, std::string type) {
   unsigned int size = 0;
   if (boost::filesystem::is_directory(path)) {
@@ -181,11 +196,11 @@ double load(RMF::FileConstHandle file, const RMF::NodeIDs& nodes) {
 std::pair<std::size_t, std::size_t> benchmark_create(RMF::FileHandle file,
                                                      std::string type) {
   RMF::NodeIDs atoms;
-  boost::timer timer;
+  Timer timer;
   boost::tuple<std::size_t> cur = create(file, atoms);
   std::cout << type << ", create, " << timer.elapsed() << ", " << cur.get<0>()
             << std::endl;
-  boost::timer frame_timer;
+  Timer frame_timer;
   boost::tuple<double, std::size_t> frames = create_frames(file, atoms);
   std::cout << type << ", create frame, " << frame_timer.elapsed() / 20.0
             << ", " << frames.get<0>() << std::endl;
@@ -194,7 +209,7 @@ std::pair<std::size_t, std::size_t> benchmark_create(RMF::FileHandle file,
 
 void benchmark_traverse(RMF::FileConstHandle file, std::string type) {
   file.set_current_frame(RMF::FrameID(0));
-  boost::timer timer;
+  Timer timer;
   double count = 0;
   double t;
   while (timer.elapsed() < 1) {
@@ -211,17 +226,18 @@ void benchmark_load(RMF::FileConstHandle file, std::string type) {
   for(RMF::NodeID n : file.get_node_ids()) {
     if (ipcf.get_is(file.get_node(n))) nodes.push_back(n);
   }
-  boost::timer timer;
+  Timer timer;
   double dist = load(file, nodes);
   std::cout << type << ", load, " << timer.elapsed() / 20.0 << ", " << dist
             << std::endl;
 }
 
 RMF::FileConstHandle benchmark_open(std::string path, std::string type) {
-  boost::timer timer;
+  Timer timer;
   RMF::FileConstHandle ret;
   double count = 0;
   while (timer.elapsed() < 1) {
+    ret.close();
     ret = RMF::open_rmf_file_read_only(path);
     ++count;
   }
@@ -268,14 +284,29 @@ int main(int, char**) {
       }
       benchmark_size(name, "rmfz");
     }
+#if RMF_HAS_DEPRECATED_BACKENDS
+    {
+      const std::string name = name_base + ".rmf-hdf5";
+      {
+        RMF::FileHandle fh = RMF::create_rmf_file(name);
+        benchmark_create(fh, "hdf5");
+      }
+      {
+        RMF::FileConstHandle fh = benchmark_open(name, "hdf5");
+        benchmark_traverse(fh, "hdf5");
+        benchmark_load(fh, "hdf5");
+      }
+      benchmark_size(name, "hdf5");
+    }
+#endif
     {
       RMF::BufferHandle buffer;
       {
         RMF::FileHandle fh = RMF::create_rmf_buffer(buffer);
         benchmark_create(fh, "buffer");
       }
       {
-        boost::timer timer;
+        Timer timer;
         RMF::FileConstHandle fh = RMF::open_rmf_buffer_read_only(buffer);
         std::cout << "buffer"
                   << ", open, " << timer.elapsed() << ", 0" << std::endl;

bin/common.h

@@ -44,7 +44,7 @@ void print_help_and_exit(char* argv[]) {
 
 void print_version_and_exit() {
   std::cout << "RMF version " << RMF_VERSION_MAJOR << "." << RMF_VERSION_MINOR
-            << std::endl;
+            << "." << RMF_VERSION_MICRO << std::endl;
   exit(0);
 }
 

bin/rmf3_dump.cpp

@@ -2,7 +2,7 @@
  * Copyright 2007-2022 IMP Inventors. All rights reserved.
  */
 
-#include <boost/shared_ptr.hpp>
+#include <memory>
 #include <stddef.h>
 #include <exception>
 #include <iostream>
@@ -38,7 +38,7 @@ int main(int argc, char** argv) {
         if (variables_map.count("verbose")) {
           internal_avro::EncoderPtr encoder =
               internal_avro::jsonEncoder(schema);
-          boost::shared_ptr<internal_avro::OutputStream> os =
+          std::shared_ptr<internal_avro::OutputStream> os =
               internal_avro::ostreamOutputStream(std::cout);
           encoder->init(*os);
           internal_avro::encode(*encoder, frame);

config.h.in

@@ -33,8 +33,10 @@
 // Version number
 #define RMF_VERSION_MAJOR @RMF_VERSION_MAJOR@
 #define RMF_VERSION_MINOR @RMF_VERSION_MINOR@
+#define RMF_VERSION_MICRO @RMF_VERSION_MICRO@
 
 #define RMF_HAS_LOG4CXX @RMF_HAS_LOG4CXX@
+#define RMF_HAS_NUMPY @RMF_HAS_NUMPY@
 
 #define RMF_HAS_DEPRECATED_BACKENDS @RMF_DEPRECATED_BACKENDS@
 

doc/Installation.md

@@ -10,6 +10,10 @@ Standalone: if you are using [Anaconda Python](https://www.anaconda.com/), insta
 
     conda install -c conda-forge rmf
 
+or on a Mac with [Homebrew](https://brew.sh/), install with
+
+    brew tap salilab/salilab; brew install rmf
+
 IMP: Download an IMP binary (which includes RMF) from the
 [IMP download page](https://integrativemodeling.org/download.html).
 

doc/Main.md

@@ -19,7 +19,7 @@ See
 Also see the [rmf examples](https://github.com/salilab/rmf_examples) repository
 for examples of interesting or problematic RMF files.
 
-Copyright 2007-2022 IMP Inventors.
+Copyright 2007-2023 IMP Inventors.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

include/RMF/BufferConstHandle.h

@@ -12,8 +12,7 @@
 #include "RMF/config.h"
 #include "infrastructure_macros.h"
 #include "exceptions.h"
-#include <boost/shared_ptr.hpp>
-#include <boost/make_shared.hpp>
+#include <memory>
 #include <limits>
 #include <stdint.h>
 
@@ -29,7 +28,7 @@ namespace RMF {
     */
 class BufferConstHandle {
  protected:
-  boost::shared_ptr<std::vector<char> > data_;
+  std::shared_ptr<std::vector<char> > data_;
   int compare(BufferConstHandle o) const {
     if (&*data_ < &*o.data_)
       return -1;
@@ -42,13 +41,13 @@ class BufferConstHandle {
  public:
 #ifndef SWIG
   explicit BufferConstHandle(std::string r)
-      : data_(boost::make_shared<std::vector<char> >(r.begin(), r.end())) {}
+      : data_(std::make_shared<std::vector<char> >(r.begin(), r.end())) {}
 #endif
   explicit BufferConstHandle(const std::vector<char> &r)
-      : data_(boost::make_shared<std::vector<char> >(r.begin(), r.end())) {}
+      : data_(std::make_shared<std::vector<char> >(r.begin(), r.end())) {}
   explicit BufferConstHandle(const std::vector<uint8_t> &r)
-      : data_(boost::make_shared<std::vector<char> >(r.begin(), r.end())) {}
-  explicit BufferConstHandle(boost::shared_ptr<std::vector<char> > r)
+      : data_(std::make_shared<std::vector<char> >(r.begin(), r.end())) {}
+  explicit BufferConstHandle(std::shared_ptr<std::vector<char> > r)
       : data_(r) {}
   const std::vector<char> &get_buffer() const { return *data_; }
 #ifndef SWIG
@@ -65,7 +64,7 @@ class BufferConstHandle {
     return std::make_pair(reinterpret_cast<const uint8_t *>(&(*data_)[0]),
                           data_->size());
   }
-  boost::shared_ptr<std::vector<char> > get() const { return data_; }
+  std::shared_ptr<std::vector<char> > get() const { return data_; }
 #endif
 };
 

include/RMF/Decorator.h

@@ -15,7 +15,7 @@
 #include "internal/SharedData.h"
 #include "NodeConstHandle.h"
 #include "NodeHandle.h"
-#include <boost/shared_ptr.hpp>
+#include <memory>
 
 RMF_ENABLE_WARNINGS
 namespace RMF {
@@ -29,7 +29,7 @@ namespace RMF {
 class Decorator {
  private:
   NodeID id_;
-  boost::shared_ptr<internal::SharedData> data_;
+  std::shared_ptr<internal::SharedData> data_;
 
  protected:
   Decorator(NodeConstHandle handle)