From e5ab828ea99c5ca9d85937ad0ae931a0b1892b99 Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Mon, 19 Apr 2021 12:34:16 -0700
Subject: [PATCH 01/19] Add DOI badge

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 6c73bc5f..d30f81ef 100644
--- a/README.md
+++ b/README.md
@@ -3,6 +3,7 @@
 [![Build Status](https://github.com/salilab/rmf/workflows/build/badge.svg?branch=develop)](https://github.com/salilab/rmf/actions?query=workflow%3Abuild)
 [![codecov](https://codecov.io/gh/salilab/rmf/branch/develop/graph/badge.svg)](https://codecov.io/gh/salilab/rmf)
 [![Code Climate](https://codeclimate.com/github/salilab/rmf/badges/gpa.svg)](https://codeclimate.com/github/salilab/rmf)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4701672.svg)](https://doi.org/10.5281/zenodo.4701672)
 
 The library provides support for the RMF file format for
 storing hierarchical molecular data (such as atomic or coarse grained

From d7da876f8024bda982d8cab6f28c4e8477bf5528 Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Mon, 19 Apr 2021 14:56:05 -0700
Subject: [PATCH 02/19] Test builds on Mac

---
 .github/workflows/build.yml | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 62986bc7..afc9d992 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -33,6 +33,12 @@ jobs:
           flags: '--coverage'
           tests: RMF
           build: Debug
+        - os: macos-latest
+          python-version: 3.9
+          install: ''
+          flags: '--coverage'
+          tests: RMF
+          build: Release
     runs-on: ${{ matrix.os }}
 
     steps:
@@ -41,11 +47,17 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+    - name: Install dependencies (Linux)
+      if: matrix.os == 'ubuntu-latest'
       run: |
         sudo apt-get update -qq
         sudo apt-get install -qq libboost-all-dev swig libc-dbg ${{ matrix.install }}
         pip install coverage
+    - name: Install dependencies (Mac)
+      if: matrix.os == 'macos-latest'
+      run: |
+        brew install swig boost ${{ matrix.install }}
+        pip install coverage
     - name: Build and test
       run: |
         mkdir build

From 934838d3a2a9a97fa0c1228d6b66f7edaa1ef9df Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Mon, 19 Apr 2021 15:07:18 -0700
Subject: [PATCH 03/19] Better document version number in header file

---
 CMakeLists.txt | 3 ++-
 config.h.in    | 7 ++++---
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index a5e811f7..b1d938fb 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -132,8 +132,9 @@ link_directories(${Boost_LIBRARY_DIRS})
 
 set(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR}/lib)
 
+# Version information
 set (RMF_VERSION_MAJOR 1)
-set (RMF_VERSION_MINOR 1)
+set (RMF_VERSION_MINOR 2)
 
 set(RMF_HAS_DEBUG_VECTOR 0 CACHE BOOL "Whether to use a bounds checked vector")
 
diff --git a/config.h.in b/config.h.in
index ff353e8f..8f2f12a7 100644
--- a/config.h.in
+++ b/config.h.in
@@ -1,7 +1,8 @@
 /*
  * \file RMF/RMF_config.h
- * \brief Provide macros to mark functions and classes as exported
- *        from a DLL/.so, and to set up namespaces
+ * \brief Configuration and utility macros
+ *        Provide version information, plus macros to mark functions and
+ *        classes as exported from a DLL/.so and to set up namespaces.
  *
  * Copyright 2007-2021 IMP Inventors. All rights reserved.
  *
@@ -24,7 +25,7 @@
 
 #endif // _MSC_VER
 
-
+// Version number
 #define RMF_VERSION_MAJOR @RMF_VERSION_MAJOR@
 #define RMF_VERSION_MINOR @RMF_VERSION_MINOR@
 

From 2beddad6d35eadf99d545cc48b843e87b7ec5a79 Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Mon, 19 Apr 2021 15:23:20 -0700
Subject: [PATCH 04/19] Drop unused files

---
 test/CppTests.cmake |  6 ------
 test/PyTests.cmake  | 22 ----------------------
 2 files changed, 28 deletions(-)
 delete mode 100644 test/CppTests.cmake
 delete mode 100644 test/PyTests.cmake

diff --git a/test/CppTests.cmake b/test/CppTests.cmake
deleted file mode 100644
index 9e3ff931..00000000
--- a/test/CppTests.cmake
+++ /dev/null
@@ -1,6 +0,0 @@
-set(cpp_tests
-${PROJECT_SOURCE_DIR}/test/test_associations.cpp
-${PROJECT_SOURCE_DIR}/test/test_buffer.cpp
-${PROJECT_SOURCE_DIR}/test/test_fill.cpp
-${PROJECT_SOURCE_DIR}/test/test_json_encode_decode.cpp
-)
diff --git a/test/PyTests.cmake b/test/PyTests.cmake
deleted file mode 100644
index ce451068..00000000
--- a/test/PyTests.cmake
+++ /dev/null
@@ -1,22 +0,0 @@
-set(python_tests 
-${PROJECT_SOURCE_DIR}/test/test_aliases.py
-${PROJECT_SOURCE_DIR}/test/test_associations.py
-${PROJECT_SOURCE_DIR}/test/test_backwards.py
-${PROJECT_SOURCE_DIR}/test/test_bad_geometry.py
-${PROJECT_SOURCE_DIR}/test/test_bulk.py
-${PROJECT_SOURCE_DIR}/test/test_closing.py
-${PROJECT_SOURCE_DIR}/test/test_copy.py
-${PROJECT_SOURCE_DIR}/test/test_data_types.py
-${PROJECT_SOURCE_DIR}/test/test_description.py
-${PROJECT_SOURCE_DIR}/test/test_errors.py
-${PROJECT_SOURCE_DIR}/test/test_external.py
-${PROJECT_SOURCE_DIR}/test/test_features.py
-${PROJECT_SOURCE_DIR}/test/test_file_level.py
-${PROJECT_SOURCE_DIR}/test/test_fill.py
-${PROJECT_SOURCE_DIR}/test/test_frame_comments.py
-${PROJECT_SOURCE_DIR}/test/test_import.py
-${PROJECT_SOURCE_DIR}/test/test_invalid.py
-${PROJECT_SOURCE_DIR}/test/test_low_level.py
-${PROJECT_SOURCE_DIR}/test/test_multikey.py
-${PROJECT_SOURCE_DIR}/test/test_static.py
-)

From dbdda18e8d9de9002e40e7b4eef209005a244338 Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Mon, 19 Apr 2021 15:24:49 -0700
Subject: [PATCH 05/19] Have all binaries report version if requested

---
 ChangeLog.md | 1 +
 bin/common.h | 9 +++++++++
 2 files changed, 10 insertions(+)

diff --git a/ChangeLog.md b/ChangeLog.md
index 80d96014..b7698148 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -1,5 +1,6 @@
 Change Log {#changelog}
 ==========
+- All RMF binaries now support the --version flag.
 
 # 1.2 - 2021-04-19 # {#changelog_1_2}
 - A new category of decorators 'provenance' allows information about how the
diff --git a/bin/common.h b/bin/common.h
index fb371f62..1b90f414 100644
--- a/bin/common.h
+++ b/bin/common.h
@@ -42,10 +42,17 @@ void print_help_and_exit(char* argv[]) {
   exit(1);
 }
 
+void print_version_and_exit() {
+  std::cerr << "RMF version " << RMF_VERSION_MAJOR << "." << RMF_VERSION_MINOR
+            << std::endl;
+  exit(0);
+}
+
 boost::program_options::variables_map process_options(int argc, char* argv[]) {
   boost::program_options::options_description all;
   std::string log_level("Off");
   options.add_options()("help,h", "Show help on command line arguments.");
+  options.add_options()("version", "Show version information.");
 #if RMF_HAS_DEPRECATED_BACKENDS
   options.add_options()("hdf5-errors", "Show hdf5 errors.");
 #endif
@@ -64,6 +71,8 @@ boost::program_options::variables_map process_options(int argc, char* argv[]) {
   boost::program_options::notify(variables_map);
   if (variables_map.count("help")) {
     print_help_and_exit(argv);
+  } else if (variables_map.count("version")) {
+    print_version_and_exit();
   }
 #if RMF_HAS_DEPRECATED_BACKENDS
   if (variables_map.count("hdf5-errors")) {

From 8745aaa16568ff4e0954c7e0351665d5c1eb9e01 Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Mon, 19 Apr 2021 15:32:11 -0700
Subject: [PATCH 06/19] Add a basic test for rmf3_dump

---
 test/test_rmf3_dump.py | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 test/test_rmf3_dump.py

diff --git a/test/test_rmf3_dump.py b/test/test_rmf3_dump.py
new file mode 100644
index 00000000..28ac2d4d
--- /dev/null
+++ b/test/test_rmf3_dump.py
@@ -0,0 +1,32 @@
+import unittest
+import RMF
+import subprocess
+
+
+class Tests(unittest.TestCase):
+
+    def test_help(self):
+        """Test rmf3_dump --help"""
+        p = subprocess.Popen(['rmf3_dump', '--help'], stdin=subprocess.PIPE,
+                             stdout=subprocess.PIPE,
+                             stderr=subprocess.PIPE,
+                             universal_newlines=True)
+        out, err = p.communicate()
+        self.assertEqual(out, "")
+        self.assertIn("Dump frames from an rmf3 file", err)
+        self.assertEqual(p.returncode, 1)
+
+    def test_version(self):
+        """Test rmf3_dump --version"""
+        p = subprocess.Popen(['rmf3_dump', '--version'], stdin=subprocess.PIPE,
+                             stdout=subprocess.PIPE,
+                             stderr=subprocess.PIPE,
+                             universal_newlines=True)
+        out, err = p.communicate()
+        self.assertEqual(out, "")
+        self.assertIn("RMF version", err)
+        self.assertEqual(p.returncode, 0)
+
+
+if __name__ == '__main__':
+    unittest.main()

From 1c7522a98a9904c8ee8177f6f4e3d8e15d7e1d31 Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Mon, 19 Apr 2021 15:34:41 -0700
Subject: [PATCH 07/19] Version information should go to stdout not stderr

---
 bin/common.h           | 2 +-
 test/test_rmf3_dump.py | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/bin/common.h b/bin/common.h
index 1b90f414..9f6ed957 100644
--- a/bin/common.h
+++ b/bin/common.h
@@ -43,7 +43,7 @@ void print_help_and_exit(char* argv[]) {
 }
 
 void print_version_and_exit() {
-  std::cerr << "RMF version " << RMF_VERSION_MAJOR << "." << RMF_VERSION_MINOR
+  std::cout << "RMF version " << RMF_VERSION_MAJOR << "." << RMF_VERSION_MINOR
             << std::endl;
   exit(0);
 }
diff --git a/test/test_rmf3_dump.py b/test/test_rmf3_dump.py
index 28ac2d4d..0621af0f 100644
--- a/test/test_rmf3_dump.py
+++ b/test/test_rmf3_dump.py
@@ -23,8 +23,8 @@ def test_version(self):
                              stderr=subprocess.PIPE,
                              universal_newlines=True)
         out, err = p.communicate()
-        self.assertEqual(out, "")
-        self.assertIn("RMF version", err)
+        self.assertEqual(err, "")
+        self.assertIn("RMF version", out)
         self.assertEqual(p.returncode, 0)
 
 

From d7792f0c9c39c5ca58c6cf07b3bb347f4f2f77f7 Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Mon, 19 Apr 2021 15:40:30 -0700
Subject: [PATCH 08/19] Ensure tests can find RMF binaries

---
 test/CMakeLists.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index 521ddf65..fda1913d 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -9,5 +9,6 @@ if (DEFINED ENV{PYTHONPATH})
 else()
   set(IMP_TESTS_PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_BINARY_DIR}/lib")
 endif()
+set(IMP_TESTS_PROPERTIES ENVIRONMENT "PATH=${CMAKE_BINARY_DIR}/bin:$ENV{PATH}")
 
 imp_add_tests("RMF" ${PROJECT_BINARY_DIR}/test RMF_TESTS test ${pyfiles} ${cppfiles})

From 2944eef914756bd71fcbb425c78a3eee1a2c2d73 Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Mon, 19 Apr 2021 16:35:31 -0700
Subject: [PATCH 09/19] Squashed 'cmake_modules/' changes from
 62a312db..6fb1fe51

6fb1fe51 Allow for multiple environment variables to be set

git-subtree-dir: cmake_modules
git-subtree-split: 6fb1fe511151e03c0ec94c1e932ce91523864669
---
 cmake_modules/IMPAddTests.cmake | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cmake_modules/IMPAddTests.cmake b/cmake_modules/IMPAddTests.cmake
index 75ad8393..97c9b778 100644
--- a/cmake_modules/IMPAddTests.cmake
+++ b/cmake_modules/IMPAddTests.cmake
@@ -30,7 +30,7 @@ function(imp_add_python_tests modulename length type)
       set_tests_properties("${modulename}-${name}" PROPERTIES TIMEOUT ${timeout})
       set_tests_properties("${modulename}-${name}" PROPERTIES COST ${IMP_${length}_COST})
       if(DEFINED IMP_TESTS_PROPERTIES)
-        set_tests_properties("${modulename}-${name}" PROPERTIES ${IMP_TESTS_PROPERTIES})
+        set_property(TEST "${modulename}-${name}" PROPERTY ${IMP_TESTS_PROPERTIES})
       endif()
   endforeach(test)
 endfunction(imp_add_python_tests)
@@ -62,7 +62,7 @@ function(imp_add_cpp_tests modulename length output target_list type)
               ${output}/${name_we}${CMAKE_EXECUTABLE_SUFFIX} ${IMP_TEST_ARGUMENTS})
      set_tests_properties("${modulename}-${name}" PROPERTIES LABELS "${modulename}-${ttype}-cpp-${length}")
      if(DEFINED IMP_TESTS_PROPERTIES)
-        set_tests_properties("${modulename}-${name}" PROPERTIES ${IMP_TESTS_PROPERTIES})
+        set_property(TEST "${modulename}-${name}" PROPERTY ${IMP_TESTS_PROPERTIES})
      endif()
      set_tests_properties("${modulename}-${name}" PROPERTIES TIMEOUT ${timeout})
      set_tests_properties("${modulename}-${name}" PROPERTIES COST ${IMP_${length}_COST})

From c85f96f165f6265c4fada390fe787268e6bfcf37 Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Mon, 19 Apr 2021 16:35:54 -0700
Subject: [PATCH 10/19] Better fix for setting PATH for tests

---
 test/CMakeLists.txt | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index fda1913d..418bdc8f 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -5,10 +5,10 @@ include_directories(BEFORE ${PROJECT_SOURCE_DIR}/src)
 include_directories(BEFORE "${PROJECT_BINARY_DIR}/src")
 set(IMP_LINK_LIBRARIES "RMF-lib" CACHE INTERNAL "")
 if (DEFINED ENV{PYTHONPATH})
-  set(IMP_TESTS_PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_BINARY_DIR}/lib:$ENV{PYTHONPATH}")
+  set(IMP_TESTS_PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_BINARY_DIR}/lib:$ENV{PYTHONPATH}" "PATH=${CMAKE_BINARY_DIR}/bin:$ENV{PATH}")
 else()
-  set(IMP_TESTS_PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_BINARY_DIR}/lib")
+  set(IMP_TESTS_PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_BINARY_DIR}/lib" "PATH=${CMAKE_BINARY_DIR}/bin:$ENV{PATH}")
 endif()
-set(IMP_TESTS_PROPERTIES ENVIRONMENT "PATH=${CMAKE_BINARY_DIR}/bin:$ENV{PATH}")
+message(set test props ${IMP_TESTS_PROPERTIES})
 
 imp_add_tests("RMF" ${PROJECT_BINARY_DIR}/test RMF_TESTS test ${pyfiles} ${cppfiles})

From 7f58f4730f257ae68c95f900cb263ab8e5f08355 Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Mon, 19 Apr 2021 16:39:37 -0700
Subject: [PATCH 11/19] Make version available in Python

---
 swig/RMF.i           | 11 +++++++++++
 test/test_version.py | 13 +++++++++++++
 2 files changed, 24 insertions(+)
 create mode 100644 test/test_version.py

diff --git a/swig/RMF.i b/swig/RMF.i
index 71d76708..dd6566cf 100644
--- a/swig/RMF.i
+++ b/swig/RMF.i
@@ -91,6 +91,17 @@
 
 %include "RMF.nullable.i"
 
+%inline %{
+std::string _get_rmf_version() {
+  std::ostringstream oss;
+  oss << RMF_VERSION_MAJOR << "." << RMF_VERSION_MINOR;
+  return oss.str();
+}
+%}
+
+%pythoncode %{
+   __version__ = _get_rmf_version()
+%}
 
 %include "RMF/Enum.h"
 namespace RMF {
diff --git a/test/test_version.py b/test/test_version.py
new file mode 100644
index 00000000..b0833d95
--- /dev/null
+++ b/test/test_version.py
@@ -0,0 +1,13 @@
+import RMF
+import unittest
+
+
+class Tests(unittest.TestCase):
+
+    def test_version(self):
+        """Test RMF.__version__"""
+        self.assertIn('.', RMF.__version__)
+
+
+if __name__ == '__main__':
+    unittest.main()

From 91f39c5bc7ab60be7f128a0409cfd1cb2218d6b4 Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Mon, 19 Apr 2021 16:52:27 -0700
Subject: [PATCH 12/19] Set version of the RMF dynamic library

---
 CMakeLists.txt     | 1 +
 ChangeLog.md       | 3 ++-
 src/CMakeLists.txt | 2 ++
 3 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index b1d938fb..b0a0d7aa 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -136,6 +136,7 @@ set(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR}/lib)
 set (RMF_VERSION_MAJOR 1)
 set (RMF_VERSION_MINOR 2)
 
+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")
 
 # configure a header file to pass some of the CMake settings
diff --git a/ChangeLog.md b/ChangeLog.md
index b7698148..375bc7ab 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -1,6 +1,7 @@
 Change Log {#changelog}
 ==========
-- All RMF binaries now support the --version flag.
+- All RMF binaries now support the --version flag, and the RMF library itself
+  is versioned.
 
 # 1.2 - 2021-04-19 # {#changelog_1_2}
 - A new category of decorators 'provenance' allows information about how the
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index c129ac40..9a5692c4 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -43,6 +43,8 @@ set_target_properties("RMF-lib" PROPERTIES
                       OUTPUT_NAME "RMF")
 set_property(TARGET "RMF-lib" PROPERTY FOLDER "RMF")
 set_property(TARGET "RMF-lib" PROPERTY COMPILE_DEFINITIONS RMF_EXPORT)
+set_property(TARGET "RMF-lib" PROPERTY VERSION ${RMF_SOVERSION})
+set_property(TARGET "RMF-lib" PROPERTY SOVERSION ${RMF_SOVERSION})
 
 target_link_libraries(RMF-lib
   ${Boost_FILESYSTEM_LIBRARY}

From d129b486e7e9717c444e3ef4d6ff1f4ed660a34b Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Tue, 20 Apr 2021 12:40:59 -0700
Subject: [PATCH 13/19] Remove debug print

---
 test/CMakeLists.txt | 1 -
 1 file changed, 1 deletion(-)

diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index 418bdc8f..fb89abee 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -9,6 +9,5 @@ if (DEFINED ENV{PYTHONPATH})
 else()
   set(IMP_TESTS_PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_BINARY_DIR}/lib" "PATH=${CMAKE_BINARY_DIR}/bin:$ENV{PATH}")
 endif()
-message(set test props ${IMP_TESTS_PROPERTIES})
 
 imp_add_tests("RMF" ${PROJECT_BINARY_DIR}/test RMF_TESTS test ${pyfiles} ${cppfiles})

From 93c97f15fc70a3377c2fcfbd49908ba19e8e14ce Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Tue, 20 Apr 2021 13:19:58 -0700
Subject: [PATCH 14/19] Set sensible default Python install location

---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index b0a0d7aa..fa432a69 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -160,7 +160,7 @@ add_subdirectory(plugins/pymol/)
 if (DEFINED CMAKE_INSTALL_PYTHONDIR)
   #message(STATUS "CMAKE_INSTALL_PYTHONDIR defined as ${CMAKE_INSTALL_PYTHONDIR}")
 else()
-  set(CMAKE_INSTALL_PYTHONDIR "${CMAKE_INSTALL_LIBDIR}/python/site_packages")
+  set(CMAKE_INSTALL_PYTHONDIR "${CMAKE_INSTALL_LIBDIR}/python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}/site-packages")
 endif()
 
 if (DEFINED CMAKE_INSTALL_SWIGDIR)

From 0990bb5f0102c454a40c009c6f9da79110109380 Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Tue, 20 Apr 2021 18:37:03 -0700
Subject: [PATCH 15/19] Don't use deprecated boost bind placeholders

---
 plugins/vmd/init.cpp           | 4 +++-
 src/avrocpp/test/CodecTests.cc | 2 +-
 src/avrocpp/test/buffertest.cc | 2 +-
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/plugins/vmd/init.cpp b/plugins/vmd/init.cpp
index a8bb1145..89a14c97 100644
--- a/plugins/vmd/init.cpp
+++ b/plugins/vmd/init.cpp
@@ -6,9 +6,11 @@
 #include "Data.h"
 #include <RMF/log.h>
 #include <RMF/exceptions.h>
-#include <boost/bind.hpp>
+#include <boost/bind/bind.hpp>
 #include <boost/lambda/construct.hpp>
 
+using namespace boost::placeholders;
+
 namespace {
 molfile_plugin_t plugin;
 molfile_plugin_t plugin3;
diff --git a/src/avrocpp/test/CodecTests.cc b/src/avrocpp/test/CodecTests.cc
index 096dd4d9..1fa9e77d 100644
--- a/src/avrocpp/test/CodecTests.cc
+++ b/src/avrocpp/test/CodecTests.cc
@@ -30,7 +30,7 @@
 #include <stack>
 #include <string>
 #include <functional>
-#include <boost/bind.hpp>
+#include <boost/bind/bind.hpp>
 
 #include <boost/test/included/unit_test_framework.hpp>
 #include <boost/test/unit_test.hpp>
diff --git a/src/avrocpp/test/buffertest.cc b/src/avrocpp/test/buffertest.cc
index 5bb83740..78818a27 100644
--- a/src/avrocpp/test/buffertest.cc
+++ b/src/avrocpp/test/buffertest.cc
@@ -19,7 +19,7 @@
 #include <boost/test/included/unit_test_framework.hpp>
 
 #include <boost/thread.hpp>
-#include <boost/bind.hpp>
+#include <boost/bind/bind.hpp>
 #include <boost/scoped_array.hpp>
 
 #ifdef HAVE_BOOST_ASIO

From 3a59fffe54d611d3d3b4f5d4f0c93671f1f3d39b Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Tue, 20 Apr 2021 18:41:43 -0700
Subject: [PATCH 16/19] Add new release checklist

---
 tools/new-release.txt | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 tools/new-release.txt

diff --git a/tools/new-release.txt b/tools/new-release.txt
new file mode 100644
index 00000000..f5a213ab
--- /dev/null
+++ b/tools/new-release.txt
@@ -0,0 +1,15 @@
+To make a new release:
+
+- Update ChangeLog.md with release date and features.
+- Add version number as RMF_VERSION_MAJOR and RMF_VERSION_MINOR
+  to CMakeLists.txt.
+- git push origin develop
+- Make sure all CI passes
+- Merge into main:
+  - git checkout main
+  - git merge --no-ff -m "Merge for x.y.z release" develop
+  - git diff develop
+  - git push origin main
+- Tag the new release:
+  - git tag -s -u 22A3BF2B x.y.z; git push origin x.y.z
+- Make new release on GitHub

From 1a32aff30bd128f4a0bd71358d6e11b245946a9b Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Wed, 21 Apr 2021 09:06:00 -0700
Subject: [PATCH 17/19] Fix use of boost::placeholders namespace

The boost::placeholders namespace only came into
existence with modern Boost, so protect its use
with a Boost version check.
---
 plugins/vmd/init.cpp | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/plugins/vmd/init.cpp b/plugins/vmd/init.cpp
index 89a14c97..1231037f 100644
--- a/plugins/vmd/init.cpp
+++ b/plugins/vmd/init.cpp
@@ -6,10 +6,13 @@
 #include "Data.h"
 #include <RMF/log.h>
 #include <RMF/exceptions.h>
+#include <boost/version.hpp>
 #include <boost/bind/bind.hpp>
 #include <boost/lambda/construct.hpp>
 
+#if BOOST_VERSION >= 107300
 using namespace boost::placeholders;
+#endif
 
 namespace {
 molfile_plugin_t plugin;

From 7d9e6075cb2539b7f64bb77f1c7faa1ff4f45026 Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Wed, 21 Apr 2021 09:24:51 -0700
Subject: [PATCH 18/19] Make sure boost placeholders are defined

---
 plugins/vmd/init.cpp | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/plugins/vmd/init.cpp b/plugins/vmd/init.cpp
index 1231037f..440eb7ba 100644
--- a/plugins/vmd/init.cpp
+++ b/plugins/vmd/init.cpp
@@ -7,7 +7,12 @@
 #include <RMF/log.h>
 #include <RMF/exceptions.h>
 #include <boost/version.hpp>
+#if BOOST_VERSION >= 107300
 #include <boost/bind/bind.hpp>
+#else
+#include <boost/bind.hpp>
+#endif
+#include <boost/bind/placeholders.hpp>
 #include <boost/lambda/construct.hpp>
 
 #if BOOST_VERSION >= 107300

From 36c8b8611e015bf274fdbbddd4afe64f557d3090 Mon Sep 17 00:00:00 2001
From: Ben Webb <ben@salilab.org>
Date: Wed, 21 Apr 2021 15:47:27 -0700
Subject: [PATCH 19/19] Prepare for 1.3 release

---
 CMakeLists.txt | 2 +-
 ChangeLog.md   | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index fa432a69..a60daaca 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -134,7 +134,7 @@ set(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR}/lib)
 
 # Version information
 set (RMF_VERSION_MAJOR 1)
-set (RMF_VERSION_MINOR 2)
+set (RMF_VERSION_MINOR 3)
 
 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")
diff --git a/ChangeLog.md b/ChangeLog.md
index 375bc7ab..55695fde 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -1,5 +1,7 @@
 Change Log {#changelog}
 ==========
+
+# 1.3 - 2021-04-21 # {#changelog_1_3}
 - All RMF binaries now support the --version flag, and the RMF library itself
   is versioned.