Merge for 1.7.0 release

.github/workflows/build.yml

@@ -63,5 +63,7 @@ jobs:
     - name: Combine coverage
       run: |
         cd build/coverage
-        coverage combine && mv .coverage ../..
-    - uses: codecov/codecov-action@v1
+        coverage combine && coverage xml && mv coverage.xml ../..
+    - uses: codecov/codecov-action@v4
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8.12...3.6.0)
+cmake_minimum_required(VERSION 3.14.0)
 project(RMF)
 
 # needs to be in main CMakeLists.txt
@@ -48,6 +48,12 @@ if(POLICY CMP0086)
   cmake_policy(SET CMP0086 NEW)
 endif(POLICY CMP0086)
 
+# Use FindBoost module rather than BoostConfig.cmake (which requires
+# Boost 1.70 or later)
+if(POLICY CMP0167)
+  cmake_policy(SET CMP0167 OLD)
+endif(POLICY CMP0167)
+
 # C++11 can use the boost version
 set(Boost_NO_BOOST_CMAKE ON)
 find_package(Boost COMPONENTS system filesystem thread program_options iostreams
@@ -139,8 +145,8 @@ set(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR}/lib)
 
 # Version information
 set (RMF_VERSION_MAJOR 1)
-set (RMF_VERSION_MINOR 6)
-set (RMF_VERSION_MICRO 1)
+set (RMF_VERSION_MINOR 7)
+set (RMF_VERSION_MICRO 0)
 math (EXPR RMF_VERSION "${RMF_VERSION_MAJOR} * 100000 + ${RMF_VERSION_MINOR} * 100 + ${RMF_VERSION_MICRO}")
 
 set(RMF_SOVERSION "${RMF_VERSION_MAJOR}.${RMF_VERSION_MINOR}" CACHE INTERNAL "" FORCE)

ChangeLog.md

@@ -1,6 +1,12 @@
 Change Log {#changelog}
 ==========
 
+# 1.7.0 - 2024-12-04 # {#changelog_1_7_0}
+- Python 2 is no longer supported; the minimum supported Python version is 3.6.
+- CMake 2 is no longer supported; the minimum supported CMake version is 3.14.
+- RMF::decorator::Chain can now store the mmCIF asym ID, which need not be
+  the same as the (author-provided) chain ID.
+
 # 1.6.1 - 2024-05-13 # {#changelog_1_6_1}
 - .deb packages for RMF for Ubuntu are now provided via the
   [Ubuntu PPA](https://launchpad.net/~salilab/+archive/ubuntu/ppa) mechanism.

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 2007-2023 IMP Inventors.
+Copyright 2007-2024 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.py

@@ -2,7 +2,6 @@
 # \brief Benchmark operations on the RMF from python to see how much overhead
 #        that adds
 
-from __future__ import print_function
 import RMF
 import datetime
 

bin/rmf3_dump.cpp

@@ -56,8 +56,11 @@ int main(int argc, char** argv) {
         std::cout << std::endl;
       }
     }
-    catch (std::exception e) {
-      std::cerr << "Caught exception " << e.what() << std::endl;
+    catch (const std::exception &e) {
+      // avro uses a plain exception to signal EOF
+      if (std::string(e.what()) != "EOF reached") {
+        std::cerr << "Caught exception " << e.what() << std::endl;
+      }
     }
     return 0;
   }

bin/rmf3_dump.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 
-from __future__ import print_function
 import avro.schema
 from avro.datafile import DataFileReader, DataFileWriter
 from avro.io import DatumReader, DatumWriter

cmake_modules/FindCurrentDoxygen.cmake

@@ -6,18 +6,11 @@ message(STATUS "Python xml.etree not found, docs disabled.")
     set(IMP_DOXYGEN_EXECUTABLE "${DOXYGEN_EXECUTABLE}" CACHE INTERNAL "")
 else()
 find_package(Doxygen QUIET)
-set(needed_doxygen_version "1.8.6")
 if(DOXYGEN_FOUND)
   imp_get_process_output("Doxygen version" doxygen_version ${CMAKE_BINARY_DIR} COMMAND ${DOXYGEN_EXECUTABLE} --version)
-  if("${doxygen_version}" STREQUAL "${needed_doxygen_version}")
-    message(STATUS "Doxygen is ${DOXYGEN_EXECUTABLE}, version ${doxygen_version}")
-    set(IMP_DOXYGEN_FOUND True CACHE INTERNAL "")
-    set(IMP_DOXYGEN_EXECUTABLE ${DOXYGEN_EXECUTABLE} CACHE INTERNAL "")
-  else()
-    message(STATUS "Wrong doxygen version at ${DOXYGEN_EXECUTABLE}. Found ${doxygen_version}, but needed ${needed_doxygen_version}")
-    set(IMP_DOXYGEN_FOUND False CACHE INTERNAL "")
-    set(IMP_DOXYGEN_EXECUTABLE "not-found" CACHE INTERNAL "")
-  endif()
+  message(STATUS "Doxygen is ${DOXYGEN_EXECUTABLE}, version ${doxygen_version}")
+  set(IMP_DOXYGEN_FOUND True CACHE INTERNAL "")
+  set(IMP_DOXYGEN_EXECUTABLE ${DOXYGEN_EXECUTABLE} CACHE INTERNAL "")
 else()
   message(STATUS "Doxygen not found")
 endif(DOXYGEN_FOUND)