Merge for 1.2 release

.codeclimate.yml

@@ -0,0 +1,33 @@
+---
+engines:
+  duplication:
+    enabled: true
+    config:
+      languages:
+      - ruby
+      - javascript
+      - python
+      - php
+  fixme:
+    enabled: true
+  radon:
+    enabled: true
+  shellcheck:
+    enabled: true
+  markdownlint:
+    enabled: true
+ratings:
+  paths:
+  - "**.inc"
+  - "**.js"
+  - "**.jsx"
+  - "**.module"
+  - "**.php"
+  - "**.py"
+  - "**.rb"
+  - "**.sh"
+  - "**.md"
+exclude_paths:
+- test/
+- tools/dev_tools/**/*
+- src/avrocpp/**/*

.codecov.yml

@@ -0,0 +1,5 @@
+ignore:
+  - test
+  - tools/dev_tools
+  - src/avrocpp
+  - benchmark

.github/workflows/build.yml

@@ -0,0 +1,62 @@
+name: build
+
+on: [push, pull_request]
+
+jobs:
+  build:
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - os: ubuntu-latest
+          python-version: 2.7
+          install: ''
+          flags: '--coverage'
+          tests: RMF
+          build: Debug
+        - os: ubuntu-latest
+          python-version: 3.9
+          install: ''
+          flags: '--coverage'
+          tests: RMF
+          build: Debug
+        - os: ubuntu-latest
+          python-version: 3.9
+          install: ''
+          flags: '--coverage'
+          tests: RMF
+          build: Release
+        - os: ubuntu-latest
+          python-version: 3.9
+          install: 'libhdf5-dev liblog4cxx-dev'
+          flags: '--coverage'
+          tests: RMF
+          build: Debug
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        sudo apt-get update -qq
+        sudo apt-get install -qq libboost-all-dev swig libc-dbg ${{ matrix.install }}
+        pip install coverage
+    - name: Build and test
+      run: |
+        mkdir build
+        cd build
+        ../tools/coverage/setup.py
+        PYTHONPATH=`pwd`/coverage cmake .. -DCMAKE_BUILD_TYPE="${{ 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: Upload coverage to codecov
+      run: |
+        cd build
+        (cd coverage && coverage combine && mv .coverage ..)
+        bash <(curl -s https://codecov.io/bash)

CMakeLists.txt

@@ -1,10 +1,24 @@
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 2.8.12)
 project(RMF)
 
 # needs to be in main CMakeLists.txt
 enable_testing()
 
-execute_process(COMMAND python setup_git.py
+# Default Python3_FIND_STRATEGY to LOCATION
+if(POLICY CMP0094)
+cmake_policy(SET CMP0094 NEW)
+endif(POLICY CMP0094)
+
+# Use new-style variables/escapes
+if(POLICY CMP0053)
+cmake_policy(SET CMP0053 NEW)
+endif(POLICY CMP0053)
+
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake_modules)
+include(cmake_modules/IMPFindPython.cmake)
+imp_find_python()
+
+execute_process(COMMAND ${PYTHON_EXECUTABLE} setup_git.py
                   RESULT_VARIABLE setup
                   OUTPUT_VARIABLE toutput
                   ERROR_VARIABLE error
@@ -14,15 +28,33 @@ if(NOT ${setup} EQUAL 0)
    message(FATAL_ERROR " Failed to run setup_git.py: ${setup}; ${error}")
 endif()
 
-set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake_modules)
+# Don't deref quoted variables in if()
+if(POLICY CMP0054)
+cmake_policy(SET CMP0054 NEW)
+endif(POLICY CMP0054)
+
+# Use new method of handling Ninja custom command byproducts
+if(POLICY CMP0058)
+  cmake_policy(SET CMP0058 NEW)
+endif(POLICY CMP0058)
+
+# Use consistent SWIG target names across all supported cmake versions
+if(POLICY CMP0078)
+  cmake_policy(SET CMP0078 OLD)
+endif(POLICY CMP0078)
+
+# Quiet warning about UseSWIG honoring SWIG_MODULE_NAME (which we don't use)
+if(POLICY CMP0086)
+  cmake_policy(SET CMP0086 NEW)
+endif(POLICY CMP0086)
 
 # C++11 can use the boost version
 set(Boost_NO_BOOST_CMAKE ON)
 find_package(Boost COMPONENTS system filesystem thread program_options iostreams
   REQUIRED)
 
 include(FindHDF5)
-find_package(HDF5)
+find_package(HDF5 1.8)
 
 if("${HDF5_INCLUDE_DIRS}" MATCHES .*NOTFOUND)
 set(RMF_DEPRECATED_BACKENDS 0 CACHE BOOL "Whether to build deprecated backends.")
@@ -45,19 +77,24 @@ include(cmake_modules/IMPFindCompilerFlags.cmake)
 
 if(RMF_DEPRECATED_BACKENDS)
 imp_execute_process("Making RMF/HDF5.h" ${PROJECT_SOURCE_DIR}
-  COMMAND "python" "${PROJECT_SOURCE_DIR}/tools/dev_tools/make_all_header.py" ${PROJECT_BINARY_DIR}/include/RMF/HDF5.h RMF/HDF5 ${PROJECT_SOURCE_DIR}/include/RMF/HDF5)
+  COMMAND ${PYTHON_EXECUTABLE}
+  "${PROJECT_SOURCE_DIR}/tools/dev_tools/make_all_header.py"
+  ${PROJECT_BINARY_DIR}/include/RMF/HDF5.h RMF/HDF5
+  ${PROJECT_SOURCE_DIR}/include/RMF/HDF5)
 endif()
 
 imp_execute_process("Making RMF.h" ${PROJECT_SOURCE_DIR}
-  COMMAND "python" "${PROJECT_SOURCE_DIR}/tools/dev_tools/make_all_header.py" ${PROJECT_BINARY_DIR}/include/RMF.h RMF ${PROJECT_SOURCE_DIR}/include/RMF)
-
+  COMMAND ${PYTHON_EXECUTABLE}
+  "${PROJECT_SOURCE_DIR}/tools/dev_tools/make_all_header.py"
+  ${PROJECT_BINARY_DIR}/include/RMF.h RMF ${PROJECT_SOURCE_DIR}/include/RMF)
 
 message(STATUS "Running setup_cmake.py")
-imp_execute_process("Running setup_cmake.py"  ${PROJECT_SOURCE_DIR} COMMAND python ${PROJECT_SOURCE_DIR}/tools/dev_tools/setup_cmake.py)
-
-include_directories("${PROJECT_BINARY_DIR}/src"
-  "${PROJECT_SOURCE_DIR}/src")
+imp_execute_process("Running setup_cmake.py" ${PROJECT_SOURCE_DIR}
+  COMMAND ${PYTHON_EXECUTABLE}
+  ${PROJECT_SOURCE_DIR}/tools/dev_tools/setup_cmake.py)
 
+include_directories(BEFORE "${PROJECT_BINARY_DIR}/include"
+  "${PROJECT_SOURCE_DIR}/include")
 
 set(RMF_INCLUDE_PATH "" CACHE INTERNAL "" FORCE)
 
@@ -68,6 +105,8 @@ if(POLICY CMP0017)
 cmake_policy(SET CMP0017 NEW)
 endif(POLICY CMP0017)
 
+# Don't set MACOSX_RPATH by default
+set(CMAKE_MACOSX_RPATH 0)
 
 if (${Log4CXX_LIBRARY} MATCHES "Log4CXX_LIBRARY-NOTFOUND")
   set(RMF_HAS_LOG4CXX "0" CACHE BOOL "Whether to use Log4CXX" FORCE)
@@ -105,9 +144,6 @@ configure_file (
   "${PROJECT_BINARY_DIR}/include/RMF/config.h"
   )
 
-include_directories("${PROJECT_BINARY_DIR}/include"
-  "${PROJECT_SOURCE_DIR}/include")
-
 add_subdirectory(data)
 add_subdirectory(include)
 

ChangeLog.md

@@ -1,4 +1,16 @@
-# Change Log #
+Change Log {#changelog}
+==========
+
+# 1.2 - 2021-04-19 # {#changelog_1_2}
+- A new category of decorators 'provenance' allows information about how the
+  structure was generated to be added to the file.
+- The new RMF::decorator::Reference decorator allows for a node to mark
+  another node as its reference.
+- The new RMF::decorator::ExplicitResolution decorator allows attaching an
+  explicitly-set resolution to a node. (This allows such values from IMP to
+  be accurately stored in the file.)
+
+# 1.1 - 2014-03-07 # {#changelog_1_1}
 - To be more consisent, RMF::decorator::Domain and
 	RMF::decorator::Fragment had their access methods modified to
 	include `residue` in the name.

README.md

@@ -1,15 +1,18 @@
 # RMF #
 
-[![Build Status](https://travis-ci.org/salilab/rmf.png?branch=develop)](https://travis-ci.org/salilab/rmf)
+[![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)
 
 The library provides support for the RMF file format for
 storing hierarchical molecular data (such as atomic or coarse grained
 representations of proteins), along with markup, including geometry
 and score data.
 
-The main documentation is found on the [web site](http://salilab.github.io/rmf).
+The main documentation is found on the
+[web site](http://integrativemodeling.org/rmf/nightly/doc/).
 
-Copyright 2013 University of California, San Francisco.
+Copyright 2007-2021 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

@@ -2,7 +2,7 @@
  * \brief Benchmark typical creation, traversal and loading with different RMF
  *        backends.
  *
- * Copyright 2007-2013 IMP Inventors. All rights reserved.
+ * Copyright 2007-2021 IMP Inventors. All rights reserved.
  */
 
 #include <boost/iterator/iterator_facade.hpp>

benchmark/benchmark_rmf.py

@@ -2,6 +2,7 @@
 # \brief Benchmark operations on the RMF from python to see how much overhead
 #        that adds
 
+from __future__ import print_function
 import RMF
 import datetime
 
@@ -94,14 +95,14 @@ def load(file, nodes):
 def benchmark_create(file, type):
     start = datetime.datetime.now()
     dist = create(file)
-    print type, "create,", datetime.datetime.now() - start, ",", dist
+    print(type, "create,", datetime.datetime.now() - start, ",", dist)
 
 
 def benchmark_traverse(file, type):
     start = datetime.datetime.now()
     file.set_current_frame(RMF.FrameID(0))
     t = traverse(file)
-    print type, "traverse,", datetime.datetime.now() - start, ",", t
+    print(type, "traverse,", datetime.datetime.now() - start, ",", t)
 
 
 def benchmark_load(file, type):
@@ -112,7 +113,7 @@ def benchmark_load(file, type):
             nodes.append(n)
     start = datetime.datetime.now()
     dist = load(file, nodes)
-    print type, "load,", datetime.datetime.now() - start, ",", dist
+    print(type, "load,", datetime.datetime.now() - start, ",", dist)
 
 name = "benchmark_python.rmf"
 fh = RMF.create_rmf_file(name)

bin/common.h

@@ -1,6 +1,6 @@
 /**
  * \file common.h
- * Copyright 2007-2013 IMP Inventors. All rights reserved.
+ * Copyright 2007-2021 IMP Inventors. All rights reserved.
  */
 
 #ifndef RMF_COMMON_H

bin/rmf3_dump.cpp

@@ -1,5 +1,5 @@
 /**
- * Copyright 2007-2013 IMP Inventors. All rights reserved.
+ * Copyright 2007-2021 IMP Inventors. All rights reserved.
  */
 
 #include <boost/shared_ptr.hpp>

bin/rmf3_dump.py

@@ -1,11 +1,12 @@
 #!/usr/bin/env python
 
+from __future__ import print_function
 import avro.schema
 from avro.datafile import DataFileReader, DataFileWriter
 from avro.io import DatumReader, DatumWriter
 import sys
 
 reader = DataFileReader(open(sys.argv[1], "r"), DatumReader())
 for user in reader:
-    print user
+    print(user)
 reader.close()

bin/rmf_cat.cpp

@@ -1,5 +1,5 @@
 /**
- * Copyright 2007-2013 IMP Inventors. All rights reserved.
+ * Copyright 2007-2021 IMP Inventors. All rights reserved.
  */
 
 #include <exception>
@@ -39,7 +39,9 @@ int main(int argc, char** argv) {
     for (unsigned int i = 0; i < inputs.size(); ++i) {
       RMF::FileConstHandle rh = RMF::open_rmf_file_read_only(inputs[i]);
       if (i == 0) {
+        RMF::clone_file_info(rh, orh); // creator etc. (not essential)
         RMF::clone_hierarchy(rh, orh);
+        RMF::clone_static_frame(rh, orh);
       }
       orh.set_description(orh.get_description() + "\n" + rh.get_description());
       RMF_FOREACH(RMF::FrameID ni, rh.get_frames()) {