Merge for 2.15.0 release

.github/workflows/ci.yml

@@ -0,0 +1,47 @@
+name: CI
+on: [push, pull_request]
+
+env:
+  CXXFLAGS: "-fprofile-arcs -ftest-coverage"
+
+jobs:
+  test:
+    name: "Python ${{ matrix.python-version }} / ${{ matrix.os }}"
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["2.7", "3.6"]
+        os: [ubuntu-18.04]
+        compiler: [gcc]
+    env:
+      CC: ${{ matrix.compiler }}
+      PY2: ${{ startsWith(matrix.python-version, 2) && 'on' || 'off' }}
+    steps:
+      - uses: actions/checkout@v2
+      - name: Install dependencies
+        run: |
+          sudo apt-get update -qq
+          sudo apt-get install -qq libboost-all-dev swig libhdf5-serial-dev libeigen3-dev \
+            cmake libcgal-dev libcgal-qt5-dev \
+            libfftw3-dev libopencv-dev libgsl0-dev libann-dev \
+            libprotobuf-dev protobuf-compiler \
+            libopenmpi-dev
+          if [ "${{ env.PY2 }}" == "on" ]
+          then
+            sudo apt-get install -qq python-dev python-numpy python-protobuf \
+                                     python-nose python-pip python-biopython
+            export PIP=pip2
+          else
+            sudo apt-get install -qq python3-dev python3-numpy python3-protobuf \
+                                     python3-nose python3-pip python3-biopython
+            export PIP=pip3
+          fi
+          $PIP install codecov
+      - name: Set up git
+        run: ./setup_git.py
+      - name: Build IMP
+        run: |
+          mkdir build
+          cd build
+          cmake .. -DUSE_PYTHON2=${{ env.PY2 }} -DCMAKE_CXX_FLAGS="${{ env.CXXFLAGS }}" -DCGAL_DIR=/usr/lib/x86_64-linux-gnu/cmake/CGAL/
+          make -k -j 2

.github/workflows/flake.yml

@@ -0,0 +1,24 @@
+name: flake
+
+on: [push, pull_request]
+
+jobs:
+  flake:
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.8]
+    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: Test
+      run: |
+        pip install flake8
+        flake8 tools modules/parallel/pyext modules/test/pyext modules/mmcif/pyext

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8.3)
+cmake_minimum_required(VERSION 2.8.12)
 
 project(IMP)
 
@@ -18,10 +18,10 @@ if(POLICY CMP0053)
 cmake_policy(SET CMP0053 NEW)
 endif(POLICY CMP0053)
 
-include(${CMAKE_SOURCE_DIR}/modules/rmf/dependency/RMF/cmake_modules/IMPFindPython.cmake)
+include(${CMAKE_SOURCE_DIR}/cmake_modules/IMPFindPython.cmake)
 imp_find_python()
 
-# Check Python version early so we can use Python >= 2.6 features in other
+# Check Python version early so we can use Python >= 2.7 features in other
 # build scripts
 execute_process(COMMAND ${PYTHON_EXECUTABLE}
                         "tools/build/check_python_version.py"
@@ -57,9 +57,9 @@ if(POLICY CMP0056)
 cmake_policy(SET CMP0056 NEW)
 endif(POLICY CMP0056)
 
-include(${CMAKE_SOURCE_DIR}/modules/rmf/dependency/RMF/cmake_modules/IMPExecuteProcess.cmake)
-include(${CMAKE_SOURCE_DIR}/modules/rmf/dependency/RMF/cmake_modules/IMPAddTests.cmake)
-include(${CMAKE_SOURCE_DIR}/modules/rmf/dependency/RMF/cmake_modules/CheckCompiles.cmake)
+include(${CMAKE_SOURCE_DIR}/cmake_modules/IMPExecuteProcess.cmake)
+include(${CMAKE_SOURCE_DIR}/cmake_modules/IMPAddTests.cmake)
+include(${CMAKE_SOURCE_DIR}/cmake_modules/CheckCompiles.cmake)
 
 imp_execute_process("check_common_problems" ${CMAKE_SOURCE_DIR}
                     COMMAND ${PYTHON_EXECUTABLE}
@@ -73,12 +73,12 @@ imp_execute_process("setup_cmake" ${CMAKE_SOURCE_DIR}
                     COMMAND ${PYTHON_EXECUTABLE}
                     ${CMAKE_SOURCE_DIR}/tools/build/setup_cmake.py)
 
-set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_SOURCE_DIR}/modules/rmf/dependency/RMF/cmake_modules)
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_SOURCE_DIR}/cmake_modules)
 
 enable_testing()
 
-include(${CMAKE_SOURCE_DIR}/modules/rmf/dependency/RMF/cmake_modules/IMPFindC++11.cmake)
-include(${CMAKE_SOURCE_DIR}/modules/rmf/dependency/RMF/cmake_modules/IMPFindCompilerFlags.cmake)
+include(${CMAKE_SOURCE_DIR}/cmake_modules/IMPFindC++11.cmake)
+include(${CMAKE_SOURCE_DIR}/cmake_modules/IMPFindCompilerFlags.cmake)
 
 if(POLICY CMP0017)
 cmake_policy(SET CMP0017 NEW)
@@ -268,11 +268,11 @@ else()
 endif()
 
 set(Boost_NO_BOOST_CMAKE ON)
-find_package(Boost 1.41.0 COMPONENTS system filesystem thread program_options REQUIRED)
+find_package(Boost 1.53.0 COMPONENTS system filesystem thread program_options REQUIRED)
 if("${Boost_SYSTEM_LIBRARY_RELEASE}" MATCHES ".*NOTFOUND.*")
   message(FATAL_ERROR "Boost is required to build IMP.")
 endif()
-find_package(Boost 1.41.0 QUIET COMPONENTS random regex graph)
+find_package(Boost 1.53.0 QUIET COMPONENTS random regex graph)
 
 if("${Boost_RANDOM_LIBRARY_RELEASE}" MATCHES ".*NOTFOUND.*")
 set(Boost_RANDOM_LIBRARY_RELEASE "" CACHE INTERNAL "" FORCE)
@@ -451,7 +451,7 @@ file(WRITE ${CMAKE_BINARY_DIR}/IMPConfig.cmake
      "set(IMP_DATA_DIR \"${CMAKE_BINARY_DIR}/data\" )\n"
      "set(IMP_SWIG_DIR \"${CMAKE_BINARY_DIR}/swig\" )\n"
      "set(RMF_SWIG_DIR \"${CMAKE_SOURCE_DIR}/modules/rmf/dependency/RMF/swig\" )\n"
-     "set(RMF_MODULES_DIR \"${CMAKE_SOURCE_DIR}/modules/rmf/dependency/RMF/cmake_modules\" )\n"
+     "set(RMF_MODULES_DIR \"${CMAKE_SOURCE_DIR}/cmake_modules\" )\n"
      "set(RMF_INCLUDE_PATH \"${RMF_INCLUDE_PATH}\" )\n"
      "set(IMP_USE_FILE \"\${IMP_MODULES_DIR}/UseIMP.cmake\" )\n")
 # Installed locations
@@ -538,7 +538,7 @@ install(DIRECTORY ${dev_tools_dir}
                                    OWNER_WRITE)
 
 # Install cmake scripts and configuration
-install(DIRECTORY ${CMAKE_SOURCE_DIR}/modules/rmf/dependency/RMF/cmake_modules/
+install(DIRECTORY ${CMAKE_SOURCE_DIR}/cmake_modules/
                   ${CMAKE_SOURCE_DIR}/tools/cmake/
                   ${CMAKE_BINARY_DIR}/cmake/
         DESTINATION ${CMAKE_INSTALL_CMAKEDIR})

CONTRIBUTING.md

@@ -23,5 +23,12 @@ and
 See the [IMP manual](https://integrativemodeling.org/nightly/doc/manual/developing.html)
 for more detail.
 
+Note that some parts of the code are actually maintained outside of the IMP
+repository, notably [PMI](https://github.com/salilab/pmi),
+[RMF](https://github.com/salilab/rmf) and
+[python-ihm](https://github.com/ihmwg/python-ihm). Issues or pull requests for
+these parts of the code should be opened in those repositories. (Changes to
+those repositories are periodically pulled in to IMP by the IMP maintainers.)
+
 To publish your protocol for applying IMP to a biological system, please
 see the [IMP manual](https://integrativemodeling.org/nightly/doc/manual/biosystem.html).

ChangeLog.md

@@ -1,6 +1,41 @@
 ChangeLog {#changelog}
 =========
 
+# 2.15.0 - 2021-06-02 # {#changelog_2_15_0}
+- The [Homebrew](https://brew.sh/) Mac packages now support Apple Silicon.
+- We no longer provide RPMs for CentOS 6, since it has reached end of life.
+- Python 2.6 is no longer supported; Python 2.7 is the oldest version of
+  Python that works with IMP (although Python 3 is recommended).
+- IMP now requires Boost 1.53 or later; support for Boost 1.41 has been dropped.
+- IMP::em::FitRestraint::cast() has been removed. Use `get_from()` instead.
+- The deprecated methods IMP::SingletonContainer::get_particle(),
+  IMP::PairContainer::get_particle_pair(),
+  IMP::TripletContainer::get_particle_triplet(), and
+  IMP::QuadContainer::get_particle_quad() have been removed. Use the
+  get_contents() method instead.
+- The IMP::em::CoarseCC class is deprecated. Use similarly-named free
+  functions instead to calculate coarse cross correlation.
+- A new numerically stable grid-based Bayesian scoring function,
+  IMP::em::FitRestraintBayesEM3D, has been added for cryo-EM data. Note that
+  this is still in development.
+- The IMP::pmi::mmcif::ProtocolOutput constructor no longer takes a file
+  handle argument, and the IMP::pmi::mmcif::ProtocolOutput::flush() method
+  has been removed. Instead, use the python-ihm library to output mmCIF
+  (or BinaryCIF).
+- IMP can now be built using external (system) copies of the RMF and/or
+  python-ihm libraries, instead of those bundled with IMP itself; use the
+  `IMP_USE_SYSTEM_RMF` or `IMP_USE_SYSTEM_IHM` CMake variables.
+- MRC file handling has been extended; MRC files not aligned with the xyz
+  axes (mapc/mapr/maps not 1,2,3) are now automatically transposed rather than
+  raising an exception, and the origin is now set from the
+  nxstart/nystart/nzstart fields if present and the file origin is zero.
+- New applications of IMP are now available:
+  - [Integrative model of the γTuSC-Spc110 complex](https://salilab.org/gtuscSpc110)
+  - [Integrative structure of the Smc5/6-Nse2/5/6 complex](https://integrativemodeling.org/systems/smc56_nse256)
+- IMP's copies of the old Template Numerical Toolkit (TNT) and
+  JAMA/C++ library have been removed from IMP::algebra::internal.
+  Use equivalent functionality in the Eigen library instead.
+
 # 2.14.0 - 2020-12-02 # {#changelog_2_14_0}
 - All IMP.parallel worker classes are now subclasses of IMP.parallel.Worker;
   the old class names still exist as aliases, but are deprecated.
@@ -462,7 +497,7 @@ ChangeLog {#changelog}
 - Generation of documentation using `doxygen` has been refactored. It is now done on a per-module basis, via targets like `IMP.core-doc`. The main advantage is that changes to the doc for a module can be tested comparatively quickly, just by building that module's docs. On the down side, docs are no longer quite so heavily interconnected, so dependencies only work to things that the module actually depends on.
 - The restraint and score state statistics functions were removed from IMP::Model. They had been broken for quite a while, with no one complaining. Statistics can be added back easily if requested.
 - Added an IMP-specific fork of `git-flow`. It handles things like `README.md` files when you start and finish feature branches and provides a tool to nicely update IMP and display the change log. The main commands of use are `git imp feature start <feature_name>`, `git imp feature finish <feature_name>`, and `git imp update`. You may want to remove the `git-flow` lines from your `.git/config` file as you may accidentally type `git flow` instead of `git imp`. You need to run `setup_git.py` to set things up.
-- [RMF](http://salilab.github.com/rmf) is now included as a git submodule rather than copied into the IMP repository. You should rerun `setup_git.py` to make sure submodule stuff is initialized.
+- [RMF](https://github.com/salilab/rmf) is now included as a git submodule rather than copied into the IMP repository. You should rerun `setup_git.py` to make sure submodule stuff is initialized.
 
 
 # For IMP 2.0 and earlier # {#changelog_2_0}

README.md

@@ -33,7 +33,7 @@ new shell.
 Copyright and License information
 =================================
 
-IMP is Copyright 2007-2020 IMP Inventors. The IMP Inventors are
+IMP is Copyright 2007-2021 IMP Inventors. The IMP Inventors are
 Andrej Sali, Ben Webb, Daniel Russel, Keren Lasker, Dina Schneidman,
 Javier Velázquez-Muriel, Friedrich Förster, Elina Tjioe, Hao Fan,
 Seung Joong Kim, Yannick Spill, Riccardo Pellarin.

VERSION

@@ -1 +1 @@
-2.14.0
+2.15.0

cmake_modules/CheckCompiles.cmake

@@ -0,0 +1,28 @@
+include(CheckCXXSourceCompiles)
+function(check_compiles name pkgname ucpkgname includes include_dir link_libs result)
+  #message(STATUS "Trying to compile ${pkgname} searching in ${include_dir} ${link_libs}")
+  set(CMAKE_REQUIRED_LIBRARIES ${link_libs})
+  set(CMAKE_REQUIRED_INCLUDES ${include_dir})
+  set(mybody "${includes}
+int main(int,char*[]) {
+  ${CHECK_COMPILES_BODY}
+  return 0;
+}")
+  set(${pkgname})
+  check_cxx_source_compiles("${mybody}" "${pkgname}${name}")
+  if ("${${pkgname}${name}}" MATCHES "1")
+    #message(STATUS "Compiled ok")
+    set(${ucpkgname}_INCLUDE_PATH ${include_dir} CACHE INTERNAL "" FORCE)
+    foreach(l ${link_libs})
+      set(${ucpkgname}_LIBRARIES ${${ucpkgname}_LIBRARIES} ${l} CACHE INTERNAL "" FORCE)
+    endforeach()
+    file(WRITE "${CMAKE_BINARY_DIR}/build_info/${pkgname}" "ok=True
+includepath=\"${${pkgname}_INCLUDE_PATH}\"
+swigpath=\"${${pkgname}_SWIG_PATH}\"
+libpath=\"${${pkgname}_LIB_PATH}\"
+")
+    set(${result} "1" PARENT_SCOPE)
+  else()
+    set(${result} "0" PARENT_SCOPE)
+  endif()
+endfunction(check_compiles)