Merge for 2.20.0 release

.github/workflows/ci.yml

@@ -10,13 +10,13 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.8"]
-        os: [ubuntu-20.04]
+        python-version: ["3.10"]
+        os: [ubuntu-22.04]
         compiler: [gcc]
     env:
       CC: ${{ matrix.compiler }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Install dependencies
         run: |
           sudo apt-get update -qq

.github/workflows/flake.yml

@@ -13,12 +13,12 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Test
       run: |
         pip install flake8
-        flake8 tools modules/parallel/pyext modules/test/pyext modules/mmcif/pyext modules/statistics/pyext modules/pepdock/pyext
+        flake8 tools modules/cnmultifit/pyext modules/EMageFit/pyext modules/parallel/pyext modules/test/pyext modules/mmcif/pyext modules/statistics/pyext modules/pepdock/pyext modules/saxs_merge/bin/saxs_merge

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8.12)
+cmake_minimum_required(VERSION 2.8.12...3.6.0)
 
 project(IMP)
 
@@ -105,7 +105,8 @@ else()
 set(IMP_MAX_CHECKS "USAGE" CACHE STRING "One of NONE, USAGE, INTERNAL")
 set(IMP_MAX_LOG "VERBOSE" CACHE STRING "One of SILENT, PROGRESS, TERSE, VERBOSE")
 endif()
-set(IMP_PER_CPP_COMPILATION "" CACHE STRING "A colon-separated list of modules to build one .cpp at a time.")
+set(IMP_PER_CPP_COMPILATION "" CACHE STRING "A colon-separated list of modules to build one .cpp at a time, or ALL to do this for all modules.")
+set(IMP_CUDA "" CACHE STRING "A colon-separated list of modules to build with CUDA support (where available), or ALL to do this for all modules.")
 
 if (${IMP_MAX_CHECKS} MATCHES "INTERNAL")
 set(timeout_factor "${timeout_factor} * 2")
@@ -139,19 +140,29 @@ else()
   SET(IMP_LIB_TYPE SHARED)
 endif()
 
-string(REGEX MATCHALL "[a-zA-Z0-9_]+" percpplist "${IMP_PER_CPP_COMPILATION}")
-foreach(m ${percpplist})
-  message(STATUS ${m} " is percpp")
-  set(IMP_${m}_IS_PER_CPP 1)
-endforeach(m)
+if("${IMP_PER_CPP_COMPILATION}" STREQUAL "ALL")
+  message(STATUS "All modules are percpp")
+  set(IMP_IS_PER_CPP 1)
+else()
+  string(REGEX MATCHALL "[a-zA-Z0-9_]+" percpplist "${IMP_PER_CPP_COMPILATION}")
+  foreach(m ${percpplist})
+    message(STATUS ${m} " is percpp")
+    set(IMP_${m}_IS_PER_CPP 1)
+  endforeach(m)
+endif()
 
-string(REGEX MATCHALL "[a-zA-Z0-9_]+" cudalist "${IMP_CUDA}")
-foreach(m ${cudalist})
-  string(TOUPPER ${m} M)
-  message(STATUS ${m} " is cuda lib")
-  set(IMP_${m}_IS_CUDA 1)
-  add_definitions( -DIMP_${M}_CUDA_LIB )
-endforeach(m)
+if("${IMP_CUDA}" STREQUAL "ALL")
+  message(STATUS "All modules are cuda lib")
+  set(IMP_IS_CUDA 1)
+  set(IMP_CUDA_REQUESTED 1)
+else()
+  string(REGEX MATCHALL "[a-zA-Z0-9_]+" cudalist "${IMP_CUDA}")
+  foreach(m ${cudalist})
+    message(STATUS ${m} " is cuda lib")
+    set(IMP_${m}_IS_CUDA 1)
+    set(IMP_CUDA_REQUESTED 1)
+  endforeach(m)
+endif()
 
 if(WIN32)
   set(IMP_SWIG_LIBRARIES ${PYTHON_LIBRARIES})
@@ -322,6 +333,26 @@ file(WRITE "${CMAKE_BINARY_DIR}/build_info/Boost.Serialization" "ok=True")
 file(WRITE "${CMAKE_BINARY_DIR}/build_info/Boost.System" "ok=True")
 file(WRITE "${CMAKE_BINARY_DIR}/build_info/Boost.Thread" "ok=True")
 
+if(DEFINED IMP_CUDA_REQUESTED)
+  find_package(CUDA REQUIRED)
+  include(FindCUDA)
+  list(APPEND CUDA_NVCC_FLAGS --compiler-options -fno-strict-aliasing -lineinfo -use_fast_math -Xptxas -dlcm=cg)
+  list(APPEND CUDA_NVCC_FLAGS -lcufft)
+  # Support for the Fermi architecture was removed in CUDA toolkit 9
+  if (CUDA_VERSION_MAJOR LESS 9)
+    list(APPEND CUDA_NVCC_FLAGS -gencode arch=compute_20,code=sm_20)
+  endif()
+  if (CUDA_VERSION_MAJOR LESS 11)
+    list(APPEND CUDA_NVCC_FLAGS -gencode arch=compute_30,code=sm_30)
+    list(APPEND CUDA_NVCC_FLAGS -gencode arch=compute_35,code=sm_35)
+  endif()
+  list(APPEND CUDA_NVCC_FLAGS -gencode arch=compute_52,code=sm_52)
+  list(APPEND CUDA_NVCC_FLAGS -arch sm_53)
+  message(STATUS "CUDA libraries: " "${CUDA_LIBRARIES}")
+  message(STATUS "CUDA curand library: " "${CUDA_curand_LIBRARY}")
+  message(STATUS "CUDA cufft library: " "${CUDA_cufft_LIBRARY}")
+endif()
+
 if(NOT IMP_STATIC)
   # Automatically enable OpenMP if available and at least version 3
   find_package(OpenMP3)

CODE_OF_CONDUCT.md

@@ -0,0 +1,77 @@
+Contributor Covenant Code of Conduct {#codeconduct}
+====================================
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at the Sali Lab. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

ChangeLog.md

@@ -1,6 +1,68 @@
 ChangeLog {#changelog}
 =========
 
+# 2.20.0 - 2023-12-21 # {#changelog_2_20_0}
+- The Windows .exe installer now supports Python 3.7 through 3.12.
+- RPM packages for IMP for RedHat Linux (and clones such as Alma or Rocky)
+  and for Fedora are now provided by the
+  [COPR project](https://copr.fedorainfracloud.org/coprs/salilab/salilab/).
+  Dependencies such as RMF and python-ihm are now packaged separately so that
+  they can be updated independently of IMP itself.
+- We no longer provide packages for Ubuntu 18.04 LTS (Bionic Beaver), as it
+  reached end of life in May 2023.
+- IMP::atom::Chain objects now track the sequence offset (if any) between
+  FASTA and PDB residue numbering, and the UniProt accession (if known) of
+  the sequence. This information is also stored in RMF files.
+- PMI's FASTA file reader now reads the UniProt accession for each sequence,
+  if provided.
+- IMP::atom::ChainPDBSelector now takes a list of chain IDs, rather than a
+  single string, so that it can select chains with multi-character IDs.
+  When working with mmCIF files, it will now select based on the author-provided
+  chain ID, if available, for consistency with the naming of IMP::atom::Chain
+  particles.
+- The IMP::rmf::load_frame and IMP::rmf::save_frame functions now warn if they
+  are called before links to IMP objects have been made (as this is a noop).
+- IMP::saxs::Restraint has seen performance improvements, and will now use a
+  GPU for speedup if IMP is built with CUDA support.
+- IMP::saxs::Restraint will now report an error if it is given invalid
+  particles; previously they would be silently ignored.
+- The IMP::mmcif module has been rewritten to work with modern RMF files
+  and IMP::sampcon output.
+- The `multi_foxs` command line tool now provides the same `--offset` option
+  that `foxs` does.
+- Model attributes can now use sparse rather than vector storage. This reduces
+  memory usage for attributes that are used by a minority of particles.
+- Previous releases would erroneously allow a single Python string to be
+  passed to any method that wants a list of strings. This would split the
+  string into a list of single-character strings, which is often not was
+  intended. Such methods now require an explicit list (or tuple) of strings.
+- The `IMP_NOEXCEPT` pre-C++11 compatibility macro has been removed; use
+  the C++ `noexcept` keyword instead.
+- The CMake `IMP_PER_CPP_COMPILATION` and `IMP_CUDA` variables can now be set
+  to `ALL` to build all IMP modules one .cpp at a time, or with CUDA support,
+  respectively.
+- PMI no longer supports old PMI1-style hierarchies. The
+  IMP::pmi::get_is_canonical function, which detects PMI2-style hierarchies,
+  should thus be assumed to always return true, and has been deprecated.
+- Windows builds now require MS Visual Studio 2017 or later.
+- IMP::algebra::Rotation3D::get_derivative(),
+  IMP::algebra::Rotation3D::get_gradient(),
+  IMP::algebra::get_gradient_of_composed_with_respect_to_first(), and
+  IMP::algebra::get_gradient_of_composed_with_respect_to_second() have been
+  removed; instead use IMP::algebra::Rotation3D::get_gradient_of_rotated(),
+  IMP::algebra::Rotation3D::get_jacobian_of_rotated(),
+  IMP::algebra::get_jacobian_of_composed_wrt_first(), and
+  IMP::algebra::get_jacobian_of_composed_wrt_second(), respectively.
+- The IMP::core::IncrementalScoringFunction class has been removed. Use
+  IMP::core::MonteCarlo::set_score_moved or
+  IMP::ScoringFunction::evaluate_moved instead.
+- The IMP::em2d::CenteredMat and IMP::em2d::Fine2DRegistrationRestraint
+  classes, which are used only internally, have been removed.
+- The base_utility.h and base_static.h headers have been removed; use utility.h
+  and static.h instead, respectively.
+- The vector_property_map.h compatibility header has been removed;
+  use Boost's boost/property_map/property_map.hpp header instead.
+
 # 2.19.0 - 2023-06-22 # {#changelog_2_19_0}
 - Most IMP Value and Object types can now be serialized (or pickled in Python).
   For example, this can be used to save the current state of an IMP::Model

VERSION

@@ -1 +1 @@
-2.19.0
+2.20.0

cmake_modules/FindRMF.cmake

@@ -1,27 +1,23 @@
-#[=======================================================================[.rst:
-FindRMF
--------
-
-Try to find RMF
-
-Result Variables
-^^^^^^^^^^^^^^^^
-
-This module defines the following variables:
-
-``RMF_FOUND``
-  system has RMF
-``RMF_INCLUDE_PATH``
-  the RMF include directory
-``RMF_SWIG_PATH``
-  the directory containing SWIG (.i) files for RMF
-``RMF_LIBRARY``
-  Link this to use RMF
-``RMF_VERSION_STRING``
-  the version of RMF found
-
-
-#]=======================================================================]
+# FindRMF
+# -------
+#
+# Try to find RMF
+#
+# Result Variables
+# ^^^^^^^^^^^^^^^^
+#
+# This module defines the following variables:
+#
+# ``RMF_FOUND``
+#   system has RMF
+# ``RMF_INCLUDE_PATH``
+#   the RMF include directory
+# ``RMF_SWIG_PATH``
+#   the directory containing SWIG (.i) files for RMF
+# ``RMF_LIBRARY``
+#   Link this to use RMF
+# ``RMF_VERSION_STRING``
+#   the version of RMF found
 
 
 find_path(RMF_INCLUDE_PATH RMF.h PATH_SUFFIXES include)
@@ -33,9 +29,15 @@ endif()
 if (RMF_INCLUDE_PATH AND EXISTS "${RMF_INCLUDE_PATH}/RMF/config.h")
   file(STRINGS "${RMF_INCLUDE_PATH}/RMF/config.h" RMF_MAJOR_H REGEX "#define RMF_VERSION_MAJOR +([0-9]+)")
   file(STRINGS "${RMF_INCLUDE_PATH}/RMF/config.h" RMF_MINOR_H REGEX "#define RMF_VERSION_MINOR +([0-9]+)")
+  file(STRINGS "${RMF_INCLUDE_PATH}/RMF/config.h" RMF_MICRO_H REGEX "#define RMF_VERSION_MICRO +([0-9]+)")
   string(REGEX REPLACE " *#define RMF_VERSION_MAJOR +([0-9]+) *" "\\1" RMF_VERSION_MAJOR "${RMF_MAJOR_H}")
   string(REGEX REPLACE " *#define RMF_VERSION_MINOR +([0-9]+) *" "\\1" RMF_VERSION_MINOR "${RMF_MINOR_H}")
-  set(RMF_VERSION_STRING "${RMF_VERSION_MAJOR}.${RMF_VERSION_MINOR}")
+  string(REGEX REPLACE " *#define RMF_VERSION_MICRO +([0-9]+) *" "\\1" RMF_VERSION_MICRO "${RMF_MICRO_H}")
+  if (RMF_MICRO_H)
+    set(RMF_VERSION_STRING "${RMF_VERSION_MAJOR}.${RMF_VERSION_MINOR}.${RMF_VERSION_MICRO}")
+  else()
+    set(RMF_VERSION_STRING "${RMF_VERSION_MAJOR}.${RMF_VERSION_MINOR}")
+  endif()
 endif()
 
 include(FindPackageHandleStandardArgs)

doc/manual/cmake_config.md

@@ -50,7 +50,7 @@ Various aspects of %IMP build behavior can be controlled via variables. These ca
 - `IMP_DISABLED_MODULES`: A colon-separated list of disabled modules.
 - `IMP_MAX_CHECKS`: One of `NONE`, `USAGE`, `INTERNAL` to control what check levels will be supported. The default is `USAGE` for release builds and `INTERNAL` for debug builds (setting this to `INTERNAL` will impact performance; `NONE` is not recommended as all sanity checks will be skipped).
 - `IMP_MAX_LOG`: One of `SILENT`, `PROGRESS`, `TERSE`, `VERBOSE` to control what log levels are supported.
-- `IMP_PER_CPP_COMPILATION`: A colon-separated list of modules to build one .cpp at a time.
+- `IMP_PER_CPP_COMPILATION`: A colon-separated list of modules to build one .cpp at a time, or `ALL` to do this for all modules.
 - `USE_PYTHON2`: Set to `on` to have CMake build %IMP with Python 2 (by default it will use Python 3 if available).
 - `IMP_USE_SYSTEM_RMF`: Set to `on` to build %IMP using an external (system) copy of the RMF library, instead of that bundled with IMP itself.
 - `IMP_USE_SYSTEM_IHM`: Set to `on` to build %IMP using an external (system) copy of the python-ihm library, instead of that bundled with IMP itself.

doc/manual/contributing.md

@@ -8,3 +8,5 @@ could include
    button at the top of each page)
  - Adding a new function, class, or module to %IMP
  - [Publishing your protocol](@ref biosystem) for applying %IMP to a biological system
+
+Please also see our [code of conduct](@ref codeconduct) for all contributions.

doc/manual/installation.md

@@ -25,8 +25,9 @@ To experiment with IMP on [Google Colaboratory](https://colab.research.google.co
 !wget -O /etc/apt/trusted.gpg.d/salilab.asc https://salilab.org/~ben/pubkey256.asc
 !apt update
 !apt install imp
-import sys
-sys.path.append('/usr/lib/python3.8/dist-packages')
+import sys, os, glob
+sys.path.append(os.path.dirname(glob.glob('/usr/lib/python*/dist-packages/IMP')[0]))
+
 \endcode
 
 # Source code installation {#installation_source}
@@ -36,7 +37,7 @@ sys.path.append('/usr/lib/python3.8/dist-packages')
 In order to build %IMP from source, you will need:
 
 - A C++ compiler that supports the C++11 standard, such as gcc, clang,
-  or Microsoft Visual Studio 2015 or later.
+  or Microsoft Visual Studio 2017 or later.
 - [CMake](https://cmake.org) (2.8.12 or later; 3.14 or later is recommended)
 - [Boost](https://www.boost.org) (1.53 or later; Boost.Iostreams must be built
   with its [zlib filter enabled](https://www.boost.org/doc/libs/1_67_0/libs/iostreams/doc/installation.html))
@@ -130,10 +131,11 @@ such as
 
 - [Conda](https://docs.conda.io/en/latest/) Once you installed conda (typically via the Miniconda or Anaconda distributions), do 
 
-        conda create -n IMP_BUILD -c conda-forge python cxx-compiler c-compiler llvm-openmp swig cmake ninja numpy rmf ihm boost-cpp hdf5 libprotobuf protobuf libopencv eigen fftw gsl libcblas  cgal-cpp gmp mpfr mpich numpy
-	conda activate IMP_BUILD
+        conda create -n IMP_BUILD -c conda-forge python cxx-compiler c-compiler llvm-openmp swig cmake ninja numpy rmf ihm boost-cpp hdf5 libopencv eigen fftw gsl libcblas  cgal-cpp gmp mpfr mpich numpy cereal
+		conda activate IMP_BUILD
+		conda install -c anaconda protobuf libprotobuf 
 
-  As in brew and Macports, some of these packages may be optional. In addition, cgal may not be identified by cmake. IMP will still run just fine. Either way, a solution could be setting the CGAL_DIR environment variable to $CONDA_PREFIX/lib/cmake/CGAL/ before running cmake, or adding a -DCGAL_DIR=$CONDA_PREFIX/lib/cmake/CGAL flag to the cmake command line ($CONDA_PREFIX is an environment variable that points to the folder of the active conda environment).
+  Conda tips: as with brew and Macports, some of these packages may be optional. It is up to you whether to use "-c anaconda" or "-c conda-forge" for either of the packages, e.g. libprotobuf and protobuf worked better with anaconda in the past. In addition, cgal may not be identified by cmake. IMP will still run just fine. Either way, a solution could be setting the CGAL_DIR environment variable to $CONDA_PREFIX/lib/cmake/CGAL/ before running cmake, or adding a -DCGAL_DIR=$CONDA_PREFIX/lib/cmake/CGAL flag to the cmake command line ($CONDA_PREFIX is an environment variable that points to the folder of the active conda environment).
 
 
 - or [Fink](http://www.finkproject.org/) (not supported)

doc/manual/mainpage.dox

@@ -98,6 +98,8 @@ complex might want to skip ahead to
 
  - [Change history](@ref changelog)
 
+ - [Code of conduct](@ref codeconduct)
+
  - [Publications](@ref publications)
 
 */