Moved the VM to this SuperBuild repo CMake: removed USE_SYSTEM_siemens_to_ismrmrd CMake: added required versions for STIR, NIFTYREG, ISMRMRD. Drop Python 2 support CMake minimum required version is set to 3.16.2, as it supports Boost 1.72 VirtualBox VM is created from the SIRF-SuperBuild repository Docker images install CIL via conda, so setting BUILD_CIL=OFF in the docker build Added jupyterhub Dockerfile and documentation to build the jupyterhub image used in training on top of SIRF docker images and jupyter datascience-notebook image with GPU access. Adds Boost random for ISMRMRD 1.5.0 https://github.com/SyneRBI/SIRF-SuperBuild/issues/636 moved the VM repository to the VirtualBox subdirectory fix usage of proj_EXTRA_CMAKE_ARGS facility (it was broken for all projects except ITK) https://github.com/SyneRBI/SIRF-SuperBuild/issues/616 Boost: fix cases where the wrong version of boost could be found https://github.com/SyneRBI/SIRF-SuperBuild/issues/627 GTest: if USE_SYSTEM_GTest=OFF, attempt to force finding our version, otherwise, pass GTest_DIR or GTEST_ROOT on to dependent projects. add the CERN ROOT library (if USE_ROOT=ON, but defaults to OFF), which can be used by STIR to read GATE ROOT files. updated versions: CMake: 3.16.2 ISMRMRD: 1.7.0 if siemens_to_ismrmrd is built, 1.4.2.1 otherwise siemens_to_ismrmrd: 6d0ab3d3d0c8ade5c0526db1c6af9825008425ad > 1.2.2 with bug-fix for boost/foreach.hpp ITK: 5.2.1 However, we now build a smaller set of modules, most (but not all) of IO, and Filtering. See SuperBuild/External_ITK.cmake) NiftyReg: 99d584e2b8ea0bffe7e65e40c8dc818751782d92 ) (fixes gcc-9 OpenMP problems) CIL: v21.4.0 GTest: 1.11.0 Boost: 1.72.0 JSON: 3.10.4 ACE: 6.5.9 parallelproj: v0.8

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