System build

[casperdcl]

• minor .bashrc fix
• docker: USE_SYSTEM_*
  • dependencies from CCPPETMR_VM/scripts/INSTALL_prerequisites_with_apt-get.sh
  • USE_SYSTEM_Armadillo=ON?
    • missing from above - add there?
    • note that according to .travis.yml#L12 can't use system's version on trusty
  • USE_SYSTEM_GTEST=ON? (add USE_SYSTEM_GTest variable #50)
  • pip install other libs from INSTALL_prerequisites_with_apt-get.sh (e.g. h5py)?
  • requirements.txt (build)
  • requirements-tests.txt (see SIRF#69)
  • requirements-runtime.txt
  • Note that USE_SYSTEM_*:
    1. halves image size (4GB -> 2GB, and compressed size ~ a CD)
    2. reduces build time
• add STIR-exercises and full STIR build as per https://github.com/CCPPETMR/CCPPETMR_VM/blob/master/scripts/update_VM_to_full_STIR.sh
• Travis: address Travis builds with system SWIG, HDF5 and FFTW3 #37
  • ccache?
  • docker?
    • cache docker layers?
  • travis_wait?

closes SyneRBI/SIRF#12

[KrisThielemans]

I don't think STIR-exercises should be a sub-project here. we could add it as an optional external-project maybe, but not more.

[casperdcl]

ok, removed STIR-exercises, -DBUILD_STIR_EXECUTABLES=ON, and -DBUILD_STIR_SWIG_PYTHON=ON. Note that that was only for the docker images (useful for the MIC workshop)