Enable CMake build on MacOS. Tested with ctffind

[arohou]

Description

The latest from repo did not build with CMake on MacOS. This fixes this problem. I have confirmed that ctffind builds on MacOS 10.15.7 using Clang and FFTW + OpenMP + OpenMPI from homebrew. I have also verified that ctffind runs to completion on test data.

In the process, I believe I fixed a bug in cistem_parameters.cpp (or at least clang thinks I did). BUT: I have not tested this functionality - I don't know where it is used. I would appreciate if someone who uses this functionality could build & test before we merge. Perhaps @bHimes or @timothygrant80 knows where this is used and can see whether I fixed or broke something.

I have rebased my feature branch to be current with the master branch using to minimize conflicts and headaches

• [ x] yes
• no

Which compilers were tested

• g++
• icpc
• clang
• [ x] other (clang 12)

These changes are isolated to the

• gui
• [x ] core library
• gpu core library
• program it modifies

How has the functionality been tested?

I can build ctffind on MacOS using CMake and clang.

Warning: I have not tested building using autotools on MacOS, or at all on linux.
Warning 2: it's likely that the GPU-enabled side of things will not build with CMake, but I believe this was already the case before these commits (I guess cmake builds just were not tested)

• Tested manually from GUI
• [ x] Tested manually from CLI
• Passed console tests
• Passed samples functional testing
• other (please specify)

Checklist:

• I have not changed anything that did not need to be changed
• I have performed a self-review of my own code
• I have commented my code, (w.r.t. why), particularly in hard-to-understand areas
• I have made corresponding changes to the documentation {Ok to pass for now}
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules

[bHimes]

Fwiw, in my local, I have removed all CMake configurations. IMO maintaining two separate build systems is just asking for trouble.

Would I set up Autotools from scratch on a new project? Probably not, but having it in place, it works just fine.

I recommend considering this for the main repo as well.

[jojoelfe]

I've pointed out the places where this PR conflicts with the current automake setup.

The CMake files don't really cause any issue, so I don't see why we can't include them as long as the "canonical" way to compile cisTEm still works.

[bHimes]

I've pointed out the places where this PR conflicts with the current automake setup.

The CMake files don't really cause any issue, so I don't see why we can't include them as long as the "canonical" way to compile cisTEm still works.

That's a fine and fair point. I just mention here b/c there is a lot of noise in the code, and I consider this a source and have removed it from my own repo.

[bHimes]

@arohou can this be closed?