Make install in atomic module does not detect changes

[Tom Goddard]

A "make install" in the atomic module sometimes does not detect changes to the atomic code. This causes confusing situations where errors in my development build persist even though a change to the atomic module fixes the error (e.g. see ticket #1214). A "make clean" followed by a "make install" fixes the problem, but the atomic build takes a few minutes after a "make clean" so I do not routinely make clean.

The failure to detect changed dependencies may be specific to the changes in Cythonized code.

[Eric Pettersen]

As far as I know, the proper dependencies are in the Makefiles to update things properly. So far, it has always updated correctly for me. Can you provide an example of updating a file where the change does not get propagated by "make install"?

[goddard@…]

Ticket #1214 describes a case where this happened but I do not know the atomic code change that caused it — it was a code change you made in atomic, I did a git pull and make install and the error in ticket #1214 persisted.  Maybe you can identify from the traceback in #1214 what code change fixed that traceback to deduce what dependency is missing.

I’ve never observed the problem when I changed atomic (because I rarely change atomic), only when I git pull changes.  You just modfied atomic/atomic_cpp/cymol.pyx and I did a make install in atomic and that one worked.

[Eric Pettersen]

Tried to reproduce this with T.G.'s help and couldn't. If some reproducible scenario can be found, the ticket will be reopened.