[chemfp] chemfp memory leak in 1.1 and older

[Andrew Dalke]

Hi all,

 Nothing like a new release to shake out bugs!

There's a chemfp memory leak bug only affects people who make and
free many arenas. I think few people actually do that.

I will put out a 1.1p1 within a day or so with this fix. If you
want it now, it's available from the Google Code repository.


Here's the full report.


I added the new "FingerprintArena.copy()" method so I could generate
extract many random subsets from an arena. This evening I realized
that my analysis code used a lot more memory than it should have.

I pinned it down to my misunderstanding in how Py_BuildValue works.
I had code like:

  PyObject *new_arena = make_string(...);
  return Py_BuildValue("O", new_arena);

The "O" character code returns a Python object, but it also adds a
new reference count to it, which I didn't expect. This meant that
my arena strings would never be deallocated. The correct version uses:

  return Py_BuildValue("N", new_arena);

which returns a Python object with "N"o reference count changes.

I've added the regression test "test_memory.py" which tests each
use of Py_BuildValue with either an "O" or an "N" to make sure that
it now returns the correct result.


				Andrew
				dalke at dalkescientific.com