Acquire GIL around every Python API call

[topolarity]

This should resolve #1096 by wrapping every Python API usage in a GIL acquire-release.

If this leads to overhead, we can probably re-export a "manual GIL" version of the API that allows consumers to manage the GIL themselves. In any case, it's worth having proper support for multi-threading.

Fixes #1096. Fixes #1095. Fixes #1090. Fixes #1088.
Fixes #1078. Fixes #1077. Fixes #1072. Fixes #1083.
Fixes timholy/Revise.jl#989.

[topolarity]

Before this can be considered complete, it needs an equivalent to JuliaMath/FFTW.jl#160 to handle:

1. Task A holds the GIL lock.
2. Task A waits for Task B to make "progress".
3. Task B waits in GC to obtain the GIL lock to run finalizers. (deadlocks)

edit: Done!

[yuyichao]

Is there any known issue with this currently? Are we going to use this approach?

I've rebased this on master at https://github.com/JuliaPy/PyCall.jl/tree/ct/with-gil-rebase with a few fixes/tweaks.

1. pydecref_ needs to hold a reference to the julia object to avoid potential race with the GC. This is really hard to happen in practice but not impossible.

   As part of it, stops returning the pointer from it since that pointer should never be used again. This PR already changed the signature of this function. The only other reference I've found for this function is in some precompilation statements which shouldn't cause any breakage.

2. Still make the finalizer clear the pointer in PyObject. I can't think of a case right now that would crash because of this but it would follow

3. Minor optimization in _drain_release_queues to use one atomic sub rather than two, and to only copy the vector if it's not empty.

One of the few issues I could think of is maybe if there are a lot of object that became garbage they can only be free'd the next time the user calls a PyCall API, which may not happen for a while. For example, the following code can place unbound number of objects in the deferred list,

[PyObject(i) for i in 1:100000];

Maybe the finalizer should detect some cases where the GIL is safe to acquire (e.g. try to acquire without waiting) and clear the queue?

[yuyichao]

I've force pushed my rebased to the original branch. As I said in #1096 (comment), unless someone come up with a better solution soon, I'd like to merge this in a few days.

[codecov-commenter]

Codecov Report

❌ Patch coverage is 90.00000% with 14 lines in your changes missing coverage. Please review.
✅ Project coverage is 70.44%. Comparing base (2f600fb) to head (a286fcd).
⚠️ Report is 7 commits behind head on master.

Files with missing lines	Patch %	Lines
src/gc.jl	87.71%	7 Missing ⚠️
src/conversions.jl	72.72%	3 Missing ⚠️
src/PyCall.jl	90.90%	2 Missing ⚠️
src/exception.jl	90.90%	1 Missing ⚠️
src/pyiterator.jl	50.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1097      +/-   ##
==========================================
+ Coverage   68.02%   70.44%   +2.41%     
==========================================
  Files          20       21       +1     
  Lines        2036     2118      +82     
==========================================
+ Hits         1385     1492     +107     
+ Misses        651      626      -25     

Flag	Coverage Δ
unittests	70.44% <90.00%> (+2.41%)	⬆️

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[topolarity]

Thanks for revisiting / rebasing @yuyichao

I am not aware of any problems with this, other than your latest fixups / tweaks. I think it's the direction we want to go in.

I'll try to reboot the context and take a look at the changes on Monday to see if we need anything else. Otherwise, sounds good to me!

[yuyichao]

The CI and local testing revealed a dead lock caused by the deferred lock. Somehow it is more likely to trigger on older julia version but in principle it could trigger on newer ones as well. See commit message for more detail but essentially I've switched the deferred unref list into an linked list instead to make atomic mutation easier.