Finalize Python runtime while shutting down Julia

src/PyCall.jl

@@ -99,7 +99,7 @@ it is equivalent to a `PyNULL()` object.
 ispynull(o::PyObject) = o.o == PyPtr_NULL
 
 function pydecref_(o::Union{PyPtr,PyObject})
-    ccall(@pysym(:Py_DecRef), Cvoid, (PyPtr,), o)
+    _finalized[] || ccall(@pysym(:Py_DecRef), Cvoid, (PyPtr,), o)
     return o
 end
 

src/pyinit.jl

@@ -62,6 +62,21 @@ end
 
 #########################################################################
 
+const _finalized = Ref(false)
+# This flag is set via `Py_AtExit` to avoid calling `pydecref_` after
+# Python is finalized.
+
+function _set_finalized()
+    # This function MUST NOT invoke any Python APIs.
+    # https://docs.python.org/3/c-api/sys.html#c.Py_AtExit
+    _finalized[] = true
+    return nothing
+end
+
+function Py_Finalize()
+    ccall(@pysym(:Py_Finalize), Cvoid, ())
+end
+
 function __init__()
     # sanity check: in Pkg for Julia 0.7+, the location of Conda can change
     # if e.g. you checkout Conda master, and we'll need to re-build PyCall
@@ -154,4 +169,25 @@ function __init__()
             end
         end
     end
+
+    # Configure finalization steps.
+    #
+    # * In julia/PyCall, `julia` needs to call `Py_Finalize` to
+    #   finalize Python runtime to invoke Python functions registered
+    #   in Python's exit hook.  This is done by Julia's `atexit` exit
+    #   hook.
+    #
+    # * In PyJulia, `python` needs to call `jl_atexit_hook` in its
+    #   exit hook instead.
+    #
+    # In both cases, it is important to not invoke GC of the finalized
+    # runtime.  This is ensured by:
+    @pycheckz ccall((@pysym :Py_AtExit), Cint, (Ptr{Cvoid},),
+                    @cfunction(_set_finalized, Cvoid, ()))
+    if !already_inited
+        # Once `_set_finalized` is successfully registered to
+        # `Py_AtExit`, it is safe to call `Py_Finalize` during
+        # finalization of this Julia process.
+        atexit(Py_Finalize)
+    end
 end

test/runtests.jl

@@ -666,4 +666,23 @@ def try_call(f):
                        pybuiltin("Exception"))
 end
 
+@testset "atexit" begin
+    if VERSION < v"0.7-"
+        setup = ""
+    else
+        setup = Base.load_path_setup_code()
+    end
+    script = """
+    $setup
+
+    using PyCall
+
+    pyimport("atexit")[:register]() do
+        println("atexit called")
+    end
+    """
+    out = read(`$(Base.julia_cmd()) -e $script`, String)
+    @test occursin("atexit called", out)
+end
+
 include("test_pyfncall.jl")