Test case for Issue #48

This is @tahorst's test case to reproduce an Arrow hang.

Is it caused by a Gillespie algorithm blowup? By integer overflow? Something else?

**Note:** `make clean compile` prints an unexpected warning
```
building 'arrow.arrowhead' extension
Warning: Can't read registry to find the necessary compiler setting
Make sure that Python modules winreg, win32api or win32con are installed.
C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include
```

**Note:** `test_flagella` also fails: `arrow/arrow.py:176: SimulationFailure`.

arrow/test/test_hang.py

@@ -0,0 +1,56 @@
+# A test case for Issue #48.
+#
+# This code should reproduce the error: the program hangs after it prints "7100"
+# and eventually runs out of memory. You'll have to Ctrl+Z to stop it.
+# Ctrl+C won't work.
+#
+# It hangs only with certain seeds and numbers of molecules. The system can
+# evolve with the same number of molecule counts for 7179 iterations before it
+# hangs. Adding 1 to all of the molecules causes it to hang at an earlier
+# iteration.
+#
+# TODO: Debug this. Is it caused by a Gillespie algorithm blowup (see below),
+# integer overflow Undefined Behavior in C, or something else?
+#
+# The Gillespie algorithm is prone to explode [symptom?] under certain
+# conditions if the exponent term in the choice calculation is too large.
+#
+# The workaround is to find the problematic reaction and decompose the
+# stoichiometry into an equivalent problem with more steps.
+#
+# The flagella example had something like 170 identical subunits which caused
+# the problem. Breaking it into 2+ equivalent reactions fixed it.
+#
+# It'd be good for the Arrow code to catch this problem when/before it happens
+# and at least identify which reactions are problematic.
+
+import os
+
+from arrow import StochasticSystem
+import numpy as np
+
+
+def np_load(filename):
+    filepath = os.path.join(os.path.dirname(__file__), filename)
+    return np.load(filepath)
+
+
+def test_hang():
+    # TODO: Use a pytest plug-in to timeout after some threshold.
+
+    seed = 807952948
+
+    stoich = np_load('stoich.npy')
+    mol = np_load('complex-counts.npy')
+    rates = np_load('rates.npy')
+
+    system = StochasticSystem(stoich, random_seed=seed)
+    for i in range(10000):
+        if i % 100 == 0:
+            print(i)
+
+        result = system.evolve(1, mol, rates)
+
+
+if __name__ == '__main__':
+    test_hang()

setup.py

@@ -1,5 +1,4 @@
 import os
-# from glob import glob
 import setuptools  # used indirectly for bdist_wheel cmd and long_description_content_type
 from distutils.core import setup
 from distutils.extension import Extension
@@ -41,8 +40,8 @@
 	name='stochastic-arrow',
 	version='0.4.4',
 	packages=['arrow'],
-	author='Ryan Spangler, John Mason, Jerry Morrison',
-	author_email='[email protected]',
+	author='Ryan Spangler, John Mason, Jerry Morrison, Chris Skalnik',
+	author_email='[email protected]',
 	url='https://github.com/CovertLab/arrow',
 	license='MIT',
 	include_dirs=include,