Merge pull request #378 from rmcgibbo/bytes

loadCheckpoint/createCheckpoint should use bytes

wrappers/python/src/swig_doxygen/OpenMM.i

@@ -13,10 +13,10 @@ See https://simtk.org/home/pyopenmm for details"
 
 %module (docstring=DOCSTRING) openmm
 
-%include "typemaps.i"
 %include "factory.i"
 %include "std_string.i"
 %include "std_iostream.i"
+%include "typemaps.i"
 
 %include "std_map.i"
 %include "std_pair.i"

wrappers/python/src/swig_doxygen/swig_lib/python/typemaps.i

@@ -156,3 +156,36 @@
   $3 = &tempC;
 }
 
+%typemap(out) std::string OpenMM::Context::createCheckpoint{
+    // createCheckpoint returns a bytes object
+    $result = PyBytes_FromStringAndSize($1.c_str(), $1.length());
+}
+
+
+%typemap(in) std::string {
+    // if we have a C++ method that takes in a std::string, we're most happy to accept
+    // a python bytes object. But if the user passes in a unicode object we'll try
+    // to recover by encoding it to UTF-8 bytes
+    PyObject* temp = NULL;
+    char* c_str = NULL;
+    Py_ssize_t len = 0;
+
+    if (PyUnicode_Check($input)) {
+        temp = PyUnicode_AsUTF8String($input);
+        if (temp == NULL) {
+            SWIG_exception_fail(SWIG_TypeError, "'utf-8' codec can't decode byte");
+        }
+        PyBytes_AsStringAndSize(temp, &c_str, &len);
+        Py_XDECREF(temp);
+    } else if (PyBytes_Check($input)) {
+        PyBytes_AsStringAndSize($input, &c_str, &len);
+    } else {
+         SWIG_exception_fail(SWIG_TypeError, "argument must be str or bytes");
+    }
+
+    if (c_str == NULL) {
+        SWIG_exception_fail(SWIG_TypeError, "argument must be str or bytes");
+    }
+
+    $1 = std::string(c_str, len);
+}
\ No newline at end of file

wrappers/python/tests/TestBytes.py

+import unittest
+import simtk.openmm as mm
+
+
+class TestBytes(unittest.TestCase):
+    def test_createCheckpoint(self):
+        system = mm.System()
+        system.addParticle(1.0)
+        refPositions = [(0,0,0)]
+
+        context = mm.Context(system, mm.VerletIntegrator(0))
+        context.setPositions(refPositions)
+        chk = context.createCheckpoint()
+        # check that the return value of createCheckpoint is of type bytes (non-unicode)
+        assert isinstance(chk, bytes)
+
+        # set the positions to something random then reload the checkpoint, and
+        # make sure that the positions get restored correctly
+        context.setPositions([(12345, 12345, 123451)])
+        context.loadCheckpoint(chk)
+        newPositions = context.getState(getPositions=True).getPositions()._value
+
+        assert newPositions == refPositions
+
+        # try encoding the checkpoint in utf-8. OpenMM should be able to handle this too
+        context.setPositions([(12345, 12345, 123451)])
+        context.loadCheckpoint(chk.decode('utf-8'))
+        newPositions = context.getState(getPositions=True).getPositions()._value
+
+        assert newPositions == refPositions
+
+
+if __name__ == '__main__':
+    unittest.main()
+
+