Init

Initial version of PySWIFTsim.

@pdraper and @matthieu, if you want to review the code. I would like to suggest starting by tests/test_cooling.py to see how the wrapper works. If you want to run it, you will need to switch on the update_cooling_grackle branch in Swift and download this file https://bitbucket.org/grackle/grackle/src/4bfba7ac54e5d878f647f7686e517f47b7e1754e/input/CloudyData_UVB=HM2012.h5?at=default. For the setup, just run python setup.py install --with-swift PATH_TO_SWIFT.

You can then look at src/parser_wrapper, src/units_wrapper or src/cooling_wrapper (do not care about how I deal with the input/output, you will need to focus on it to understand it).

At the end, you can look at how I deal with the python/C interface. First you can look at pyswiftsim/structure.py where I define a python class for each struct that I am wrapping (using https://docs.python.org/3/library/struct.html) and then to src/pyswiftsim_tools where I define the C methods to transform a python object to a C object. The big advantage of my method is that you can modify any non pointer field (I would like to allow changing a pointer, but it may be tricky).

src/cooling_wrapper.c

@@ -14,6 +14,7 @@ PyObject* pycooling_init(PyObject* self, PyObject* args) {
   PyObject *pyus;
   PyObject *pypconst;
 
+  /* parse arguments */
   if (!PyArg_ParseTuple(args, "OOO", &pyparams, &pyus, &pypconst))
       return NULL;
 
@@ -32,8 +33,10 @@ PyObject* pycooling_init(PyObject* self, PyObject* args) {
 
   struct cooling_function_data cooling;
 
+  /* init cooling */
   cooling_init_backend(params, us, pconst, &cooling);
 
+  /* construct python object */
   PyObject *pycooling = pytools_return(&cooling, class_cooling_function_data);
 
   return pycooling;
@@ -51,6 +54,7 @@ PyArrayObject* pycooling_rate(PyObject* self, PyObject* args) {
 
   float dt = 1e-3;
 
+  /* parse argument */
   if (!PyArg_ParseTuple(args,
 			"OOOOO|f",
 			&pypconst,
@@ -61,6 +65,7 @@ PyArrayObject* pycooling_rate(PyObject* self, PyObject* args) {
 			&dt))
     return NULL;
 
+  /* check numpy array */
   if (pytools_check_array(energy, 1, NPY_FLOAT) != SUCCESS)
     {
       return NULL;
@@ -76,7 +81,9 @@ PyArrayObject* pycooling_rate(PyObject* self, PyObject* args) {
       pyerror("Density and energy should have the same dimension");
     }
 
-    size_t N = PyArray_DIM(energy, 0);
+  size_t N = PyArray_DIM(energy, 0);
+
+  /* transform PyObject to C struct */
 
   struct cooling_function_data *cooling = (struct cooling_function_data*) pytools_construct(pycooling, class_cooling_function_data);
   if (cooling == NULL)
@@ -92,20 +99,19 @@ PyArrayObject* pycooling_rate(PyObject* self, PyObject* args) {
 
   struct part p;
 
-#ifdef COOLING_GRACKLE
-  grackle_data.grackle_data_file = cooling->GrackleCloudyTable;
-#endif
-
+  /* return object */
   PyArrayObject *rate = PyArray_NewLikeArray(energy, NPY_ANYORDER, NULL, 1);
 
+  /* loop over all particles */
   for(size_t i = 0; i < N; i++)
     {
+      /* set particle data */
       p.rho = *(float*) PyArray_GETPTR1(rho, i);
       float u = *(float*) PyArray_GETPTR1(energy, i);
       p.entropy = gas_entropy_from_internal_energy(p.rho, u);
 
+      /* compute cooling rate */
       float *tmp = PyArray_GETPTR1(rate, i);
-
 #ifdef COOLING_GRACKLE
       *tmp = cooling_rate(pconst, us, cooling, &p, dt);
 #else