added make test and cleanup

src/ClusterReader.c

@@ -1,29 +1,15 @@
 #include "ClusterReader.h"
+#include "arr_desc.h"
 #include "cluster_reader.h"
 #include "data_types.h"
-#include "arr_desc.h"
-
 
+//clang-format off
 typedef struct {
     PyObject_HEAD 
     FILE *fp;
     int n_left;
 } ClusterFileReader;
-
-
-
-// static PyArray_Descr *cluster_analysis_dt() {
-//     PyObject *dtype_dict;
-//     PyArray_Descr *dtype;
-//     dtype_dict = Py_BuildValue("[(s, s),(s, s),(s, s)]", "tot3", "i4", "tot2",
-//                                "i4", "corner", "u4");
-
-//     PyArray_DescrConverter(dtype_dict, &dtype);
-//     Py_DECREF(dtype_dict);
-//     return dtype;
-// }
-
-
+//clang-format on
 
 // Constructor: sets the fp to NULL then tries to open the file
 // raises python exception if something goes wrong
@@ -74,10 +60,9 @@ static PyObject *ClusterFileReader_read(ClusterFileReader *self, PyObject *args,
 
     // Create an uninitialized numpy array
     PyObject *clusters = PyArray_SimpleNewFromDescr(ndim, dims, cluster_dt());
-    
+
     // Fill with zeros
-    PyArray_FILLWBYTE((PyArrayObject *)clusters,
-                      0);
+    PyArray_FILLWBYTE((PyArrayObject *)clusters, 0);
 
     // Get a pointer to the array memory
     void *buf = PyArray_DATA((PyArrayObject *)clusters);
@@ -105,71 +90,6 @@ static PyObject *ClusterFileReader_read(ClusterFileReader *self, PyObject *args,
     return clusters;
 }
 
-// // read method
-// static PyObject *ClusterFileReader_clusterize(ClusterFileReader *self,
-//                                               PyObject *args,
-//                                               PyObject *Py_UNUSED(kwds)) {
-
-//     // Create an uninitialized numpy array
-//     PyArray_Descr *dtypeIn = cluster_dt();
-//     PyArray_Descr *dtypeOut = cluster_analysis_dt();
-
-    // PyObject *cl_obj;
-    // if (!PyArg_ParseTuple(args, "O", &cl_obj))
-    //     return NULL;
-
-//     // Create two numpy arrays from the passed objects, if possible numpy will
-//     // use the underlying buffer, otherwise it will create a copy, for example
-//     // if data type is different or we pass in a list. The
-// //     // NPY_ARRAY_C_CONTIGUOUS flag ensures that we have contiguous memory.
-//     PyObject *cl_array = PyArray_FromArray((PyArrayObject *)cl_obj, cluster_dt,
-//                                           NPY_ARRAY_C_CONTIGUOUS);
-
-//     // If parsing of a or b fails we throw an exception in Python
-//     if (cl_array == NULL) {
-//         PyErr_SetString(
-//             PyExc_TypeError,
-//             "Could not convert one of the arguments to a numpy array.");
-//         return NULL;
-//     }
-
-//     const int ndim = PyArray_NDIM((PyArrayObject *)c_array);
-
-//     npy_intp *dims = PyArray_SHAPE((PyArrayObject *)c_array);
-
-//     Py_ssize_t size = dims[0];
-//     // printf("%d size %d %d\n",ndim,size,sizeof(ClusterAnalysis));
-//     // dims[0]=size;
-
-//     // Cluster *clusters = reinterpret_cast<Cluster *>(
-//     // PyArray_DATA(reinterpret_cast<PyArrayObject *>(c_array)));
-
-//     Cluster *clusters = (Cluster *)(PyArray_DATA((PyArrayObject *)(c_array)));
-
-//     // PyObject *PyArray_SimpleNewFromDescr(int nd, npy_int const *dims,
-//     // PyArray_Descr *descr)
-//     PyObject *clustersA = PyArray_SimpleNewFromDescr(ndim, dims, dtypeOut);
-//     // PyArray_FILLWBYTE((PyArrayObject *)clustersA, 0); //zero initialization
-//     // can be removed later
-//     npy_intp *strides = PyArray_STRIDES(((PyArrayObject *)(clustersA)));
-//     //  printf("strides %d %d\n", strides[0],sizeof(ClusterAnalysis));
-
-//     // Get a pointer to the array memory
-//     ClusterAnalysis *buf = PyArray_DATA((PyArrayObject *)clustersA);
-
-//     // Call the standalone C code to read clusters from file
-//     // Here goes the looping, removing frame numbers etc.
-//     int nc = analyze_clusters(size, clusters, buf);
-//     // printf("%d %d\n",nc,size);
-
-//     if (nc != size) {
-
-//         PyErr_SetString(PyExc_TypeError, "Parsed wrong size array!");
-//     }
-
-//     return clustersA;
-// }
-
 // List all methods in our ClusterFileReader class
 static PyMethodDef ClusterFileReader_methods[] = {
     {"read", (PyCFunction)ClusterFileReader_read, METH_VARARGS,
@@ -192,8 +112,7 @@ static PyTypeObject ClusterFileReaderType = {
     .tp_methods = ClusterFileReader_methods,
 };
 
-void init_ClusterFileReader(PyObject *m){
-
+PyObject *init_ClusterFileReader(PyObject *m) {
     import_array();
     if (PyType_Ready(&ClusterFileReaderType) < 0)
         return NULL;
@@ -205,4 +124,5 @@ void init_ClusterFileReader(PyObject *m){
         Py_DECREF(m);
         return NULL;
     }
+    return m;
 }

src/ClusterReader.h

@@ -1,7 +1,7 @@
-# pragma once
+#pragma once
 #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
 #define PY_SSIZE_T_CLEAN
 #include <Python.h>
 #include <numpy/arrayobject.h>
 
-void init_ClusterFileReader(PyObject *m);
+PyObject* init_ClusterFileReader(PyObject *m);

src/arr_desc.c

@@ -1,17 +1,18 @@
 #include "arr_desc.h"
 
+// Numpy data type holding a cluster
 PyArray_Descr* cluster_dt(){
     import_array();
     PyObject *dict;
     PyArray_Descr *dtype = NULL;
     dict = Py_BuildValue("[(s, s),(s, s),(s, s, (i))]", "x", "u2", "y",
                             "u2", "data", "i4", 9);
-    // return dict;
     PyArray_DescrConverter(dict, &dtype);
     Py_DECREF(dict);
     return dtype;
 }
 
+// Numpy data type holding the result of a cluster analysis
 PyArray_Descr *cluster_analysis_dt() {
     import_array(); //TODO! Correct placement for this?
     PyObject *dict;

src/creader_module.c

@@ -100,6 +100,6 @@ PyMODINIT_FUNC PyInit_creader(void) {
         return NULL;
     import_array();
 
-    init_ClusterFileReader(m);
+    m = init_ClusterFileReader(m);
     return m;
 }