Remove PyInt references, work around Py3.11 Cython default argument p…

…roblem

setup.py

@@ -58,7 +58,6 @@ def Extension(*args, **kwargs):
         else:
             ext.extra_compile_args.append("-g3")
             ext.extra_compile_args.append("-O0")
-    # ext.extra_compile_args.append("/fsanitize=address")
     return ext
 
 def OpenMPExtension(*args, **kwargs):

src/ms_peak_picker/_c/peak_picker.pxd

@@ -13,6 +13,34 @@ cpdef enum PeakFit:
     apex = 3
 
 
+cdef enum range_tag:
+    mz_range = 1
+    index_range = 2
+    full_range = 3
+
+
+cdef struct mz_range_t:
+    range_tag tag
+    double start_mz
+    double stop_mz
+
+
+cdef struct index_range_t:
+    range_tag tag
+    Py_ssize_t start_index
+    Py_ssize_t stop_index
+
+
+cdef struct full_range_t:
+    range_tag tag
+
+
+cdef union discovery_range_t:
+    mz_range_t mz
+    index_range_t index
+    full_range_t full
+
+
 cdef class PartialPeakFitState(object):
     cdef:
         public bint set
@@ -48,10 +76,9 @@ cdef class PeakProcessor(object):
     cpdef object set_intensity_threshold(self, double intensity_threshold)
 
 
-    cpdef size_t _discover_peaks(self, np.ndarray[cython.floating, ndim=1, mode='c'] mz_array,
+    cdef size_t _discover_peaks(self, np.ndarray[cython.floating, ndim=1, mode='c'] mz_array,
                                        np.ndarray[cython.floating, ndim=1, mode='c'] intensity_array,
-                                       double start_mz, double stop_mz,
-                                       Py_ssize_t start_index=*, Py_ssize_t stop_index=*) noexcept
+                                       discovery_range_t discovery_range) noexcept
 
     cpdef double find_full_width_at_half_max(self, Py_ssize_t index,
                                              np.ndarray[cython.floating, ndim=1, mode='c'] mz_array,

src/ms_peak_picker/_c/peak_picker.pyx

@@ -223,30 +223,41 @@ cdef class PeakProcessor(object):
         cdef:
             double _start_mz, _stop_mz
             Py_ssize_t _start_index, _stop_index
+            discovery_range_t discovery_range
 
-        if start_mz is None:
-            _start_mz = -1
-        else:
-            _start_mz = start_mz
-        if stop_mz is None:
-            _stop_mz = -1
-        else:
-            _stop_mz = stop_mz
-        if start_index is None:
-            _start_index = 0
-        else:
-            _start_index = start_index
-        if stop_index is None:
-            _stop_index = 0
+        if start_mz is not None or stop_mz is not None:
+            if start_mz is None:
+                _start_mz = -1
+            else:
+                _start_mz = start_mz
+            if stop_mz is None:
+                _stop_mz = -1
+            else:
+                _stop_mz = stop_mz
+            discovery_range.mz.tag = range_tag.mz_range
+            discovery_range.mz.start_mz = _start_mz
+            discovery_range.mz.stop_mz = _stop_mz
+        elif start_index is not None or stop_index is not None:
+            if start_index is None:
+                _start_index = 0
+            else:
+                _start_index = start_index
+            if stop_index is None:
+                _stop_index = 0
+            else:
+                _stop_index = stop_index
+            discovery_range.index.tag = range_tag.index_range
+            discovery_range.index.start_index = _start_index
+            discovery_range.index.stop_index = _stop_index
         else:
-            _stop_index = stop_index
-        return self._discover_peaks(mz_array, intensity_array, _start_mz, _stop_mz, _start_index, _stop_index)
+            discovery_range.full.tag = range_tag.full_range
+        return self._discover_peaks(mz_array, intensity_array, discovery_range)
 
     @cython.nonecheck(False)
     @cython.cdivision(True)
     @cython.boundscheck(False)
-    cpdef size_t _discover_peaks(self, np.ndarray[cython.floating, ndim=1, mode='c'] mz_array, np.ndarray[cython.floating, ndim=1, mode='c'] intensity_array,
-                                 double start_mz, double stop_mz, Py_ssize_t start_index=0, Py_ssize_t stop_index=0) noexcept:
+    cdef size_t _discover_peaks(self, np.ndarray[cython.floating, ndim=1, mode='c'] mz_array, np.ndarray[cython.floating, ndim=1, mode='c'] intensity_array,
+                                discovery_range_t discovery_range) noexcept:
         """Carries out the peak picking process on `mz_array` and `intensity_array`. All
         peaks picked are appended to :attr:`peak_data`.
 
@@ -277,8 +288,32 @@ cdef class PeakProcessor(object):
             size_t offset
             bint infer_range
 
+            double start_mz, stop_mz
+            ssize_t start_index, stop_index
+
             FittedPeak peak
 
+        if discovery_range.mz.tag == range_tag.mz_range:
+            start_mz = discovery_range.mz.start_mz
+            stop_mz = discovery_range.mz.stop_mz
+        else:
+            start_mz = -1
+            stop_mz = -1
+
+        if discovery_range.index.tag == range_tag.index_range:
+            start_index = discovery_range.index.start_index
+            stop_index = discovery_range.index.stop_index
+        else:
+            start_index = 0
+            stop_index = 0
+
+        if discovery_range.full.tag == range_tag.full_range:
+            start_mz = -1
+            stop_mz = -1
+            start_index = 0
+            stop_index = 0
+
+
         verbose = self.verbose
         is_centroid = self.peak_mode == PeakMode.centroid
 

src/ms_peak_picker/_c/scan_averaging.pyx

@@ -11,7 +11,7 @@ import numpy as np
 cdef extern from * nogil:
     int printf (const char *template, ...)
 
-from cpython cimport PyFloat_AsDouble, PyInt_AsLong, PyErr_SetString, PyErr_Format
+from cpython cimport PyFloat_AsDouble, PyLong_AsLong, PyErr_SetString, PyErr_Format
 from cpython.list cimport PyList_GET_SIZE, PyList_GET_ITEM
 from cpython.tuple cimport PyTuple_GET_SIZE, PyTuple_GET_ITEM
 from cpython.slice cimport PySlice_GetIndicesEx
@@ -40,7 +40,7 @@ from ms_peak_picker._c.interval_t_vector cimport (
 
 cnp.import_array()
 
-cdef long num_processors = PyInt_AsLong(cpu_count())
+cdef long num_processors = PyLong_AsLong(cpu_count())
 
 
 @cython.cdivision(True)
@@ -266,7 +266,7 @@ cdef class GridAverager(object):
 
         if n_workers is None:
             n_workers = min(num_processors, len(spectra))
-        n_threads = PyInt_AsLong(n_workers)
+        n_threads = PyLong_AsLong(n_workers)
 
 
         prepare_arrays(spectra, &spectrum_pairs)
@@ -314,7 +314,7 @@ cdef class GridAverager(object):
         if n_workers is None:
             n_threads = 1
         else:
-            n_threads = PyInt_AsLong(n_workers)
+            n_threads = PyLong_AsLong(n_workers)
 
         if start > stop:
             stop, start = start, stop

src/ms_peak_picker/_c/size_t_vector.pyx

@@ -11,7 +11,7 @@ from cpython.sequence cimport (
     PySequence_Fast_GET_ITEM, PySequence_Fast_GET_SIZE)
 from cpython.slice cimport PySlice_GetIndicesEx
 
-from cpython.int cimport PyInt_FromSize_t, PyInt_AsLong
+from cpython.long cimport PyLong_FromSize_t, PyLong_AsLong
 
 cdef enum VectorStateEnum:
     should_free = 1
@@ -333,7 +333,7 @@ cdef class SizeTVector(object):
             qsort(self.get_data(), self.size(), sizeof(size_t), compare_value_size_t)
 
     cpdef object _to_python(self, size_t value):
-        return PyInt_FromSize_t(value)
+        return PyLong_FromSize_t(value)
 
     cpdef size_t _to_c(self, object value) except *:
-        return PyInt_AsLong(value)
+        return PyLong_AsLong(value)