Add explicit noexcept in nogil function declaration

libmetgem/_cosine.pxd

@@ -10,4 +10,4 @@ cpdef enum SpectraMatchState:
 
 cdef double cosine_score_nogil(double, peak_t*, np.npy_intp,
                                double, peak_t*, np.npy_intp,
-                               double, int) nogil
+                               double, int) noexcept nogil

libmetgem/_cosine.pyx

@@ -24,10 +24,10 @@ from ._common cimport (score_t, np_arr_pointer,
                        arr_from_score_vector,
                        arr_from_1d_vector)
 
-cdef double addScore(double sum, const score_t &b) nogil:
+cdef double addScore(double sum, const score_t &b) noexcept nogil:
     return sum + b.value
 
-cdef bool compareByScore(const score_t &a, const score_t &b) nogil:
+cdef bool compareByScore(const score_t &a, const score_t &b) noexcept nogil:
     return a.value > b.value
 
 
@@ -37,7 +37,7 @@ cdef vector[score_t] compare_spectra_nogil(double spectrum1_mz,
                                            double spectrum2_mz,
                                            peak_t *spectrum2_data,
                                            np.npy_intp spectrum2_size,
-                                           double mz_tolerance) nogil:
+                                           double mz_tolerance) noexcept nogil:
     cdef:
         double dm
         vector[score_t] scores
@@ -117,7 +117,7 @@ cdef double cosine_score_nogil(double spectrum1_mz,
                                peak_t *spectrum2_data,
                                np.npy_intp spectrum2_size,
                                double mz_tolerance,
-                               int min_matched_peaks) nogil:
+                               int min_matched_peaks) noexcept nogil:
     cdef:
         vector[score_t] matches = compare_spectra_nogil(spectrum1_mz,
                                                         spectrum1_data,

libmetgem/_database.pyx

@@ -171,7 +171,7 @@ cdef query_result_t query_nogil(char *fname, vector[int] indices,
                                 double analog_mz_tolerance=0.,
                                 bool positive_polarity=True,
                                 double mz_min = 50.,
-                                object callback=None) nogil:
+                                object callback=None) noexcept nogil:
     cdef:
         sqlite3 *db
         sqlite3_stmt *stmt

libmetgem/_filter.pxd

@@ -4,4 +4,4 @@ from libcpp.vector cimport vector
 cimport numpy as np
 from ._common cimport peak_t
 
-cdef vector[peak_t] filter_data_nogil(double, const peak_t *, np.npy_intp, int, int, int, int, double) nogil
+cdef vector[peak_t] filter_data_nogil(double, const peak_t *, np.npy_intp, int, int, int, int, double) noexcept nogil

libmetgem/_filter.pyx

@@ -28,7 +28,7 @@ cdef bool compareByMz(const peak_t &a, const peak_t &b) nogil:
 cdef vector[peak_t] parent_filter_nogil(double mz_parent, vector[peak_t] data,
                                         int min_intensity,
                                         int parent_filter_tolerance,
-                                        double mz_min = 50.) nogil:
+                                        double mz_min = 50.) noexcept nogil:
     cdef:
         int i
         float mz, intensity
@@ -64,7 +64,7 @@ cdef vector[peak_t] parent_filter_nogil(double mz_parent, vector[peak_t] data,
 @cython.cdivision(True)    
 cdef vector[peak_t] window_rank_filter_nogil(vector[peak_t] data,
                                              int matched_peaks_window,
-                                             int min_matched_peaks_search) nogil:
+                                             int min_matched_peaks_search) noexcept nogil:
     cdef:
         int i, j, count=0
         float mz
@@ -93,7 +93,7 @@ cdef vector[peak_t] window_rank_filter_nogil(vector[peak_t] data,
 @cython.boundscheck(False)
 @cython.wraparound(False)
 @cython.cdivision(True)
-cdef vector[peak_t] square_root_and_normalize_data_nogil(vector[peak_t] data) nogil:
+cdef vector[peak_t] square_root_and_normalize_data_nogil(vector[peak_t] data) noexcept nogil:
     cdef:
         int i
         double dot_product = 0.
@@ -123,7 +123,7 @@ cdef vector[peak_t] filter_data_nogil(double mz_parent, const peak_t *data,
                                       int parent_filter_tolerance,
                                       int matched_peaks_window,
                                       int min_matched_peaks_search,
-                                      double mz_min) nogil:
+                                      double mz_min) noexcept nogil:
     cdef vector[peak_t] peaks
 
     if data_size == 0:
@@ -156,7 +156,7 @@ cdef vector[vector[peak_t]] filter_data_multi_nogil(vector[double] mzvec,
                                                     int matched_peaks_window,
                                                     int min_matched_peaks_search,
                                                     double mz_min,
-                                                    object callback=None) nogil:
+                                                    object callback=None) noexcept nogil:
     cdef:
         vector[vector[peak_t]] spectra
         int i

libmetgem/_mgf.pyx

@@ -46,7 +46,7 @@ cdef extern from *:
     extern const char* CHARSET
 
 
-cdef inline double strtof(char* string, char **endptr) nogil:
+cdef inline double strtof(char* string, char **endptr) noexcept nogil:
     cdef char *ptr = NULL
 
     # Allow comma as decimal separator
@@ -56,7 +56,7 @@ cdef inline double strtof(char* string, char **endptr) nogil:
     return std_strtof(string, endptr)
 
 
-cdef void read_data(char line[MAX_LINE_SIZE], vector[peak_t] *peaklist, FILE *fp) nogil:
+cdef void read_data(char line[MAX_LINE_SIZE], vector[peak_t] *peaklist, FILE *fp) noexcept nogil:
     """Read peak list from file.
        First line has already been read and has to be passed as first argument.
        peak list is read into `peaklist`, which is cleared as first step."""

libmetgem/_msp.pyx

@@ -57,11 +57,11 @@ cdef extern from *:
     extern const char* CHARSET
 
 
-cdef inline bool isdelim(char s) nogil:
+cdef inline bool isdelim(char s) noexcept nogil:
     return strchr(b'()[]{},;:', s) != NULL
 
 
-cdef inline void trim(char* string) nogil:
+cdef inline void trim(char* string) noexcept nogil:
     cdef:
         int i = 0
         int index = 0
@@ -91,7 +91,7 @@ cdef inline void trim(char* string) nogil:
 
 
 cdef void read_data(char line[MAX_LINE_SIZE], vector[peak_t] *peaklist,
-                    FILE *fp, int num_peaks) nogil:
+                    FILE *fp, int num_peaks) noexcept nogil:
     """Read peak list from file.
        First line has already been read and has to be passed as first argument.
        peak list is read into `peaklist`, which is cleared as first step."""

libmetgem/_network.pyx

@@ -19,10 +19,10 @@ ctypedef struct element_t:
     int index
     double cosine
 
-cdef bool compareElementsByCosine(const element_t &a, const element_t &b) nogil:
+cdef bool compareElementsByCosine(const element_t &a, const element_t &b) noexcept nogil:
     return a.cosine > b.cosine
 
-cdef bool compareInteractionsByCosine(const interaction_t &a, const interaction_t &b) nogil:
+cdef bool compareInteractionsByCosine(const interaction_t &a, const interaction_t &b) noexcept nogil:
     if a.cosine > b.cosine:
         return True
     elif a.cosine < b.cosine:
@@ -41,14 +41,14 @@ cdef bool compareInteractionsByCosine(const interaction_t &a, const interaction_
         return False
     else:
         return False
- 
+
 @cython.boundscheck(False)
 @cython.wraparound(False)
 cdef vector[interaction_t] generate_network_nogil(const float[:,:] scores_matrix,
                                                   vector[double] mzvec,
                                                   double pairs_min_cosine,
                                                   size_t top_k,
-                                                  object callback=None) nogil:
+                                                  object callback=None) noexcept nogil:
     cdef:
         vector[interaction_t] interactions, interactions2
         interaction_t inter