Mark callback functions used from C as nogil and (mostly) noexcept

Prevents "Casting a GIL-requiring function into a nogil function" warnings.

Author: jmarshall

pysam/libcalignmentfile.pyx

@@ -2320,38 +2320,30 @@ cdef class IteratorRowSelection(IteratorRow):
             raise IOError(read_failure_reason(ret))
 
 
-cdef int __advance_nofilter(void *data, bam1_t *b):
+cdef int __advance_nofilter(void *data, bam1_t *b) noexcept nogil:
     '''advance without any read filtering.
     '''
     cdef __iterdata * d = <__iterdata*>data
-    cdef int ret
-    with nogil:
-        ret = sam_itr_next(d.htsfile, d.iter, b)
-    return ret
+    return sam_itr_next(d.htsfile, d.iter, b)
 
 
-cdef int __advance_raw_nofilter(void *data, bam1_t *b):
+cdef int __advance_raw_nofilter(void *data, bam1_t *b) noexcept nogil:
     '''advance (without iterator) without any read filtering.
     '''
     cdef __iterdata * d = <__iterdata*>data
-    cdef int ret
-    with nogil:
-        ret = sam_read1(d.htsfile, d.header, b)
-    return ret
+    return sam_read1(d.htsfile, d.header, b)
 
 
-cdef int __advance_all(void *data, bam1_t *b):
+cdef int __advance_all(void *data, bam1_t *b) noexcept nogil:
     '''only use reads for pileup passing basic filters such as
 
     BAM_FUNMAP, BAM_FSECONDARY, BAM_FQCFAIL, BAM_FDUP
     '''
 
     cdef __iterdata * d = <__iterdata*>data
-    cdef mask = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP
     cdef int ret
     while 1:
-        with nogil:
-            ret = sam_itr_next(d.htsfile, d.iter, b)
+        ret = sam_itr_next(d.htsfile, d.iter, b)
         if ret < 0:
             break
         if b.core.flag & d.flag_filter:
@@ -2360,7 +2352,7 @@ cdef int __advance_all(void *data, bam1_t *b):
     return ret
 
 
-cdef int __advance_raw_all(void *data, bam1_t *b):
+cdef int __advance_raw_all(void *data, bam1_t *b) noexcept nogil:
     '''only use reads for pileup passing basic filters such as
 
     BAM_FUNMAP, BAM_FSECONDARY, BAM_FQCFAIL, BAM_FDUP
@@ -2369,8 +2361,7 @@ cdef int __advance_raw_all(void *data, bam1_t *b):
     cdef __iterdata * d = <__iterdata*>data
     cdef int ret
     while 1:
-        with nogil:
-            ret = sam_read1(d.htsfile, d.header, b)
+        ret = sam_read1(d.htsfile, d.header, b)
         if ret < 0:
             break
         if b.core.flag & d.flag_filter:
@@ -2379,7 +2370,7 @@ cdef int __advance_raw_all(void *data, bam1_t *b):
     return ret
 
 
-cdef int __advance_samtools(void * data, bam1_t * b):
+cdef int __advance_samtools(void * data, bam1_t *b) nogil:
     '''advance using same filter and read processing as in
     the samtools pileup.
     '''
@@ -2388,8 +2379,7 @@ cdef int __advance_samtools(void * data, bam1_t * b):
     cdef int q
 
     while 1:
-        with nogil:
-            ret = sam_itr_next(d.htsfile, d.iter, b) if d.iter else sam_read1(d.htsfile, d.header, b)
+        ret = sam_itr_next(d.htsfile, d.iter, b) if d.iter else sam_read1(d.htsfile, d.header, b)
         if ret < 0:
             break
         if b.core.flag & d.flag_filter:
@@ -2402,13 +2392,7 @@ cdef int __advance_samtools(void * data, bam1_t * b):
             if d.seq != NULL:
                 free(d.seq)
             d.tid = b.core.tid
-            with nogil:
-                d.seq = faidx_fetch_seq(
-                    d.fastafile,
-                    d.header.target_name[d.tid],
-                    0, MAX_POS,
-                    &d.seq_len)
-
+            d.seq = faidx_fetch_seq(d.fastafile, d.header.target_name[d.tid], 0, MAX_POS, &d.seq_len)
             if d.seq == NULL:
                 raise ValueError(
                     "reference sequence for '{}' (tid={}) not found".format(
@@ -2560,19 +2544,13 @@ cdef class IteratorColumn:
 
         if self.stepper is None or self.stepper == "all":
             with nogil:
-                self.pileup_iter = bam_mplp_init(1,
-                                                 <bam_plp_auto_f>&__advance_all,
-                                                 data)
+                self.pileup_iter = bam_mplp_init(1, __advance_all, data)
         elif self.stepper == "nofilter":
             with nogil:
-                self.pileup_iter = bam_mplp_init(1,
-                                                 <bam_plp_auto_f>&__advance_nofilter,
-                                                 data)
+                self.pileup_iter = bam_mplp_init(1, __advance_nofilter, data)
         elif self.stepper == "samtools":
             with nogil:
-                self.pileup_iter = bam_mplp_init(1,
-                                                 <bam_plp_auto_f>&__advance_samtools,
-                                                 data)
+                self.pileup_iter = bam_mplp_init(1, <bam_plp_auto_f>__advance_samtools, data)
         else:
             raise ValueError(
                 "unknown stepper option `%s` in IteratorColumn" % self.stepper)
@@ -2609,19 +2587,13 @@ cdef class IteratorColumn:
 
         if self.stepper is None or self.stepper == "all":
             with nogil:
-                self.pileup_iter = bam_mplp_init(1,
-                                                 <bam_plp_auto_f>&__advance_raw_all,
-                                                 data)
+                self.pileup_iter = bam_mplp_init(1, __advance_raw_all, data)
         elif self.stepper == "nofilter":
             with nogil:
-                self.pileup_iter = bam_mplp_init(1,
-                                                 <bam_plp_auto_f>&__advance_raw_nofilter,
-                                                 data)
+                self.pileup_iter = bam_mplp_init(1, __advance_raw_nofilter, data)
         elif self.stepper == "samtools":
             with nogil:
-                self.pileup_iter = bam_mplp_init(1,
-                                                 <bam_plp_auto_f>&__advance_samtools,
-                                                 data)
+                self.pileup_iter = bam_mplp_init(1, <bam_plp_auto_f>__advance_samtools, data)
         else:
             raise ValueError(
                 "unknown stepper option `%s` in IteratorColumn" % self.stepper)