Fix array reallocation formula causing segfaults in nhmmer (#62)

include/capacity.pxd

@@ -3,11 +3,6 @@ cdef inline size_t new_capacity(size_t capacity, size_t length) nogil:
 
     Compute a new capacity for a buffer reallocation.
 
-    This is how CPython computes the allocation sizes for the array storing
-    the references for a `list` object.
-
     """
-    cdef size_t new_cap = (<size_t> capacity + (capacity >> 3) + 6) & ~(<size_t> 3)
-    if (capacity - length) > (new_cap - capacity):
-        new_cap = (<size_t> capacity + 3) & ~(<size_t> 3)
-    return new_cap
+    return (<size_t> capacity + (capacity >> 3) + 6) & ~(<size_t> 3)
+

include/libhmmer/nhmmer.pxd

@@ -1,6 +1,5 @@
 from libc.stdint cimport int64_t, uint64_t
 from libc.stdlib cimport calloc, malloc, realloc, free
-from libc.stdio cimport printf
 
 cimport libeasel
 from libhmmer.p7_tophits cimport P7_TOPHITS
@@ -19,7 +18,7 @@ ctypedef struct ID_LENGTH_LIST:
     size_t     size
 
 
-cdef inline ID_LENGTH_LIST* idlen_list_init(size_t size) nogil:
+cdef inline ID_LENGTH_LIST* idlen_list_init(size_t size) noexcept nogil:
     cdef ID_LENGTH_LIST* l = <ID_LENGTH_LIST*> malloc(sizeof(ID_LENGTH_LIST))
     if l != NULL:
         l.count = 0
@@ -30,13 +29,13 @@ cdef inline ID_LENGTH_LIST* idlen_list_init(size_t size) nogil:
             l = NULL
     return l
 
-cdef inline void idlen_list_destroy(ID_LENGTH_LIST* l) nogil:
+cdef inline void idlen_list_destroy(ID_LENGTH_LIST* l) noexcept nogil:
     if l != NULL:
         if l.id_lengths != NULL:
             free(l.id_lengths)
         free(l)
 
-cdef inline int idlen_list_add(ID_LENGTH_LIST* l, int64_t id, int64_t L) nogil:
+cdef inline int idlen_list_add(ID_LENGTH_LIST* l, int64_t id, int64_t L) noexcept nogil:
     if l.count > 0 and l.id_lengths[l.count - 1].id == id:
         l.id_lengths[l.count - 1].length = L
     else:
@@ -50,7 +49,7 @@ cdef inline int idlen_list_add(ID_LENGTH_LIST* l, int64_t id, int64_t L) nogil:
         l.count += 1
     return libeasel.eslOK
 
-cdef inline int idlen_list_assign(ID_LENGTH_LIST* l, P7_TOPHITS* th) nogil:
+cdef inline int idlen_list_assign(ID_LENGTH_LIST* l, P7_TOPHITS* th) noexcept nogil:
     cdef uint64_t i
     cdef int64_t  j = 0
     for i in range(th.N):
@@ -61,5 +60,5 @@ cdef inline int idlen_list_assign(ID_LENGTH_LIST* l, P7_TOPHITS* th) nogil:
         th.hit[i].dcl[0].ad.L = l.id_lengths[j].length
     return libeasel.eslOK
 
-cdef inline int idlen_list_clear(ID_LENGTH_LIST* l) nogil:
+cdef inline int idlen_list_clear(ID_LENGTH_LIST* l) noexcept nogil:
     l.count = 0