Remove reexports from pyhmmer module and update Cython headers directly

Author: althonos

include/libhmmer/p7_hmmfile.pxd

@@ -1,3 +1,4 @@
+from libc.stdint cimport uint32_t
 from libc.stdio cimport FILE
 from posix.types cimport off_t
 
@@ -57,3 +58,16 @@ cdef extern from "hmmer.h" nogil:
     int  p7_hmmfile_Read(P7_HMMFILE *hfp, ESL_ALPHABET **ret_abc,  P7_HMM **opt_hmm)# except *
     int  p7_hmmfile_PositionByKey(P7_HMMFILE *hfp, const char *key)
     int  p7_hmmfile_Position(P7_HMMFILE *hfp, const off_t offset)
+
+    # Private re-exports
+
+    cdef uint32_t v3a_magic
+    cdef uint32_t v3b_magic
+    cdef uint32_t v3c_magic
+    cdef uint32_t v3d_magic
+    cdef uint32_t v3e_magic
+    cdef uint32_t v3f_magic
+
+    int read_asc20hmm(P7_HMMFILE* hfp, ESL_ALPHABET** ret_abc, P7_HMM** opt_hmm)
+    int read_asc30hmm(P7_HMMFILE* hfp, ESL_ALPHABET** ret_abc, P7_HMM** opt_hmm)
+    int read_bin30hmm(P7_HMMFILE* hfp, ESL_ALPHABET** ret_abc, P7_HMM** opt_hmm)

include/libhmmer/p7_tophits.pxd

@@ -31,6 +31,7 @@ cdef extern from "hmmer.h" nogil:
     P7_TOPHITS *p7_tophits_Create()
     P7_TOPHITS *p7_tophits_Clone(const P7_TOPHITS* h)
     int         p7_tophits_Grow(P7_TOPHITS *h)
+    int         p7_tophits_Reuse(P7_TOPHITS* h)
     int         p7_tophits_CreateNextHit(P7_TOPHITS *h, P7_HIT **ret_hit)
     int         p7_tophits_Add(P7_TOPHITS *h,
     				  char *name, char *acc, char *desc,

src/pyhmmer/plan7.pyx

@@ -104,8 +104,20 @@ from libhmmer.p7_pipeline cimport P7_PIPELINE, p7_pipemodes_e, p7_zsetby_e, p7_s
 from libhmmer.p7_profile cimport p7_LOCAL, p7_GLOCAL, p7_UNILOCAL, p7_UNIGLOCAL
 from libhmmer.p7_trace cimport P7_TRACE, p7t_statetype_e
 from libhmmer.p7_prior cimport P7_PRIOR
+from libhmmer.p7_tophits cimport p7_tophits_Reuse
 from libhmmer.nhmmer cimport ID_LENGTH_LIST
 from capacity cimport new_capacity
+from libhmmer.p7_hmmfile cimport (
+    read_asc20hmm,
+    read_asc30hmm,
+    read_bin30hmm,
+    v3a_magic,
+    v3b_magic,
+    v3c_magic,
+    v3d_magic,
+    v3e_magic,
+    v3f_magic
+)
 
 if HMMER_IMPL == "VMX":
     from libhmmer.impl_vmx cimport p7_oprofile, p7_omx, impl_Init, p7O_EXTRA_SB
@@ -181,18 +193,6 @@ from .easel cimport (
     Randomness,
     RandomnessOrSeed,
 )
-from .reexports.p7_tophits cimport p7_tophits_Reuse
-from .reexports.p7_hmmfile cimport (
-    read_asc20hmm,
-    read_asc30hmm,
-    read_bin30hmm,
-    v3a_magic,
-    v3b_magic,
-    v3c_magic,
-    v3d_magic,
-    v3e_magic,
-    v3f_magic
-)
 
 if TARGET_SYSTEM == "Linux":
     from .fileobj.linux cimport fileobj_linux_open as fopen_obj
@@ -8662,8 +8662,8 @@ cdef class TopHits:
                 fname = "p7_tophits_TabularTargets"
                 status = libhmmer.p7_tophits.p7_tophits_TabularTargets(
                     file,
-                    qname,
-                    qacc,
+                    <char*> qname,
+                    <char*> qacc,
                     self._th,
                     &self._pli,
                     header
@@ -8672,8 +8672,8 @@ cdef class TopHits:
                 fname = "p7_tophits_TabularDomains"
                 status = libhmmer.p7_tophits.p7_tophits_TabularDomains(
                     file,
-                    qname,
-                    qacc,
+                    <char*> qname,
+                    <char*> qacc,
                     self._th,
                     &self._pli,
                     header
@@ -8682,8 +8682,8 @@ cdef class TopHits:
                 fname = "p7_tophits_TabularXfam"
                 status = libhmmer.p7_tophits.p7_tophits_TabularXfam(
                     file,
-                    qname,
-                    qacc,
+                    <char*> qname,
+                    <char*> qacc,
                     self._th,
                     &self._pli,
                 )