Expose additional private fields of `skch::Sketch` in Cython headers

include/fastani/map/common_func.pxd

+from libc.stdint cimport uint64_t
+from libcpp.string cimport string
+from libcpp.vector cimport vector
+
+from fastani.map.base_types cimport hash_t, seqno_t
+
+cdef extern from "map/include/commonFunc.hpp" namespace "skch::CommonFunc" nogil:
+
+    cdef int seed
+
+    void reverseComplement(const char * src, char * dest, int length)
+    hash_t getHash(const char * seq, int length)
+
+    void addMinimizers[T, KSEQ](
+        vector[T] &minimizerIndex,
+        KSEQ kseq,
+        int kmerSize,
+        int windowSize,
+        int alphabetSize,
+        seqno_t seqCounter
+    )
+
+    uint64_t getReferenceSize(const vector[string] &refSequences)
+
+    void ltrim(string &s)
+    void rtrim(string &s)
+    void trim(string &s)

include/fastani/map/win_sketch.pxd

 cimport libcpp11.iostream
+from libcpp.map cimport map
 from libcpp.unordered_map cimport unordered_map
 from libcpp.vector cimport vector
 
@@ -15,18 +16,47 @@ from fastani.map.map_parameters cimport Parameters
 
 cdef extern from "map/include/winSketch.hpp" namespace "skch" nogil:
 
-    cdef cppclass Sketch:
+    IF FASTANI_PRIVATE_ACCESS:
 
-        ctypedef vector[MinimizerInfo].const_iterator MIIter_t
-        ctypedef unordered_map[MinimizerMapKeyType, MinimizerMapValueType] MI_Map_t
-        ctypedef vector[MinimizerInfo] MI_Type
+        cdef cppclass Sketch:
 
-        vector[ContigInfo] metadata
-        vector[seqno_t]    sequencesByFileInfo
-        MI_Map_t minimizerPosLookupIndex
+            ctypedef vector[MinimizerInfo].const_iterator MIIter_t
+            ctypedef unordered_map[MinimizerMapKeyType, MinimizerMapValueType] MI_Map_t
+            ctypedef vector[MinimizerInfo] MI_Type
 
-        Sketch(const Parameters &p)
+            float              percentageThreshold # private
+            int                freqThreshold # private
+            Parameters&        param # private
+            MI_Type            minimizerIndex # private
+            map[int, int]      minimizerFreqHistogram # private
+            vector[ContigInfo] metadata
+            vector[seqno_t]    sequencesByFileInfo
+            MI_Map_t           minimizerPosLookupIndex
 
-        int getFreqThreshold()
-        MIIter_t searchIndex(seqno_t seqId, offset_t winpos)
-        MIIter_t getMinimizerIndexEnd()
+            Sketch() # private
+            Sketch(const Parameters &p)
+
+            void build() # private
+            void index() # private
+            void computeFreqHist() # private
+            int getFreqThreshold()
+            MIIter_t searchIndex(seqno_t seqId, offset_t winpos)
+            MIIter_t getMinimizerIndexEnd()
+
+    ELSE:
+
+        cdef cppclass Sketch:
+
+            ctypedef vector[MinimizerInfo].const_iterator MIIter_t
+            ctypedef unordered_map[MinimizerMapKeyType, MinimizerMapValueType] MI_Map_t
+            ctypedef vector[MinimizerInfo] MI_Type
+
+            vector[ContigInfo] metadata
+            vector[seqno_t]    sequencesByFileInfo
+            MI_Map_t           minimizerPosLookupIndex
+
+            Sketch(const Parameters &p)
+
+            int getFreqThreshold()
+            MIIter_t searchIndex(seqno_t seqId, offset_t winpos)
+            MIIter_t getMinimizerIndexEnd()

setup.py

@@ -93,9 +93,13 @@ class publicize_headers(_build_ext):
     def patch_header(self, old_path, new_path):
         self.mkpath(os.path.dirname(new_path))
         with open(old_path, "r") as src:
-            with open(new_path, "w") as dst:
-                for line in src:
-                    dst.write( line.replace("private:", "public:") )
+            source = src.read()
+
+        source = re.sub("private:", "public:", source)
+        source = re.sub(r"class (.+\s*)\{(\s*)", r"class \1 {\npublic:\n\2", source)
+
+        with open(new_path, "w") as dst:
+            dst.write(source)
 
 
 class build_ext(_build_ext):
@@ -121,7 +125,7 @@ class build_ext(_build_ext):
 
         # use debug directives with Cython if building in debug mode
         cython_args = {"include_path": ["include", "pyfastani"], "compiler_directives": {}}
-        cython_args["compile_time_env"] = {"SYS_IMPLEMENTATION": SYS_IMPLEMENTATION}
+        cython_args["compile_time_env"] = {"FASTANI_PRIVATE_ACCESS": 1}
         if self.force:
             cython_args["force"] = True
         if self.debug: