dna.pyi

@@ -1 +0,0 @@
-def dna_reverse(input_file_path: str, output_file_path: str):...

py_example.py

@@ -1,5 +0,0 @@
-import dna
-
-help(dna)
-
-dna.dna_reverse("filteredReads.txt","reversedSequence.txt")

src/main.cpp

@@ -1,12 +1,5 @@
 #include "dna.hpp"
 
-#ifdef DNA_IS_PYBIND
-#include <pybind11/pybind11.h>
-// #include <pybind11/stl_bind.h>
-namespace py = pybind11;
-#endif
-
-
 //注意，这个函数会被并行执行，请只访问begin<=i<end之间的内容，以免出现数据竞争导致程序异常
 void reverseComplement(char *begin, char *end) 
 {
@@ -21,7 +14,7 @@ void reverseComplement(char *begin, char *end)
     std::reverse(begin, end); //翻转DNA序列
 
     for (ptrdiff_t i = 0; i < (end - begin); ++i) {
-        // static int _ = (zt::print(NAME_VALUE(omp_get_num_threads()),"\n"),0); // 打印线程数量
+        static int _ = (zt::print(NAME_VALUE(omp_get_num_threads()),"\n"),0); // 打印线程数量
         auto it = complement.find(begin[i]);
         if (it != complement.end()) {
             begin[i] = it->second;
@@ -29,7 +22,6 @@ void reverseComplement(char *begin, char *end)
     }
 }
 
-#ifndef DNA_IS_PYBIND
 int main()
 {
 	try{
@@ -54,34 +46,3 @@ int main()
         throw;
     }
 }
-
-#else
-
-void bind_func(std::string input_file_name,std::string out_put_file_name){
-    try{
-       dna::open_file_and_calculate<(size_t)4*1024 * 1024 *1024 , (size_t)5e4+5>(input_file_name, out_put_file_name,reverseComplement);
-    // dna::open_file_and_calculate<(size_t)1 * 1024 *1024 , (size_t)5e4+5>(input_file_name, out_put_file_name,reverseComplement);
-   }catch(const std::exception &e){
-       zt::eprint(
-           "Caught an error because:\n",
-           "\t",NAME_VALUE(e.what()),"\n"
-           "Closing\n"
-       );
-       throw  e;
-   }catch(...){
-       zt::eprint(
-           "Caught an unknown error :\n",
-           "Closing\n"
-       );
-       throw;
-   }
-}
-
-PYBIND11_MODULE(dna, m){
-    m.doc() = "DNASequence processing functions"; // optional module docstring
-
-    m.def("dna_reverse", &bind_func, "DNA is double-stranded and complementary to each other, and when sequencing a DNA sample you can't be sure which strand is being measured, so the complementary strands of all the DNA fragments are counted and assembled together with the original file."
-        ,py::arg("input_file_path"),py::arg("output_file_path"));
-}
-
-#endif

xmake.lua

@@ -1,8 +1,6 @@
 add_rules("mode.debug","mode.release")
 set_languages("c++23")
 
-add_requires("pybind11")
-
 if is_mode("release")then
     set_optimize("aggressive") --这里使用了激进的优化，可能会导致浮点数计算不准确，考虑到本项目没有浮点计算，酌情考虑开启
     -- set_optimize("fastest") --上面和下面的二选一，--表示注释
@@ -26,20 +24,5 @@ end
 add_includedirs("src/tools")
 set_rundir("./")
 
-target("dna_pybind")
-    add_defines("DNA_IS_PYBIND")
-    add_packages("pybind11")
-    set_kind("shared")
-    set_extension(".pyd")
-    add_files("src/main.cpp")
-    set_basename("dna")
-    after_build(
-        function (target) 
-            print(target:targetdir())
-            os.cp("*.py*",target:targetdir())
-        end
-    )
-
 target("dna")
-    set_kind("binary")
     add_files("src/main.cpp")