cython setup imc_termite pytho module

.gitignore

@@ -10,7 +10,7 @@ nohup.out
 raw_eater.cpp
 raw_meat.cpp
 
-cyt/*.cpp
+cython/*.cpp
 /build
 
 *.log

cython/imc_termite.pxd

@@ -0,0 +1,18 @@
+# cython: language_level = 3
+
+# use some C++ STL libraries
+from libcpp.string cimport string
+from libcpp.vector cimport vector
+from libcpp cimport bool
+
+cdef extern from "imc_raw.hpp" namespace "imc":
+  cdef cppclass imc_termite "imc::raw":
+    # constructor(s)
+    imc_termite() except +
+    imc_termite(string rawfile) except +
+    # provide raw file
+    void submit_file(string rawfile) except+
+    # get JSON list of channels
+    vector[string] get_channels() except+
+    # print all channels
+    void print_channels(string outputdir) except+

cython/py_imc_termite.pyx

@@ -0,0 +1,27 @@
+# distutils: language = c++
+
+from imc_termite cimport imc_termite
+
+import json as jn
+# import numpy as np
+
+cdef class imctermite:
+
+  # C++ instance of class => stack allocated (requires nullary constructor!)
+  cdef imc_termite cpp_imc
+
+  # constructor
+  def __cinit__(self, string rawfile):
+    self.cpp_imc = imc_termite(rawfile)
+
+  # provide raw file
+  def submit_file(self,string rawfile):
+    self.cpp_tdm.set_file(rawfile)
+
+  # get JSON list of channels
+  def get_channels(self, bool data):
+    return self.cpp_imc.get_channels()
+
+  # print a channels
+  def print_channel(self, string outputdir):
+    self.cpp_tdm.print_channels(outputdir)

cython/setup.py

@@ -0,0 +1,24 @@
+from distutils.core import setup
+from distutils.extension import Extension
+from Cython.Build import cythonize
+
+extensions = Extension(
+    name="imc_termite",
+    sources=["cython/py_imc_termite.pyx"],
+    # libraries=[""],
+    # library_dirs=["lib"],
+    include_dirs=["lib"],
+    language='c++',
+    extra_compile_args=['-std=c++17','-Wno-unused-variable'],
+    extra_link_args=['-std=c++17'],
+)
+
+setup(
+    version='0.1',
+    description='IMCtermite cython extension',
+    author='Record Evolution GmbH',
+    author_email='mario.fink@record-evolution.de',
+    url='https://github.com/RecordEvolution/IMCtermite.git',
+    name="imc_termite",
+    ext_modules=cythonize(extensions)
+)

lib/imc_raw.hpp

@@ -5,6 +5,7 @@
 
 #include <fstream>
 #include <filesystem>
+#include <iostream>
 
 #include "hexshow.hpp"
 #include "imc_key.hpp"

makefile

@@ -58,36 +58,14 @@ docker-build :
 docker-run:
 	docker run -it --rm imctermite:0.1 /bin/bash
 
-# # build CLI executable
-# $(EXE) : $(SRC)main.cpp $(LIB)raweat.hpp $(LIB)hexshow.hpp $(LIB)rawmerge.hpp output
-# 	$(CCC) $(OPT) $< -o $@
+#-----------------------------------------------------------------------------#
+# python
 
-# # development version
-# eatdev : $(SRC)main_dev.cpp $(LIB)raweat.hpp
-# 	$(CCC) $(OPT) $< -o $@
-#
-# # build target for conversion set of .raw files
-# eatall : $(SRC)eatall.cpp $(LIB)raweat.hpp
-# 	$(CCC) $(OPT) $< -o $@
-
-# check existence of name of executable globally
-# chexe:=$(shell command -v $(EXE))
-#
-# # install executable if name does not exist yet
-# install : $(EXE)
-# ifeq ($(chexe),)
-# 	cp $(EXE) /usr/local/bin/
-# else
-# 	@echo "executable with name already exists! choose different name!"
-# 	@exit 1
-# endif
-
-# # uninstall
-# uninstall :
-# 	rm /usr/local/bin/$(EXE)
+cython-build : $(CYT)setup.py $(CYT)imc_termite.pxd $(CYT)py_imc_termite.pyx $(HPP)
+	python3 $< build_ext --inplace
 
 #-----------------------------------------------------------------------------#
-# Python
+# Python (to be removed)
 
 # build python module
 py : $(CYT)setup_raw_eater.py $(CYT)raw_eater.pyx $(CYT)raw_eater.pxd $(LIB)raweat.hpp \

src/main.cpp

@@ -1,10 +1,11 @@
 //---------------------------------------------------------------------------//
 
 #include <iostream>
+#include <vector>
 #include <filesystem>
 
-#include "imc_key.hpp"
-#include "imc_block.hpp"
+// #include "imc_key.hpp"
+// #include "imc_block.hpp"
 #include "imc_raw.hpp"
 
 //---------------------------------------------------------------------------//