* add github workflow for building wheels

* rename cython module for more consistency
* restructure python code
* proper python module setup
* bump major version 2.0.0

.github/workflows/wheels.yml

@@ -0,0 +1,34 @@
+
+name: Build Python Wheels
+on:
+  schedule:
+  push:
+    branches:
+      - master
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, windows-2019, macOS-10.15]
+        arch: [auto32, auto64, aarch64, ppc64le, s390x]
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==2.1.2
+      - name: Build wheels
+        run: python -m cibuildwheel --output-dir wheelhouse
+
+  upload_wheels:
+    name: Upload binary wheels to PyPI
+    needs: [build_wheels]
+    
+    steps:
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.IMCTERMITE_GITHUB_WORKFLOW_PYPI_API_TOKEN }}
+

.gitignore

@@ -31,3 +31,13 @@ pip/LICENSE
 pip/*egg-info
 pip/dist/
 pip/build/
+
+python/README.md
+python/LICENSE
+python/VERSION
+python/build
+python/*.egg-info
+python/dist
+python/*.soc
+python/lib/
+python/*.cpp

README.md

@@ -211,9 +211,9 @@ channels = imcraw.get_channels(False)
 print(channels)
 ```
 
-A more complete [example](python/usage.py), including the methods for obtaining the
-channels, i.a. their data and/or directly printing them to files, can be found
-in the Python folder.
+A more complete [example](python/examples/usage.py), including the methods for
+obtaining the channels, i.a. their data and/or directly printing them to files,
+can be found in the `python/examples` folder.
 
 ## References
 

python/IMCtermite.pxd

@@ -0,0 +1,24 @@
+
+# use some C++ STL libraries
+from libcpp.string cimport string
+from libcpp.vector cimport vector
+from libcpp cimport bool
+
+cdef extern from "lib/imc_raw.hpp" namespace "imc":
+
+  cdef cppclass cppimctermite "imc::raw":
+
+    # constructor(s)
+    cppimctermite() except +
+    cppimctermite(string rawfile) except +
+
+    # provide raw file
+    void set_file(string rawfile) except +
+
+    # get JSON list of channels
+    vector[string] get_channels(bool json, bool data) except +
+
+    # print single channel/all channels
+    void print_channel(string channeluuid, string outputdir, char delimiter) except +
+    void print_channels(string outputdir, char delimiter) except +
+    void print_table(string outputfile) except +

python/IMCtermite.pyx

@@ -0,0 +1,44 @@
+# distutils: language = c++
+# cython: language_level = 3
+
+from IMCtermite cimport cppimctermite
+
+import json as jn
+import decimal
+
+cdef class imctermite:
+
+  # C++ instance of class => stack allocated (requires nullary constructor!)
+  cdef cppimctermite cppimc
+
+  # constructor
+  def __cinit__(self, string rawfile):
+    self.cppimc = cppimctermite(rawfile)
+
+  # provide raw file
+  def submit_file(self,string rawfile):
+    self.cppimc.set_file(rawfile)
+
+  # get JSON list of channels
+  def get_channels(self, bool data):
+    chnlst = self.cppimc.get_channels(True,data)
+    chnlstjn = [jn.loads(chn.decode(errors="ignore")) for chn in chnlst]
+    return chnlstjn
+
+  # print single channel/all channels
+  def print_channel(self, string channeluuid, string outputfile, char delimiter):
+    self.cppimc.print_channel(channeluuid,outputfile,delimiter)
+  def print_channels(self, string outputdir, char delimiter):
+    self.cppimc.print_channels(outputdir,delimiter)
+
+  # print table including channels
+  def print_table(self, string outputfile):
+    chnlst = self.cppimc.get_channels(True,True)
+    chnlstjn = [jn.loads(chn.decode(errors="ignore")) for chn in chnlst]
+    with open(outputfile.decode(),'w') as fout:
+      for chn in chnlstjn:
+        fout.write('#' +str(chn['xname']).rjust(19)+str(chn['yname']).rjust(20)+'\n')
+        fout.write('#'+str(chn['xunit']).rjust(19)+str(chn['yunit']).rjust(20)+'\n')
+        for n in range(0,len(chn['ydata'])):
+          fout.write(str(chn['xdata'][n]).rjust(20)+
+                     str(chn['ydata'][n]).rjust(20)+'\n')

python/examples/usage.py

@@ -1,11 +1,11 @@
 
-import imc_termite
+import IMCtermite
 import json
 import os
 
 # declare and initialize instance of "imctermite" by passing a raw-file
 try :
-    imcraw = imc_termite.imctermite(b"samples/exampleB.raw")
+    imcraw = IMCtermite.imctermite(b"samples/exampleB.raw")
 except RuntimeError as e :
     raise Exception("failed to load/parse raw-file: " + str(e))
 

python/examples/usage_adv.py

@@ -1,5 +1,5 @@
 
-import imc_termite
+import IMCtermite
 import json
 import os
 
@@ -15,7 +15,7 @@ for fl in rawlist1:
 
     # declare and initialize instance of "imctermite" by passing a raw-file
     try :
-        imcraw = imc_termite.imctermite(fl.encode())
+        imcraw = IMCtermite.imctermite(fl.encode())
     except RuntimeError as e :
         raise Exception("failed to load/parse raw-file: " + str(e))
 
@@ -24,7 +24,7 @@ for fl in rawlist1:
     print(json.dumps(channels,indent=4, sort_keys=False))
 
     # print the channels into a specific directory
-    imcraw.print_channels(b"./")
+    imcraw.print_channels(b"./",ord(','))
 
     # print all channels in single file
     imcraw.print_table(("./"+str(os.path.basename(fl).split('.')[0])+"_allchannels.csv").encode())

python/examples/usage_ext.py

@@ -1,12 +1,12 @@
 
-import imc_termite
+import IMCtermite
 import json
 import os
 import datetime
 
 # declare and initialize instance of "imctermite" by passing a raw-file
 try :
-    imcraw = imc_termite.imctermite(b"samples/sampleB.raw")
+    imcraw = IMCtermite.imctermite(b"samples/sampleB.raw")
 except RuntimeError as e :
     raise Exception("failed to load/parse raw-file: " + str(e))
 

python/examples/usage_files.py

@@ -0,0 +1,29 @@
+
+from IMCtermite import imctermite
+
+def show_results(imcraw) :
+
+    channels = imcraw.get_channels(False)
+    print(channels)
+
+    channelsData = imcraw.get_channels(True)
+    print("number of channels: " + str(len(channelsData)))
+
+    for (i,chn) in enumerate(channelsData) :
+        print(str(i) +  " | " + chn['name'])
+        print(chn['xname'] + " | " + chn['xunit'])
+        print(chn['xdata'][:10])
+        print(chn['yname'] + " | " + chn['yunit'])
+        print(chn['ydata'][:10])
+
+    print("")
+
+# create instance of 'imctermite'
+imcraw = imctermite(b'samples/sampleA.raw')
+
+show_results(imcraw)
+
+# use previous instance of 'imctermite' to provide new file
+imcraw.submit_file(b'samples/sampleB.raw')
+
+show_results(imcraw)

python/makefile

@@ -0,0 +1,44 @@
+
+GITAG := $(shell git tag -l --sort=version:refname | tail -n1 | sed 's/^v//g')
+
+setup:
+	echo $(GITAG) > VERSION
+	cat ../README.md | grep '^# IMCtermite' -A 50000 > ./README.md
+	cp -r ../lib ./
+	cp -v ../LICENSE ./
+
+setup-clean:
+	rm -vf README.md VERSION LICENSE
+	rm -rf lib/
+
+build: setup
+	python setup.py build
+
+build-inplace: setup
+	python setup.py build_ext --inplace
+
+build-sdist: setup
+	python setup.py sdist
+
+build-bdist: setup
+	python setup.py bdist
+
+build-clean:
+	python setup.py clean --all
+	rm -vf imctermite*.so imctermite*.cpp
+	rm -vf IMCtermite*.so IMCtermite*.cpp
+	rm -rvf dist/ IMCtermite.egg-info/
+
+cibuildwheel-build: setup
+	cibuildwheel --platform linux
+
+cibuildwheel-clean:
+	rm -rvf wheelhouse/
+
+pypi-upload:
+	python -m twine upload dist/$(shell ls -t dist/ | head -n1)
+
+clean: setup build-clean cibuildwheel-clean setup-clean
+
+run-example:
+	PYTHONPATH=$(pwd) python examples/usage_files.py

python/pyproject.toml

@@ -0,0 +1,7 @@
+[build-system]
+requires = ["setuptools", "wheel","Cython"]
+build-backend = "setuptools.build_meta"
+
+[tool.cibuildwheel]
+before-all = ""
+

python/setup.cfg

@@ -0,0 +1,19 @@
+
+[metadata]
+name = IMCtermite
+description = Enables extraction of measurement data from binary files with extension 'raw' used by proprietary software imcFAMOS/imcSTUDIO and facilitates its storage in open source file formats
+long_description = file: README.md
+version = file: VERSION
+author = Record Evolution GmbH
+author_email = mario.fink@record-evolution.de
+maintainer = Record Evolution GmbH
+url= 'https://github.com/RecordEvolution/IMCtermite.git'
+license = MIT License
+license_files = LICENSE
+keywords = IMC, raw, imcFAMOS, imcSTUDIO, imcCRONOS
+classifiers =
+  Programming Language :: Python :: 3,
+  License :: OSI Approved :: MIT License,
+  Operating System :: OS Independent
+
+[options]

python/setup.py

@@ -0,0 +1,6 @@
+from setuptools import setup
+from Cython.Build import cythonize
+
+setup(
+  ext_modules=cythonize(["IMCtermite.pyx"],language_level=3)
+)