* README.md: adjust python examples to renaming of module

* bump new major version 2.0.0

.github/workflows/pypi-deploy.yml

@@ -0,0 +1,97 @@
+
+name: Build Python Wheels
+
+on:
+  push:
+    #branches: [master]
+    tags: ["v[0-9]+.[0-9]+.[0-9]+"]
+
+jobs:
+
+  build_setup:
+    name: Prepare environment for wheel builds
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v2
+      - name: Prepare wheel build
+        run: make -C python/ setup
+      - name: Store wheel configuration files
+        uses: actions/upload-artifact@v2
+        with:
+          name: wheel-config
+          path: python/
+
+  build_wheels:
+    name: Build binary wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    needs: [build_setup]
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, windows-2019]
+        arch: [auto32, auto64, aarch64]
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==2.1.2
+      - name: Get wheel configuration files
+        uses: actions/download-artifact@v2
+        with:
+          name: wheel-config
+          path: python/
+      - name: Build wheels
+        run: python -m cibuildwheel --output-dir wheelhouse
+        working-directory: python/
+        # env:
+        #   CIBW_BUILD: cp36-* cp37-* cp38-* cp39-* cp310-*
+      - name: Store binary wheels
+        uses: actions/upload-artifact@v2
+        with:
+          name: binary-wheels
+          path: python/wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    needs: [build_setup]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Install cython
+        run: python -m pip install cython==0.29.24
+      - name: Get wheel configuration files
+        uses: actions/download-artifact@v2
+        with:
+          name: wheel-config
+          path: python/
+      - name: Build sdist
+        run: python setup.py sdist
+        working-directory: python/
+      - name: Store source wheels
+        uses: actions/upload-artifact@v2
+        with:
+          name: source-wheels
+          path: python/dist/*.tar.gz
+
+
+  upload_pypi:
+    name: Upload binary wheels to PyPI
+    runs-on: ubuntu-20.04
+    needs: [build_wheels, build_sdist]
+
+    steps:
+      - name: Get source wheels
+        uses: actions/download-artifact@v2
+        with:
+          name: source-wheels
+          path: dist/
+      - name: Get binary wheels
+        uses: actions/download-artifact@v2
+        with:
+          name: binary-wheels
+          path: dist/
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.TDMTERMITE_GITHUB_WORKFLOW_PYPI_API_TOKEN }}

README.md

@@ -160,19 +160,21 @@ make cython-requirements
 make cython-install
 ```
 
-That makes the module available for import as a `import tdm_termite` .
+which makes the module available for import by `import tdm_termite` .
 
 #### Installation with pip
 
-The package is also available via the [Python Package Index](https://pypi.org) at 
+The package is also available via the [Python Package Index](https://pypi.org) at
 [TDMtermite](https://pypi.org/project/TDMtermite/). To install the latest version simply do
 
 ```Shell
 python3 -m pip install TDMtermite
 ```
 
-Note, that _python3_setuptools_ and _gcc version >= 10.2.0_ are required to 
+##### Unix
-successfully install and use it. 
+
+Note, that _python3_setuptools_ and _gcc version >= 10.2.0_ are required to
+successfully install and use it.
 
 ## Usage
 
@@ -223,21 +225,21 @@ To be able to use the Python module _tdm_termite_, it first has to be built loca
 or installed on the system. In the Python interpreter, simply do:
 
 ```Python
-import tdm_termite
+import TDMtermite
 ```
 
 This will import the module. The TDM files are provided by creating an instance of
-the _tdm_termite_ class:
+the _tdmtermite_ class:
 
 ```Python
-# create 'tdm_termite' instance object
+# create 'tdmtermite' instance object
 try :
-    jack = tdm_termite.tdmtermite(b'samples/SineData.tdm',b'samples/SineData.tdx')
+    jack = TDMtermite.tdmtermite(b'samples/SineData.tdm',b'samples/SineData.tdx')
 except RuntimeError as e:
     print("failed to load/decode TDM files: " + str(e))
 ```
 
-After initializing the _tdm_termite_ object, it can be used to extract any of the
+After initializing the _tdmtermite_ object, it can be used to extract any of the
 available data. For instance, to list the included channelgroups and channels:
 
 ```Python
@@ -253,12 +255,12 @@ As a use case, we have a look at listing the ids of all channelgroups and printi
 their data to separate files:
 
 ```Python
-import tdm_termite
+import TDMtermite
 import re
 
-# create 'tdm_termite' instance object
+# create 'tdmtermite' instance object
 try :
-    jack = tdm_termite.tdmtermite(b'samples/SineData.tdm',b'samples/SineData.tdx')
+    jack = TDMtermite.tdmtermite(b'samples/SineData.tdm',b'samples/SineData.tdx')
 except RuntimeError as e :
     print("failed to load/decode TDM files: " + str(e))
 
@@ -292,8 +294,8 @@ to simply extract all data of the TDM datatset and dump it to files in a given
 (existing!) directory, do
 
 ```Python
-import tdm_termite
+import TDMtermite
-jack = tdm_termite.tdmtermite(b'samples/SineData.tdm',b'samples/SineData.tdx')
+jack = TDMtermite.tdmtermite(b'samples/SineData.tdm',b'samples/SineData.tdx')
 jack.write_all(b"./my_tdm_data_directory/")
 ```
 

cython/requirements.txt

@@ -1 +0,0 @@
-Cython==0.29.21

cython/setup.py

@@ -1,35 +0,0 @@
-from distutils.core import setup
-from distutils.extension import Extension
-from Cython.Build import cythonize
-import os
-
-extensions = Extension(
-    name="tdm_termite",
-    sources=["cython/py_tdm_termite.pyx"],
-    # libraries=[""],
-    # library_dirs=["lib"],
-    include_dirs=["lib","3rdparty/pugixml"],
-    language='c++',
-    extra_compile_args=['-std=c++17','-Wno-unused-variable'],
-    extra_link_args=['-std=c++17'],
-)
-
-os.system("git tag > gittags.log")
-with open ("gittags.log","r") as gt:
-    taglst = gt.readlines()
-os.remove("gittags.log")
-if len(taglst) > 0 :
-    version = taglst[-1].replace('\n','').replace('v','')
-else:
-    version = 'unkown'
-print("building version: "+version)
-
-setup(
-    version=version,
-    description='TDMtermite cython extension',
-    author='Record Evolution GmbH',
-    author_email='mario.fink@record-evolution.de',
-    url='https://github.com/RecordEvolution/TDMtermite.git',
-    name="tdm_termite",
-    ext_modules=cythonize(extensions)
-)

lib/tdm_datatype.hpp

@@ -14,6 +14,7 @@ typedef unsigned short int eUInt16Usi;
 typedef unsigned int eUInt32Usi;
 typedef float eFloat32Usi;
 typedef double eFloat64Usi;
+typedef char eStringUsi;
 
 class tdmdatatype
 {
@@ -26,12 +27,13 @@ protected:
   eUInt32Usi uint32_;   // 4
   eFloat32Usi float32_; // 5
   eFloat64Usi float64_; // 6
-  short int dtidx_;     // \in \{0,...,6\}
+  eStringUsi string_;   // 7
+  short int dtidx_;     // \in \{0,...,7\}
 
 public:
   tdmdatatype(): sint16_(0), sint32_(0),
                  uint8_(0), uint16_(0), uint32_(0),
-                 float32_(0.0), float64_(0.0),
+                 float32_(0.0), float64_(0.0), string_(0),
                  dtidx_(0) { };
   // every supported datatype gets its own constructor
   tdmdatatype(eInt16Usi num): sint16_(num), dtidx_(0) {};
@@ -41,6 +43,7 @@ public:
   tdmdatatype(eUInt32Usi num): uint32_(num), dtidx_(4) {};
   tdmdatatype(eFloat32Usi num): float32_(num), dtidx_(5) {};
   tdmdatatype(eFloat64Usi num): float64_(num), dtidx_(6) {};
+  tdmdatatype(eStringUsi num): string_(num), dtidx_(7) {};
 
   // identify type
   short int& dtype() { return dtidx_; }
@@ -55,6 +58,7 @@ public:
     this->uint32_ = num.uint32_;
     this->float32_ = num.float32_;
     this->float64_ = num.float64_;
+    this->string_ = num.string_;
     this->dtidx_ = num.dtidx_;
   }
 
@@ -70,6 +74,7 @@ public:
       this->uint32_ = num.uint32_;
       this->float32_ = num.float32_;
       this->float64_ = num.float64_;
+      this->string_ = num.string_;
       this->dtidx_ = num.dtidx_;
     }
 
@@ -119,6 +124,12 @@ public:
     this->dtidx_ = 6;
     return *this;
   }
+  tdmdatatype& operator=(const eStringUsi &num)
+  {
+    this->string_ = num;
+    this->dtidx_ = 7;
+    return *this;
+  }
 
   // obtain number as double
   double as_double()
@@ -131,6 +142,7 @@ public:
     else if ( dtidx_ == 4 ) num = (double)uint32_;
     else if ( dtidx_ == 5 ) num = (double)float32_;
     else if ( dtidx_ == 6 ) num = (double)float64_;
+    else if ( dtidx_ == 7 ) num = (double)(int)string_;
     return num;
   }
 
@@ -144,6 +156,7 @@ public:
     else if ( num.dtidx_ == 4 ) out<<num.uint32_;
     else if ( num.dtidx_ == 5 ) out<<num.float32_;
     else if ( num.dtidx_ == 6 ) out<<num.float64_;
+    else if ( num.dtidx_ == 7 ) out<<num.string_;
     return out;
   }
 
@@ -332,7 +345,7 @@ const std::vector<tdm_datatype> tdm_datatypes = {
   {"eFloat32Usi","DT_FLOAT",3,"float_sequence",4,"32 bit float"},
   {"eFloat64Usi","DT_DOUBLE",7,"double_sequence",8,"64 bit double"},
 
-  // {"eStringUsi","DT_STRING",1,"string_sequence",0,"text"}
+  {"eStringUsi","DT_STRING",1,"string_sequence",1,"text"}
 
 };
 

lib/tdm_termite.cpp

@@ -445,9 +445,14 @@ void tdm_termite::process_localcolumns(bool showlog, pugi::xml_document& xml_doc
     {
       locc.values_ = vl.at(0);
     }
+    else if ( vl.size() == 0 )
+    {
+      //std::cerr<<"localcolumn ("<<locc.id_<<","<<locc.name_<<") misses any value-ids"<<"\n";
+      locc.values_ = "none";
+    }
     else
     {
-      throw std::logic_error("localcolumn with out/multiple values id(s)");
+      throw std::logic_error("localcolumn with multiple values id(s)");
     }
 
     // add external id referring to block in <usi:include>
@@ -460,7 +465,7 @@ void tdm_termite::process_localcolumns(bool showlog, pugi::xml_document& xml_doc
       {
         throw std::runtime_error(std::string("measurement_quantity: ")
                                  + locc.measurement_quantity_
-                                 + std::string(" is ambiguous") );
+                                 + std::string(" is missing/ambiguous") );
       }
       std::string dt = tdmchannels_.at(locc.measurement_quantity_).datatype_;
       std::string sequence_type;
@@ -482,8 +487,10 @@ void tdm_termite::process_localcolumns(bool showlog, pugi::xml_document& xml_doc
 
       if ( locc.external_id_.empty() )
       {
-        throw std::logic_error( std::string("no external id found for ")
+        //throw std::logic_error( std::string("no external id found for ")
-                              + sequence_type + std::string(" with ") + locc.values_ );
+        //                      + sequence_type + std::string(" with ") + locc.values_ );
+        //std::cerr<<"no external id found for "<<sequence_type<<" with "<<locc.values_<<"\n";
+        locc.external_id_ = "none";
       }
     }
 
@@ -508,8 +515,8 @@ std::string tdm_termite::get_channel_overview(format chformatter)
 
   // compose header
   chformatter.set_header(true);
-  tdm_channelgroup grp;
+  //tdm_channelgroup grp;
-  channels_summary += grp.get_info(chformatter);
+  //channels_summary += grp.get_info(chformatter);
   tdm_channel chn;
   channels_summary += chn.get_info(chformatter);
   std::string rule; // = std::string("#");
@@ -526,8 +533,9 @@ std::string tdm_termite::get_channel_overview(format chformatter)
                                                    it!=tdmchannels_.end(); ++it)
   {
     // get corresponding group
-    tdm_channelgroup grp = tdmchannelgroups_.at(it->second.group_);
+    // tdm_channelgroup grp = tdmchannelgroups_.at(it->second.group_);
-    channels_summary += grp.get_info(chformatter);
+    // channels_summary += grp.get_info(chformatter);
+
     // ...and actual channel
     channels_summary += it->second.get_info(chformatter);
     channels_summary += std::string("\n");
@@ -619,7 +627,7 @@ std::vector<tdmdatatype> tdm_termite::get_channel(std::string& id)
     // retrieve full channel info
     tdm_channel chn = tdmchannels_.at(id);
 
-    // extract (first) "localcolumn" for channel
+    // extract (first) "localcolumn" for channel TODO there should only be a single!! local_column!!
     if ( chn.local_columns_.size() != 1 )
     {
       throw std::runtime_error(std::string("invalid local_columns_ of channel: ") + id);
@@ -636,8 +644,28 @@ std::vector<tdmdatatype> tdm_termite::get_channel(std::string& id)
     }
 
     // use "values" id to map to external block
+    if ( loccol.external_id_ == "none" )
+    {
+      //throw std::runtime_error(std::string("missing external_id in local_column ")+loccol.id_);
+      //std::cerr<<"missing external_id in local_column "<<loccol.id_<<"\n";
+      return std::vector<tdmdatatype>(0);
+    }
     block blk = tdx_blocks_.at(loccol.external_id_);
 
+    // find corresponding submatrix
+    if ( submatrices_.count(loccol.submatrix_) != 1 )
+    {
+      throw std::runtime_error(std::string("no associated submatrix for localcolumn found: ") + loccol.id_);
+    }
+    submatrix subm = submatrices_.at(loccol.submatrix_);
+    if ( subm.number_of_rows_ != blk.length_ )
+    {
+      std::stringstream ss;
+      ss<<"number of rows in submatrix "<<subm.id_<<" ("<<subm.number_of_rows_<<") "
+        <<" does not agree with length of associated block "<<blk.id_<<" ("<<blk.length_<<")";
+      throw std::runtime_error(ss.str());
+    }
+
     // declare vector of appropriate length
     std::vector<tdmdatatype> datavec(blk.length_);
 
@@ -691,6 +719,10 @@ std::vector<tdmdatatype> tdm_termite::get_channel(std::string& id)
     {
       this->convert_data_to_type<eFloat64Usi>(tdxblk,datavec);
     }
+    else if ( blk.value_type_ == std::string("eStringUsi") )
+    {
+      this->convert_data_to_type<eStringUsi>(tdxblk,datavec);
+    }
     else
     {
       throw std::runtime_error(std::string("unsupported/unknown datatype") + blk.value_type_);
@@ -852,7 +884,7 @@ void tdm_termite::print_group(std::string &id, const char* filename, bool includ
     for ( std::string chn: chngrp.channels_ )
     {
       std::vector<tdmdatatype> chndat = this->get_channel(chn);
-      if ( chndat.size() > maxrows ) maxrows = chndat.size();
+      if ( chndat.size() > maxrows ) maxrows = (unsigned int)chndat.size();
       allchns.push_back(chndat);
     }
 
@@ -917,7 +949,7 @@ void tdm_termite::check_filename_path(const char* filename)
 
   if ( !std::filesystem::is_directory(pt) )
   {
-    throw std::runtime_error(std::string("directory does not exist: ") + pt.c_str() );
+    throw std::runtime_error( std::string("directory does not exist: ") + pt.u8string() );
   }
 }
 
@@ -987,6 +1019,10 @@ void tdm_termite::check_datatype_consistency()
     {
       if ( el.size_ != sizeof(eFloat64Usi) ) throw std::logic_error("invalid representation of eFloat64Usi");
     }
+    else if ( el.name_ == "eStringUsi" )
+    {
+      if ( el.size_ != sizeof(eStringUsi) ) throw std::logic_error("invalid representation of eStringUsi");
+    }
     else
     {
       throw std::logic_error("missing datatype validation");

makefile

@@ -13,15 +13,19 @@ HPP = $(wildcard lib/*.hpp)
 CC = g++ -std=c++17
 
 # compiler options and optimization flags
-OPT = -O3 -Wall -Werror -Wunused-variable -Wsign-compare
+OPT = -O3 -Wall -Wconversion -Wpedantic -Wunused-variable -Wsign-compare
 
 # include 3rd party libraries paths
 LIBB := 3rdparty/
 LIB := $(foreach dir,$(shell ls $(LIBB)),-I $(LIBB)$(dir))
 
 # determine git version/commit tag
-GTAG := $(shell git tag | tail -n1)
+GTAG := $(shell git tag -l --sort=version:refname | tail -n1 | sed "s/$^v//g")
 GHSH := $(shell git rev-parse HEAD | head -c8)
+GVSN := $(shell cat python/VERSION | tr -d ' \n')
+
+# current timestamp
+TMS = $(shell date +%Y%m%dT%H%M%S)
 
 # define install location
 INST := /usr/local/bin
@@ -31,33 +35,39 @@ OST := $(shell uname)
 CWD := $(shell pwd)
 
 # --------------------------------------------------------------------------- #
-# CLI tool
+# C++ and CLI tool
 
-$(EXE) : main.o $(SRC).o
+# check tags and build executable
+exec: check-tags $(GVSN) $(EXE)
+
+# build executable
+$(EXE): $(SRC).o main.o
 	$(CC) $(OPT) $^ -o $@
 
-install : $(EXE)
+$(SRC).o : lib/$(SRC).cpp lib/$(SRC).hpp $(HPP)
-	cp $< $(INST)/
+	$(CC) -c $(OPT) $(LIB) $< -o $@
-
-uninstall : $(INST)/$(EXE)
-	rm $<
 
 # build main.cpp object file and include git version/commit tag
-main.o : src/main.cpp lib/$(SRC).hpp $(HPP)
+main.o: src/main.cpp lib/$(SRC).hpp $(HPP)
 	@cp $< $<.cpp
 	@if [ $(OST) = "Linux" ]; then\
 		sed -i 's/TAGSTRING/$(GTAG)/g' $<.cpp; \
 		sed -i 's/HASHSTRING/$(GHSH)/g' $<.cpp; \
+		sed -i 's/TIMESTAMPSTRING/$(TMS)/g' $<.cpp; \
 	fi
 	@if [ $(OST) = "Darwin" ]; then\
 		sed -i '' 's/TAGSTRING/$(GTAG)/g' $<.cpp; \
 		sed -i '' 's/HASHSTRING/$(GHSH)/g' $<.cpp; \
+		sed -i '' 's/TIMESTAMPSTRING/$(TMS)/g' $<.cpp; \
 	fi
 	$(CC) -c $(OPT) $(LIB) -I lib/ $<.cpp -o $@
 	@rm $<.cpp
 
-$(SRC).o : lib/$(SRC).cpp lib/$(SRC).hpp $(HPP)
+install: $(EXE)
-	$(CC) -c $(OPT) $(LIB) $< -o $@
+	cp $< $(INST)/
+
+uninstall : $(INST)/$(EXE)
+	rm $<
 
 tdmtest : tdmtest.o
 	$(CC) $(OPT) $^ -o $@
@@ -66,38 +76,19 @@ tdmtest.o : src/test.cpp lib/$(SRC).hpp $(HPP)
 	$(CC) -c $(OPT) $(LIB) -I lib/ $< -o $@
 
 cpp-clean :
-	rm -f $(EXE) *.o src/main.cpp.cpp tdmtest
+	rm -vf $(EXE)
+	rm -vf *.o src/main.cpp.cpp tdmtest
 
-# --------------------------------------------------------------------------- #
+#-----------------------------------------------------------------------------#
-# check process
+# versions
 
-checkps :
+$(GTAG):
-	@ps aux | head -n1
+	@echo "consistent versions check successful: building $(GTAG)"
-	@ps aux | grep $(EXE) | grep -v "grep"
 
-# --------------------------------------------------------------------------- #
+check-tags:
-# python/cython module
+	@echo "latest git tag:  $(GTAG)"
-
+	@echo "latest git hash: $(GHSH)"
-cython-requirements: cython/requirements.txt
+	@echo "python version:  $(GVSN)"
-	python3 -m pip install -r $<
-
-cython-help : cython/setup.py
-	python3 $< --help
-
-cython-list : cython/setup.py
-	python3 $< --name --description --author --author-email --url
-
-cython-build : cython/setup.py cython/tdm_termite.pxd cython/py_tdm_termite.pyx $(HPP) lib/tdm_termite.cpp
-	python3 $< build_ext --inplace
-	cp -v tdm_termite.cpython-*.so python/
-
-cython-install : cython/setup.py cython/tdm_termite.pxd cython/py_tdm_termite.pyx $(HPP) lib/tdm_termite.cpp
-	python3 $< install
-
-cython-clean :
-	rm -vf cython/py_tdm_termite.c* cython/tdm_termite.c*
-	rm -vf tdm_termite.cpython-*.so python/tdm_termite.cpython-*.so
-	rm -rf build
 
 # --------------------------------------------------------------------------- #
 # docker
@@ -114,17 +105,32 @@ docker-clean:
 	docker image remove tdmtermite
 
 # --------------------------------------------------------------------------- #
-# pip
+# check process
 
-pip-publish: cython-build
+checkps :
-	cd pip/ && make pip-publish
+	@ps aux | head -n1
-
+	@ps aux | grep $(EXE) | grep -v "grep"
-pip-test:
-	cd pip/ && make pip-test
 
 # --------------------------------------------------------------------------- #
+# python
 
-clean : cpp-clean cython-clean
+python-build: check-tags $(GVSN)
-	cd pip/ && make pip-clean
+	make -C python/ build-inplace
+	cp python/TDMtermite*.so ./ -v
+
+python-install: check-tags $(GVSN)
+	make -C python/ install
+
+python-clean:
+	make -C python/ clean
+	rm -vf TDMtermite*.so
+
+python-test:
+	PYTHONPATH=./ python python/examples/usage.py
+
+# --------------------------------------------------------------------------- #
+# clean
+
+clean : cpp-clean python-clean
 
 # --------------------------------------------------------------------------- #

pip/Dockerfile

@@ -1,15 +0,0 @@
-
-FROM debian:bullseye
-
-RUN DEBIAN_FRONTEND=noninteractive \
-  apt-get update && apt-get upgrade -y && apt-get install -y \
-  python3 \
-  python3-pip \
-  python3-setuptools
-
-# RUN python3 -m pip install -i https://test.pypi.org/simple/ TDMtermite-RecordEvolution==0.6.7 && \
-#   python3 -m pip install --upgrade TDMtermite-RecordEvolution
-RUN python3 -m pip install TDMtermite
-
-# CMD ["sleep","3600"]
-CMD ["python3","-m","pip","freeze"]

pip/Dockerfile-manylinux

@@ -1,25 +0,0 @@
-
-FROM quay.io/pypa/manylinux2010_x86_64
-
-RUN yum -y install \
-    git \
-    python34-devel \
-    gcc-c++ \
-    python34-tkinter \
-    make \
-    python34-pip \
-    
-RUN sudo yum -y install rh-python36-python-devel.x86_64 rh-python35-python-devel.x86_64 python27-python-devel.x86_64
-
-ENV PATH /opt/rh/python27/root/usr/bin:/opt/rh/rh-python35/root/usr/bin/:/opt/rh/rh-python36/root/usr/bin/:$PATH
-
-RUN  python3.6 -m pip install --user --upgrade cython wheel twine auditwheel
-
-WORKDIR /home/${USERNAME}/neuron-yale
-
-RUN  git checkout setuppy \
-     && python3.6 setup.py bdist_wheel
-
-# repair wheel? see : https://malramsay.com/post/perils_of_packaging/
-RUN python3.6 -m pip install --user --upgrade auditwheel
-RUN LD_LIBRARY_PATH=`pwd`/_install/lib auditwheel repair dist/NEURON-7.8-cp36-cp36m-linux_x86_64.whl

pip/bkup.pyproject.toml

@@ -1,4 +0,0 @@
-[build-system]
-requires = [
-    "setuptools"
-]

pip/makefile

@@ -1,62 +0,0 @@
-# --------------------------------------------------------------------------- #
-
-pip-publish: pip-sdist pip-upload
-
-pip-sdist: ../cython/py_tdm_termite.pyx ../cython/tdm_termite.pxd ../cython/py_tdm_termite.cpp
-	cp -v ../cython/py_tdm_termite.pyx ../cython/tdm_termite.pxd ./
-	cp -v ../cython/py_tdm_termite.cpp ./
-	cp -v ../lib/*.hpp ../lib/*.cpp ./
-	cp -v ../3rdparty/pugixml/* ./
-	cat ../README.md | head -n316 | tail -n306 > ./README.md
-	cp -v ../LICENSE ./
-	# cython py_tdm_termite.pyx -o py_tdm_termite.cpp
-	python3 setup.py sdist
-
-pip-setup:
-	apt-get install -y python3-setuptools \
-	                   python3-pip \
-	                   python3-venv
-	python3 -m pip install --upgrade build
-	python3 -m pip install twine wheel auditwheel cython
-	python3 -m pip install --user --upgrade twine
-
-pip-build:
-	#python3 -m build
-	# python3 setup.py sdist bdist_wheel
-	python3 setup.py bdist_wheel
-
-# actually it seems we have to use CentOS container
-# docker run -i -t -v `pwd`:/io quay.io/pypa/manylinux1_x86_64 /bin/bash
-# see https://github.com/neuronsimulator/nrn/issues/329 for setup of the container
-
-pip-audit:
-	auditwheel repair $(shell find dist/ -name "*-cp38-cp38-linux_x86_64.whl")
-
-# username: __token__
-# password: API-token including "pypi-"
-# !! RUN AS ROOT!! (only for bdist_wheel + auditwheel)
-pip-upload-test:
-	python3 -m twine upload --repository testpypi dist/$(shell ls -t dist/ | head -n1)
-
-pip-upload:
-	python3 -m twine upload dist/$(shell ls -t dist/ | head -n1)
-
-pip-test-install:
-	python3 -m pip install --index-url https://test.pypi.org/simple --no-deps TDMtermite-RecordEvolution
-	# python3 -m pip install -i https://test.pypi.org/simple/ TDMtermite-RecordEvolution==0.5
-
-pip-test:
-	docker build . --tag tdmtermite-piptest
-	docker run -it --rm tdmtermite-piptest
-
-pip-clean:
-	rm -rvf dist/
-	rm -rvf *.egg-info
-	rm -rvf build/
-	rm -rvf cython/
-	rm -rvf wheelhouse/
-	rm -vf *.pyx *.pxd
-	rm -vf *.cpp *.c *.hpp
-	rm -vf README.md LICENSE
-
-# --------------------------------------------------------------------------- #

pip/setup.cfg

@@ -1,21 +0,0 @@
-[metadata]
-name = TDMtermite-RecordEvolution
-version = 0.5
-author = Record Evolution GmbH
-author_email = mario.fink@record-evolution.de
-maintainer = Record Evolution GmbH
-license = MIT
-description = Extract and read data from National Instruments LabVIEW tdx/tdm files and export them as csv files
-long_description = file: README.md
-long_description_content_type = text/markdown
-url = https://github.com/RecordEvolution/TDMtermite.git
-project_urls =
-    Bug Tracker = https://github.com/RecordEvolution/TDMtermite/issues
-classifiers =
-    Programming Language :: Python :: 3
-    License :: OSI Approved :: MIT License
-    Operating System :: OS Independent
-
-[options]
-packages = find:
-python_requires = >=3.6

pip/setup.py

@@ -1,36 +0,0 @@
-
-from setuptools import setup, Extension
-
-with open("README.md", "r", encoding="utf-8") as fh:
-    long_description = fh.read()
-
-setup(
-    name="TDMtermite",
-    version="1.0.0", #version,
-    author="Record Evolution GmbH",
-    author_email="mario.fink@record-evolution.de",
-    maintainer="Record Evolution GmbH",
-    license="MIT",
-    description="Extract and read data from National Instruments LabVIEW tdx/tdm files and export them as csv files",
-    keywords="TDM/TDX NationalInstruments LabVIEW decode",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    url="https://github.com/RecordEvolution/TDMtermite.git",
-    project_urls={
-        "Bug Tracker": "https://github.com/RecordEvolution/TDMtermite/issues",
-    },
-    classifiers=[
-        "Programming Language :: Python :: 3",
-        "License :: OSI Approved :: MIT License",
-        "Operating System :: OS Independent",
-    ],
-    ext_modules=[Extension("tdm_termite",
-                           ["py_tdm_termite.cpp"],
-                           # libraries_dirs=["cython/"],
-                           # include_dirs=["3rdparty/pugixml/","lib/"],
-                           # depends=["../lib/tdm_termite.hpp"]
-                           language='c++',
-                           extra_compile_args=['-std=c++17','-Wno-unused-variable'],
-                           extra_link_args=['-std=c++17'],
-                           )],
-)

python/MANIFEST.in

@@ -1,4 +1,4 @@
-include *.hpp
+include lib/*.hpp
 include *.cpp
 include *.pyx
 include *.pxd

python/TDMtermite.pxd

@@ -1,28 +1,34 @@
-# 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 "tdm_termite.cpp":
+cdef extern from "lib/tdm_termite.cpp":
   pass
 
-cdef extern from "tdm_termite.hpp":
+cdef extern from "lib/tdm_termite.hpp":
-  cdef cppclass tdm_termite:
+
+  cdef cppclass cpptdmtermite "tdm_termite":
+
     # constructor(s)
-    tdm_termite() except +
+    cpptdmtermite() except +
-    tdm_termite(string tdmfile, string tdxfile) except +
+    cpptdmtermite(string tdmfile, string tdxfile) except +
+
     # provide TDM files
     void submit_files(string tdmfile, string tdxfile) except+
+
     # get list of channel(-group) ids
     vector[string] get_channelgroup_ids() except+
     vector[string] get_channel_ids() except+
+
     # get data of specific channel
     vector[double] get_channel_as_double(string id) except+
+
     # get meta-data
     string get_channelgroup_info(string id) except+
     string get_channel_info(string id) except+
+
     # print a channel(-group)
     void print_group(string id, const char* filename, bool include_meta,
                      char delimiter, string column_header) except+

python/TDMtermite.pyx

@@ -1,51 +1,52 @@
 # distutils: language = c++
+# cython: language_level = 3
+
+from TDMtermite cimport cpptdmtermite
 
-from tdm_termite cimport tdm_termite
 import json as jn
-# import numpy as np
 
 cdef class tdmtermite:
 
   # C++ instance of class => stack allocated (requires nullary constructor!)
-  cdef tdm_termite cpp_tdm
+  cdef cpptdmtermite cpptdm
 
   # constructor
   def __cinit__(self, string tdmfile, string tdxfile):
-    self.cpp_tdm = tdm_termite(tdmfile,tdxfile)
+    self.cpptdm = cpptdmtermite(tdmfile,tdxfile)
 
   # provide TDM files
   def submit_files(self,string tdmfile, string tdxfile):
-    self.cpp_tdm.submit_files(tdmfile,tdxfile)
+    self.cpptdm.submit_files(tdmfile,tdxfile)
 
   # get list of channel(-group) ids
   def get_channelgroup_ids(self):
-    return self.cpp_tdm.get_channelgroup_ids()
+    return self.cpptdm.get_channelgroup_ids()
   def get_channel_ids(self):
-    return self.cpp_tdm.get_channel_ids()
+    return self.cpptdm.get_channel_ids()
 
   # get data of specific channel
   def get_channel(self, string id):
-    return self.cpp_tdm.get_channel_as_double(id)
+    return self.cpptdm.get_channel_as_double(id)
 
   # get meta-data of channel(-group) (as dictionary)
   def get_channelgroup_info(self, string id):
-    grpstr = self.cpp_tdm.get_channelgroup_info(id)
+    grpstr = self.cpptdm.get_channelgroup_info(id)
     return jn.loads(grpstr.decode())
   def get_channel_info(self, string id):
-    chnstr = self.cpp_tdm.get_channel_info(id)
+    chnstr = self.cpptdm.get_channel_info(id)
     return jn.loads(chnstr.decode())
 
   # print a channel(-group)
   def print_channelgroup(self, string id, const char* filename, bool include_meta,
                                char delimiter, string column_header):
-    self.cpp_tdm.print_group(id,filename,include_meta,delimiter,column_header)
+    self.cpptdm.print_group(id,filename,include_meta,delimiter,column_header)
   def print_channel(self, string id, const char* filename,
                           bool include_meta):
-    self.cpp_tdm.print_channel(id,filename,include_meta)
+    self.cpptdm.print_channel(id,filename,include_meta)
 
   # print all data grouped by channelgroups
   def write_all(self, string outputdir) :
-    grpids = self.cpp_tdm.get_channelgroup_ids()
+    grpids = self.cpptdm.get_channelgroup_ids()
     for id in grpids :
       grpfile = outputdir.decode() + "/channelgroup_" + id.decode() + ".csv"
-      self.cpp_tdm.print_group(id,grpfile.encode(),True,ord(','),"".encode())
+      self.cpptdm.print_group(id,grpfile.encode(),True,ord(','),"".encode())

python/VERSION

@@ -0,0 +1 @@
+2.0.0

python/examples/custom.py

@@ -1,11 +1,11 @@
 
-import tdm_termite
+import TDMtermite
 import json
 import re
 
 # create 'tdm_termite' instance object
 try :
-    jack = tdm_termite.tdmtermite(b'samples/SineData.tdm',b'samples/SineData.tdx')
+    jack = TDMtermite.tdmtermite(b'samples/SineData.tdm',b'samples/SineData.tdx')
 except RuntimeError as e :
     print("failed to load/decode TDM files: " + str(e))
 

python/examples/minimal.py

@@ -1,9 +1,9 @@
 
-import tdm_termite
+import TDMtermite
 
 # create 'tdm_termite' instance object
 try :
-    jack = tdm_termite.tdmtermite(b'samples/SineData.tdm',b'samples/SineData.tdx')
+    jack = TDMtermite.tdmtermite(b'samples/SineData.tdm',b'samples/SineData.tdx')
     # list ids of channelgroups
     grpids = jack.get_channelgroup_ids()
     # iterate through groups

python/examples/usage.py

@@ -1,12 +1,12 @@
 
-import tdm_termite
+import TDMtermite
 # import numpy as np
 import json
 import re
 
 # create 'tdm_termite' instance object
 try :
-    jack = tdm_termite.tdmtermite(b'samples/SineData.tdm',b'samples/SineData.tdx')
+    jack = TDMtermite.tdmtermite(b'samples/SineData.tdm',b'samples/SineData.tdx')
 except RuntimeError as e :
     print("failed to load/decode TDM files: " + str(e))
 

python/makefile

@@ -0,0 +1,60 @@
+
+setup:
+	cat ../README.md | grep '^# TDMtermite' -A 50000 > ./README.md
+	#pandoc -f markdown -t rst -o README.rst README.md
+	#python -m rstvalidator README.rst
+	cp -r ../lib ./
+	cp -r ../3rdparty ./
+	cp -v ../LICENSE ./
+
+setup-clean:
+	rm -vf README.md README.rst LICENSE
+	rm -rf lib/ 3rdparty/
+
+build: setup
+	python setup.py build
+
+build-inplace: setup
+	python setup.py build_ext --inplace
+
+build-install: setup
+	python setup.py install
+
+build-sdist: setup
+	python setup.py sdist
+	python -m twine check dist/*
+
+build-bdist: setup
+	python setup.py bdist
+	python -m twine check dist/*
+
+build-clean:
+	python setup.py clean --all
+	rm -vf TDMtermite*.so TDMtermite*.cpp
+	rm -rvf dist/ IMCtermite.egg-info/
+
+cibuildwheel-build: setup
+	cibuildwheel --platform linux
+
+cibuildwheel-clean:
+	rm -rvf wheelhouse/
+
+pypi-audit:
+	auditwheel repair $(shell find dist/ -name "*-linux_x86_64.whl")
+
+# username: __token__
+# password: API-token including "pypi-"
+pypi-upload-test:
+	python -m twine upload --repository testpypi dist/$(shell ls -t dist/ | head -n1)
+
+pypi-install-test:
+	python -m pip install --index-url https://test.pypi.org/simple --no-deps TDMtermite-RecordEvolution
+	# python3 -m pip install -i https://test.pypi.org/simple/ TDMtermite-RecordEvolution==0.5
+
+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.py

python/pyproject.toml

@@ -0,0 +1,6 @@
+[build-system]
+requires = ["setuptools", "wheel","Cython"]
+build-backend = "setuptools.build_meta"
+
+[tool.cibuildwheel]
+before-all = ""

python/setup.cfg

@@ -0,0 +1,23 @@
+
+[metadata]
+name = TDMtermite
+description = Extract and read data from National Instruments LabVIEW tdx/tdm files and export them as csv files
+long_description = file: README.md
+# long_description_content_type = text/x-rst
+long_description_content_type = text/markdown
+version = file: VERSION
+author = Record Evolution GmbH
+author_email = mario.fink@record-evolution.de
+maintainer = Record Evolution GmbH
+url= https://github.com/RecordEvolution/TDMtermite.git
+license = MIT License
+license_files = LICENSE
+keywords = TDM, TDX, National Instruments, DIAdem, LabVIEW, Measurement Studio, SignalExpress
+classifiers =
+  Programming Language :: Python :: 3
+  License :: OSI Approved :: MIT License
+  Operating System :: OS Independent
+  Topic :: Scientific/Engineering
+  Topic :: Software Development :: Libraries :: Python Modules
+
+[options]

python/setup.py

@@ -0,0 +1,23 @@
+from setuptools import Extension, setup
+from Cython.Build import cythonize
+import sys
+
+print("building on platform: "+sys.platform)
+
+cmpArgs = {
+    "linux": ['-std=c++17','-Wno-unused-variable'],
+    "darwin": ['-std=c++17','-Wno-unused-variable'],
+    "win32": ['/EHsc','/std:c++17']
+}
+
+extension = Extension(
+    "TDMtermite",
+    language='c++',
+    sources=["TDMtermite.pyx"],
+    include_dirs=["lib","3rdparty/pugixml"],
+    extra_compile_args=cmpArgs[sys.platform]
+)
+
+setup(
+    ext_modules=cythonize(extension,language_level=3)
+)

src/main.cpp

@@ -11,11 +11,12 @@
 
 const std::string gittag("TAGSTRING");
 const std::string githash("HASHSTRING");
+const std::string timestamp("TIMESTAMPSTRING");
 
 void show_usage()
 {
   std::cout<<"\n"
-           <<"tdmtermite ["<<gittag<<"-g"<<githash<<"] (github.com/RecordEvolution/TDMtermite.git)"
+           <<"tdmtermite ["<<gittag<<"-g"<<githash<<"-"<<timestamp<<"] (https://github.com/RecordEvolution/TDMtermite.git)"
            <<"\n\n"
            <<"Decode TDM/TDX files and dump data as *.csv"
            <<"\n\n"
@@ -78,7 +79,7 @@ optkeys parse_args(int argc, char* argv[], bool showargs = false)
     else if ( std::string(argv[1]) == std::string("--version")
            || std::string(argv[1]) == std::string("-v") )
     {
-      std::cout<<"tdmtermite "<<gittag<<"-g"<<githash<<"\n";
+      std::cout<<"tdmtermite "<<gittag<<"-g"<<githash<<"-"<<timestamp<<"\n";
     }
     else
     {
@@ -284,13 +285,13 @@ int main(int argc, char* argv[])
     if ( showroot ) std::cout<<"\n"<<jack.get_root().get_info()<<"\n";
 
     // get complete channel(-group) overview
-    format grpformatter(26,false,false,' ');
+    format grpformatter(16,false,false,' ');
     if (listgroups) std::cout<<"\n"<<jack.get_overview<tdm_channelgroup>(grpformatter)<<"\n";
-    format chformatter(14,false,false,' ');
+    format chformatter(16,false,false,' ');
     if (listchannels) std::cout<<"\n"<<jack.get_channel_overview(chformatter)<<"\n";
 
     // get complete submatrix/localcolumns overview
-    format formatter(18,false,false,' ');
+    format formatter(16,false,false,' ');
     if (listblocks) std::cout<<jack.get_overview<block>(formatter)<<"\n";
     if (listsubmatrices) std::cout<<jack.get_overview<submatrix>(formatter)<<"\n";
     if (listlocalcolumns) std::cout<<jack.get_overview<localcolumn>(formatter)<<"\n";