PyPI setup

.gitignore

@@ -12,3 +12,5 @@ tdmripper
 tdmreaper
 cython/*.cpp
 tdmtermite
+dist/
+*.egg-info/

README.md

@@ -313,3 +313,16 @@ meta-data and provide these headers for usage in file output (see this
 - https://pugixml.org/
 - https://github.com/zeux/pugixml
 - https://cython.readthedocs.io/en/latest/src/userguide/wrapping_CPlusPlus.html
+
+### Packaging
+
+- https://packaging.python.org/tutorials/packaging-projects/
+- https://medium.com/swlh/distributing-python-packages-protected-with-cython-40fc29d84caf
+- https://levelup.gitconnected.com/how-to-deploy-a-cython-package-to-pypi-8217a6581f09
+- https://setuptools.readthedocs.io/en/latest/userguide/declarative_config.html
+- https://test.pypi.org/account/register/
+- https://malramsay.com/post/perils-of-packaging/
+- https://github.com/pypa/auditwheel
+- https://github.com/pypa/python-manylinux-demo
+- https://github.com/pypa/manylinux
+- https://github.com/neuronsimulator/nrn/issues/329

makefile

@@ -58,7 +58,7 @@ main.o : src/main.cpp lib/$(SRC).hpp $(HPP)
 $(SRC).o : lib/$(SRC).cpp lib/$(SRC).hpp $(HPP)
 	$(CC) -c $(OPT) -I $(LIB) $< -o $@
 
-clean-cpp :
+cpp-clean :
 	rm -f $(EXE) *.o src/main.cpp.cpp
 
 # --------------------------------------------------------------------------- #
@@ -87,7 +87,7 @@ cython-build : cython/setup.py cython/tdm_termite.pxd cython/py_tdm_termite.pyx
 cython-install : cython/setup.py cython/tdm_termite.pxd cython/py_tdm_termite.pyx $(HPP) lib/tdm_termite.cpp
 	python3 $< install
 
-clean-cython :
+cython-clean :
 	rm -vf cython/py_tdm_termite.cpp
 	rm -vf tdm_termite.cpython-*.so python/tdm_termite.cpython-*.so
 	rm -rf build
@@ -102,8 +102,50 @@ docker-run:
 	mkdir -pv data/{input,output}
 	docker run -it --rm --volume $(CWD)/data:/home/data tdmtermite:latest /bin/bash
 
-# --------------------------------------------------------------------------- #
+docker-clean:
-
+	rm -rv data
-clean : clean-cpp clean-cython
+	docker image remove tdmtermite
+
+# --------------------------------------------------------------------------- #
+# pip
+
+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!!
+pip-upload:
+	python3 -m twine upload --repository testpypi dist/*
+
+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-clean:
+	rm -rvf dist/
+	rm -rvf *.egg-info
+	rm -rvf build/ wheelhouse/
+
+# --------------------------------------------------------------------------- #
+
+clean : cpp-clean cython-clean pip-clean
 
 # --------------------------------------------------------------------------- #

pip/Dockerfile

@@ -0,0 +1,25 @@
+
+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/MANIFEST.in

@@ -0,0 +1 @@
+include cython/tdm_termite.pxd

pip/pyproject.toml

@@ -0,0 +1,7 @@
+[build-system]
+requires = [
+  "setuptools",
+  "wheel",
+  "Cython>=0.29.21"
+]
+build-backend = "setuptools.build_meta"

pip/setup.cfg

@@ -0,0 +1,21 @@
+[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

@@ -0,0 +1,40 @@
+import setuptools
+from distutils.core import setup
+from distutils.extension import Extension
+from Cython.Build import cythonize
+
+with open("README.md", "r", encoding="utf-8") as fh:
+    long_description = fh.read()
+
+extensions = Extension(
+    name="tdm_termite",
+    sources=["cython/py_tdm_termite.pyx"],
+    # libraries=[""],
+    # library_dirs=["lib"],
+    include_dirs=["lib","pugixml"],
+    language='c++',
+    extra_compile_args=['-std=c++17','-Wno-unused-variable'],
+    extra_link_args=['-std=c++17'],
+)
+
+setuptools.setup(
+    name="TDMtermite-RecordEvolution",
+    version="0.5",
+    author="Record Evolution GmbH",
+    author_email="mario.fink@record-evolution.de",
+    description="Extract and read data from National Instruments LabVIEW tdx/tdm files and export them as csv files",
+    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=cythonize(extensions),
+    packages=setuptools.find_packages(),
+    python_requires=">=3.6",
+)