pytrexio build and pip install working

Makefile.am

@@ -137,7 +137,7 @@ tests_test_f_SOURCES = $(test_trexio_f) tests/test_f.f90
 tests_test_f_LDFLAGS = -no-install
 
 clean-local:
-	-rm -rf -- *.dir/ *.h5
+	-rm -rf -- *.dir/ *.h5 __pycache__/
 
 # =============== DOCUMENTATION =============== #
 
@@ -184,60 +184,43 @@ cppcheck.out: $(trexio_h)
 	  -I../include *.c *.h 2>../$@
 
 
-setup_py  = $(srcdir)/setup.py
+setup_py    = $(srcdir)/python/setup.py
-setup_cfg = $(srcdir)/setup.cfg
+setup_cfg   = $(srcdir)/python/setup.cfg
-pytrexio_py = $(srcdir)/src/pytrexio.py
+pytrexio_py = $(srcdir)/python/pytrexio.py
-pytrexio_c = $(srcdir)/src/pytrexio_wrap.c
+TESTS_PY    = $(srcdir)/python/test/test_py.py
-pytrexio_i = $(srcdir)/src/pytrexio.i
+pytrexio_c  = $(srcdir)/src/pytrexio_wrap.c
-TESTS_PY  = $(srcdir)/tests/test_py.py
+pytrexio_i  = $(srcdir)/src/pytrexio.i
+numpy_i     = $(srcdir)/src/numpy.i
 
-#python-prepare: 
-#	cp include/trexio.h src/*.c src/*.h python/src/
 
-python: _pytrexio*.so
+python-test: $(pytrexio_py) $(TESTS_PY)
-
-python-test: $(TESTS_PY) $(pytrexio_py)
-	cp $(pytrexio_py) .
 	python3 $(TESTS_PY)
-	$(RM) -r -- __pycache__ pytrexio.py
+	$(RM) -r -- __pycache__
 
-python-sdist: $(setup_py) $(pytrexio_py)
+python-install: $(pytrexio_py) $(setup_py) $(setup_cfg)
-	python3 setup.py sdist
+	cd python && ./install_pytrexio.sh
 
-python-build: $(setup_py) $(pytrexio_py) pyproject.toml
+$(pytrexio_py): $(pytrexio_c) 
-	python3 -m build
+	cd tools && ./prepare_python.sh
 
-python-release: $(setup_py) $(pytrexio_py) pyproject.toml
+# Build Python module and C wrapper code for TREXIO using SWIG
-	python3 -m twine upload --repository testpypi dist/*
+# [?] swig -python -threads pytrexio.i ----> Add thread support for all the interface
-
+$(pytrexio_c): $(ORG_FILES) $(trexio_h) $(pytrexio_i) $(numpy_i)
-# Advanced compilation using Python-native distutils
-#
-# swig -python -threads pytrexio.i ----> Add thread support for all the interface
-# 
-$(pytrexio_c): $(ORG_FILES) $(trexio_h) $(pytrexio_i)
 	cp $(trexio_h) src/
 	cd src/ && swig -python -py3 -o pytrexio_wrap.c pytrexio.i
-
-_pytrexio*.so: $(pytrexio_c) $(setup_py)
-	python3 setup.py build_ext --inplace --swig-opts="-modern"
 	$(RM) -- src/trexio.h
 
-# Manual compilation of Python module
+$(numpy_i):
-#
+	wget https://raw.githubusercontent.com/numpy/numpy/main/tools/swig/numpy.i -O $(numpy_i) 
-#src/_pytrexio.so: $(ORG_FILES) $(trexio_h) src/pytrexio.i
-#       cp $(trexio_h) src/
-#       cd src/ && \
-#       swig -python -py3 -o pytrexio_wrap.c pytrexio.i && \
-#       $(CC) $(CPPFLAGS) -I/usr/include/python3.8 -fPIC -Wno-discarded-qualifiers \
-#       	-c trexio.c trexio_hdf5.c trexio_text.c pytrexio_wrap.c && \
-#       $(CC) -shared trexio.o trexio_hdf5.o trexio_text.o pytrexio_wrap.o \
-#       	$(LDFLAGS) $(LIBS) -o _pytrexio.so
-#       $(RM) -- src/trexio.h
-#
 
-CLEANFILES += src/pytrexio_wrap.c src/pytrexio.py _pytrexio*.so 
 
-.PHONY: cppcheck python python-build python-test python-release
+CLEANFILES += src/pytrexio_wrap.c \
+	      src/pytrexio.py \
+	      python/pytrexio.py \
+	      python/src/*.c \
+	      python/src/*.h
+
+.PHONY: cppcheck python-test python-install
 
 endif
 

python/.gitignore

@@ -0,0 +1,10 @@
+AUTHORS
+LICENSE
+README.md
+pytrexio.py
+src/
+
+build/
+dist/
+*.egg-info/
+__pycache__/

python/install_pytrexio.sh

@@ -0,0 +1,47 @@
+#!/bin/bash                                                    
+
+set -x
+set -e
+
+# This script should update the version of the Python package
+#source version.py
+#exit 0
+
+# Install/upgrade packages required for the installation
+python3 -m pip install --upgrade setuptools wheel twine
+
+# Create build directory and compile extension files (*.c)
+# --no-user-cfg disables custom .cfg files of the user machine, so that only setup.cfg is used
+python3 -s setup.py --no-user-cfg build 
+
+# Local inplace build of the .so module with SWIG-produced pytrexio_wrap.c (from the SWIG documentation)
+#python3 setup.py build_ext --inplace --swig-opts="-modern"
+
+# Create distributions: 
+#   1) sdist produces .tar.gz with all files necessary for manual compilation;
+#   2) bdist_whell produces .whl wheel distribution (see https://www.python.org/dev/peps/pep-0425/).
+python3 setup.py sdist bdist_wheel
+
+# Install pytrexio in the current environment from the aforementioned wheel
+# --force-reinstall is needed here because build-system pre-installs pytrexio in the environment 
+#                   but does not install things in the corresponding site-packages directory
+python3 -m pip install dist/pytrexio-0.1-*.whl --force-reinstall
+
+# Uninstall pytrexio: this only works from the pytrexio root directory (more likely python/ folder) and only after --force-reinstall
+#python3 -m pip uninstall pytrexio
+
+# Test the current release by uploading to TestPyPI sandbox
+#python3 -m twine upload --repository testpypi dist/pytrexio-*.tar.gz
+
+# NOTE:I get an error: 
+#      Binary wheel 'pytrexio-0.1-cp38-cp38-linux_x86_64.whl' has an unsupported platform tag 'linux_x86_64'.
+# when uploading the wheel instead of the tar.gz file to testpypi
+# This is a well-known issue, see https://stackoverflow.com/questions/59451069/binary-wheel-cant-be-uploaded-on-pypi-using-twine
+# Once fixed both .tar.gz and .whl distribution can be uploaded, meaning that dist/pytrexio-*.tar.gz can be replaced by dist/*
+
+# Upload updated version of PyTREXIO to PyPI
+#python3 -m twine upload dist/pytrexio-*.tar.gz
+
+# Cleaning
+rm -rf build dist pytrexio.egg-info
+

python/test-pypi-release-pytrexio.sh

@@ -1,27 +0,0 @@
-#!/bin/bash                                                    
-
-set -x
-set -e
-
-#source version.py
-
-python3 -m pip install --upgrade setuptools wheel twine
-#python3 -s setup.py --no-user-cfg build
-python3 -s setup.py build
-python3 setup.py sdist bdist_wheel
-python3 -m pip install dist/pytrexio-0.1-*.whl --force-reinstall
-
-# remove
-#python3 -m pip uninstall pytrexio
-
-#python3 -m twine upload dist/pytrexio-0.1.tar.gz
-
-# NOTE:I get an error: 
-#      Binary wheel 'pytrexio-0.1-cp38-cp38-linux_x86_64.whl' has an unsupported platform tag 'linux_x86_64'.
-# when uploading the wheel instead of the tar.gz file to testpypi
-# This is a well-known issue, see https://stackoverflow.com/questions/59451069/binary-wheel-cant-be-uploaded-on-pypi-using-twine
- 
-#python3 -m twine upload --repository testpypi dist/pytrexio-0.1.tar.gz
-
-rm -rf build pytrexio.egg-info
-rm -rf dist

tools/prepare_python.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+
+# Check that script is executed from tools directory
+if [[ $(basename $PWD) != "tools" ]] ; then
+  echo "This script should run in the tools directory"
+  exit -1
+fi
+
+TREXIO_ROOT=$(dirname "${PWD}../")
+
+#   First define readonly global variables.
+readonly SRC=${TREXIO_ROOT}/src
+readonly INCLUDIR=${TREXIO_ROOT}/include
+readonly TOOLS=${TREXIO_ROOT}/tools
+readonly PYDIR=${TREXIO_ROOT}/python
+
+# We want the script to crash on the 1st error:
+set -e
+
+# Create src directory in the python folder if not yet done
+mkdir -p ${PYDIR}/src
+
+# Copy all the source code and header files in the corresponding python directory
+cp ${SRC}/*.py ${PYDIR}
+cp ${SRC}/*.c ${PYDIR}/src
+cp ${SRC}/*.h ${PYDIR}/src
+cp ${INCLUDIR}/trexio.h ${PYDIR}/src 
+
+# Copy additional info
+cp ${TREXIO_ROOT}/AUTHORS ${TREXIO_ROOT}/LICENSE ${TREXIO_ROOT}/README.md ${PYDIR}
+