more portable build of the Python extension module with HDF5 paths propagated from configure script

Makefile.am

@@ -157,6 +157,10 @@ $(HTML_FILES): docs/index.html
 
 # =============== DEVELOPER MODE =============== #
 
+SWIG          = @SWIG@ 
+HDF5_LDFLAGS  = @HDF5_LDFLAGS@ 
+HDF5_CFLAGS   = @HDF5_CFLAGS@ 
+
 if TREXIO_DEVEL
 
 CLEANFILES += $(SOURCES) $(trexio_f) $(trexio_h)
@@ -183,7 +187,6 @@ cppcheck.out: $(trexio_h)
 	  --language=c --std=c99 -rp --platform=unix64  \
 	  -I../include *.c *.h 2>../$@
 
-
 setup_py      = $(srcdir)/python/setup.py
 setup_cfg     = $(srcdir)/python/setup.cfg
 pytrexio_py   = $(srcdir)/python/pytrexio/pytrexio.py
@@ -199,7 +202,8 @@ python-test: $(TEST_PY)
 	$(RM) -r -- __pycache__
 
 python-install: $(pytrexio_py) $(setup_py) $(setup_cfg)
-	cd python && ./install_pytrexio.sh
+	cd python && \
+		./install_pytrexio.sh $(HDF5_LDFLAGS) $(HDF5_CFLAGS)
 
 $(pytrexio_py): $(pytrexio_c) 
 	cd tools && ./prepare_python.sh
@@ -208,7 +212,8 @@ $(pytrexio_py): $(pytrexio_c)
 # [?] swig -python -threads pytrexio.i ----> Add thread support for all the interface
 $(pytrexio_c): $(ORG_FILES) $(trexio_h) $(pytrexio_i) $(numpy_i)
 	cp $(trexio_h) src/
-	cd src/ && swig -python -py3 -o pytrexio_wrap.c pytrexio.i
+	cd src/ && \
+		$(SWIG) -python -py3 -o pytrexio_wrap.c pytrexio.i
 	$(RM) -- src/trexio.h
 
 $(numpy_i):

python/install_pytrexio.sh

@@ -3,6 +3,9 @@
 set -x
 set -e
 
+H5_LDFLAGS_LOCAL=$1
+H5_CFLAGS_LOCAL=$2
+
 # This script should update the version of the Python package
 #source version.py
 
@@ -11,7 +14,7 @@ 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 
+H5_LDFLAGS=${H5_LDFLAGS_LOCAL} H5_CFLAGS=${H5_CFLAGS_LOCAL} 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"

python/setup.py

@@ -14,13 +14,16 @@ c_files = ['trexio.c', 'trexio_hdf5.c', 'trexio_text.c', 'pytrexio_wrap.c']
 with open("README.md", "r") as fh:
     long_description = fh.read()
 
+h5_ldflags = str(os.environ.get("H5_LDFLAGS", None ))
+h5_cflags_withI  = str(os.environ.get("H5_CFLAGS", None ))
+h5_cflags = h5_cflags_withI.replace("-I","")
 
 pytrexio_module = Extension('pytrexio._pytrexio',
                             sources = [os.path.join(srcpath, code) for code in c_files],
-                            include_dirs = ['/usr/include/hdf5/serial', srcpath],
+                            include_dirs = [h5_cflags, srcpath],
                             libraries = ['hdf5', 'hdf5_hl'],
                             extra_compile_args = ['-Wno-discarded-qualifiers'],
-                            extra_link_args = ['-L/usr/lib/x86_64-linux-gnu/hdf5/serial']
+                            extra_link_args = [h5_ldflags]
                             )