better structure of the python directory

Makefile.am

@@ -186,8 +186,8 @@ cppcheck.out: $(trexio_h)
 
 setup_py      = $(srcdir)/python/setup.py
 setup_cfg     = $(srcdir)/python/setup.cfg
-pytrexio_py   = $(srcdir)/python/trexio/pytrexio.py
-trexio_api_py = $(srcdir)/python/trexio/trexio_api.py
+pytrexio_py   = $(srcdir)/python/pytrexio/pytrexio.py
+trexio_py     = $(srcdir)/python/trexio.py
 TEST_PY       = $(srcdir)/python/test/test_api.py
 pytrexio_c    = $(srcdir)/src/pytrexio_wrap.c
 pytrexio_i    = $(srcdir)/src/pytrexio.i
@@ -219,7 +219,7 @@ check-numpy:
 
 CLEANFILES += $(pytrexio_c) \
               $(pytrexio_py) \
-              $(trexio_api_py) \
+              $(trexio_py) \
               python/src/*.c \
               python/src/*.h
 

python/setup.py

@@ -15,7 +15,7 @@ with open("README.md", "r") as fh:
     long_description = fh.read()
 
 
-pytrexio_module = Extension('trexio._pytrexio',
+pytrexio_module = Extension('pytrexio._pytrexio',
                             sources = [os.path.join(srcpath, code) for code in c_files],
                             include_dirs = ['/usr/include/hdf5/serial', srcpath],
                             libraries = ['hdf5', 'hdf5_hl'],
@@ -32,7 +32,8 @@ setup(name             = 'trexio',
       long_description = long_description,
       long_description_content_type = "text/markdown",
       ext_modules      = [pytrexio_module],
-      packages         = ['trexio'],
+      py_modules       = ['trexio'],
+      packages         = ['pytrexio'],
       url              = 'https://github.com/TREX-CoE/trexio',
       license          = 'BSD',
       classifiers=[

src/templates_front/build.sh

@@ -10,7 +10,7 @@ echo "" >> trexio.h
 
 cat prefix_s_front.h > trexio_s.h
 cat prefix_fortran.f90   > trexio_f.f90
-cat prefix_python.py   > trexio_api.py
+cat prefix_python.py   > trexio.py
 
 # c front end
 cat populated/pop_*.c >> trexio.c
@@ -23,7 +23,7 @@ cat helper_fortran.f90 >> trexio_f.f90
 cat populated/pop_*.fh_90 >> trexio_f.f90
 
 # python front end
-cat populated/pop_*.py >> trexio_api.py
+cat populated/pop_*.py >> trexio.py
 
 # suffixes
 cat suffix_s_front.h >> trexio_s.h

src/templates_front/templator_front.org

@@ -21,7 +21,7 @@
 ** Python
   #+begin_src python :tangle prefix_python.py
 try:
-    from trexio.pytrexio import *
+    from pytrexio.pytrexio import *
 except ImportError:
     raise Exception("Could not import pytrexio module from trexio package")
 

tools/prepare_python.sh

@@ -13,7 +13,7 @@ readonly SRC=${TREXIO_ROOT}/src
 readonly INCLUDIR=${TREXIO_ROOT}/include
 readonly TOOLS=${TREXIO_ROOT}/tools
 readonly PYDIR=${TREXIO_ROOT}/python
-readonly PYTREXIODIR=${PYDIR}/trexio
+readonly PYTREXIODIR=${PYDIR}/pytrexio
 
 # We want the script to crash on the 1st error:
 set -e
@@ -24,7 +24,7 @@ mkdir -p ${PYTREXIODIR}
 
 # Copy all the source code and header files in the corresponding python directory
 mv ${SRC}/pytrexio.py ${PYTREXIODIR}
-mv ${SRC}/trexio_api.py ${PYTREXIODIR}
+mv ${SRC}/trexio.py ${PYDIR}
 cp ${SRC}/*.c ${PYDIR}/src
 cp ${SRC}/*.h ${PYDIR}/src
 cp ${INCLUDIR}/trexio.h ${PYDIR}/src