Standardize package structure to respect python standard (#164)

* putting the SO in a morphio folder

* Is it using pip from the virtualenv ?

* Add morphio.mut and morphio.vasculature

* Do not run the tests from inside the folder

MANIFEST.in

@@ -2,4 +2,4 @@ recursive-include src *
 recursive-include binds *
 recursive-include include *
 recursive-include 3rdparty *
-include CMakeLists.txt
+include CMakeLists.txt

binds/python/CMakeLists.txt

@@ -1,4 +1,4 @@
-pybind11_add_module(morphio
+pybind11_add_module(_morphio
     SYSTEM
     morphio.cpp
     bind_immutable.cpp
@@ -8,11 +8,11 @@ pybind11_add_module(morphio
     bind_vasculature.cpp
     )
 
-target_include_directories(morphio
+target_include_directories(_morphio
   PRIVATE
   ${CMAKE_CURRENT_SOURCE_DIR}/../../include
   )
 
-target_link_libraries(morphio
+target_link_libraries(_morphio
     PRIVATE
     morphio_static)

binds/python/morphio.cpp

@@ -7,7 +7,7 @@
 
 namespace py = pybind11;
 
-PYBIND11_MODULE(morphio, m) {
+PYBIND11_MODULE(_morphio, m) {
     bind_misc(m);
     bind_immutable_module(m);
 

ci/python_test.sh

@@ -11,10 +11,15 @@ set +u  # ignore errors in virtualenv's activate
 source "$VENV/bin/activate"
 set -u
 
+which pip
+
 pip install --upgrade pip setuptools
 
 # install
 pip install .
 
 pip install -r tests/requirement_tests.txt
-nosetests
+CURRENT=$(pwd)
+
+cd ..
+nosetests ${CURRENT}/tests

morphio/__init__.py

@@ -0,0 +1 @@
+from ._morphio import *

morphio/mut/__init__.py

@@ -0,0 +1 @@
+from .._morphio.mut import *

morphio/vasculature/__init__.py

@@ -0,0 +1 @@
+from .._morphio.vasculature import *

setup.py

@@ -79,7 +79,7 @@ def build_extension(self, ext, cmake):
             os.makedirs(self.build_temp)
         try:
             subprocess.check_call([cmake, ext.sourcedir] + cmake_args, cwd=self.build_temp)
-            subprocess.check_call([cmake, '--build', '.', '--target', 'morphio'] + build_args, cwd=self.build_temp)
+            subprocess.check_call([cmake, '--build', '.', '--target', '_morphio'] + build_args, cwd=self.build_temp)
         except subprocess.CalledProcessError as exc:
             print("Status : FAIL", exc.returncode, exc.output)
             raise
@@ -96,8 +96,10 @@ def build_extension(self, ext, cmake):
     long_description_content_type="text/markdown",
     install_requires=['numpy>=1.14.1'],
     url='https://github.com/BlueBrain/MorphIO/',
-    ext_modules=[CMakeExtension('morphio')],
+    ext_modules=[CMakeExtension('morphio._morphio')],
     cmdclass=dict(build_ext=CMakeBuild),
+    packages=['morphio', 'morphio.mut', 'morphio.vasculature'],
+
     license="BBP-internal-confidential",
     keywords=('computational neuroscience',
               'morphology',