Create paackage folder structure

Author: Francesco Beghini

panphlan_map.py panphlan/panphlan_map.pypanphlan_map.py renamed to panphlan/panphlan_map.py

@@ -17,7 +17,7 @@
 from argparse import ArgumentParser
 from collections import defaultdict
 from shutil import copyfileobj
-from utils import end_program, show_interruption_message, show_error_message, time_message, find
+from .utils import end_program, show_interruption_message, show_error_message, time_message, find
 import bz2, fnmatch, multiprocessing, operator, os, subprocess, sys, tempfile, time
 from distutils.version import LooseVersion
 

panphlan_new_pangenome_generation.py …lan/panphlan_new_pangenome_generation.pypanphlan_new_pangenome_generation.py renamed to panphlan/panphlan_new_pangenome_generation.py panphlan_new_pangenome_generation.py renamed to panphlan/panphlan_new_pangenome_generation.py

@@ -19,7 +19,7 @@
 from argparse import ArgumentParser
 from collections import defaultdict
 from random import randint
-from utils import end_program, show_interruption_message, show_error_message, time_message, find
+from .utils import end_program, show_interruption_message, show_error_message, time_message, find
 import fnmatch, operator, os, subprocess, sys, time
 import bz2
 

panphlan_pangenome_generation.py panphlan/panphlan_pangenome_generation.pypanphlan_pangenome_generation.py renamed to panphlan/panphlan_pangenome_generation.py

@@ -10,11 +10,14 @@
     author='Matthias Scholz',
     author_email='matthias.scholz.de@gmail.com',
     url='http://github.com/SegataLab/panphlan/',
-    py_modules=['panphlan_map', 'panphlan_profile', 'panphlan_new_pangenome_generation', 'panphlan_pangenome_generation', 'utils'],
-    entry_points = { "console_scripts" : [ "panphlan_map = panphlan_map:main",
-                                           "panphlan_profile = panphlan_profile:main",
-                                           "panphlan_new_pangenome_generation = panphlan_new_pangenome_generation:main",
-                                           "panphlan_pangenome_generation = panphlan_pangenome_generation:main"
+    packages=setuptools.find_namespace_packages(),
+    package_data = { 'panphlan' : [
+        'panphlan/tools/*'
+    ]},
+    entry_points = { "console_scripts" : [ "panphlan_map.py = panphlan.panphlan_map:main",
+                                           "panphlan_profile.py = panphlan.panphlan_profile:main",
+                                           "panphlan_new_pangenome_generation.py = panphlan.panphlan_new_pangenome_generation:main",
+                                           "panphlan_pangenome_generation.py = panphlan.panphlan_pangenome_generation:main"
                                          ] },
     long_description_content_type='text/markdown',
     long_description=open('README.md').read(),