Merge pull request #3 from dstrib/master

Merge Release 0.1.9

Author: dstrib

README.rst

@@ -2,13 +2,16 @@
 hybkit
 ==================================
 .. image:: https://img.shields.io/github/v/release/RenneLab/hybkit?include_prereleases
+   :target: https://github.com/RenneLab/hybkit/releases
    :alt: GitHub release (latest by date including pre-releases)
 .. image:: https://badge.fury.io/py/hybkit.svg
-   :target: https://badge.fury.io/py/hybkit
+   :target: https://pypi.org/project/hybkit/
+   :alt: PyPI Package Version
 .. image:: https://readthedocs.org/projects/hybkit/badge/?version=latest
    :target: https://hybkit.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status
 .. image:: https://img.shields.io/pypi/pyversions/hybkit
+   :target: https://pypi.org/project/hybkit/
    :alt: PyPI - Python Version
 
 

docs/source/about.rst

@@ -34,6 +34,8 @@ Lead Developer
 Changelog
 ---------
 
+    * 0.1.9 Fix for Module Path Finding for Python > 3.6
+    * 0.1.8 Streamlining, PyPI / PIP Initial Release
     * 0.1.0 (-present) Beta Implementation
 
 

hybkit/__about__.py

@@ -10,21 +10,26 @@
 import os
 import sys
 if sys.version_info.major >= 3 and sys.version_info.minor >= 7:
-    from importlib import resources as importlib_resources
+    from importlib import resources
 else:
     import importlib_resources
+    module_path_find_function = importlib_resources.files
 
 project_name = 'hybkit'
-version = "0.1.8"
+version = "0.1.9"
 description = 'Toolkit for analysis of .hyb format genomic '
 description += 'sequence data from ribonomics experiments.'
 project_url = 'https://github.com/RenneLab/hybkit'
-project_download_url = 'https://github.com/RenneLab/hybkit' + '/tarball/' + version
 keywords = 'genetics genomics ribonomics bioinformatics hyb CLASH qCLASH miRNA '
 keywords += 'RNA DNA vienna viennad unafold'
 name_and_version = project_name + '-' + version
 
-module_dir = importlib_resources.files('hybkit')
+if sys.version_info.major >= 3 and sys.version_info.minor >= 7:
+    with resources.path('hybkit', '__init__.py') as path_obj:
+        module_dir = os.path.dirname(path_obj)
+else:
+    module_dir = importlib_resources.files('hybkit')
+
 prefix_data_dir = os.path.join(sys.prefix, name_and_version)
 #Putting in try block to allow use with exec()
 try:
@@ -37,7 +42,7 @@
 elif os.path.isdir(os.path.join(local_data_dir, 'databases')):
     hybkit_data_dir = local_data_dir
 else:
-    print('WARNING: hybkit_data_dir variable cannot be set.')
+    print('WARNING: hybkit_data_dir variable cannot be set, ignore during setup.py.')
     hybkit_data_dir = ''
 
 databases_dir = os.path.join(hybkit_data_dir, 'databases')
@@ -65,6 +70,7 @@
     ]
 
 info_urls = {
+    'Download as TAR': ('https://github.com/RenneLab/hybkit/tarball/' + version),
     'Renne Lab Github': 'https://github.com/RenneLab',
     'Renne Lab Mainpage': 'https://www.rennelab.com/',
     'Hyb Format Specification':

setup.py

@@ -11,6 +11,7 @@
 import os
 import hybkit
 import glob
+import fnmatch
 
 # Set project directory
 proj_dir = os.path.abspath(os.path.dirname(__file__))
@@ -26,25 +27,26 @@
 
 # Dynamically generate reference data file tuples:
 data_files = []
-data_file_dirs = ['scripts', 'scripts_extra', 'databases', 'reference_data', 'hybkit']
+data_file_dirs = ['', 'scripts', 'scripts_extra', 'databases', 'reference_data', 'hybkit']
 sample_directory_dirs = glob.glob('sample_0*')
 data_file_dirs += sample_directory_dirs
 for item in glob.glob('docs/**', recursive=True):
     if os.path.isdir(item) and not item.startswith(os.path.join('docs','_')):
         data_file_dirs.append(item)
 
+ignore_file_patterns = []
+with open('.gitignore', 'r') as git_ignore:
+    for line in git_ignore:
+        line = line.strip()
+        if line.startswith('#') or not line:
+            continue
+        ignore_file_patterns.append(line)
+
 for dir_name in data_file_dirs:
     file_list = [f for f in glob.glob(os.path.join(dir_name, '*'))
                  if not (
-                         (os.path.isdir(f)) 
-                         or ('/output' in f)
-                         or (f.endswith('.hyb'))
-                         or (f.endswith('.viennad'))
-                         or (f.endswith('.vienna'))
-                         or (f.endswith('.ct'))
-                         or (f.endswith('__'))
-                         or (f.endswith('.pyc'))
-                  
+                         os.path.isdir(f)
+                         or any(fnmatch.fnmatch(f, ignore) for ignore in ignore_file_patterns)
                         )]
     target_dir_name = os.path.join(about_vars['name_and_version'], dir_name)
     data_files.append((target_dir_name, file_list))
@@ -56,7 +58,6 @@
     long_description=long_description,
     long_description_content_type='text/x-rst',
     url=about_vars['project_url'],
-    download_url=about_vars['project_download_url'],
     author=about_vars['__author__'],
     author_email=about_vars['__contact__'],
     classifiers=about_vars['classifiers'],