diff --git a/README.rst b/README.rst index 09d0d33..b70a4e6 100644 --- a/README.rst +++ b/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 diff --git a/docs/source/about.rst b/docs/source/about.rst index db175d5..a0b4777 100644 --- a/docs/source/about.rst +++ b/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 diff --git a/hybkit/__about__.py b/hybkit/__about__.py index 719a1ec..57100c5 100644 --- a/hybkit/__about__.py +++ b/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': diff --git a/setup.py b/setup.py index 002b4d2..8f6a475 100644 --- a/setup.py +++ b/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'],