From a1c2f69688042017ae5d740eb9f2837832abdc31 Mon Sep 17 00:00:00 2001 From: Dan Stribling Date: Tue, 10 Mar 2020 19:18:07 -0400 Subject: [PATCH 1/6] Readme Tweak. --- README.rst | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 09d0d33..5c9dbde 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/0.1.8/ + :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 From 3b5c5314496a66408042b33463e063f7fe63fc63 Mon Sep 17 00:00:00 2001 From: Dan Stribling Date: Tue, 10 Mar 2020 19:19:16 -0400 Subject: [PATCH 2/6] Readme Tweak. --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 5c9dbde..b70a4e6 100644 --- a/README.rst +++ b/README.rst @@ -5,7 +5,7 @@ hybkit :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://pypi.org/project/hybkit/0.1.8/ + :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 From 48ba87e6f123bd3f6fac0bd863ddbc588e1f70cb Mon Sep 17 00:00:00 2001 From: Dan Stribling Date: Tue, 10 Mar 2020 21:30:08 -0400 Subject: [PATCH 3/6] Fix module_dir variable for Python>=3.7 . --- hybkit/__about__.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/hybkit/__about__.py b/hybkit/__about__.py index 719a1ec..d04e57b 100644 --- a/hybkit/__about__.py +++ b/hybkit/__about__.py @@ -10,9 +10,10 @@ 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" @@ -24,7 +25,12 @@ 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: From 96c57b3c2e3dfc006028c1e9e4e88d6cb3594007 Mon Sep 17 00:00:00 2001 From: Dan Stribling Date: Wed, 11 Mar 2020 07:56:34 -0400 Subject: [PATCH 4/6] PyPI setup.py Tweaks. --- hybkit/__about__.py | 2 +- setup.py | 27 ++++++++++++++++----------- 2 files changed, 17 insertions(+), 12 deletions(-) diff --git a/hybkit/__about__.py b/hybkit/__about__.py index 719a1ec..d6ff35e 100644 --- a/hybkit/__about__.py +++ b/hybkit/__about__.py @@ -19,7 +19,6 @@ 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 @@ -65,6 +64,7 @@ ] 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..79fbb2d 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__)) @@ -26,29 +27,34 @@ # 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)) +for items in data_files: + print(items) +sys.exit() + setuptools.setup( name='hybkit', version=about_vars['__version__'], @@ -56,7 +62,6 @@ 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'], From aaec2e57bcacea84a33c0775bf03696e56fd1cb9 Mon Sep 17 00:00:00 2001 From: Dan Stribling Date: Wed, 11 Mar 2020 08:02:52 -0400 Subject: [PATCH 5/6] __about__.py Tweak. --- hybkit/__about__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hybkit/__about__.py b/hybkit/__about__.py index 65fa34a..8b4dc03 100644 --- a/hybkit/__about__.py +++ b/hybkit/__about__.py @@ -42,7 +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') From 1c14589f0744db2a87c65f4b19c3893d901fe658 Mon Sep 17 00:00:00 2001 From: Dan Stribling Date: Wed, 11 Mar 2020 11:36:25 -0400 Subject: [PATCH 6/6] Bump Version to 0.1.9 . --- docs/source/about.rst | 2 ++ hybkit/__about__.py | 2 +- setup.py | 4 ---- 3 files changed, 3 insertions(+), 5 deletions(-) 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 8b4dc03..57100c5 100644 --- a/hybkit/__about__.py +++ b/hybkit/__about__.py @@ -16,7 +16,7 @@ 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' diff --git a/setup.py b/setup.py index 79fbb2d..8f6a475 100644 --- a/setup.py +++ b/setup.py @@ -51,10 +51,6 @@ target_dir_name = os.path.join(about_vars['name_and_version'], dir_name) data_files.append((target_dir_name, file_list)) -for items in data_files: - print(items) -sys.exit() - setuptools.setup( name='hybkit', version=about_vars['__version__'],