From 3405adbca64645ed158db43c259401692424d3a5 Mon Sep 17 00:00:00 2001 From: Peter Kruczkiewicz Date: Thu, 26 Sep 2019 15:32:12 -0500 Subject: [PATCH 1/6] Version bump v2.4.0; fix prog desc Harmonize program description with README --- bio_hansel/__init__.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bio_hansel/__init__.py b/bio_hansel/__init__.py index 0aff8c3..d0ceda6 100644 --- a/bio_hansel/__init__.py +++ b/bio_hansel/__init__.py @@ -1,9 +1,9 @@ # -*- coding: utf-8 -*- -__version__ = '2.3.0' +__version__ = '2.4.0' program_name = 'bio_hansel' program_summary = 'Subtype microbial genomes using SNV targeting k-mer subtyping schemes.' program_desc = program_summary + ''' Includes schemes for Salmonella enterica spp. enterica serovar Heidelberg, Enteritidis, Typhi, and Typhimurium subtyping. Also includes a Mycobacterium tuberculosis scheme called 'tb_lineage'. -Developed by Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Marisa Rankin, Matthew Gopez, Chad R. Laing, Philip Mabon, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, David Son, Darian Hole, Philip Mabon, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Marisa Rankin, Joanne MacKinnon, Roger Johnson, John H.E. Nash. +Developed by Geneviève Labbé, Peter Kruczkiewicz, Philip Mabon, James Robertson, Justin Schonfeld, Daniel Kein, Marisa A. Rankin, Matthew Gopez, Darian Hole, David Son, Natalie Knox, Chad R. Laing, Kyrylo Bessonov, Eduardo Taboada, Catherine Yoshida, Roger P. Johnson, Gary Van Domselaar and John H.E. Nash. ''' From b340888850c9122a8029057388cc43e850394099 Mon Sep 17 00:00:00 2001 From: Peter Kruczkiewicz Date: Thu, 26 Sep 2019 15:53:17 -0500 Subject: [PATCH 2/6] Update setup.py --- setup.py | 71 ++++++++++++++++++++++++++++---------------------------- 1 file changed, 36 insertions(+), 35 deletions(-) diff --git a/setup.py b/setup.py index 2911c70..fa09949 100644 --- a/setup.py +++ b/setup.py @@ -3,50 +3,51 @@ from setuptools import setup, find_packages -from bio_hansel import __version__, program_name, program_desc - -classifiers = """ -Development Status :: 3 - Alpha -Environment :: Console -License :: OSI Approved :: Apache Software License -Intended Audience :: Science/Research -Topic :: Scientific/Engineering -Topic :: Scientific/Engineering :: Bio-Informatics -Programming Language :: Python :: 3.5 -Programming Language :: Python :: 3.6 -Programming Language :: Python :: Implementation :: CPython -Operating System :: POSIX :: Linux -""".strip().split('\n') - with open('README.rst') as readme_file: readme = readme_file.read() +requirements=['numpy>=1.12.1', + 'pandas>=0.20.1', + 'pyahocorasick>=1.1.6', + 'attrs'] + +setup_requirements = ['pytest-runner', ] + +test_requirements = ['pytest', ] + setup( - name=program_name, - version=__version__, - packages=find_packages(exclude=['tests']), - url='https://github.com/phac-nml/{}'.format(program_name), - license='Apache Software License 2.0', author='Peter Kruczkiewicz', author_email='peter.kruczkiewicz@gmail.com', - description=program_desc, - long_description=readme, - keywords='Salmonella enterica Heidelberg Enteritidis SNP kmer subtyping Aho-Corasick', - classifiers=classifiers, - package_dir={program_name: program_name}, - package_data={program_name: ['data/*/*.fasta', 'data/*/*.tsv',]}, - install_requires=[ - 'numpy>=1.12.1', - 'pandas>=0.20.1', - 'pyahocorasick>=1.1.6', - 'attrs', + classifiers=[ + 'Development Status :: 3 - Alpha', + 'Environment :: Console', + 'Intended Audience :: Science/Research', + 'License :: OSI Approved :: Apache Software License', + 'Operating System :: POSIX :: Linux', + 'Programming Language :: Python :: 3.5', + 'Programming Language :: Python :: 3.6', + 'Programming Language :: Python :: Implementation :: CPython', + 'Topic :: Scientific/Engineering :: Bio-Informatics', + 'Topic :: Scientific/Engineering' ], - extras_require={ - 'test': ['pytest>=3.0.7',], - }, + description='Subtype microbial whole-genome sequencing (WGS) data using SNV targeting k-mer subtyping schemes.', entry_points={ 'console_scripts': [ 'hansel={}.main:main'.format(program_name), ], - } + }, + install_requires=requirements, + keywords='Salmonella enterica Heidelberg Enteritidis SNP kmer subtyping Aho-Corasick', + license='Apache Software License 2.0', + long_description=readme, + name='bio_hansel', + package_data={'bio_hansel': ['data/*/*.fasta', 'data/*/*.tsv',]}, + package_dir={'bio_hansel': 'bio_hansel'}, + packages=find_packages(include=['bio_hansel']), + setup_requires=setup_requirements, + test_suite='tests', + tests_require=test_requirements, + url='https://github.com/phac-nml/biohansel', + version='2.4.0', + zip_safe=False, ) From ae769fbc2f3da0e61da3abb0abe5adaf5f7a640d Mon Sep 17 00:00:00 2001 From: Peter Kruczkiewicz Date: Thu, 26 Sep 2019 15:55:47 -0500 Subject: [PATCH 3/6] Update setup.py --- setup.py | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/setup.py b/setup.py index fa09949..18c7a48 100644 --- a/setup.py +++ b/setup.py @@ -31,11 +31,7 @@ 'Topic :: Scientific/Engineering' ], description='Subtype microbial whole-genome sequencing (WGS) data using SNV targeting k-mer subtyping schemes.', - entry_points={ - 'console_scripts': [ - 'hansel={}.main:main'.format(program_name), - ], - }, + entry_points={'console_scripts': ['hansel=bio_hansel.main:main']}, install_requires=requirements, keywords='Salmonella enterica Heidelberg Enteritidis SNP kmer subtyping Aho-Corasick', license='Apache Software License 2.0', From a2d0c832d56fbe4c483e03a388a3608d98a24269 Mon Sep 17 00:00:00 2001 From: Peter Kruczkiewicz Date: Fri, 4 Oct 2019 10:20:16 -0500 Subject: [PATCH 4/6] Update setup.py --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 18c7a48..2f1be9d 100644 --- a/setup.py +++ b/setup.py @@ -24,8 +24,8 @@ 'Intended Audience :: Science/Research', 'License :: OSI Approved :: Apache Software License', 'Operating System :: POSIX :: Linux', - 'Programming Language :: Python :: 3.5', 'Programming Language :: Python :: 3.6', + 'Programming Language :: Python :: 3.7', 'Programming Language :: Python :: Implementation :: CPython', 'Topic :: Scientific/Engineering :: Bio-Informatics', 'Topic :: Scientific/Engineering' From e3a411f10453ede2f976ffe6722ad1f3c61f66b5 Mon Sep 17 00:00:00 2001 From: Peter Kruczkiewicz Date: Fri, 4 Oct 2019 10:21:04 -0500 Subject: [PATCH 5/6] Update .travis.yml --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index a983763..0459496 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,6 +1,7 @@ language: python python: - '3.6' +- '3.7' os: - linux branches: From a08206b9a95b9eeb51210b0242eb05171770579e Mon Sep 17 00:00:00 2001 From: Peter Kruczkiewicz Date: Fri, 4 Oct 2019 10:21:34 -0500 Subject: [PATCH 6/6] Update tox.ini --- tox.ini | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tox.ini b/tox.ini index cfa182b..9a4486f 100644 --- a/tox.ini +++ b/tox.ini @@ -1,9 +1,10 @@ [tox] -envlist = py36, flake8 +envlist = py36, py37, flake8 [travis] python = 3.6: py36 + 3.7: py37 [testenv:flake8] basepython = python