Prepare release v2.4.0

.travis.yml

@@ -1,6 +1,7 @@
 language: python
 python:
 - '3.6'
+- '3.7'
 os:
 - linux
 branches:

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.
 '''

setup.py

@@ -3,50 +3,47 @@
 
 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='[email protected]',
-    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 :: 3.6',
+        'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: Implementation :: CPython',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
+        'Topic :: Scientific/Engineering'
     ],
-    extras_require={
-        'test': ['pytest>=3.0.7',],
-    },
-    entry_points={
-        'console_scripts': [
-            'hansel={}.main:main'.format(program_name),
-        ],
-    }
+    description='Subtype microbial whole-genome sequencing (WGS) data using SNV targeting k-mer subtyping schemes.',
+    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',
+    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,
 )

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