diff --git a/PanACoTA/__init__.py b/PanACoTA/__init__.py index 121fd20451e97502656c178ca58963ab2c028651..318e01994a20fd88276abb6d070a971128142caf 100755 --- a/PanACoTA/__init__.py +++ b/PanACoTA/__init__.py @@ -1,3 +1,3 @@ """PanACoTA""" -__version__ = "1.0.1.0" +__version__ = "1.0.1-2" diff --git a/PanACoTA/bin/__init__.py b/PanACoTA/bin/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..5980e95b3aade7155ba7f992cf5c15066cb38c46 --- /dev/null +++ b/PanACoTA/bin/__init__.py @@ -0,0 +1,31 @@ +# ############################################################################### +# This file is part of PanACOTA. # +# # +# Authors: Amandine Perrin # +# Copyright © 2018-2020 Institut Pasteur (Paris). # +# See the COPYRIGHT file for details. # +# # +# PanACOTA is a software providing tools for large scale bacterial comparative # +# genomics. From a set of complete and/or draft genomes, you can: # +# - Do a quality control of your strains, to eliminate poor quality # +# genomes, which would not give any information for the comparative study # +# - Uniformly annotate all genomes # +# - Do a Pan-genome # +# - Do a Core or Persistent genome # +# - Align all Core/Persistent families # +# - Infer a phylogenetic tree from the Core/Persistent families # +# # +# PanACOTA is free software: you can redistribute it and/or modify it under the # +# terms of the Affero GNU General Public License as published by the Free # +# Software Foundation, either version 3 of the License, or (at your option) # +# any later version. # +# # +# PanACOTA is distributed in the hope that it will be useful, but WITHOUT ANY # +# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS # +# FOR A PARTICULAR PURPOSE. See the Affero GNU General Public License # +# for more details. # +# # +# You should have received a copy of the Affero GNU General Public License # +# along with PanACOTA (COPYING file). # +# If not, see <https://www.gnu.org/licenses/>. # +# ############################################################################### diff --git a/bin/PanACoTA b/PanACoTA/bin/run_panacota.py similarity index 73% rename from bin/PanACoTA rename to PanACoTA/bin/run_panacota.py index 007a25bde0f0c43d046e44661b64eca702975008..a4d3c97271dd9df5aaa83bb10f29fc7fa2e4e867 100755 --- a/bin/PanACoTA +++ b/PanACoTA/bin/run_panacota.py @@ -1,6 +1,40 @@ #!/usr/bin/env python3 # coding: utf-8 + +# ############################################################################### +# This file is part of PanACOTA. # +# # +# Authors: Amandine Perrin # +# Copyright © 2018-2020 Institut Pasteur (Paris). # +# See the COPYRIGHT file for details. # +# # +# PanACOTA is a software providing tools for large scale bacterial comparative # +# genomics. From a set of complete and/or draft genomes, you can: # +# - Do a quality control of your strains, to eliminate poor quality # +# genomes, which would not give any information for the comparative study # +# - Uniformly annotate all genomes # +# - Do a Pan-genome # +# - Do a Core or Persistent genome # +# - Align all Core/Persistent families # +# - Infer a phylogenetic tree from the Core/Persistent families # +# # +# PanACOTA is free software: you can redistribute it and/or modify it under the # +# terms of the Affero GNU General Public License as published by the Free # +# Software Foundation, either version 3 of the License, or (at your option) # +# any later version. # +# # +# PanACOTA is distributed in the hope that it will be useful, but WITHOUT ANY # +# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS # +# FOR A PARTICULAR PURPOSE. See the Affero GNU General Public License # +# for more details. # +# # +# You should have received a copy of the Affero GNU General Public License # +# along with PanACOTA (COPYING file). # +# If not, see <https://www.gnu.org/licenses/>. # +# ############################################################################### + + import sys from textwrap import dedent diff --git a/setup.py b/setup.py index 1d763e24925d3e8a60b61761dfc79bb218fed5cb..ddc049ddcc0d97b047bc6223d455c0c44686ac3f 100755 --- a/setup.py +++ b/setup.py @@ -7,13 +7,12 @@ Setup script import PanACoTA try: - from setuptools import setup + from setuptools import setup, find_packages from setuptools.command.test import test as TestCommand except ImportError: - from distutils.core import setup + from distutils.core import setup, find_packages from distutils.core import Command as TestCommand - class PyTest(TestCommand): def initialize_options(self): pass @@ -38,11 +37,11 @@ def parse_requirements(requirements): and not l.startswith('#')] -packages = ['PanACoTA', 'PanACoTA.prepare_module', 'PanACoTA.annotate_module', - 'PanACoTA.pangenome_module', 'PanACoTA.corepers_module', - 'PanACoTA.align_module', 'PanACoTA.tree_module', 'PanACoTA.subcommands'] +# packages = ['PanACoTA', 'PanACoTA.prepare_module', 'PanACoTA.annotate_module', +# 'PanACoTA.pangenome_module', 'PanACoTA.corepers_module', +# 'PanACoTA.align_module', 'PanACoTA.tree_module', 'PanACoTA.subcommands'] requires = parse_requirements("requirements.txt") -scripts = ['bin/PanACoTA'] +scripts = ['PanACoTA/bin/run_panacota.py'] classifiers = [ "Environment :: Console", @@ -58,7 +57,7 @@ with open('README.md') as f: setup( name='PanACoTA', - packages=packages, + packages=find_packages(), version=PanACoTA.__version__, description="Large scale comparative genomics tools: annotate genomes, do pangenome, " "core/persistent genome, align core/persistent families, infer phylogenetic tree.", @@ -71,8 +70,13 @@ setup( package_data={'': ['LICENSE']}, url='https://github.com/gem-pasteur/PanACoTA', scripts=scripts, + entry_points={ + 'console_scripts': ['PanACoTA=PanACoTA.bin.run_panacota:main'] + }, + python_requires='>=3.4', include_package_data=True, install_requires=requires, + extras_require={'dev': parse_requirements("requirements-dev.txt")}, tests_require=['pytest'], cmdclass={'test': PyTest}, classifiers=classifiers