Merge pull request #1 from Ecogenomics/conda_updates

packaging for conda

.gitignore

@@ -127,3 +127,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# IntelliJ
+.idea

README.md

@@ -1,2 +1,4 @@
 # gtdb-migration-tk
+[![ace-internal](https://img.shields.io/conda/vn/ace-internal/gtdb_migration_tk.svg?color=green)](https://anaconda.org/ace-internal/gtdb_migration_tk)
+
 Toolkit for updating the GTDB to the next release and test data 

bin/gtdb_migration_tk

@@ -24,35 +24,25 @@ __maintainer__ = "Pierre Chaumeil"
 __email__ = "uqpchaum@uq.edu.au"
 __status__ = "Development"
 
+import argparse
 import os
 import sys
-import ntpath
-import logging
-import argparse
 
 sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
 
-
 from gtdb_migration_tk.main import OptionsParser
 
 from biolib.logger import logger_setup
 from biolib.misc.custom_help_formatter import CustomHelpFormatter
-from biolib.common import make_sure_path_exists
-
-
-def version():
-    """Read program version from file."""
-    import gtdb_migration_tk
-    version_file = open(os.path.join(gtdb_migration_tk.__path__[0], 'VERSION'))
-    return version_file.readline().strip()
+from gtdb_migration_tk import __version__
 
 
 def print_help():
     """Help menu."""
 
     print('')
     print('                ...::: GTDB Migration Toolkit v' +
-          version() + ' :::...''')
+          __version__ + ' :::...''')
     print('''\
 
     NCBI folder to GTDB folder:
@@ -274,7 +264,7 @@ if __name__ == '__main__':
 
     # get and check options
     args = None
-    if(len(sys.argv) == 1 or sys.argv[1] == '-h' or sys.argv == '--help'):
+    if len(sys.argv) == 1 or sys.argv[1] in {'-h', '--help'}:
         print_help()
         sys.exit(0)
     else:
@@ -284,13 +274,13 @@ if __name__ == '__main__':
         logger_setup(args.output_dir,
                      'gtdb_migration_tk.log',
                      'GTDB Migration Tk',
-                     version(),
+                     __version__,
                      args.silent)
     except:
         logger_setup(None,
                      'gtdb_migration_tk.log',
                      'GTDB Migration Tk',
-                     version(),
+                     __version__,
                      args.silent)
 
     # do what we came here to do

gtdb_migration_tk/__init__.py

@@ -0,0 +1,22 @@
+###############################################################################
+#                                                                             #
+#    This program is free software: you can redistribute it and/or modify     #
+#    it under the terms of the GNU General Public License as published by     #
+#    the Free Software Foundation, either version 3 of the License, or        #
+#    (at your option) any later version.                                      #
+#                                                                             #
+#    This program 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            #
+#    GNU General Public License for more details.                             #
+#                                                                             #
+#    You should have received a copy of the GNU General Public License        #
+#    along with this program. If not, see <http://www.gnu.org/licenses/>.     #
+#                                                                             #
+###############################################################################
+
+import os
+
+# Set the module version.
+with open(os.path.join(__path__[0], 'VERSION'), 'r') as f:
+    __version__ = f.readline().strip()

setup.py

@@ -0,0 +1,28 @@
+#!/usr/bin/env python
+
+import os
+
+from setuptools import setup
+
+
+def version():
+    setup_dir = os.path.dirname(os.path.realpath(__file__))
+    with open(os.path.join(setup_dir, 'gtdb_migration_tk', 'VERSION'), 'r') as f:
+        return f.readline().strip()
+
+
+setup(
+    name='gtdb_migration_tk',
+    python_requires='>=3.6',
+    version=version(),
+    author='Pierre-Alain Chaumeil',
+    author_email='p.chaumeil@uq.edu.au',
+    maintainer='Pierre-Alain Chaumeil, Aaron Mussig, and Donovan Parks',
+    maintainer_email='p.chaumeil@uq.edu.au',
+    packages=['gtdb_migration_tk'],
+    scripts=['bin/gtdb_migration_tk'],
+    package_data={'gtdb_migration_tk': ['VERSION']},
+    url='https://github.com/Ecogenomics/gtdb-migration-tk',
+    description='Toolkit for updating the GTDB to the next release and test data.',
+    install_requires=['requests', 'unidecode', 'biolib>=0.1.0', 'pandas', 'numpy'],
+)