Make sourcetracker2 gibbs work as a command

setup.py

@@ -71,7 +71,7 @@ def run(self):
 
 description = "Python implementation of the SourceTracker R package."
 
-standalone = ['sourcetracker2=sourcetracker._cli.gibbs:gibbs']
+standalone = ['sourcetracker2=sourcetracker._cli.cli:cli']
 q2cmds = ['q2-sourcetracker2=sourcetracker._q2.plugin_setup:plugin']
 
 with open('README.md') as f:

sourcetracker/_cli/__init__.py

@@ -1,20 +0,0 @@
-# ----------------------------------------------------------------------------
-# Copyright (c) 2016--, Biota Technology.
-#
-# Distributed under the terms of the Modified BSD License.
-#
-# The full license is in the file LICENSE, distributed with this software.
-# ----------------------------------------------------------------------------
-from importlib import import_module
-import click
-
-from sourcetracker import __version__
-
-
-@click.group()
-@click.version_option(__version__)
-def cli():
-    pass
-
-
-import_module('sourcetracker._cli.gibbs')

sourcetracker/_cli/cli.py

@@ -0,0 +1,19 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2016--, Biota Technology.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+import click
+
+from importlib import import_module
+from sourcetracker import __version__
+
+
+@click.group()
+@click.version_option(__version__)
+def cli():
+    pass
+
+import_module('sourcetracker._cli.gibbs')

sourcetracker/_cli/gibbs.py

@@ -17,7 +17,7 @@
 from biom import Table, load_table
 from matplotlib import pyplot as plt
 
-from sourcetracker._cli import cli
+from sourcetracker._cli.cli import cli
 from sourcetracker._gibbs import gibbs_helper
 from sourcetracker._plot import plot_heatmap
 from sourcetracker._util import parse_sample_metadata, biom_to_df