Merge pull request #43 from gregcaporaso/issue-40

ENH: support discovery of plugin citations and user support text

q2cli/_info.py

@@ -34,11 +34,10 @@ def _echo_plugins():
  # https://github.com/qiime2/qiime2/issues/82
  click.secho('No plugins are currently installed.\nYou can browse '
  'the official QIIME 2 plugins at: '
- 'https://github.com/qiime2')
+ 'http://2.qiime.org/Plugins')
  else:
  for name, plugin in installed_plugins.items():
- click.echo('%s %s (%s)' %
- (name, plugin.version, plugin.website))
+ click.echo('%s %s' % (name, plugin.version))
 
 
 def _echo_installed_packages():
@@ -62,6 +61,12 @@ def info(py_packages):
  if py_packages:
  click.secho('\nInstalled Python packages', fg='green')
  _echo_installed_packages()
- click.secho('\nTo get help with QIIME, visit %s.' % qiime.sdk.HELP_URL)
- click.secho('If you use QIIME in any published work, please cite %s' %
- qiime.sdk.CITATION)
+
+ click.secho('\nGetting help', fg='green')
+ click.secho('To get help with QIIME 2, visit %s.' % qiime.sdk.HELP_URL)
+
+ click.secho('\nCiting QIIME 2', fg='green')
+ click.secho('If you use QIIME 2 in any published work, you should cite '
+ 'QIIME 2 and the plugins that you used. To find the relevant '
+ 'citations, run:')
+ click.secho('\tqiime tools citations')

q2cli/_tools.py

@@ -136,3 +136,19 @@ def extract(path, output_dir):
  raise click.BadParameter(
  '%s is not a QIIME Result. Only QIIME Visualizations and Artifacts'
  ' can be extracted.' % path)
+
+
+@tools.command(help='Present citations for QIIME and installed plugins.')
+def citations():
+ click.secho('If you use QIIME 2 in any published work, you should cite '
+ 'QIIME 2 and the plugins that you used. The citations for '
+ 'QIIME and all installed plugins follow.')
+ click.secho('\nQIIME 2 framework and command line interface', fg='green')
+ click.secho('Pending a QIIME 2 publication, please cite QIIME using the '
+ 'original publication: %s' % qiime.sdk.CITATION)
+
+ plugin_manager = qiime.sdk.PluginManager()
+ installed_plugins = plugin_manager.plugins
+ for name, plugin in sorted(installed_plugins.items()):
+ click.secho('\n%s' % name, fg='green')
+ click.secho(plugin.citation_text)

q2cli/cli.py

@@ -72,9 +72,13 @@ def get_command(self, ctx, name):
  else:
  return _build_visualizer_command(
  name, plugin.visualizers[action_name])
- # TODO: pass help=plugin.description, pending its existence:
- # https://github.com/qiime2/qiime2/issues/81
- return PluginCommand(ctx)
+ # TODO: pass short_help=plugin.description, pending its
+ # existence: https://github.com/qiime2/qiime2/issues/81
+ _support = 'Getting user support: %s' % plugin.user_support_text
+ _citing = 'Citing this plugin: %s' % plugin.citation_text
+ _website = 'Plugin website: %s' % plugin.website
+ _help = '\n\n'.join([_website, _support, _citing])
+ return PluginCommand(ctx, short_help='', help=_help)
  else:
  return None
 

setup.py

@@ -14,7 +14,7 @@
  license='BSD-3-Clause',
  packages=find_packages(),
  include_package_data=True,
- install_requires=['click', 'qiime >= 2.0.0', 'pip'],
+ install_requires=['click', 'qiime >= 2.0.2', 'pip'],
  entry_points='''
  [console_scripts]
  qiime=q2cli.cli:main