Prefer dashes instead of underscores in flags

Author: natefoo

setup.py

@@ -36,7 +36,9 @@ def get_var(var_name):
         workflow-to-tools=ephemeris.generate_tool_list_from_ga_workflow_files:main
         setup-data-libraries=ephemeris.setup_data_libraries:main
         galaxy-wait=ephemeris.sleep:main
+        install-tool-deps=ephemeris.install_tool_deps:main
         install_tool_deps=ephemeris.install_tool_deps:main
+        set-library-permissions=ephemeris.set_library_permissions:main
         set_library_permissions=ephemeris.set_library_permissions:main
 '''
 PACKAGE_DATA = {

src/ephemeris/common_parser.py

@@ -3,13 +3,28 @@
 import argparse
 
 
+class HideUnderscoresHelpFormatter(argparse.HelpFormatter):
+    def add_arguments(self, actions):
+        for action in actions:
+            action.option_strings = list(s for s in action.option_strings if "_" not in s)
+            self.add_argument(action)
+
+
+class RawDescriptionHideUnderscoresHelpFormatter(HideUnderscoresHelpFormatter, argparse.RawDescriptionHelpFormatter):
+    pass
+
+
+class ArgumentDefaultsHideUnderscoresHelpFormatter(HideUnderscoresHelpFormatter, argparse.ArgumentDefaultsHelpFormatter):
+    pass
+
+
 def get_common_args(login_required=True, log_file=False):
 
     parser = argparse.ArgumentParser(add_help=False)
     general_group = parser.add_argument_group('General options')
     general_group.add_argument("-v", "--verbose", help="Increase output verbosity.", action="store_true")
     if log_file:
-        general_group.add_argument("--log_file",
+        general_group.add_argument("--log-file", "--log_file",
                                    dest="log_file",
                                    help="Where the log file should be stored. "
                                    "Default is a file in your system's temp folder",
@@ -25,7 +40,7 @@ def get_common_args(login_required=True, log_file=False):
                                help="Galaxy user email address")
         con_group.add_argument("-p", "--password",
                                help="Password for the Galaxy user")
-        con_group.add_argument("-a", "--api_key",
+        con_group.add_argument("-a", "--api-key", "--api_key",
                                dest="api_key",
                                help="Galaxy admin user API key (required if not defined in the tools list file)")
 

src/ephemeris/generate_tool_list_from_ga_workflow_files.py

@@ -1,10 +1,11 @@
 #!/usr/bin/env python
 '''Tool to generate tools from workflows'''
 import json
-from argparse import ArgumentParser, RawDescriptionHelpFormatter
+from argparse import ArgumentParser
 
 import yaml
 
+from .common_parser import RawDescriptionHideUnderscoresHelpFormatter
 from .shed_tools_methods import format_tool_shed_url
 
 INSTALL_TOOL_DEPENDENCIES = 'install_tool_dependencies: True'
@@ -21,7 +22,7 @@ def _parse_cli_options():
 
 
 def _parser():
-    parser = ArgumentParser(formatter_class=RawDescriptionHelpFormatter,
+    parser = ArgumentParser(formatter_class=RawDescriptionHideUnderscoresHelpFormatter,
                             usage="%(prog)s <options>",
                             epilog="Workflow files must have been exported from Galaxy release 16.04 or newer.\n\n"
                                    "example:\n"
@@ -37,7 +38,7 @@ def _parser():
                         required=True,
                         dest='output_file',
                         help='The output file with a yml tool list')
-    parser.add_argument('-l', '--panel_label',
+    parser.add_argument('-l', '--panel-label', '--panel_label',
                         dest='panel_label',
                         default='Tools from workflows',
                         help='The name of the panel where the tools will show up in Galaxy.'

src/ephemeris/get_tool_list_from_galaxy.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 """Tool to extract a tool list from galaxy."""
 
-from argparse import ArgumentDefaultsHelpFormatter
 from argparse import ArgumentParser
 from distutils.version import StrictVersion
 
@@ -10,7 +9,7 @@
 from bioblend.galaxy.toolshed import ToolShedClient
 
 from . import get_galaxy_connection
-from .common_parser import get_common_args
+from .common_parser import ArgumentDefaultsHideUnderscoresHelpFormatter, get_common_args
 from .shed_tools_methods import format_tool_shed_url
 
 
@@ -216,29 +215,29 @@ def _parser():
     """Creates the parser object."""
     parent = get_common_args(login_required=True)
     parser = ArgumentParser(parents=[parent],
-                            formatter_class=ArgumentDefaultsHelpFormatter)
+                            formatter_class=ArgumentDefaultsHideUnderscoresHelpFormatter)
     parser.add_argument("-o", "--output-file",
                         required=True,
                         dest="output",
                         help="tool_list.yml output file")
-    parser.add_argument("--include_tool_panel_id",
+    parser.add_argument("--include-tool-panel-id", "--include_tool_panel_id",
                         action="store_true",
                         help="Include tool_panel_id in tool_list.yml ? "
                              "Use this only if the tool panel id already exists. See "
                              "https://github.com/galaxyproject/ansible-galaxy-tools/blob/master/files/tool_list.yaml.sample")
-    parser.add_argument("--skip_tool_panel_name",
+    parser.add_argument("--skip-tool-panel-name", "--skip_tool_panel_name",
                         action="store_true",
                         help="Do not include tool_panel_name in tool_list.yml ?")
-    parser.add_argument("--skip_changeset_revision",
+    parser.add_argument("--skip-changeset-revision", "--skip_changeset_revision",
                         action="store_true",
                         help="Do not include the changeset revision when generating the tool list."
                              "Use this if you would like to use the list to update all the tools in"
                              "your galaxy instance using shed-install."
                         )
-    parser.add_argument("--get_data_managers",
+    parser.add_argument("--get-data-managers", "--get_data_managers",
                         action="store_true",
                         help="Include the data managers in the tool list. Requires admin login details")
-    parser.add_argument("--get_all_tools",
+    parser.add_argument("--get-all-tools", "--get_all_tools",
                         action="store_true",
                         help="Get all tools and revisions, not just those which are present on the web ui."
                              "Requires login details.")

src/ephemeris/install_tool_deps.py

@@ -10,14 +10,14 @@
 from bioblend.galaxy.tools import ToolClient
 
 from ephemeris import get_galaxy_connection
-from ephemeris.common_parser import get_common_args
+from ephemeris.common_parser import get_common_args, HideUnderscoresHelpFormatter
 
 timeout_codes = (408, 502, 504)
 
 
 def _parser():
     parent = get_common_args()
-    parser = argparse.ArgumentParser(parents=[parent])
+    parser = argparse.ArgumentParser(parents=[parent], formatter_class=HideUnderscoresHelpFormatter)
     parser.add_argument("-t", "--tool", help='Path to a tool file, tool_conf file, or yaml file containing a sequence of tool ids', nargs='*')
     parser.add_argument("-i", "--id", help='Space-separated list of tool ids', nargs='*')
 

src/ephemeris/run_data_managers.py

@@ -35,7 +35,7 @@
 
 from . import get_galaxy_connection
 from . import load_yaml_file
-from .common_parser import get_common_args
+from .common_parser import get_common_args, HideUnderscoresHelpFormatter
 from .ephemeris_log import disable_external_library_logging, setup_global_logger
 
 DEFAULT_URL = "http://localhost"
@@ -288,13 +288,14 @@ def _parser():
 
     parser = argparse.ArgumentParser(
         parents=[parent],
+        formatter_class=HideUnderscoresHelpFormatter,
         description='Running Galaxy data managers in a defined order with defined parameters.'
                     "'watch_tool_data_dir' in galaxy config should be set to true.'")
     parser.add_argument("--config", required=True,
                         help="Path to the YAML config file with the list of data managers and data to install.")
     parser.add_argument("--overwrite", action="store_true",
                         help="Disables checking whether the item already exists in the tool data table.")
-    parser.add_argument("--ignore_errors", action="store_true",
+    parser.add_argument("--ignore-errors", "--ignore_errors", action="store_true",
                         help="Do not stop running when jobs have failed.")
     return parser
 

src/ephemeris/set_library_permissions.py

@@ -8,7 +8,7 @@
 from bioblend import galaxy
 from rich.progress import Progress
 
-from .common_parser import get_common_args
+from .common_parser import get_common_args, HideUnderscoresHelpFormatter
 
 # Print iterations progress
 
@@ -74,7 +74,9 @@ def _parser():
     """Constructs the parser object"""
     parent = get_common_args()
     parser = argparse.ArgumentParser(
-        parents=[parent], description="Populate the Galaxy data library with data."
+        parents=[parent],
+        formatter_class=HideUnderscoresHelpFormatter,
+        description="Populate the Galaxy data library with data."
     )
     parser.add_argument("library", help="Specify the data library ID")
     parser.add_argument("--roles", nargs="+", help="Specify a list of comma separated role IDs")

src/ephemeris/setup_data_libraries.py

@@ -8,7 +8,7 @@
 import yaml
 from bioblend import galaxy
 
-from .common_parser import get_common_args
+from .common_parser import get_common_args, HideUnderscoresHelpFormatter
 
 
 def create_legacy(gi, desc):
@@ -189,6 +189,7 @@ def _parser():
     parent = get_common_args()
     parser = argparse.ArgumentParser(
         parents=[parent],
+        formatter_class=HideUnderscoresHelpFormatter,
         description='Populate the Galaxy data library with data.'
     )
     parser.add_argument('-i', '--infile', required=True, type=argparse.FileType('r'))