Prefer dashes instead of underscores in flags

src/ephemeris/common_parser.py

@@ -3,6 +3,21 @@
 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")
@@ -11,6 +26,8 @@ def get_common_args(login_required=True, log_file=False):
     )
     if log_file:
         general_group.add_argument(
+        general_group.add_argument(
+            "--log-file",
             "--log_file",
             dest="log_file",
             help="Where the log file should be stored. "
@@ -31,6 +48,7 @@ def get_common_args(login_required=True, log_file=False):
         con_group.add_argument("-p", "--password", help="Password for the Galaxy user")
         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

@@ -1,17 +1,15 @@
 #!/usr/bin/env python
 """Tool to generate tools from workflows"""
 import json
-from argparse import (
-    ArgumentParser,
-    RawDescriptionHelpFormatter,
-)
+from argparse import ArgumentParser
 from typing import (
     Iterable,
     List,
 )
 
 import yaml
 
+from .common_parser import RawDescriptionHideUnderscoresHelpFormatter
 from .shed_tools import InstallRepoDict
 from .shed_tools_methods import format_tool_shed_url
 
@@ -30,7 +28,7 @@ def _parse_cli_options():
 
 def _parser():
     parser = ArgumentParser(
-        formatter_class=RawDescriptionHelpFormatter,
+        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"
@@ -55,6 +53,7 @@ def _parser():
     )
     parser.add_argument(
         "-l",
+        "--panel-label",
         "--panel_label",
         dest="panel_label",
         default="Tools from workflows",

src/ephemeris/get_tool_list_from_galaxy.py

@@ -1,18 +1,18 @@
 #!/usr/bin/env python
 """Tool to extract a tool list from galaxy."""
 
-from argparse import (
-    ArgumentDefaultsHelpFormatter,
-    ArgumentParser,
-)
+from argparse import ArgumentParser
 from distutils.version import StrictVersion
 
 import yaml
 from bioblend.galaxy.tools import ToolClient
 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
 
 
@@ -245,7 +245,7 @@ def _parser():
     """Creates the parser object."""
     parent = get_common_args(login_required=True)
     parser = ArgumentParser(
-        parents=[parent], formatter_class=ArgumentDefaultsHelpFormatter
+        parents=[parent], formatter_class=ArgumentDefaultsHideUnderscoresHelpFormatter
     )
     parser.add_argument(
         "-o",
@@ -255,30 +255,35 @@ def _parser():
         help="tool_list.yml output file",
     )
     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",
         "--skip_tool_panel_name",
         action="store_true",
         help="Do not include tool_panel_name in tool_list.yml ?",
     )
     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",
         "--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",
         "--get_all_tools",
         action="store_true",
         help="Get all tools and revisions, not just those which are present on the web ui."

src/ephemeris/install_tool_deps.py

@@ -10,14 +10,17 @@
 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",

src/ephemeris/run_data_managers.py

@@ -37,7 +37,10 @@
     get_galaxy_connection,
     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,
@@ -320,6 +323,7 @@ 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.'",
     )
@@ -334,6 +338,7 @@ def _parser():
         help="Disables checking whether the item already exists in the tool data table.",
     )
     parser.add_argument(
+        "--ignore-errors",
         "--ignore_errors",
         action="store_true",
         help="Do not stop running when jobs have failed.",

src/ephemeris/set_library_permissions.py

@@ -9,7 +9,10 @@
 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
 
@@ -75,7 +78,9 @@ 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(

src/ephemeris/setup_data_libraries.py

@@ -8,7 +8,10 @@
 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):
@@ -211,7 +214,9 @@ 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("-i", "--infile", required=True, type=argparse.FileType("r"))
     parser.add_argument(