Merge branch 'main' into 1044-get-rid-of-all-global-variables-and-mov…

…e-to-a-config-data-class

src/sorcha/sorcha.py

@@ -183,7 +183,6 @@ def runLSSTSimulation(args, sconfigs):
         if sconfigs.input.ephemerides_type.casefold() == "external":
             verboselog("Reading in chunk of orbits and associated ephemeris from an external file")
             observations = reader.read_block(block_size=sconfigs.input.size_serial_chunk)
-            observations.to_csv("post_readin_ephem_nonprimary.csv")
         else:
             verboselog("Ingest chunk of orbits")
             orbits_df = reader.read_aux_block(block_size=sconfigs.input.size_serial_chunk)

src/sorcha_cmdline/bootstrap.py

@@ -1,15 +1,17 @@
 #
 # The `sorcha run` subcommand implementation
 #
-import argparse
 import pooch
+from sorcha_cmdline.sorchaargumentparser import SorchaArgumentParser
 
 
 def main():  # pragma: no cover
     # parse the input arguments
-    parser = argparse.ArgumentParser(
-        description="Fetch the NAIF high precision EOP kernel file store its checksum."
+    parser = SorchaArgumentParser(
+        prog="sorcha bootstrap",
+        description="Fetch the NAIF high precision EOP kernel file store its checksum.",
     )
+
     parser.add_argument(
         "--cache",
         type=str,

src/sorcha_cmdline/demo.py

@@ -1,4 +1,4 @@
-import argparse
+from sorcha_cmdline.sorchaargumentparser import SorchaArgumentParser
 
 #
 # sorcha demo prepare
@@ -47,11 +47,14 @@ def cmd_demo_howto(args):  # pragma: no cover
 
 def main():
     # Create the top-level parser
-    parser = argparse.ArgumentParser(
-        prog="sorcha-demo", description="Prepare and explain how to run sorcha demos"
+    parser = SorchaArgumentParser(
+        prog="sorcha demo", description="Prepare and explain how to run sorcha demos"
     )
     subparsers = parser.add_subparsers(
-        title="commands", description="Available commands", help="Command to execute", dest="command"
+        title="commands",
+        description="Available commands",
+        help="Command to execute",
+        dest="command",
     )
 
     # Add the `prepare` subcommand

src/sorcha_cmdline/init.py

@@ -1,4 +1,4 @@
-import argparse
+from sorcha_cmdline.sorchaargumentparser import SorchaArgumentParser
 import sys
 
 #
@@ -72,8 +72,8 @@ def execute(args):  # pragma: no cover
 
 def main():
     # Create the top-level parser
-    parser = argparse.ArgumentParser(
-        prog="sorcha-init", description="Initialize configuration files for a new simulation."
+    parser = SorchaArgumentParser(
+        prog="sorcha init", description="Initialize configuration files for a new simulation."
     )
     parser.add_argument("-v", "--verbose", action="store_true", help="Enable verbose output")
     parser.add_argument(

src/sorcha_cmdline/outputs.py

@@ -1,4 +1,4 @@
-import argparse
+from sorcha_cmdline.sorchaargumentparser import SorchaArgumentParser
 
 #
 # sorcha outputs create-sqlite
@@ -69,7 +69,7 @@ def cmd_outputs_check_logs(args):  # pragma: no cover
 
 def main():
     # Create the top-level parser
-    parser = argparse.ArgumentParser(prog="sorcha-outputs", description="Sorcha outputs manipulation utility")
+    parser = SorchaArgumentParser(prog="sorcha outputs", description="Sorcha outputs manipulation utility")
     subparsers = parser.add_subparsers(
         title="commands", description="Available commands", help="Command to execute", dest="command"
     )

src/sorcha_cmdline/run.py

@@ -2,12 +2,18 @@
 # The `sorcha run` subcommand implementation
 #
 import argparse
+from sorcha_cmdline.sorchaargumentparser import SorchaArgumentParser
 
 
 def main():
-    parser = argparse.ArgumentParser(
-        formatter_class=argparse.ArgumentDefaultsHelpFormatter, description="Run a simulation."
+    parser = SorchaArgumentParser(
+        prog="sorcha run",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        description="Run a simulation.",
     )
+
+    # parser = SorchaArgparse(parser)
+
     required = parser.add_argument_group("Required arguments")
     required.add_argument(
         "-c",

src/sorcha_cmdline/sorchaargumentparser.py

@@ -0,0 +1,37 @@
+from argparse import ArgumentParser
+
+
+class SorchaArgumentParser(ArgumentParser):
+    """A subclass of the argparse.ArgumentParser that adds in a print statement
+    to make it clearer how to get detailed help for new users who may not be
+    as familiar with linux/unix"""
+
+    def __init__(self, *args, **kwargs):
+        """A subclass of the argparse.ArgumentParser that adds in a print statement
+        to make it clearer how to get detailed help for new users who may not be
+        as familiar with linux/unix
+
+        Parameters
+        -----------
+        *args: Variable length argument list.
+        **kwargs: Arbitrary keyword arguments.
+        """
+        super().__init__(*args, **kwargs)
+
+    def print_usage(self, file=None):
+        """Print a brief description of how the ArgumentParser should be invoked
+        on the command line. If file is None, sys.stdout is assumed.
+
+
+        Parameters
+        -----------
+        file: str or None
+            Variable length argument list.
+
+        Returns
+        -----------
+        None.
+
+        """
+        super().print_usage(file)
+        print(f"For more detailed help try: {self.prog} -h ", file=file)