Rework the way arguments are passed throughout the modules using a config factory pattern

pyproject.toml

@@ -110,3 +110,10 @@ ignore = [
 
 [tool.ruff.lint.per-file-ignores]
 "src/data/dorado_info.py" = ["E501"]
+# Legacy module names that don't follow PEP 8 naming convention
+"src/data/AUV.py" = ["N999"]
+"src/data/BLFilter.py" = ["N999"] 
+"src/data/lopcMEP.py" = ["N999"]
+"src/data/lopcToNetCDF.py" = ["N999"]
+"src/data/process_Dorado389.py" = ["N999"]
+"src/data/usblToNetCDF.py" = ["N999"]

src/data/align.py

@@ -12,32 +12,25 @@
 __author__ = "Mike McCann"
 __copyright__ = "Copyright 2021, Monterey Bay Aquarium Research Institute"
 
-import argparse
-import json
+import json  # noqa: I001
 import logging
 import os
 import re
 import sys
 import time
-from argparse import RawTextHelpFormatter
 from datetime import UTC, datetime
 from pathlib import Path
 from socket import gethostname
 
 import git
 import numpy as np
 import pandas as pd
+from scipy.interpolate import interp1d
 import xarray as xr
-from logs2netcdfs import (
-    BASE_PATH,
-    MISSIONNETCDFS,
-    SUMMARY_SOURCE,
-    TIME,
-    TIME60HZ,
-    AUV_NetCDF,
-)
+
+from common_args import get_standard_lrauv_parser
+from logs2netcdfs import AUV_NetCDF, MISSIONNETCDFS, SUMMARY_SOURCE, TIME, TIME60HZ
 from nc42netcdfs import BASE_LRAUV_PATH
-from scipy.interpolate import interp1d
 
 
 class InvalidCalFile(Exception):
@@ -679,6 +672,7 @@ def write_netcdf(self, netcdfs_dir, vehicle: str = "", name: str = "") -> None:
         )
 
     def process_command_line(self):
+        """Process command line arguments using shared parser infrastructure."""
         examples = "Examples:" + "\n\n"
         examples += "  Align calibrated data for some missions:\n"
         examples += "    " + sys.argv[0] + " --mission 2020.064.10\n"
@@ -691,57 +685,19 @@ def process_command_line(self):
             + "202509140809_202509150109.nc4\n"
         )
 
-        parser = argparse.ArgumentParser(
-            formatter_class=RawTextHelpFormatter,
+        # Use shared LRAUV parser since align handles both Dorado and LRAUV
+        parser = get_standard_lrauv_parser(
             description=__doc__,
             epilog=examples,
         )
 
-        parser.add_argument(
-            "--base_path",
-            action="store",
-            default=BASE_PATH,
-            help=f"Base directory for missionlogs and missionnetcdfs, default: {BASE_PATH}",
-        )
-        parser.add_argument(
-            "--auv_name",
-            action="store",
-            default="Dorado389",
-            help="Dorado389 (default), i2MAP, or Multibeam",
-        )
-        parser.add_argument(
-            "--mission",
-            action="store",
-            help="Mission directory, e.g.: 2020.064.10",
-        )
-        parser.add_argument(
-            "--log_file",
-            action="store",
-            help=(
-                "Path to the log file of original LRAUV data, e.g.: "
-                "brizo/missionlogs/2025/20250903_20250909/"
-                "20250905T072042/202509050720_202509051653.nc4"
-            ),
-        )
+        # Add align-specific arguments
         parser.add_argument(
             "--plot",
             action="store_true",
             help="Create intermediate plots to validate data operations.",
         )
-        parser.add_argument(
-            "-v",
-            "--verbose",
-            type=int,
-            choices=range(3),
-            action="store",
-            default=0,
-            const=1,
-            nargs="?",
-            help="verbosity level: "
-            + ", ".join(
-                [f"{i}: {v}" for i, v in enumerate(("WARN", "INFO", "DEBUG"))],
-            ),
-        )
+
         self.args = parser.parse_args()
         self.logger.setLevel(self._log_levels[self.args.verbose])
         self.commandline = " ".join(sys.argv)

src/data/archive.py

@@ -9,19 +9,22 @@
 __author__ = "Mike McCann"
 __copyright__ = "Copyright 2022, Monterey Bay Aquarium Research Institute"
 
-import argparse
-import logging
+import logging  # noqa: I001
 import os
 import shutil
 import sys
 import time
 from pathlib import Path
 
+from common_args import DEFAULT_BASE_PATH, get_standard_dorado_parser
 from create_products import MISSIONIMAGES, MISSIONODVS
-from logs2netcdfs import BASE_PATH, LOG_FILES, MISSIONNETCDFS, AUV_NetCDF
+from logs2netcdfs import AUV_NetCDF, LOG_FILES, MISSIONNETCDFS
 from nc42netcdfs import BASE_LRAUV_PATH, GROUP
 from resample import FREQ
 
+# Define BASE_PATH for backward compatibility
+BASE_PATH = DEFAULT_BASE_PATH
+
 LOG_NAME = "processing.log"
 AUVCTD_VOL = "/Volumes/AUVCTD"
 LRAUV_VOL = "/Volumes/LRAUV"
@@ -226,33 +229,13 @@ def copy_to_LRAUV(self, log_file: str, freq: str = FREQ) -> None:  # noqa: C901,
                 )
 
     def process_command_line(self):
-        parser = argparse.ArgumentParser(
-            formatter_class=argparse.RawTextHelpFormatter,
+        """Process command line arguments using shared parser infrastructure."""
+        # Use shared parser with archive-specific additions
+        parser = get_standard_dorado_parser(
             description=__doc__,
         )
-        parser.add_argument(
-            "--base_path",
-            action="store",
-            default=BASE_PATH,
-            help="Base directory for missionlogs and missionnetcdfs, default: auv_data",
-        )
-        parser.add_argument(
-            "--auv_name",
-            action="store",
-            default="Dorado389",
-            help="Dorado389 (default), i2map, or Multibeam",
-        )
-        parser.add_argument(
-            "--mission",
-            action="store",
-            help="Mission directory, e.g.: 2020.064.10",
-        )
-        parser.add_argument(
-            "--freq",
-            action="store",
-            default=FREQ,
-            help="Resample freq",
-        )
+
+        # Add archive-specific arguments
         parser.add_argument(
             "--M3",
             action="store_true",
@@ -263,11 +246,6 @@ def process_command_line(self):
             action="store_true",
             help="Copy reampled netCDF file(s) to appropriate place on AUVCTD",
         )
-        parser.add_argument(
-            "--clobber",
-            action="store_true",
-            help="Remove existing netCDF files before copying to the AUVCTD directory",
-        )
         parser.add_argument(
             "--archive_only_products",
             action="store_true",
@@ -278,20 +256,7 @@ def process_command_line(self):
             action="store_true",
             help="Create products from the resampled netCDF file(s)",
         )
-        parser.add_argument(
-            "-v",
-            "--verbose",
-            type=int,
-            choices=range(3),
-            action="store",
-            default=0,
-            const=1,
-            nargs="?",
-            help="verbosity level: "
-            + ", ".join(
-                [f"{i}: {v}" for i, v in enumerate(("WARN", "INFO", "DEBUG"))],
-            ),
-        )
+
         self.args = parser.parse_args()
         self.logger.setLevel(self._log_levels[self.args.verbose])
         self.commandline = " ".join(sys.argv)

src/data/calibrate.py

@@ -27,15 +27,13 @@
 __author__ = "Mike McCann"
 __copyright__ = "Copyright 2020, Monterey Bay Aquarium Research Institute"
 
-import argparse  # noqa: I001
-import logging
+import logging  # noqa: I001
 import os
 import shlex
 import shutil
 import subprocess
 import sys
 import time
-from argparse import RawTextHelpFormatter
 from collections import OrderedDict
 from datetime import UTC, datetime
 from pathlib import Path
@@ -46,16 +44,17 @@
 import defusedxml.ElementTree as ET  # noqa: N817
 import matplotlib.pyplot as plt
 import numpy as np
+import pandas as pd
+import pyproj
 import xarray as xr
+from scipy import signal
 from scipy.interpolate import interp1d
-from seawater import eos80
 
-import pandas as pd
-import pyproj
 from AUV import monotonic_increasing_time_indices, nudge_positions
+from common_args import get_standard_dorado_parser
 from hs2_proc import compute_backscatter, hs2_calc_bb, hs2_read_cal_file
-from logs2netcdfs import BASE_PATH, MISSIONLOGS, MISSIONNETCDFS, TIME, TIME60HZ, AUV_NetCDF
-from scipy import signal
+from logs2netcdfs import AUV_NetCDF, MISSIONLOGS, MISSIONNETCDFS, TIME, TIME60HZ
+from seawater import eos80
 
 AVG_SALINITY = 33.6  # Typical value for upper 100m of Monterey Bay
 
@@ -3282,64 +3281,29 @@ def process_logs(self, vehicle: str = "", name: str = "", process_gps: bool = Tr
         return netcdfs_dir
 
     def process_command_line(self):
+        """Process command line arguments using shared parser infrastructure."""
         examples = "Examples:" + "\n\n"
         examples += "  Calibrate original data for some missions:\n"
         examples += "    " + sys.argv[0] + " --mission 2020.064.10\n"
         examples += "    " + sys.argv[0] + " --auv_name i2map --mission 2020.055.01\n"
 
-        parser = argparse.ArgumentParser(
-            formatter_class=RawTextHelpFormatter,
+        # Use shared parser with calibrate-specific additions
+        parser = get_standard_dorado_parser(
             description=__doc__,
             epilog=examples,
         )
 
-        parser.add_argument(
-            "--base_path",
-            action="store",
-            default=BASE_PATH,
-            help=f"Base directory for missionlogs and missionnetcdfs, default: {BASE_PATH}",
-        )
-        parser.add_argument(
-            "--auv_name",
-            action="store",
-            default="Dorado389",
-            help="Dorado389 (default), i2MAP, or Multibeam",
-        )
-        parser.add_argument(
-            "--mission",
-            action="store",
-            help="Mission directory, e.g.: 2020.064.10",
-        )
-        parser.add_argument(
-            "--noinput",
-            action="store_true",
-            help="Execute without asking for a response, e.g. to not ask to re-download file",
-        )
+        # Add calibrate-specific arguments
         parser.add_argument(
             "--plot",
             action="store",
             help="Create intermediate plots"
             " to validate data operations. Use first<n> to plot <n>"
             " points, e.g. first2000. Program blocks upon show.",
         )
-        parser.add_argument(
-            "-v",
-            "--verbose",
-            type=int,
-            choices=range(3),
-            action="store",
-            default=0,
-            const=1,
-            nargs="?",
-            help="verbosity level: "
-            + ", ".join(
-                [f"{i}: {v}" for i, v in enumerate(("WARN", "INFO", "DEBUG"))],
-            ),
-        )
 
         self.args = parser.parse_args()
         self.logger.setLevel(self._log_levels[self.args.verbose])
-
         self.commandline = " ".join(sys.argv)