use configargparse in all scripts

AegeanTools/CLI/AeReg.py

@@ -1,6 +1,6 @@
 #! /usr/bin/env python
 
-import argparse
+import configargparse
 import os
 import sys
 
@@ -13,25 +13,22 @@
 from AegeanTools.logging import logger, logging
 
 __author__ = ["PaulHancock"]
-__date__ = "2024-01-24"
-__version__ = "0.9"
+__version__ = "0.9.1"
+__date__ = "2025-01-14"
 
 
 def main():
     """
     A regrouping tool to accompany the Aegean source finding program.
     """
 
-    parser = argparse.ArgumentParser(prog="regroup", prefix_chars="-")
+    parser = configargparse.ArgumentParser(prog="AeReg", prefix_chars="-")
     group1 = parser.add_argument_group("Required")
-    group1.add_argument(
-        "--input", dest="input", type=str, required=True, help="The input catalogue."
-    )
+    group1.add_argument("--input", dest="input", type=str, help="The input catalogue.")
     group1.add_argument(
         "--table",
         dest="tables",
         type=str,
-        required=True,
         help="Table outputs, format inferred from extension.",
     )
 
@@ -72,15 +69,20 @@ def main():
     group4.add_argument(
         "--debug", dest="debug", action="store_true", default=False, help="Debug mode."
     )
+    group4.add_argument("--config", is_config_file=True, help="Path to the config file")
 
     options = parser.parse_args()
 
+    if not options.input or not options.tables:
+        parser.print_help()
+        return 0
+
     invocation_string = " ".join(sys.argv)
 
     # configure logging
     logging_level = logging.DEBUG if options.debug else logging.INFO
     logger.setLevel(logging_level)
-    logger.info("This is regroup {0}-({1})".format(__version__, __date__))
+    logger.info("This is AeReg {0}-({1})".format(__version__, __date__))
     logger.debug("Run as:\n{0}".format(invocation_string))
 
     # check that a valid intput filename was entered

AegeanTools/CLI/AeRes.py

@@ -1,24 +1,21 @@
 #! /usr/bin/env python
 
-import argparse
+import configargparse
 
 from AegeanTools.AeRes import make_residual
 from AegeanTools.logging import logger, logging
 
 __author__ = "Paul Hancock"
 __version__ = "v0.2.7"
-__date__ = "2024-01-24"
-
-
-# global constants
+__date__ = "2025-01-14"
 
 
 def main():
     """
     Tool for making residual images with Aegean tables as input
     """
 
-    parser = argparse.ArgumentParser(prog="AeRes", prefix_chars="-")
+    parser = configargparse.ArgumentParser(prog="AeRes", prefix_chars="-")
     group1 = parser.add_argument_group("I/O arguments")
     group1.add_argument(
         "-c",
@@ -100,6 +97,7 @@ def main():
     group4.add_argument(
         "--debug", dest="debug", action="store_true", default=False, help="Debug mode."
     )
+    group4.add_argument("--config", is_config_file=True, help="Path to the config file")
 
     options = parser.parse_args()
 

AegeanTools/CLI/MIMAS.py

@@ -1,10 +1,13 @@
 #! /usr/bin/env python
-import argparse
+import configargparse
 import sys
 
 from AegeanTools import MIMAS, __citation__
 from AegeanTools.logging import logger, logging
 
+__author__ = "Paul Hancock"
+__date__ = "2025-01-14"
+
 
 def main():
     """
@@ -15,7 +18,7 @@ def main():
         "+r -r +c -c +p -p. This means that you might have to take "
         "multiple passes to construct overly complicated regions."
     )
-    parser = argparse.ArgumentParser(epilog=epilog, prefix_chars="+-")
+    parser = configargparse.ArgumentParser(epilog=epilog, prefix_chars="+-")
 
     group1 = parser.add_argument_group(
         "Creating/modifying regions", "Must specify -o, plus or more [+-][cr]"
@@ -247,6 +250,8 @@ def main():
         help="Show citation information.",
     )
 
+    group4.add_argument("--config", is_config_file=True, help="Path to the config file")
+
     results = parser.parse_args()
 
     # print help if the user enters no options or filename

AegeanTools/CLI/SR6.py

@@ -1,5 +1,5 @@
 #! /usr/bin/env python
-import argparse
+import configargparse
 import os
 import sys
 
@@ -12,8 +12,8 @@
 from AegeanTools.logging import logger, logging
 
 __author__ = "Paul Hancock"
-__version__ = "v1.2"
-__date__ = "2024-01-24"
+__version__ = "v1.2.1"
+__date__ = "2025-01-14"
 
 
 # command line version of this program runs from here.
@@ -24,7 +24,7 @@ def main():
     """
 
     epilog = ""
-    parser = argparse.ArgumentParser(epilog=epilog, prefix_chars="-")
+    parser = configargparse.ArgumentParser(epilog=epilog, prefix_chars="-")
 
     # tools for shrinking files
     group1 = parser.add_argument_group("Shrinking and expanding files")
@@ -81,8 +81,10 @@ def main():
         default=False,
         help="Show citation information.",
     )
+    group2.add_argument("--config", is_config_file=True, help="Path to the config file")
 
     results = parser.parse_args()
+
     # print help if the user enters no options or filename
     if len(sys.argv) == 1:
         parser.print_help()
@@ -92,6 +94,10 @@ def main():
         print(__citation__)
         return 0
 
+    if results.infile is None:
+        parser.print_help()
+        return 0
+
     logging_level = logging.DEBUG if results.debug else logging.INFO
     logger.setLevel(logging_level)
     logger.info("This is SR6 {0}-({1})".format(__version__, __date__))

AegeanTools/CLI/aegean.py

@@ -1,6 +1,6 @@
 #! /usr/bin/env python
 
-import argparse
+import configargparse
 
 # import logging.config
 import multiprocessing
@@ -51,10 +51,12 @@ def main():
     The Aegean source finding program.
     """
 
-    parser = argparse.ArgumentParser(prog="aegean", prefix_chars="-")
+    parser = configargparse.ArgumentParser(prog="aegean", prefix_chars="-")
     parser.add_argument("image", nargs="?", default=None)
     group1 = parser.add_argument_group("Configuration Options")
 
+    group1.add_argument("--config", is_config_file=True, help="Path to the config file")
+
     group1.add_argument(
         "--find",
         dest="find",

pyproject.toml

@@ -16,7 +16,8 @@ dependencies = [
     "astropy>=2.0",
     "healpy >=1.10",
     "lmfit>=0.9.2",
-    "scikit-learn>=0.24.2"
+    "scikit-learn>=0.24.2",
+    "configargparse>=1.7"
 ]
 classifiers=[
     "Development Status :: 5 - Production/Stable",

tests/integration/test_script_AeReg.py

@@ -87,6 +87,18 @@ def test_broken_catalogue():
             os.remove(tempfile + "_comp")
 
 
+def test_configfile():
+    cfile = "AeReg.ini"
+    try:
+        with open(cfile, "w") as config:
+            config.write("debug = False")
+        sys.argv = ["", "--config", cfile]
+        AeReg.main()
+    finally:
+        if os.path.exists(cfile):
+            os.remove(cfile)
+
+
 if __name__ == "__main__":
     # introspect and run all the functions starting with 'test'
     for f in dir():

tests/integration/test_script_AeRes.py

@@ -41,6 +41,18 @@ def test_nocat():
         os.remove(tempfile + "_model")
 
 
+def test_configfile():
+    cfile = "AeRes.ini"
+    try:
+        with open(cfile, "w") as config:
+            config.write("debug = False")
+        sys.argv = ["", "--config", cfile]
+        AeRes.main()
+    finally:
+        if os.path.exists(cfile):
+            os.remove(cfile)
+
+
 if __name__ == "__main__":
     # introspect and run all the functions starting with 'test'
     for f in dir():

tests/integration/test_script_MIMAS.py

@@ -102,6 +102,18 @@ def test_make_region():
         os.remove(tempfile)
 
 
+def test_configfile():
+    cfile = "MIMAS.ini"
+    try:
+        with open(cfile, "w") as config:
+            config.write("debug = False")
+        sys.argv = ["", "--config", cfile]
+        MIMAS.main()
+    finally:
+        if os.path.exists(cfile):
+            os.remove(cfile)
+
+
 if __name__ == "__main__":
     # introspect and run all the functions starting with 'test'
     for f in dir():

tests/integration/test_script_SR6.py

@@ -55,6 +55,18 @@ def test_expand():
         os.remove(tempfile + ".fits")
 
 
+def test_configfile():
+    cfile = "SR6.ini"
+    try:
+        with open(cfile, "w") as config:
+            config.write("debug = False")
+        sys.argv = ["", "--config", cfile]
+        SR6.main()
+    finally:
+        if os.path.exists(cfile):
+            os.remove(cfile)
+
+
 if __name__ == "__main__":
     # introspect and run all the functions starting with 'test'
     for f in dir():

tests/integration/test_script_aegean.py

@@ -105,6 +105,18 @@ def test_priorized():
     aegean.main()
 
 
+def test_configfile():
+    cfile = "aegean.ini"
+    try:
+        with open(cfile, "w") as config:
+            config.write("debug = False")
+        sys.argv = ["", "--config", cfile]
+        aegean.main()
+    finally:
+        if os.path.exists(cfile):
+            os.remove(cfile)
+
+
 if __name__ == "__main__":
     # introspect and run all the functions starting with 'test'
     for f in dir():