Apple set_argparse_from_dict to all arg parsers

artistools/__init__.py

@@ -97,7 +97,7 @@
 from artistools.misc import read_linestatfile
 from artistools.misc import readnoncommentline
 from artistools.misc import roman_numerals
-from artistools.misc import set_argparse_from_dict
+from artistools.misc import set_args_from_dict
 from artistools.misc import showtimesteptimes
 from artistools.misc import split_dataframe_dirbins
 from artistools.misc import stripallsuffixes

artistools/deposition.py

@@ -57,7 +57,7 @@ def main_analytical(args: argparse.Namespace | None = None, argsraw: list[str] |
     if args is None:
         parser = argparse.ArgumentParser(formatter_class=at.CustomArgHelpFormatter, description=__doc__)
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         args = parser.parse_args([] if kwargs else argsraw)
     dfmodel, modelmeta = at.inputmodel.get_modeldata(args.modelpath, derived_cols=["mass_g", "vel_r_min_kmps"])
 
@@ -127,7 +127,7 @@ def main(args: argparse.Namespace | None = None, argsraw: list[str] | None = Non
     if args is None:
         parser = argparse.ArgumentParser(formatter_class=at.CustomArgHelpFormatter, description=__doc__)
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         args = parser.parse_args([] if kwargs else argsraw)
 
         # TODO: plot deposition.out file!

artistools/estimators/exportmassfractions.py

@@ -19,7 +19,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
         )
 
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         args = parser.parse_args([] if kwargs else argsraw)
 
     modelpath: Path = Path()

artistools/estimators/plotestimators.py

@@ -1013,7 +1013,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
     if args is None:
         parser = argparse.ArgumentParser(formatter_class=at.CustomArgHelpFormatter, description=__doc__)
         addargs(parser)
-        at.set_argparse_from_dict(parser, kwargs)
+        at.set_args_from_dict(parser, kwargs)
         argcomplete.autocomplete(parser)
         args = parser.parse_args([] if kwargs else argsraw)
 

artistools/gsinetwork.py

@@ -663,7 +663,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
         parser = argparse.ArgumentParser(formatter_class=at.CustomArgHelpFormatter, description=__doc__)
 
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         argcomplete.autocomplete(parser)
         args = parser.parse_args([] if kwargs else argsraw)
 

artistools/inputmodel/1dslicefrom3d.py

@@ -7,7 +7,7 @@
 
 import matplotlib.pyplot as plt
 
-from artistools import CustomArgHelpFormatter
+import artistools as at
 
 
 def addargs(parser: argparse.ArgumentParser) -> None:
@@ -27,11 +27,11 @@ def addargs(parser: argparse.ArgumentParser) -> None:
 def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None = None, **kwargs: t.Any) -> None:
     if args is None:
         parser = argparse.ArgumentParser(
-            formatter_class=CustomArgHelpFormatter,
+            formatter_class=at.CustomArgHelpFormatter,
             description="Covert abundances.txt and model.txt from 3D to a one dimensional slice.",
         )
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         args = parser.parse_args()
 
     if not Path(args.outputfolder).exists():

artistools/inputmodel/botyanski2017.py

@@ -33,7 +33,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
         parser = argparse.ArgumentParser(formatter_class=at.CustomArgHelpFormatter, description=__doc__)
 
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         args = parser.parse_args([] if kwargs else argsraw)
 
     e_k = 1.2  # in units of 10^51 erg

artistools/inputmodel/describeinputmodel.py

@@ -47,7 +47,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
         )
 
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         argcomplete.autocomplete(parser)
         args = parser.parse_args([] if kwargs else argsraw)
 

artistools/inputmodel/from_alcar.py

@@ -336,7 +336,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
         parser = argparse.ArgumentParser(formatter_class=at.CustomArgHelpFormatter, description=__doc__)
 
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         argcomplete.autocomplete(parser)
         args = parser.parse_args([] if kwargs else argsraw)
 

artistools/inputmodel/fullymixed.py

@@ -22,7 +22,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
         )
 
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         args = parser.parse_args([] if kwargs else argsraw)
 
     dfmodel, t_model_init_days, _ = at.inputmodel.get_modeldata_tuple(args.inputpath, derived_cols=["mass_g"])

artistools/inputmodel/makeartismodel.py

@@ -56,7 +56,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
     if args is None:
         parser = argparse.ArgumentParser(formatter_class=at.CustomArgHelpFormatter, description=__doc__)
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         argcomplete.autocomplete(parser)
         args = parser.parse_args([] if kwargs else argsraw)
 

artistools/inputmodel/maptogrid.py

@@ -481,7 +481,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
         )
 
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         argcomplete.autocomplete(parser)
         args = parser.parse_args([] if kwargs else argsraw)
 

artistools/inputmodel/modelfromhydro.py

@@ -438,7 +438,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
         parser = argparse.ArgumentParser(formatter_class=at.CustomArgHelpFormatter, description=__doc__)
 
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         argcomplete.autocomplete(parser)
         args = parser.parse_args([] if kwargs else argsraw)
 

artistools/inputmodel/plotdensity.py

@@ -31,7 +31,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
         )
 
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         argcomplete.autocomplete(parser)
         args = parser.parse_args([] if kwargs else argsraw)
 

artistools/inputmodel/plotinitialcomposition.py

@@ -471,7 +471,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
     if args is None:
         parser = argparse.ArgumentParser(formatter_class=at.CustomArgHelpFormatter, description=__doc__)
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         argcomplete.autocomplete(parser)
         args = parser.parse_args([] if kwargs else argsraw)
 

artistools/inputmodel/recombinationenergy.py

@@ -197,7 +197,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
         )
 
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         argcomplete.autocomplete(parser)
         args = parser.parse_args([] if kwargs else argsraw)
 

artistools/inputmodel/rprocess_from_trajectory.py

@@ -512,7 +512,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
         )
 
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         argcomplete.autocomplete(parser)
         args = parser.parse_args([] if kwargs else argsraw)
 

artistools/inputmodel/rprocess_solar.py

@@ -20,7 +20,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
         parser = argparse.ArgumentParser(formatter_class=at.CustomArgHelpFormatter, description=__doc__)
 
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         args = parser.parse_args([] if kwargs else argsraw)
 
     dfsolarabund = pd.read_csv(

artistools/inputmodel/scalevelocity.py

@@ -36,7 +36,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
         )
 
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         args = parser.parse_args([] if kwargs else argsraw)
 
     dfmodel, t_model_init_days, _ = at.inputmodel.get_modeldata_tuple(args.inputfile)

artistools/inputmodel/shen2018.py

@@ -21,7 +21,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
         parser = argparse.ArgumentParser(formatter_class=at.CustomArgHelpFormatter, description=__doc__)
 
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         args = parser.parse_args([] if kwargs else argsraw)
 
     with Path(args.inputpath).open() as infile:

artistools/inputmodel/slice1dfromconein3dmodel.py

@@ -236,7 +236,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
             description=__doc__,
         )
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         args = parser.parse_args([] if kwargs else argsraw)
 
     if not args.modelpath:

artistools/inputmodel/test_inputmodel.py

@@ -21,11 +21,11 @@ def clear_modelfiles() -> None:
 
 
 def test_describeinputmodel() -> None:
-    at.inputmodel.describeinputmodel.main(argsraw=[], inputfile=modelpath, get_elemabundances=True)
+    at.inputmodel.describeinputmodel.main(argsraw=[], inputfile=modelpath, isotopes=True)
 
 
 def test_describeinputmodel_3d() -> None:
-    at.inputmodel.describeinputmodel.main(argsraw=[], inputfile=modelpath_3d, get_elemabundances=True)
+    at.inputmodel.describeinputmodel.main(argsraw=[], inputfile=modelpath_3d, isotopes=True)
 
 
 def test_get_modeldata_1d() -> None:
@@ -234,9 +234,7 @@ def test_makemodel() -> None:
 
 def test_makemodel_energyfiles() -> None:
     clear_modelfiles()
-    at.inputmodel.makeartismodel.main(
-        argsraw=[], modelpath=modelpath, makeenergyinputfiles=True, modeldim=1, outputpath=outputpath
-    )
+    at.inputmodel.makeartismodel.main(argsraw=[], modelpath=modelpath, makeenergyinputfiles=True, outputpath=outputpath)
 
 
 def test_maketardismodel() -> None:

artistools/inputmodel/to_tardis.py

@@ -35,7 +35,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
         parser = argparse.ArgumentParser(formatter_class=at.CustomArgHelpFormatter, description=__doc__)
 
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         argcomplete.autocomplete(parser)
         args = parser.parse_args([] if kwargs else argsraw)
 

artistools/lightcurve/plotlightcurve.py

@@ -1576,7 +1576,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
     if args is None:
         parser = argparse.ArgumentParser(formatter_class=at.CustomArgHelpFormatter, description=__doc__)
         addargs(parser)
-        at.set_argparse_from_dict(parser, kwargs)
+        at.set_args_from_dict(parser, kwargs)
         argcomplete.autocomplete(parser)
         args = parser.parse_args([] if kwargs else argsraw)
         if args.average_every_tenth_viewing_angle:

artistools/linefluxes.py

@@ -898,7 +898,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
             description=(__doc__),
         )
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         args = parser.parse_args([] if kwargs else argsraw)
 
     if not args.modelpath:

artistools/logfiles.py

@@ -130,7 +130,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
             formatter_class=at.CustomArgHelpFormatter, description="Plot durations from log files."
         )
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         args = parser.parse_args([] if kwargs else argsraw)
 
     if not args.modelpath:

artistools/macroatom.py

@@ -32,7 +32,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
             formatter_class=at.CustomArgHelpFormatter, description="Plot ARTIS macroatom transitions."
         )
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         args = parser.parse_args([] if kwargs else argsraw)
 
     if Path(args.outputfile).is_dir():

artistools/misc.py

@@ -726,7 +726,7 @@ def get_ionstring(
     return f"{get_elsymbol(atomic_number)}{strcharge}"
 
 
-def set_argparse_from_dict(parser: argparse.ArgumentParser, kwargs: dict[str, t.Any]) -> None:
+def set_args_from_dict(parser: argparse.ArgumentParser, kwargs: dict[str, t.Any]) -> None:
     """Set argparse defaults from a dictionary."""
     # set_defaults expects the dest of an argument. Here we allow the option strings to be used as keys
     for arg in parser._actions:

artistools/nltepops/plotnltepops.py

@@ -733,7 +733,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
     if args is None:
         parser = argparse.ArgumentParser(description=__doc__)
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         args = parser.parse_args([] if kwargs else argsraw)
 
     at.set_mpl_style()

artistools/nonthermal/plotnonthermal.py

@@ -291,7 +291,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
         parser = argparse.ArgumentParser(formatter_class=at.CustomArgHelpFormatter, description=__doc__)
 
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         args = parser.parse_args([] if kwargs else argsraw)
 
     if not args.modelpath:

artistools/nonthermal/solvespencerfanocmd.py

@@ -145,7 +145,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
             description=__doc__,
         )
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         args = parser.parse_args([] if kwargs else argsraw)
 
     if args.plotstats:

artistools/plotspherical.py

@@ -287,7 +287,7 @@ def main(args: argparse.Namespace | None = None, argsraw: list[str] | None = Non
     if args is None:
         parser = argparse.ArgumentParser(formatter_class=at.CustomArgHelpFormatter, description=__doc__)
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         argcomplete.autocomplete(parser)
         args = parser.parse_args([] if kwargs else argsraw)
 

artistools/radfield.py

@@ -959,7 +959,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
     if args is None:
         parser = argparse.ArgumentParser(formatter_class=at.CustomArgHelpFormatter, description=__doc__)
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         args = parser.parse_args([] if kwargs else argsraw)
 
     at.set_mpl_style()

artistools/spectra/plotspectra.py

@@ -1361,8 +1361,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
             description=__doc__,
         )
         addargs(parser)
-        at.set_argparse_from_dict(parser, kwargs)
-
+        at.set_args_from_dict(parser, kwargs)
         argcomplete.autocomplete(parser)
         args = parser.parse_args([] if kwargs else argsraw)
         if args.average_every_tenth_viewing_angle:

artistools/spectra/writespectra.py

@@ -70,7 +70,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
             description=__doc__,
         )
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         argcomplete.autocomplete(parser)
         args = parser.parse_args([] if kwargs else argsraw)
 

artistools/transitions.py

@@ -233,7 +233,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
             description=__doc__,
         )
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         args = parser.parse_args([] if kwargs else argsraw)
 
     if Path(args.outputfile).is_dir():

artistools/writecomparisondata.py

@@ -196,7 +196,7 @@ def main(args: argparse.Namespace | None = None, argsraw: t.Sequence[str] | None
             description=__doc__,
         )
         addargs(parser)
-        parser.set_defaults(**kwargs)
+        at.set_args_from_dict(parser, kwargs)
         args = parser.parse_args([] if kwargs else argsraw)
 
     if not args.modelpath: