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Merged
sbillinge merged 5 commits into from
Feb 24, 2026
Merged

Update error message #292

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eab8da0
Update error message
Sparks29032 Feb 24, 2026
9d08723
Remove SystemExit
Sparks29032 Feb 24, 2026
1ac2cf9
News
Sparks29032 Feb 24, 2026
6d5abca
Refactor default labels from [r],[gr]->[x],[fx] when saving (#294)
Sparks29032 Feb 24, 2026
8a8f008
Fixed tests for squeeze morph warnings (#295)
Sparks29032 Feb 24, 2026
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23 changes: 23 additions & 0 deletions news/error-message.rst
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Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
**Added:**

* <news item>

**Changed:**

* Program no longer gives SystemExit. Proper errors are assigned to each case.

**Deprecated:**

* <news item>

**Removed:**

* <news item>

**Fixed:**

* <news item>

**Security:**

* <news item>
137 changes: 79 additions & 58 deletions src/diffpy/morph/morphapp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,13 +41,13 @@ class CustomParser(optparse.OptionParser):
def __init__(self, *args, **kwargs):
super(CustomParser, self).__init__(*args, **kwargs)

def custom_error(self, msg):
"""custom_error(msg : string)
def morph_error(self, msg, error):
"""morph_error(msg : string)

@sbillinge sbillinge Feb 24, 2026

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Let's make the docstring a bit better (and also accurate)


Print a message incorporating 'msg' to stderr and exit. Does
not print usage.
"""
self.exit(2, "%s: error: %s\n" % (self.get_prog_name(), msg))
raise error(f"{self.get_prog_name()}: {msg}")

parser = CustomParser(
usage="\n".join(
Expand Down Expand Up @@ -507,14 +507,17 @@ def single_morph(
parser, opts, pargs, stdout_flag=True, python_wrap=False, pymorphs=None
):
if len(pargs) < 2:
parser.error("You must supply MORPHFILE and TARGETFILE.")
parser.morph_error(
"You must supply MORPHFILE and TARGETFILE.", TypeError
)
elif len(pargs) > 2 and not python_wrap:
parser.error(
parser.morph_error(
"Too many arguments. Make sure you only supply "
"MORPHFILE and TARGETFILE."
"MORPHFILE and TARGETFILE.",
TypeError,
)
elif not (len(pargs) == 2 or len(pargs) == 6) and python_wrap:
parser.error("Python wrapper error.")
parser.morph_error("Python wrapper error.", RuntimeError)

# Get the PDFs
# If we get from python, we may wrap, which has input size 4
Expand All @@ -528,9 +531,9 @@ def single_morph(
x_target, y_target = getPDFFromFile(pargs[1])

if y_morph is None:
parser.error(f"No data table found in: {pargs[0]}.")
parser.morph_error(f"No data table found in: {pargs[0]}.", ValueError)
if y_target is None:
parser.error(f"No data table found in: {pargs[1]}.")
parser.morph_error(f"No data table found in: {pargs[1]}.", ValueError)

# Get tolerance
tolerance = 1e-08
Expand All @@ -549,8 +552,8 @@ def single_morph(
and opts.xmax is not None
and opts.xmax <= opts.xmin
):
e = "xmin must be less than xmax"
parser.custom_error(e)
emsg = "xmin must be less than xmax"
parser.morph_error(emsg, ValueError)

# Set up the morphs
chain = morphs.MorphChain(config)
Expand Down Expand Up @@ -607,7 +610,9 @@ def single_morph(
squeeze_dict_in.update({f"a{idx}": float(coeff)})
idx += 1
except ValueError:
parser.error(f"{coeff} could not be converted to float.")
parser.morph_error(
f"{coeff} could not be converted to float.", ValueError
)
squeeze_poly_deg = len(squeeze_dict_in.keys())
squeeze_morph = morphs.MorphSqueeze()
chain.append(squeeze_morph)
Expand Down Expand Up @@ -727,7 +732,7 @@ def single_morph(
# Adjust all parameters
refiner.refine(*refpars)
except ValueError as e:
parser.custom_error(str(e))
parser.morph_error(str(e), ValueError)
# Smear is not being refined, but baselineslope needs to refined to apply
# smear
# Note that baselineslope is only added to the refine list if smear is
Expand All @@ -738,7 +743,7 @@ def single_morph(
"baselineslope", baselineslope=config["baselineslope"]
)
except ValueError as e:
parser.custom_error(str(e))
parser.morph_error(str(e), ValueError)
else:
chain(x_morph, y_morph, x_target, y_target)

Expand Down Expand Up @@ -827,9 +832,9 @@ def single_morph(
stdout_flag=stdout_flag,
)

except (FileNotFoundError, RuntimeError):
except (FileNotFoundError, RuntimeError) as e:
save_fail_message = "Unable to save to designated location."
parser.custom_error(save_fail_message)
parser.morph_error(save_fail_message, type(e))

if opts.plot:
pairlist = [chain.xy_target_out, chain.xy_morph_out]
Expand Down Expand Up @@ -871,25 +876,29 @@ def multiple_targets(parser, opts, pargs, stdout_flag=True, python_wrap=False):
# Custom error messages since usage is distinct when --multiple tag is
# applied
if len(pargs) < 2:
parser.custom_error(
parser.morph_error(
"You must supply a FILE and DIRECTORY. "
"See --multiple-targets under --help for usage."
"See --multiple-targets under --help for usage.",
Comment thread
sbillinge marked this conversation as resolved.
TypeError,
)
elif len(pargs) > 2:
parser.custom_error(
"Too many arguments. You must only supply a FILE and a DIRECTORY."
parser.morph_error(
"Too many arguments. You must only supply a FILE and a DIRECTORY.",

@sbillinge sbillinge Feb 24, 2026

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File or a directory?

TypeError,
)

# Parse paths
morph_file = Path(pargs[0])
if not morph_file.is_file():
parser.custom_error(
f"{morph_file} is not a file. Go to --help for usage."
parser.morph_error(
f"{morph_file} is not a file. Go to --help for usage.",
FileNotFoundError,
)
target_directory = Path(pargs[1])
if not target_directory.is_dir():
parser.custom_error(
f"{target_directory} is not a directory. Go to --help for usage."
parser.morph_error(
f"{target_directory} is not a directory. Go to --help for usage.",
NotADirectoryError,
)

# Get list of files from target directory
Expand Down Expand Up @@ -926,12 +935,14 @@ def multiple_targets(parser, opts, pargs, stdout_flag=True, python_wrap=False):
)
except KeyError:
if opts.serfile is not None:
parser.custom_error(
"The requested field was not found in the metadata file."
parser.morph_error(
"The requested field was not found in the metadata file.",
KeyError,
)
else:
parser.custom_error(
"The requested field is missing from a file header."
parser.morph_error(
"The requested field is missing from a file header.",
KeyError,
)
else:
# Default is alphabetical sort
Expand All @@ -953,9 +964,9 @@ def multiple_targets(parser, opts, pargs, stdout_flag=True, python_wrap=False):
save_morphs_here = io.create_morphs_directory(save_directory)

# Could not create directory or find names to save morphs as
except (FileNotFoundError, RuntimeError):
except (FileNotFoundError, RuntimeError) as e:
save_fail_message = "\nUnable to create directory"
parser.custom_error(save_fail_message)
parser.morph_error(save_fail_message, type(e))

try:
save_names = io.get_multisave_names(
Expand All @@ -964,7 +975,7 @@ def multiple_targets(parser, opts, pargs, stdout_flag=True, python_wrap=False):
# Could not create directory or find names to save morphs as
except FileNotFoundError:
save_fail_message = "\nUnable to read from save names file"
parser.custom_error(save_fail_message)
parser.morph_error(save_fail_message, FileNotFoundError)

# Morph morph_file against all other files in target_directory
morph_results = {}
Expand Down Expand Up @@ -1013,9 +1024,9 @@ def multiple_targets(parser, opts, pargs, stdout_flag=True, python_wrap=False):
verbose=opts.verbose,
stdout_flag=stdout_flag,
)
except (FileNotFoundError, RuntimeError):
except (FileNotFoundError, RuntimeError) as e:
save_fail_message = "Unable to save summary to directory."
parser.custom_error(save_fail_message)
parser.morph_error(save_fail_message, type(e))

# Plot the values of some parameter for each target if requested
if plot_opt:
Expand All @@ -1032,8 +1043,9 @@ def multiple_targets(parser, opts, pargs, stdout_flag=True, python_wrap=False):
# Not an available parameter to plot or no values found for the
# parameter
if param_list is None:
parser.custom_error(
"Cannot find specified plot parameter. No plot shown."
parser.morph_error(
"Cannot find specified plot parameter. No plot shown.",
KeyError,
)
else:
try:
Expand All @@ -1045,9 +1057,10 @@ def multiple_targets(parser, opts, pargs, stdout_flag=True, python_wrap=False):
# i.e. --smear is not selected as an option, but smear is the
# plotting parameter
except ValueError:
parser.custom_error(
parser.morph_error(
"The plot parameter is missing values for at least one "
"morph and target pair. No plot shown."
"morph and target pair. No plot shown.",
ValueError,
)

return morph_results
Expand All @@ -1057,25 +1070,29 @@ def multiple_morphs(parser, opts, pargs, stdout_flag=True, python_wrap=False):
# Custom error messages since usage is distinct when --multiple tag is
# applied
if len(pargs) < 2:
parser.custom_error(
parser.morph_error(
"You must supply a DIRECTORY and FILE. "
"See --multiple-morphs under --help for usage."
"See --multiple-morphs under --help for usage.",
TypeError,
)
elif len(pargs) > 2:
parser.custom_error(
"Too many arguments. You must only supply a DIRECTORY and FILE."
parser.morph_error(
"Too many arguments. You must only supply a DIRECTORY and FILE.",
TypeError,
)

# Parse paths
target_file = Path(pargs[1])
if not target_file.is_file():
parser.custom_error(
f"{target_file} is not a file. Go to --help for usage."
parser.morph_error(
f"{target_file} is not a file. Go to --help for usage.",
FileNotFoundError,
)
morph_directory = Path(pargs[0])
if not morph_directory.is_dir():
parser.custom_error(
f"{morph_directory} is not a directory. Go to --help for usage."
parser.morph_error(
f"{morph_directory} is not a directory. Go to --help for usage.",
NotADirectoryError,
)

# Get list of files from morph directory
Expand Down Expand Up @@ -1112,12 +1129,14 @@ def multiple_morphs(parser, opts, pargs, stdout_flag=True, python_wrap=False):
)
except KeyError:
if opts.serfile is not None:
parser.custom_error(
"The requested field was not found in the metadata file."
parser.morph_error(
"The requested field was not found in the metadata file.",
KeyError,
)
else:
parser.custom_error(
"The requested field is missing from a PDF file header."
parser.morph_error(
"The requested field is missing from a PDF file header.",
KeyError,
)
else:
# Default is alphabetical sort
Expand All @@ -1139,9 +1158,9 @@ def multiple_morphs(parser, opts, pargs, stdout_flag=True, python_wrap=False):
save_morphs_here = io.create_morphs_directory(save_directory)

# Could not create directory or find names to save morphs as
except (FileNotFoundError, RuntimeError):
except (FileNotFoundError, RuntimeError) as e:
save_fail_message = "\nUnable to create directory"
parser.custom_error(save_fail_message)
parser.morph_error(save_fail_message, type(e))

try:
save_names = io.get_multisave_names(
Expand All @@ -1150,7 +1169,7 @@ def multiple_morphs(parser, opts, pargs, stdout_flag=True, python_wrap=False):
# Could not create directory or find names to save morphs as
except FileNotFoundError:
save_fail_message = "\nUnable to read from save names file"
parser.custom_error(save_fail_message)
parser.morph_error(save_fail_message, FileNotFoundError)

# Morph morph_file against all other files in target_directory
morph_results = {}
Expand Down Expand Up @@ -1200,9 +1219,9 @@ def multiple_morphs(parser, opts, pargs, stdout_flag=True, python_wrap=False):
stdout_flag=stdout_flag,
mm=True,
)
except (FileNotFoundError, RuntimeError):
except (FileNotFoundError, RuntimeError) as e:
save_fail_message = "Unable to save summary to directory."
parser.custom_error(save_fail_message)
parser.morph_error(save_fail_message, type(e))

# Plot the values of some parameter for each target if requested
if plot_opt:
Expand All @@ -1219,8 +1238,9 @@ def multiple_morphs(parser, opts, pargs, stdout_flag=True, python_wrap=False):
# Not an available parameter to plot or no values found for the
# parameter
if param_list is None:
parser.custom_error(
"Cannot find specified plot parameter. No plot shown."
parser.morph_error(
"Cannot find specified plot parameter. No plot shown.",
KeyError,
)
else:
try:
Expand All @@ -1232,9 +1252,10 @@ def multiple_morphs(parser, opts, pargs, stdout_flag=True, python_wrap=False):
# i.e. --smear is not selected as an option, but smear is the
# plotting parameter
except ValueError:
parser.custom_error(
parser.morph_error(
"The plot parameter is missing values for at least one "
"morph and target pair. No plot shown."
"morph and target pair. No plot shown.",
ValueError,
)

return morph_results
Expand Down
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