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Deprecate petablint with individual tables #274

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merged 4 commits into from
Jun 26, 2024
Merged

Deprecate petablint with individual tables #274

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9f68596
Deprecated petablint with individual tables
dweindl Jun 25, 2024
2b5c474
Update petab/petablint.py
dweindl Jun 25, 2024
32523fd
..
dweindl Jun 25, 2024
f39e1ea
Merge branch 'develop' into deprecate_petablint_files
dweindl Jun 26, 2024
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Deprecated petablint with individual tables
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@dweindl
dweindl committed Jun 25, 2024
commit 9f68596293628438c9a91d3f68c690b6ce3ad0f1
46 changes: 33 additions & 13 deletions petab/petablint.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,34 +49,35 @@ def parse_cli_args():
)

# Call with set of files
parser.add_argument(
group = parser.add_argument_group("Check individual files *DEPRECATED*")
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group.add_argument(
"-s", "--sbml", dest="sbml_file_name", help="SBML model filename"
)
parser.add_argument(
group.add_argument(
"-o",
"--observables",
dest="observable_file_name",
help="Observable table",
)
parser.add_argument(
group.add_argument(
"-m",
"--measurements",
dest="measurement_file_name",
help="Measurement table",
)
parser.add_argument(
group.add_argument(
"-c",
"--conditions",
dest="condition_file_name",
help="Conditions table",
)
parser.add_argument(
group.add_argument(
"-p",
"--parameters",
dest="parameter_file_name",
help="Parameter table",
)
parser.add_argument(
group.add_argument(
"--vis",
"--visualizations",
dest="visualization_file_name",
Expand All @@ -87,13 +88,18 @@ def parse_cli_args():
group.add_argument(
"-y",
"--yaml",
dest="yaml_file_name_deprecated",
help="PEtab YAML problem filename. "
"*DEPRECATED* pass the file name as positional argument instead.",
)
group.add_argument(
dest="yaml_file_name",
help="PEtab YAML problem filename",
nargs="?",
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I wonder if it's possible to say yaml_file_name_deprecated takes 0 arguments, i.e. it's treated as just a "flag", and instead its argument then gets treated as a positional argument, and hence saved to yaml_file_name. Anyway, not important

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@dweindl dweindl Jun 25, 2024 •
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It can be done and would slightly simplify the code, but the petablint --help output would be more confusing, I think.

)

args = parser.parse_args()

if args.yaml_file_name and any(
if (args.yaml_file_name or args.yaml_file_name_deprecated) and any(
(
args.sbml_file_name,
args.condition_file_name,
Expand All @@ -102,24 +108,37 @@ def parse_cli_args():
)
):
parser.error(
"When providing a yaml file, no other files may " "be specified."
"When providing a yaml file, no other files may be specified."
)

if args.yaml_file_name_deprecated:
logger.warning(
"The -y/--yaml option is deprecated. "
"Please provide the YAML file as a positional argument."
)
if args.yaml_file_name:
parser.error(
"Please provide only one of --yaml or positional argument."
)

args.yaml_file_name = args.yaml_file_name or args.yaml_file_name_deprecated

return args


def main():
"""Run PEtab validator"""
args = parse_cli_args()
init_colorama(autoreset=True)

ch = logging.StreamHandler()
ch.setFormatter(LintFormatter())
logging.basicConfig(level=logging.DEBUG, handlers=[ch])

args = parse_cli_args()

if args.verbose:
ch.setLevel(logging.DEBUG)
else:
ch.setLevel(logging.WARN)
ch.setFormatter(LintFormatter())
logging.basicConfig(level=logging.DEBUG, handlers=[ch])

if args.yaml_file_name:
from jsonschema.exceptions import ValidationError
Expand All @@ -143,6 +162,7 @@ def main():
problem = petab.Problem.from_yaml(args.yaml_file_name)

else:
# DEPRECATED
logger.debug("Looking for...")
if args.sbml_file_name:
logger.debug(f"\tSBML model: {args.sbml_file_name}")
Expand Down