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add -swc in pynml #326

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Merged
merged 5 commits into from
Apr 9, 2024
Merged

add -swc in pynml #326

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8cee5dc
add -swc in pynml
YBCS Mar 24, 2024
ecf3113
adress comments
YBCS Mar 27, 2024
92fc66b
update logger output
YBCS Mar 27, 2024
1ba6112
Merge branch 'development' into dev-buda-development
YBCS Apr 9, 2024
2d4a7ea
run generate man in right dir, check cell length
YBCS Apr 9, 2024
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13 changes: 13 additions & 0 deletions pyneuroml/pynml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@
import lems.model.model as lems_model
from pyneuroml import DEFAULTS, JNEUROML_VERSION, __version__
from pyneuroml.errors import ARGUMENT_ERR, UNKNOWN_ERR
from pyneuroml.swc.ExportSWC import convert_to_swc
from pyneuroml.utils import extract_lems_definition_files

# these imports are included for backwards compatibility
Expand Down Expand Up @@ -415,6 +416,11 @@ def _parse_arguments():
action="store_true",
help=("Validate SEDML file(s)"),
)
mut_exc_opts.add_argument(
"-swc",
action="store_true",
help=("Load a NeuroML file, and convert it to swc format\n"),
)

return parser.parse_args()

Expand Down Expand Up @@ -852,6 +858,13 @@ def _evaluate_arguments(args):
exit_on_fail = True
run_multi = True

elif args.swc:
for f in args.input_files:
logger.info(f"converting {f} to swc format...")
convert_to_swc(f)
logger.info(f"Done converting {len(args.input_files)} files to swc format")
sys.exit(0)

if run_multi is False:
run_jneuroml(
pre_args,
Expand Down