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Fix nbopen standard output and error handling in notebook generation #89

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Merged
akutuva21 merged 2 commits into from
Apr 13, 2026
Merged

Fix nbopen standard output and error handling in notebook generation #89

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0a606a1
Fix nbopen standard output and error handling in notebook generation
google-labs-jules[bot] Apr 13, 2026
52bd0f6
chore: PR #89 remove forbidden artifacts and run black
akutuva21 Apr 13, 2026
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2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -10,3 +10,5 @@ temp_testing/*
build
dist
Issues/rule_keywords/test_DeleteMolecules_changed.bngl
.jules/
__pycache__/
19 changes: 15 additions & 4 deletions bionetgen/core/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -233,13 +233,24 @@ def generate_notebook(app):
app.log.debug(f"Writing notebook to file: {fname}", f"{__file__} : notebook()")
notebook.write(fname)
# open the notebook with nbopen
# TODO: deal with stdout/err
app.log.debug(
f"Attempting to open notebook {fname} with nbopen",
f"{__file__} : notebook()",
)
stdout = getattr(subprocess, app.config["bionetgen"]["stdout"])
stderr = getattr(subprocess, app.config["bionetgen"]["stderr"])
try:
stdout_loc = getattr(subprocess, app.config["bionetgen"]["stdout"])
except (AttributeError, KeyError):
stdout_loc = subprocess.PIPE
try:
stderr_loc = getattr(subprocess, app.config["bionetgen"]["stderr"])
except (AttributeError, KeyError):
stderr_loc = subprocess.STDOUT

if args.open:
command = ["nbopen", fname]
rc, _ = run_command(command)
process = subprocess.Popen(
command,
stdout=stdout_loc,
stderr=stderr_loc,
)
rc = process.wait()
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