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Properly handle and route stdout/err from nbopen subprocess #40

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Properly handle and route stdout/err from nbopen subprocess #40

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8d4f20c
Properly route standard output and standard error from nbopen subproc…
google-labs-jules[bot] Apr 9, 2026
1060596
chore: PR #40 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__/
8 changes: 6 additions & 2 deletions bionetgen/core/main.py
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Expand Up @@ -233,7 +233,6 @@ 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()",
Expand All @@ -242,4 +241,9 @@ def generate_notebook(app):
stderr = getattr(subprocess, app.config["bionetgen"]["stderr"])
if args.open:
command = ["nbopen", fname]
rc, _ = run_command(command)
process = subprocess.Popen(command, stdout=stdout, stderr=stderr)
p_out, p_err = process.communicate()
if p_out:
app.log.info(p_out.decode("utf-8") if isinstance(p_out, bytes) else p_out)
if p_err:
app.log.error(p_err.decode("utf-8") if isinstance(p_err, bytes) else p_err)
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