Location: bionetgen/core/utils/utils.py:651
Original marker:
# TODO: Figure out how to use the BNG2.pl if it's set
# in the PATH variable. Solution: set os.environ BNGPATH
# and make everything use that route
test_bngexec resolves BNG2.pl from explicit candidate paths today. Users who already manage BNG2.pl via $PATH (the conventional Unix install pattern) still have to set the path explicitly.
What would unblock this: the original author already proposed the path forward — read $BNGPATH from os.environ, and route all BNG2.pl invocations through that. Concretely, add a fallback chain to the resolver: explicit candidate → $BNGPATH → shutil.which("BNG2.pl") → error.
Discovered during: non-Atomizer TODO/FIXME triage sweep, 2026-05-08.
Location:
bionetgen/core/utils/utils.py:651Original marker:
test_bngexecresolvesBNG2.plfrom explicit candidate paths today. Users who already manageBNG2.plvia$PATH(the conventional Unix install pattern) still have to set the path explicitly.What would unblock this: the original author already proposed the path forward — read
$BNGPATHfromos.environ, and route allBNG2.plinvocations through that. Concretely, add a fallback chain to the resolver: explicit candidate →$BNGPATH→shutil.which("BNG2.pl")→ error.Discovered during: non-Atomizer TODO/FIXME triage sweep, 2026-05-08.