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Adds §4a to notes/CASCOR_CONDA_ENV_FIX_2026-05-07.md describing the secondary failure mode hit during the 2026-05-08 plant_all run and the out-of-repo fix applied to both env-local activate hooks. Symptom: juniper_plant_all.bash aborted silently on ``conda activate JuniperCanopy1`` with exit code 1, the cleanup ERR trap output also swallowed. Root cause: the LIBTORCH-strip activate hooks in JuniperCanopy1 and JuniperCascor used a ``grep -v /rust_mudgeon/`` pipeline. When LD_LIBRARY_PATH consisted of *only* a rust_mudgeon segment (which is the default state set by ~/.bashrc), grep exited 1 → pipefail → set -e killed the activate hook mid-flight → conda's var-context bookkeeping was left inconsistent → bash emitted the ``pop_var_context: head of shell_variables not a function context`` cascade. Fix: replaced the grep+paste pipeline in both hooks with a pure-bash ``IFS=':' read -ra _segs`` split + filter loop — no subprocess that can fail under pipefail. Both hooks now activate cleanly under ``set -euo pipefail`` and plant_all runs end-to-end with all four services healthy. The hook files themselves live under /opt/miniforge3/envs/<env>/etc/conda/activate.d/ and are not part of the repo; documenting the diagnosis and the canonical fix here so a future env rebuild reinstates the pure-bash split instead of the fragile grep pipeline. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Adds §4a to
notes/CASCOR_CONDA_ENV_FIX_2026-05-07.mddocumenting asecondary failure mode discovered during a fresh
./util/juniper_plant_all.bashrun on 2026-05-08:conda activate JuniperCanopy1with
exit_code=1and no error output (even the cleanup ERR-trapmessage was swallowed).
JuniperCanopy1and
JuniperCascorused agrep -v /rust_mudgeon/pipeline. WhenLD_LIBRARY_PATHis only a single rust_mudgeon segment (the defaultstate set by
~/.bashrc), grep exits 1 → pipefail fails the pipeline→
set -ekills the activate hook mid-flight → conda's var-contextbookkeeping is inconsistent → bash emits
pop_var_context: head of shell_variables not a function contextcascades.IFS=':' read -ra _segssplit + filter loop inboth hooks. No subprocess that can fail under pipefail. Confirmed all
four services (data / cascor / canopy / worker) come up healthy after
the fix.
The hook files live under
/opt/miniforge3/envs/<env>/etc/conda/activate.d/(out-of-repo); this PR captures the diagnosis and canonical replacement
inline so a future env rebuild reinstates the safe pattern.
Test plan
set -euo pipefailbefore the fix🤖 Generated with Claude Code