fix: prevent settings.json race that drops MLflow env vars#154
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datasciencemonkey merged 5 commits intomainfrom Apr 30, 2026
Merged
fix: prevent settings.json race that drops MLflow env vars#154datasciencemonkey merged 5 commits intomainfrom
datasciencemonkey merged 5 commits intomainfrom
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Two changes: 1. setup_claude.py and _configure_all_cli_auth() now read-merge-write settings.json instead of overwriting it. This preserves env vars added by other setup scripts (e.g. setup_mlflow.py). 2. setup_mlflow.py now runs sequentially after the parallel agent setup batch, not inside it. This eliminates the race where setup_claude.py and setup_mlflow.py both write settings.json concurrently. Fixes #153
The test_returns_empty_list test failed when run after other test classes because sessions leaked across classes. Adding session cleanup at fixture setup (not just teardown) fixes the ordering dependency.
- setup_codex.py, setup_gemini.py, setup_opencode.py: retry npm install up to 3 times with 5s delay, print full stderr/stdout on failure - tests/test_session_limit.py: clear leaked sessions before slot-freeing test - .gitignore: add codex and agent-plane-ref entries
Skills already live in ~/.agents/skills/ (copied by setup_codex.py). Copying them again into ~/.gemini/skills/ caused Gemini CLI to log "Skill conflict detected" warnings for every skill on startup.
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Summary
setup_claude.pyand_configure_all_cli_auth()were overwriting~/.claude/settings.jsonfrom scratch, nuking MLflow env vars added bysetup_mlflow.pysetup_mlflow.pyran in parallel withsetup_claude.py, creating a race condition on the same fileChanges
setup_claude.py: read-merge-write instead of overwrite — preserves existing env vars (hooks, MLflow config, etc.)app.py:_configure_all_cli_auth(): same read-merge-write patternapp.py:run_setup():setup_mlflow.pynow runs sequentially after the parallel agent setup batch, not inside itTest plan
~/.claude/settings.jsonafter setup completesFixes #153