clinosim 0.6.4__tar.gz

clinosim-0.6.4/.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*.egg-info/
+dist/
+build/
+.eggs/
+
+# Virtual environment
+.venv/
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Output (generated data — not clinosim/modules/output/ which is source code)
+# Preserved sample outputs are tracked via Git LFS (see .gitattributes)
+/output/*
+!/output/fhir_jp_v2/
+/output_*/
+
+# Installers and generated tarballs (do not commit — keep local only)
+Miniconda3*.sh
+*.tar.gz
+
+# Test artifacts
+.pytest_cache/
+htmlcov/
+.coverage
+
+# Working scratchpad — maintainer per-session investigation files
+# (past archives live under docs/history/scratchpad-archive/)
+/scratchpad/
+
+# Claude Code
+.claude/
+venv/
+
+# Superpowers subagent-driven-development scratch state
+.superpowers/
+
+# Scratchpad: ignore generated cohort outputs + run logs (keep tracked dev scripts).
+# Prevents accidental commit of large generated data (see session-38 84GB cleanup).
+scratchpad/*/
+scratchpad/*_gen.log
+scratchpad/*_audit.txt
+scratchpad/*_narrate.log
+scratchpad/*_mock.log
+scratchpad/*_report.txt
+
+# session 49 F4 memoize + smoke output directories
+# `/` anchors to repo root, so `tests/unit/output/` etc. are NOT matched.
+/output-p*-seed*/
+/output/
+# Session 57: catch scratch CIF/FHIR generation dirs a maintainer may create
+# in-repo by accident when passing a relative `-o` to `clinosim generate`.
+/test_*_output/
+/verify-*/
+/pre-verify*/
+
+# LLM narrative eval outputs — accumulated locally, not versioned data.
+# Nothing under `tests/` or `clinosim/` references this path; keeping it
+# tracked would ship 200MB of past run artifacts to every clone. Same
+# rationale as the .tar.gz maintainer artifacts above (session 82 PR C).
+/test_data/
+
+# Maintainer-local continuation notes(shared repo has only the shared roadmap).
+# Contributors may keep private session-scoped resume prompts here without
+# tracking them in git.
+docs/session-resume/
+
+# Session-local resume prompts at repo root (personal / one-off).
+# `.resume-prompt-<name>.md` for named variants; `.resume-prompt.md` for the
+# default one written at end of a session (see s78 handover convention).
+.resume-prompt.md
+.resume-prompt-*.md
+
+# Personal roadmap / backlog. TODO.md was previously tracked (contributor-
+# facing docs), but per session 80 convention it is now personal / per-
+# session-local — the shared roadmap lives in GitHub Issues, and
+# per-session narrative lives in `docs/session-NN-resume-prompt.md`
+# (for numbered wraps that ARE tracked) or `.resume-prompt.md`
+# (for the current session's personal one).
+TODO.md
+
+# mkdocs local build output (`mkdocs build` default writes here). CI uses
+# a fresh runner directory; contributors keep the artifact locally without
+# committing it. Sibling to the existing session-local ignore convention.
+site/
+
+# Baseline cohorts generated for local data-quality / clinical-coherence
+# analysis. Deterministic per (country, population, seed, dates), so any
+# session can regenerate — no need to version, and dropping 500-patient
+# JP + US cohorts here would be tens of MB per commit.
+/baseline/
+verify/boot_*/case_*_scratch/
+
+# Large boot data tarballs (kept local-only, too big for git)
+verify/boot_*/*_narratives.tar.gz
+verify/boot_*/*_cohort_cif.tar.gz
+verify/boot_*/*_fhir_r4.tar.gz
+verify/boot_*/*_artifacts.tar.gz