BioProject01/.gitignore at main · biospin/BioProject01 · GitHub

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.DS_Store
.playwright-cli/

# Claude Code local state (per-machine, not for sharing)
.claude/*
# ...but DO share the ported Claude harness layer (skills + agents) for web/team use.
# settings*.json and worktrees/ stay per-machine (ignored by .claude/* above).
!.claude/skills/
!.claude/agents/
!.claude/rules/

# Python virtual environment (per-machine, not for sharing)
.venv/

# Presentation slides — local-only, not committed to shared repo
presentation/

# humanize/윤문 에이전트 임시 작업폴더 (캐노니컬 산출은 manuscript/*.md)
_workspace/

# Python bytecode cache
__pycache__/
*.pyc

# 논문 산출물 레이어 — 요약/스크립트만 tracked, 대용량·이미지·컴파일물은 ignore
# results/: csv·md·json 요약만 commit (대용량 중간산출 제외)
pipeline/**/results/**/*.h5ad
pipeline/**/results/**/*.h5mu
pipeline/**/results/**/*.npz
pipeline/**/results/**/*.npy
pipeline/**/results/**/*.parquet
pipeline/**/results/**/*.pkl
# bootstrap 재fit raw 중간산출(12×) — 요약은 bootstrap_refit_pergene.csv/.md만 track
pipeline/**/results/bootstrap_refit/
# scratchpad: 임시 작업파일
pipeline/**/scratchpad/
# proxy_join/out_gate/: gate 플롯(png)은 제외, gate_report.json(요약)만 commit
pipeline/**/proxy_join/out_gate/*.png
# figures/: 생성 스크립트(*.py)만 commit, 출력 이미지는 제외
pipeline/**/figures/**/*.png
pipeline/**/figures/**/*.pdf
pipeline/**/figures/**/*.svg
pipeline/**/figures/**/*.tif
pipeline/**/figures/**/*.tiff
# manuscript/: md·bib만 commit, 컴파일 산출물은 제외
pipeline/**/manuscript/**/*.pdf
pipeline/**/manuscript/**/*.docx
pipeline/**/manuscript/**/*.aux
pipeline/**/manuscript/**/*.log

# cross-dataset 무인 드라이버 런타임 산출 — 로그·sentinel은 일시적, 추적 안 함
pipeline/**/cross_dataset/*.log
pipeline/**/cross_dataset/AUTOPIPE_*

# Source binaries — copyrighted, never commit. Stubs (.url, .bib, abstract.txt)
# under sources/ are NOT excluded by these patterns and may be committed.
analysis/**/sources/*.pdf
analysis/**/sources/*.PDF
analysis/**/sources/*.xlsx
analysis/**/sources/*.docx
analysis/**/sources/*.pptx
analysis/**/sources/*.zip
analysis/**/sources/*.tar.gz
analysis/**/sources/*.tgz
# Cached text dump of PDF (created by build_html.py for figure detection)
analysis/**/sources/.paper_text.txt

# Generated artifacts (re-built by build_html.py / build_index.py from yaml + sources)
# Keep figure-map.json (may be hand-edited).
analysis/**/figures/*.png
analysis/**/figures/.table_cache.json
analysis/**/*_core.html
analysis/**/*_core-with-figures.md
# Legacy unprefixed names (pre-paper-id naming convention)
analysis/**/core.html
analysis/**/core-with-figures.md

# paper_analysis/ — 외부 하네스 산출물 반입 위치 (analysis/와 동일 규칙)
paper_analysis/**/sources/*.pdf
paper_analysis/**/sources/*.PDF
paper_analysis/**/sources/*.xlsx
paper_analysis/**/sources/*.docx
paper_analysis/**/sources/*.pptx
paper_analysis/**/sources/*.zip
paper_analysis/**/sources/*.tar.gz
paper_analysis/**/sources/*.tgz
paper_analysis/**/sources/.paper_text.txt
paper_analysis/**/figures/*.png
paper_analysis/**/figures/.table_cache.json
paper_analysis/**/*_core.html
paper_analysis/**/*_core-with-figures.md
paper_analysis/**/core.html
paper_analysis/**/core-with-figures.md

# Web dashboard runtime artifacts (per-run, not for sharing).
# Keep run records (request.json, prompt.md, <engine>-job.json); ignore raw logs + uploads.
artifacts/web-runs/**/*.log
artifacts/uploads/
# Pipeline runtime data + large intermediates (per-machine, not for sharing)
pipeline/**/data/
pipeline/**/*.h5ad
pipeline/**/*.h5mu
pipeline/**/*.loom

# stray runtime dump
settings.txt

# vendored 외부 repo (MoFlow 등) — clone, not tracked
pipeline/**/vendor/

# MoFlow 기본 출력 폴더(stray)
pipeline/**/MoFlow_velocity_/

# 개인 작업기록(연구 산출물 아님, 편의상 로컬 유지) — untrack 2026-07-01
HANDOFF.md
TODO.md
SESSION-LOG.md

# cross-dataset 복구 드라이버 런타임 sentinel/heartbeat(생성물, 커밋 대상 아님) — 2026-07-06
pipeline/hspc-velocity-benchmark/cross_dataset/BMMC_PROGRESS
pipeline/hspc-velocity-benchmark/cross_dataset/BMMC_DONE
pipeline/hspc-velocity-benchmark/cross_dataset/BMMC_FAILED

# 블로그 정리 초안(구글드라이브/JIRA용, 로컬 md 유지) — 2026-07-04
blog_HSPC_velocity_lag.md
# blog/ 폴더 전체(canonical=/workspace/blog + 구글드라이브, 생성물 00_*_blog_all.md·심링크 build_index.py 포함) — 로컬 유지
blog/

# 세션 잡동사니(백업·jupyter collab db·인증 qr) — 커밋 대상 아님
.jupyter_ystore.db
blog_backup_*/
gdrive_auth_qr.png
docs/PROGRAM-PRESENTATION-ROADMAP.md

# 실행 부산물 — 로그·진행 마커·락·smoke 산출 (2026-07-22)
pipeline/hspc-velocity-benchmark/results/logs/
pipeline/hspc-velocity-benchmark/results/sim_pc_logs/
pipeline/hspc-velocity-benchmark/results/*.log
*.smoke.csv
pipeline/hspc-velocity-benchmark/cross_dataset/*_DONE
pipeline/hspc-velocity-benchmark/cross_dataset/*_PROGRESS
*.lock
evals/**/logs/