PeakATail/.gitignore at develop · BMGLab/PeakATail · GitHub

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/test/testdata
/data/
**/__pycache__
**/*.egg-info
**/emaout
**/emaout_*
peakatail_runs/
**/cbtotal.py
*.pyc
/dist/
*.bed
*.tsv
*.csv
*.mtx
*.bam
*.bai
*.h5ad
**/.vscode
Emaenv
.venv/
prompts/
other_repos/
references/
test_run/
logs/
reports/figures/*.png
reports/figures/*.svg
gtf_cache/
reports/PeakATail_Technical_Report.pdf

# Local-only project notes / specs / plans (not for upstream)
docs/superpowers/
.peakatail/
**/.claude/site/

# MkDocs build output (regenerated on every `mkdocs build`)
/site/
.claude/
reports/.claude/

# AI agent artefacts (plans, prompts, scratch analyses — kept on disk locally)
plans/
*plan*.md
*PLAN*.md
*prompt*.md
*PROMPT*.md
*analysis*.md
*ANALYSIS*.md
*.local.md
notes/
scratch/
analysis/

# Agent-generated delivery notes / dev-phase scratch at repo root
TECHNICAL_REPORT_COMPLETE.md
README_TECHNICAL_REPORT.md
REPORT_DELIVERY.txt

# Reports directory (local technical write-up scratch, not upstream content)
reports/technical_report.md
reports/README.md
reports/PDF_CONVERSION_INSTRUCTIONS.txt
reports/build_report.sh
reports/build_simple.py
reports/convert_to_pdf.py
reports/generate_figures_simple.py
reports/generate_report.py
reports/run_build_simple.sh
reports/build_pdf.sh
reports/build_latex.sh
reports/subset_heavy_strategies.py
# LaTeX source and build artefacts
reports/PeakATail_Technical_Report.tex
reports/*.aux
reports/*.log
reports/*.toc
reports/*.out
reports/explainer_figures.py
reports/baseline_apa_completeness/
reports/subset_curated.h5ad
reports/diff_compare/
reports/length_compare/
reports/subset_diff_compare/
reports/subset_length_compare/

# Root-level report build helpers (invoke scripts inside reports/)
run_build.sh
run_generate_figures.sh

# Performance report (local-only artefacts, same pattern as Technical Report)
reports/PeakATail_Performance_Report.tex
reports/PeakATail_Performance_Report.pdf
reports/PeakATail_Performance_Report.md
reports/perf_figures.py
reports/build_perf.sh
reports/figures/perf/

# PR scratch (paste into GitHub — not for upstream)
PR_DESCRIPTION.md

# Dev caches and editor artefacts
.pytest_cache/
.mypy_cache/
.ruff_cache/
htmlcov/
coverage.xml
.coverage
.DS_Store
Thumbs.db
*~
*.swp