﻿# Python
__pycache__/
*.py[cod]
*.egg-info/
.eggs/
build/
dist/
.installed.cfg
*.egg

# Environments
.venv/
venv/
env/
.python-version

# Test / coverage / cache
.pytest_cache/
.pytest_tmp/
.hypothesis/
.mypy_cache/
.ruff_cache/
.coverage
.coverage.*
htmlcov/
coverage.xml
junit*.xml
pytest-tmp/

# Tooling
.tox/
.nox/

# Docs
site/
.ipynb_checkpoints/

# Workflow engines
.nextflow/
.nextflow.log*
work/
.snakemake/

# Generated outputs
*.html
!docs/**/*.html
!leaderboard/index.html
histoweave_report.html
*.zarr/
*.h5ad
results/
*.params.json
pipeline_trace.tsv

# Repository-local data and scratch artifacts
/data/
/datasets_cache/
/tmp/
/*.patch
*.orig
*.rej
*.bak

# Reference artefacts (JSON/MD/CSV summaries are tracked — see docs/reference-artefacts.md).
# Ignore only bulky regenerables / logs inside those directories.
/independent_personalisation_results/**/*.log
/independent_personalisation_results/**/checkpoints/
/independent_personalisation_results/**/*.h5ad
/protocol_endpoints_results/**/*.log
/protocol_endpoints_results/**/checkpoints/
/protocol_endpoints_results/**/*.h5ad
/non_oracle_k_sota/**/checkpoints/
/non_oracle_k_sota/**/*.log
/non_oracle_k_sota/run.log
/non_oracle_k_sota/**/*.h5ad
# Per-seed SOTA cell dumps (summaries dual_track_k / summary stay tracked)
/non_oracle_k_sota/cells/

# Generated benchmark and case-study artifacts (keep source scripts trackable)
/5x15_spatial_aware/checkpoints/
/5x15_spatial_aware/figures/
/5x15_spatial_aware/*.csv
/5x15_spatial_aware/*.json
# Audited SOTA evidence artifacts are part of the reproducible benchmark.
!/5x15_spatial_aware/sota_benchmark_long.csv
!/5x15_spatial_aware/sota_method_means.csv
!/5x15_spatial_aware/performance_matrix_mean_full.csv
!/5x15_spatial_aware/sota_merge_manifest.json
/benchmark_crossplatform/checkpoints/
/benchmark_crossplatform/figures/
/benchmark_crossplatform/*.csv
/benchmark_crossplatform/*.json
/case_study_dlpfc_consistency/figures/
/case_study_dlpfc_consistency/vitessce_config.json
/variance_decomposition/figures/
/variance_decomposition/variance_*.csv

# OS / editor
.DS_Store
Thumbs.db
.idea/
.vscode/
*.swp

# Failure-boundary mapping generated artifacts (keep source scripts trackable)
/failure_boundary_mapping/figures/
/failure_boundary_mapping/results/
/failure_boundary_mapping/*.csv
/failure_boundary_mapping/*.json

# Local raw/intermediate research data (recreate via checked-in preparers)
/research/cross_tissue_niches/.patch_probe
/research/cross_tissue_niches/Puck_200115_08_count_location.RData
/research/cross_tissue_niches/slideseq_raw/intermediate/
/tmp_perf.json

# Federated evidence network
# NEVER commit Ed25519 private keys.
federation/*.key.json
federation/**/*.key.json
# Derived / local aggregation layer — rebuilt by `histoweave fed pull` and
# `histoweave fed consensus` (and by pages.yml from committed bundles).
federation/evidence_store.jsonl
federation/consensus.json
