# -------------------------------
# Python / Packaging
# -------------------------------
__pycache__/
*.py[cod]
*$py.class

# Hatchling / builds / wheels / eggs
dist/
build/
*.egg-info/
*.egg
.eggs/
pip-wheel-metadata/

# Virtual environments
.venv/
venv/
env/
.env
.env.*
.python-version

# Tool caches
.pytest_cache/
.mypy_cache/
.ruff_cache/
.coverage
.coverage.*
coverage.xml
htmlcov/

# IDE / OS
.vscode/
.idea/
*.iml
.DS_Store
Thumbs.db

# Logs / temp
*.log
*.tmp
tmp/
temp/

# -------------------------------
# Project-specific outputs
# -------------------------------

# CLI results and large bioinformatics artifacts (keep fixtures explicitly later)
ambiguous_summary.tsv
*_ambiguous_summary.tsv
test_*_ambiguous_summary.tsv
*.run_provenance.json
*.multiqc.tsv
*.per_contig_summary.tsv
*.variant_matrix.tsv
*.variant_matrix.tsv.gz

# Mapping / calling intermediates & outputs
*.bam
*.bai
*.cram
*.crai
*.sam

*.vcf
*.vcf.gz
*.tbi
*.bcf
*.bcf.csi

# Reference/index files (admin refs and local)
refs/
*.fa
*.fna
*.fasta
*.fa.gz
*.fna.gz
*.fasta.gz
*.fai
*.gzi
*.mmi
*.amb
*.ann
*.pac
*.bwt*
*.0123

# mosdepth & depth summaries
*.mosdepth.global.dist.txt
*.mosdepth.region.dist.txt
*.mosdepth.summary.txt
*.per-base.bed.gz
*.regions.bed.gz
*.depth.txt

# Other common genomics temps
*.idx
*.dict
*.sai
*.pileup
*.tmp.*

# -------------------------------
# Galaxy / Planemo
# -------------------------------
.planemo*

# -------------------------------
# Conda / Bioconda / Containers
# -------------------------------
conda-bld/
*.conda
*.tar.bz2
.mamba/
.conda/

# -------------------------------
# LLM agent local notes (do not commit)
# -------------------------------
LLM/

# -------------------------------
# Re-include tiny fixtures for tests/docs
# -------------------------------
!fixtures/**

# But exclude large potential test data
fixtures/potential_data/
