dnallmmark/.gitignore at main · zhangtaolab/dnallmmark · GitHub

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# Python
__pycache__/
*.py[cod]
*$py.class
*.so
.Python
.python-version
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.cfg
*.egg

# Virtual Environment
venv/
env/
ENV/
.env
.venv

# IDE
.idea/
.vscode/
*.swp
*.swo
.project
.pydevproject
.settings/

# Jupyter & Marimo
.ipynb_checkpoints
.marimo-cache/
.marimo-env/

# uv
.uv.toml
uv.lock

# Testing
.coverage
.coverage.*
coverage.xml
.pytest_cache/
htmlcov/

# Training outputs
outputs/
runs/
wandb/
checkpoints/
logs/
benchmark_results/
test_demo/

# Data
*.fasta
*.fa
*.fna
*.fastq
*.fq
*.sam
*.bam
*.gz
*.zip
*.tar
*.tar.gz

# OS
.DS_Store
Thumbs.db
*.db
*.sqlite
*.log
*.bak

# Project specific
dnallm/models/downloads/
dnallm/data/cache/
dnallm/ui/tmp/
.planning/

# Jupyter Notebook tmp files
.ipynb_checkpoints/
*.output.txt
example/notebooks/*/output*/
example/notebooks/*/*.pdf
example/notebooks/*/results*/

# Marimo cache
.marimo-cache/
.marimo-env/
example/marimo/*/__marimo__/

# Mkdocs cache
site

# MyPy cache
.mypy_cache/

results/

.ruff_cache/

test/inference/pdf/
tests/inference/pdf/demo_attention_pdf.pdf
tests/inference/pdf/demo_bars_pdf.pdf
tests/inference/pdf/demo_curves_pdf.pdf
tests/inference/pdf/demo_embeddings_pdf.pdf
tests/inference/pdf/demo_scatter_pdf.pdf
tests/inference/pdf/format_compatibility_test_pdf.pdf


datasets/
models/
finetuned/
.DS_Store
Arena/
instruct/

# Worktrees
.worktrees/
worktrees/