spatial_transcriptomics/.gitignore at main · pandeyravi15/spatial_transcriptomics · GitHub

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# =============================================================================
# DATA FILES — too large for GitHub (100MB limit)
# =============================================================================
# Raw Visium data — download from 10x Genomics instead
data/visium_human_brain/
data/*.h5
data/*.tar.gz
data/*.gz
data/*.mtx
data/*.tsv.gz
data/*.csv.gz

# =============================================================================
# LARGE RESULT FILES — generated by running the pipeline
# =============================================================================
# Saved AnnData objects (.h5ad) can be 500MB+
results/real_data/visium_brain_analyzed.h5ad
results/**/*.h5ad

# PDF figures (keep PNGs, ignore PDFs)
results/**/*.pdf

# =============================================================================
# PYTHON
# =============================================================================
__pycache__/
*.py[cod]
*.pyo
*.pyd
*.egg-info/
*.egg
dist/
build/
.eggs/

# Virtual environments
.env
.venv/
venv/
env/
ENV/

# =============================================================================
# JUPYTER
# =============================================================================
# Jupyter checkpoint files (auto-saved backups — not needed in repo)
.ipynb_checkpoints/
*/.ipynb_checkpoints/

# Jupyter config
.jupyter/

# =============================================================================
# OS FILES
# =============================================================================
# Mac
.DS_Store
.AppleDouble
.LSOverride

# Windows
Thumbs.db
Desktop.ini
$RECYCLE.BIN/

# Linux
*~

# =============================================================================
# IDE & EDITORS
# =============================================================================
.vscode/
.idea/
*.swp
*.swo
.spyderproject.cfg
.ropeproject/

# =============================================================================
# KEEP THESE — explicit exceptions
# =============================================================================
# Keep all PNG figures in results/
!results/**/*.png

# Keep all CSV tables in results/
!results/**/*.csv

# Keep all JSON summaries
!results/**/*.json

# Keep the data README (instructions only, no actual data)
!data/README.md