# === OS Files ===
.DS_Store
*~
~$*

# === Python ===
__pycache__/
*.py[cod]
*$py.class
*.egg-info/
*.egg
.eggs/
*.pth

# === Build / Distribution ===
dist/
build/
*.whl

# === Development ===
.vscode/
.idea/
*.log
.backup_before_pip_packaging/
.gemini/
scripts/
instructions/
modeling/TASEP/test_*.py
*_executed.ipynb

# === Jupyter Notebooks ===
.ipynb_checkpoints/

# === Local Config ===
config.yml
config/
**/[C]onfig*

# === Output / Results ===
Output/
temp/
temp_*
results*/
analyses/
analyses_*
filtered_images_*/
test_simulation/
out.txt
output.txt
output__*
slurm-*
out-*

# === Generated Files ===
dataframe.csv
*.csv
df*
Figure_Distributions_*
*particle*.png
masks_*
mask_*
kk*

# === Large Data Files ===
*.tif
*.lif
*.jpg
*.pdf
*.pptx
*.ppt
*.dna
*.cds.all.fa

# === Project-Specific Excludes ===
dataBases/
database*
OneDrive*/
spatio_temporal_models/
gene_sequences/
human_genome/
circular_RNA/
dev/
revision/
revision_data/
writing/
docs/paper_microlive_12112025/
merged
testing/
video_youtube/
IMPLEMENTATION_PLAN.md
dev_pipelines/

*.aux
*.bbl
*.blg
*.log
*.out
*.pdf
*.synctex.gz
*.toc
*fdb_latexmk
*.log
*.out
*.pdf
*.fls
writing/latex/Fig/
writing/latex/readme
writing/latex/reference.bib


