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*-latex-*.sh
*overleaf*.md
*overleaf*.sh
*_test_report.md
*_REPORT.md
*_PLAN.md
*_MIGRATION_GUIDE.md
*_REFACTOR_PLAN*.md
*_DEPENDENCY_*.md
*_SUMMARY.md
*SUMMARY*.md
*_ANALYSIS*.md
*ANALYSIS*.md
*_VERIFICATION*.md
*VERIFICATION*.md
*_IMPLEMENTATION*.md
*IMPLEMENTATION*.md
*_OPTIMIZATION*.md
*OPTIMIZATION*.md
*_FIX*.md
*FIX*.md
*_COMPLETE*.md
*COMPLETE*.md
*_GUIDE*.md
*GUIDE*.md
*_INDEX*.md
*_README.md
*README*.md
*_FINDINGS*.md
*FINDINGS*.md
*_PHASE*.md
*PHASE*.md
*_REPORT*.md
*REPORT*.md
*_FLOW*.md
*FLOW*.md
quick_reference.md
duplicate_code_analysis.md
check_*.md
MEMORY_PATTERN_SCANNER.py
docs/*_REPORT.md
docs/*_PLAN.md
docs/DOCUMENTATION_IMPROVEMENT_PLAN.md
docs/IMPROVEMENT_COMPLETION_REPORT.md
docs/WEBSITE_STRUCTURE_IMPROVEMENT_PLAN.md
# Exclude internal GitHub configuration docs
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ChatSpatial_Claude_Desktop_Testing_Guide.md
docs/examples/guides/ChatSpatial_Claude_Desktop_Testing_Guide.md
docs/examples/guides/GITHUB_ACTIONS_OPTIMIZATION.md
ChatSpatial_Claude_Desktop_Testing_Guide.md
DATASET_DOWNLOAD_REPORT.md
DATASET_SURVEY_REPORT.md
FINAL_MCP_DATASETS_REPORT.md
LLM_Parameter_Mismatch_Analysis.md
Spatial_Analysis_Parameter_Dependency_Fix_Plan.md
direct_tools_test_report.md
enrichment_analysis_test_report.md
tools_test_report.md
# Exclude temporary development files
=3.6
dataset_survey_code.py
deep_organize_data.py
download_reliable_datasets.py
download_standard_datasets.py
verify_*.py
analyze_*.py
investigate_*.py
demo_*.py
check_*.py
check_*.R
filter_*.py
sparse_matrix_*.py
convert_*.py
convert_*.R
fix_*.py
compare_*.py
prepare_*.py
quick_*.py
survey_*.py
# Exclude large data directories that shouldn't be in git
data/V1_*/
data/large_datasets/
data/merfish_large/
data/slideseq_large/
data/modern_spatial/
data/real_datasets/visium_*/
data/gaston_tutorial/
data/merfish_data/
# Exclude data verification scripts
data/verify_large_datasets.py
data/test_chatspatial_large_data.py
# Exclude internal data reports
data/BIG_DATASETS_FINAL_REPORT.md
data/QUICK_START_DEMO.py
data/STANDARD_DATASETS_GUIDE.md
data/*TESTING*.md
data/*LOG*.md
data/card_example/*.RData
# Personal development files (should never be committed)
Group*_Fixes_Summary.md
fallback_analysis_*.md
GEMINI.md
*_test_report.md
chatspatial.egg-info/
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site/
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scripts/tests/
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outputs/*.jpg
outputs/*.jpeg
outputs/*.pdf
outputs/*.svg
exports/*.png
exports/*.jpg
exports/*.jpeg
exports/*.pdf
exports/*.svg
# Internal development files in outputs/
outputs/*.py
outputs/*.R
outputs/*.md
outputs/*/*.md
# Keep README files
!outputs/README.md
!exports/README.md
