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# =============================================================================
# System and development tools related
# =============================================================================
.DS_Store
.vscode/
.tox/
wandb/
# =============================================================================
# Build and cache
# =============================================================================
*.egg*
__pycache__/
build/
_build/
*.log
# =============================================================================
# Data files
# =============================================================================
*.pkl
*.pt
*.zip
*.h5
*.h5ad
*.gz
*.tif
# =============================================================================
# Temporary files
# =============================================================================
temp_ans.csv
temp_ans.json
check_time.py
t.py
t.ipynb
del.sh
data.yaml
proxy.txt
readme.txt
# =============================================================================
# Result files
# =============================================================================
results - cell type deconvolution.csv
results - spatial domain.csv
# =============================================================================
# Examples directory
# =============================================================================
# Common data files
examples/**/*.h5ad
examples/**/*.h5
examples/**/*.zip
examples/**/*.gz
examples/**/*.tif
# tuning subdirectory
examples/tuning/**/*.yaml
examples/tuning/**/*.csv
examples/tuning/**/*.sh
examples/tuning/**/*.tar.gz
examples/tuning/**/*.txt
examples/tuning/figures/
examples/tuning/imputation_magic/data/
examples/tuning/domain_EfNST/Image_crop/
examples/tuning/cta_scdeepsort/f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas)/
examples/tuning/cta_scdeepsort/old/f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas)/
examples/tuning/joint_embedding_scmvae/get_run_kwargs.py
examples/tuning/joint_embedding_scmvae/openproblems_2022_multi_atac2gex/config.png
examples/tuning/imputation_graphsci/tsne_visualization.png
examples/tuning/imputation_deepimpute/*.png
examples/tuning/check_sweep.py
examples/tuning/result.md
examples/tuning/joint_embedding_scmogcn/models/model_joint_embedding_1.pth
# tuning retention rules - keep one example result folder for each algorithm folder
!examples/tuning/cluster_graphsc/human_pbmc2_cell/**
!examples/tuning/cluster_scdcc/human_pbmc2_cell/**
!examples/tuning/cluster_scdsc/human_pbmc2_cell/**
!examples/tuning/cluster_scdeepcluster/human_pbmc2_cell/**
!examples/tuning/cluster_sctag/human_pbmc2_cell/**
!examples/tuning/domain_louvain/sub_mba/**
!examples/tuning/domain_spagcn/sub_mba/**
!examples/tuning/domain_stagate/sub_mba/**
!examples/tuning/domain_stlearn/sub_mba/**
!examples/tuning/domain_EfNST/sub_mba/**
!examples/tuning/deconv_card/hcc_liver/**
!examples/tuning/deconv_spotlight/hcc_liver/**
!examples/tuning/deconv_stdgcn/hcc_liver/**
!examples/tuning/deconv_dstg/hcc_liver/**
!examples/tuning/deconv_spatialdecon/hcc_liver/**
!examples/tuning/joint_embedding_dcca/GSE140203_SKIN_atac2gex/**
!examples/tuning/joint_embedding_jae/GSE140203_SKIN_atac2gex/**
!examples/tuning/joint_embedding_scmogcn/GSE140203_SKIN_atac2gex/**
!examples/tuning/joint_embedding_scmvae/GSE140203_SKIN_atac2gex/**
!examples/tuning/imputation_deepimpute/human_melanoma_data/**
!examples/tuning/imputation_graphsci/human_melanoma_data/**
!examples/tuning/imputation_scgnn2/human_melanoma_data/**
!examples/tuning/custom-methods/**
examples/tuning/custom-methods/wandb
# tuning retention rules
!examples/tuning/cta_scheteronet/328_138/**
!examples/tuning/cta_celltypist/328_138/**
!examples/tuning/cta_scdeepsort/328_138/**
!examples/tuning/cta_singlecellnet/328_138/**
!examples/tuning/cta_svm/328_138/config_yamls/params/0_params_tuning_config.yaml
!examples/tuning/cta_svm/328_138/config_yamls/params/1_params_tuning_config.yaml
!examples/tuning/cta_svm/328_138/config_yamls/params/2_params_tuning_config.yaml
!examples/tuning/cta_svm/328_138/results/**
!examples/tuning/cta_svm/328_138/pipeline_params_tuning_config.yaml
!examples/tuning/cta_svm/328_138/pipeline_tuning_config.yaml
!examples/tuning/cta_actinn/328_138/**
!examples/tuning/step3_default_params.yaml
# atlas subdirectory
examples/atlas/demos/atlas_csvs/
examples/atlas/demos/atlas_patterns/
examples/atlas/metadatas/
examples/atlas/sc_similarity_examples/temp/
examples/atlas/sc_similarity_examples/visualization/*
examples/atlas/sc_similarity_examples/data/*
examples/atlas/sc_similarity_examples/similarity/temp.ipynb
examples/atlas/dropbox_token.txt
examples/atlas/generate_method.ipynb
examples/atlas/config/run_config.csv
# atlas retention rules
!examples/atlas/sc_similarity_examples/visualization/*.py
!examples/atlas/sc_similarity_examples/data/Cell Type Annotation Atlas.xlsx
# single_modality subdirectory
examples/single_modality/cell_type_annotation/**/*.xlsx
examples/single_modality/cell_type_annotation/**/*.csv
examples/single_modality/imputation/data/
# Other Examples
examples/spatial/spatial_domain/data/spatial/
examples/spatial/cell_type_deconvo/data/spatial/
examples/computer_resources/
examples/temp_hpancreas/
examples/result_analysis/*
examples/multi_modality/joint_embedding/models/*.pth
# Keep specific scripts under result_analysis
!examples/result_analysis/get_important_pattern_sweep.py
!examples/result_analysis/get_important_pattern.py
!examples/result_analysis/get_num.py
# =============================================================================
# Model files
# =============================================================================
models/model_joint_embedding_1.pth
examples/tuning/joint_embedding_scmogcn/models/model_joint_embedding_1.pth
examples/multi_modality/joint_embedding/models/*.pth
# =============================================================================
# Others
# =============================================================================
trash
out.log
temp_data