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remove deprecated args #102

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merged 1 commit into from
Dec 26, 2022
Merged

remove deprecated args #102

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24 changes: 12 additions & 12 deletions tests/test_bench.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,9 +24,9 @@
# {task}-{method}-{dataset}: {command_line_options}
# Single modality
"cell_type_annotation-actinn-spleen": "--species mouse --tissue Spleen --train_dataset 1970 --test_dataset 1759 --lambd 0.0001 --device cuda --num_epochs 2 --runs 1",
"cell_type_annotation-celltypist-spleen": "--species mouse --tissue Kidney --train_dataset 4682 --test_dataset 203 --label_conversion False",
"cell_type_annotation-scdeepsort-spleen": "--data_type scdeepsort --tissue Spleen --test_data 1759 --gpu 0 --n_epochs 2",
"cell_type_annotation-singlecellnet-spleen": "--species mouse --tissue Spleen --train_dataset 1970 --test_dataset 1759 --dLevel Cell_type --dtype Cell_type",
"cell_type_annotation-celltypist-spleen": "--species mouse --tissue Kidney --train_dataset 4682 --test_dataset 203",
"cell_type_annotation-scdeepsort-spleen": "--data_type scdeepsort --tissue Spleen --test_data 1759 --device cuda --n_epochs 2",
"cell_type_annotation-singlecellnet-spleen": "--species mouse --tissue Spleen --train_dataset 1970 --test_dataset 1759 --dLevel Cell_type",
"cell_type_annotation-svm-spleen": "--species mouse --tissue Spleen --train_dataset 1970 --test_dataset 1759",
"clustering-graphsc-10X_PBMC": "--dataset 10X_PBMC --epochs 2",
"clustering-scdcc-10X_PBMC": "--data_file 10X_PBMC --label_cells_files label_10X_PBMC.txt --gamma 1.5 --maxiter 2 --pretrain_epochs 2",
Expand Down Expand Up @@ -64,15 +64,15 @@
"cell_type_annotation-actinn-brain": "--species mouse --tissue Brain --train_dataset 753 3285 --test_dataset 2695 --lambd 0.1 --device cuda:0",
"cell_type_annotation-actinn-kidney": "--species mouse --tissue Kidney --train_dataset 4682 --test_dataset 203 --lambd 0.01 --device cuda:0",
"cell_type_annotation-actinn-spleen": "--species mouse --tissue Spleen --train_dataset 1970 --test_dataset 1759 --lambd 0.0001 --device cuda:0",
"cell_type_annotation-celltypist-brain": "--species mouse --tissue Brain --train_dataset 753 --test_dataset 2695 --label_conversion True",
"cell_type_annotation-celltypist-kidney": "--species mouse --tissue Spleen --train_dataset 1970 --test_dataset 1759 --label_conversion False",
"cell_type_annotation-celltypist-spleen": "--species mouse --tissue Kidney --train_dataset 4682 --test_dataset 203 --label_conversion False",
"cell_type_annotation-scdeepsort-brain": "--data_type scdeepsort --tissue Brain --test_data 2695 --gpu 0",
"cell_type_annotation-scdeepsort-kidney": "--data_type scdeepsort --tissue Kidney --test_data 203 --gpu 0",
"cell_type_annotation-scdeepsort-spleen": "--data_type scdeepsort --tissue Spleen --test_data 1759 --gpu 0",
"cell_type_annotation-singlecellnet-brain": "--species mouse --tissue Brain --train_dataset 753 --test_dataset 2695 --dLevel Cell_type --dtype Cell_type",
"cell_type_annotation-singlecellnet-kidney": "--species mouse --tissue Kidney --train_dataset 4682 --test_dataset 203 --dLevel Cell_type --dtype Cell_type",
"cell_type_annotation-singlecellnet-spleen": "--species mouse --tissue Spleen --train_dataset 1970 --test_dataset 1759 --dLevel Cell_type --dtype Cell_type",
"cell_type_annotation-celltypist-brain": "--species mouse --tissue Brain --train_dataset 753 --test_dataset 2695",
"cell_type_annotation-celltypist-kidney": "--species mouse --tissue Spleen --train_dataset 1970 --test_dataset 1759",
"cell_type_annotation-celltypist-spleen": "--species mouse --tissue Kidney --train_dataset 4682 --test_dataset 203",
"cell_type_annotation-scdeepsort-brain": "--data_type scdeepsort --tissue Brain --test_data 2695 --device cuda",
"cell_type_annotation-scdeepsort-kidney": "--data_type scdeepsort --tissue Kidney --test_data 203 --device cuda",
"cell_type_annotation-scdeepsort-spleen": "--data_type scdeepsort --tissue Spleen --test_data 1759 --device cuda",
"cell_type_annotation-singlecellnet-brain": "--species mouse --tissue Brain --train_dataset 753 --test_dataset 2695 --dLevel Cell_type",
"cell_type_annotation-singlecellnet-kidney": "--species mouse --tissue Kidney --train_dataset 4682 --test_dataset 203 --dLevel Cell_type",
"cell_type_annotation-singlecellnet-spleen": "--species mouse --tissue Spleen --train_dataset 1970 --test_dataset 1759 --dLevel Cell_type",
"cell_type_annotation-svm-brain": "--species mouse --tissue Brain --train_dataset 753 3285 --test_dataset 2695",
"cell_type_annotation-svm-kidney": "--species mouse --tissue Kidney --train_dataset 4682 --test_dataset 203",
"cell_type_annotation-svm-spleen": "--species mouse --tissue Spleen --train_dataset 1970 --test_dataset 1759",
Expand Down