From f59f86ebc10e7c87fa743eb3717c2a8ac1c7e401 Mon Sep 17 00:00:00 2001 From: Bora Uyar Date: Sat, 2 Mar 2024 15:48:37 +0100 Subject: [PATCH] fix issue with path to env --- .github/workflows/benchmarks.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml index 71e6e61..5f5d4b1 100644 --- a/.github/workflows/benchmarks.yml +++ b/.github/workflows/benchmarks.yml @@ -66,29 +66,29 @@ jobs: - name: Run DirectPred shell: bash -l {0} run: | - source ~/.venv/my_env/bin/activate + source ~/.venv/bin/activate flexynesis --data_path dataset1 --model_class DirectPred --target_variables Erlotinib --batch_variables Crizotinib --fusion_type early --hpo_iter 1 --features_min 50 --features_top_percentile 5 --log_transform False --data_types gex,cnv --outdir . --prefix erlotinib_direct --early_stop_patience 3 --use_loss_weighting False --evaluate_baseline_performance False - name: Run DirectPred_TestSurvival shell: bash -l {0} run: | - source ~/.venv/my_env/bin/activate + source ~/.venv/bin/activate flexynesis --data_path lgggbm_tcga_pub_processed --model_class DirectPred --target_variables STUDY --fusion_type intermediate --hpo_iter 1 --features_min 50 --features_top_percentile 5 --log_transform False --data_types mut,cna --outdir . --prefix lgg_surv --early_stop_patience 3 --use_loss_weighting False --evaluate_baseline_performance False --surv_event_var OS_STATUS --surv_time_var OS_MONTHS - name: Run supervised_vae shell: bash -l {0} run: | - source ~/.venv/my_env/bin/activate + source ~/.venv/bin/activate flexynesis --data_path dataset1 --model_class supervised_vae --target_variables Erlotinib,Crizotinib --fusion_type early --hpo_iter 1 --features_min 50 --features_top_percentile 5 --log_transform False --data_types gex,cnv --outdir . --prefix erlotinib_svae --early_stop_patience 3 --use_loss_weighting True --evaluate_baseline_performance False - name: Run MultiTripletNetwork shell: bash -l {0} run: | - source ~/.venv/my_env/bin/activate + source ~/.venv/bin/activate flexynesis --data_path dataset2 --model_class MultiTripletNetwork --target_variables y --fusion_type early --hpo_iter 1 --features_min 50 --features_top_percentile 5 --log_transform False --data_types gex,meth --outdir . --prefix msi_triplet --early_stop_patience 3 --evaluate_baseline_performance False - name: Run DirectPredGCNN shell: bash -l {0} run: | - source ~/.venv/my_env/bin/activate + source ~/.venv/bin/activate flexynesis --data_path dataset1 --model_class DirectPredGCNN --target_variables Erlotinib --batch_variables Crizotinib --fusion_type intermediate --hpo_iter 1 --features_min 50 --features_top_percentile 5 --log_transform False --data_types gex,cnv --outdir . --prefix erlotinib_direct --early_stop_patience 3 --use_loss_weighting False --evaluate_baseline_performance False