updated inference scripts

Author: aghktb

infer_grn.py

@@ -99,7 +99,7 @@
     TestDatasets = ConcatDataset(All_test_dataset)
 
     test_loader = DataListLoader(dataset=TestDatasets, batch_size=BATCH_SIZE, shuffle=False, num_workers=1)
-    model = GRNFormerLitModule(totalnodes=numnodes, tf_file = tffile, exp_file = os.path.abspath(args.exp_file), net_file=os.path.abspath(args.net_file), output_file=os.path.abspath(args.output_file))
+    model = GRNFormerLitModule(totalnodes=numnodes, tf_file = tffile, exp_file = os.path.abspath(args.exp_file), output_file=os.path.abspath(args.output_file))
     print("Model loaded")
     # trainer = pl.Trainer.from_argparse_args(args)
     trainer = Trainer(devices=[0], num_nodes=1, accelerator = ACCELERATOR, detect_anomaly = True, enable_model_summary = True)

setup.sh

@@ -8,10 +8,20 @@ if [[ ! -d "$HOME/miniconda" ]]; then
 fi
 export PATH="$HOME/miniconda/bin:$PATH"
 source "$HOME/miniconda/etc/profile.d/conda.sh"
-# Create Conda environment if it doesn't exist
-if ! conda env list | grep -qw grnformer; then
+# Create Conda environment if it doesn't exist (check by name in this install)
+if ! conda env list | awk 'NR>2 && $1=="grnformer" { exit 0 } END { exit 1 }'; then
   conda env create -f environment.yml -n grnformer
 fi
 conda activate grnformer
-echo "Setup complete. Use: conda activate grnformer"
+
+# Ensure this Miniconda is used in new shells so "conda activate grnformer" works by name
+CONDA_INIT="source \"$HOME/miniconda/etc/profile.d/conda.sh\""
+if [[ -f "$HOME/.bashrc" ]] && ! grep -q "miniconda/etc/profile.d/conda.sh" "$HOME/.bashrc"; then
+  echo "" >> "$HOME/.bashrc"
+  echo "# GRNformer: use this Miniconda so 'conda activate grnformer' works" >> "$HOME/.bashrc"
+  echo "$CONDA_INIT" >> "$HOME/.bashrc"
+  echo "Added Miniconda init to ~/.bashrc"
+fi
+echo "Setup complete. In new terminals use: conda activate grnformer"
+echo "In this shell you are already in the grnformer env."