Revert "call rfd3 with process.Popen to allow cancellation" and do not pass subprocess to go back to working version

This reverts commit f8364c2c939323a000f5524e96fdc3653ed5d200.

app.py

@@ -13,7 +13,6 @@ from utils.pipelines import *
 #from gradio_molecule3d import Molecule3D
 from utils.handle_events import *
 from utils.handle_files import *
-import signal
 
 download_weights()
 
@@ -132,13 +131,19 @@ with gr.Blocks(title="RFD3 Test") as demo:
     display_state = gr.Textbox(label="Selected Batch and Design", visible=True)
     display_state.value = "Please Select a Batch and Design number to show sequence"
     
-
+    def generate(config_upload, scaffold_upload, num_batches, num_designs_per_batch, extra_args, max_duration):
+        if config_upload is None:
+            return gr.update(), None, None
+        else:
+            textbox_update, gen_directory, gen_results = generation_with_input_config(config_upload, scaffold_upload, num_batches, num_designs_per_batch, extra_args, max_duration)
+            print(textbox_update)
+            return textbox_update, gen_directory, gen_results
         
     generation_event = run_btn.click(
         lambda: (gr.update(visible=False), gr.update(visible=True)),
         outputs=[run_btn, stop_btn]
     ).then(
-        generation_with_input_config, inputs=[config_upload, scaffold_upload, num_batches, num_designs_per_batch, extra_args, max_duration], outputs=[runtextbox, gen_directory, gen_results]
+        generate, inputs=[config_upload, scaffold_upload, num_batches, num_designs_per_batch, extra_args, max_duration], outputs=[runtextbox, gen_directory, gen_results]
     ).then(
         update_batch_choices,
         inputs=gen_results,
@@ -151,7 +156,7 @@ with gr.Blocks(title="RFD3 Test") as demo:
         lambda: (gr.update(visible=True), gr.update(visible=False)),
         outputs=[run_btn, stop_btn]
     )
-
+    
     stop_btn.click(
         lambda: gr.update(value="Generation cancelled by user."),
         outputs=runtextbox,
@@ -178,6 +183,5 @@ with gr.Blocks(title="RFD3 Test") as demo:
     #visualize_btn.click(load_viewer, inputs=[batch_dropdown, design_dropdown, gen_results], outputs=viewer)
 
 if __name__ == "__main__":
-
     demo.queue()
     demo.launch()

utils/pipelines.py

@@ -53,7 +53,6 @@ def generation_with_input_config(input_file, pdb_file, num_batches, num_designs_
     directory = f"./outputs/generation_with_input_config/session_{session_hash}_{time_stamp}"
     os.makedirs(directory, exist_ok=False)
 
-    process = None
     try: 
         if pdb_file is not None:
             # I need to do this because uploading files to a HF space stores each file in a separate temp directory so I need to copy them again to the same place.
@@ -71,37 +70,11 @@ def generation_with_input_config(input_file, pdb_file, num_batches, num_designs_
         print(f"Running command: {command}")
         status_update += f"\nRunning command: {command}."
         start = perf_counter()
-        
-        # Start the process with Popen to allow cancellation
-        process = subprocess.Popen(
-            command,
-            shell=True,
-            stdout=subprocess.PIPE,
-            stderr=subprocess.PIPE,
-            text=True,
-            preexec_fn=os.setsid,  # For Unix-like systems, start a new process group
-        )
-        
-        # Immediately yield to make process available in State
-        yield gr.update(value=status_update), gr.update(), gr.update()
-        
-        # Poll the process - yield regularly to allow Gradio to stop calling the generator
-        while process.poll() is None:
-            time.sleep(2)  # Wait before checking again
-            yield gr.update(value=status_update), gr.update(), gr.update()
-        
-        # Get the output after process completes
-        stdout, stderr = process.communicate()
-        
-        # Check if process succeeded
-        if process.returncode != 0:
-            raise subprocess.CalledProcessError(process.returncode, command, stdout, stderr)
-        
-        elapsed_time = perf_counter() - start
-        print(f"Command took {elapsed_time:.2f} seconds to run.")
-        status_update += f"\nGeneration successful! Command took {elapsed_time:.2f} seconds to run."
+        res = subprocess.run(command, shell=True, check=True, text=True, capture_output=True)
+        print("Command took", perf_counter() - start, "seconds to run.")
+        status_update += f"\nGeneration successful! Command took {perf_counter() - start:.2f} seconds to run."
+
 
-        # Collect results from output directory
         results = []
         for file_name in os.listdir(directory):
             if file_name.endswith(".cif.gz"):
@@ -120,23 +93,6 @@ def generation_with_input_config(input_file, pdb_file, num_batches, num_designs_
     except subprocess.CalledProcessError as e:
         print("subprocess threw an error", e.stderr)
         return gr.update(value=f"Generation failed:\n{e.stderr}"), None, None
-    
-    except Exception as e:
-        # Handle cancellation or other errors - terminate the subprocess if it's still running
-        if process and process.poll() is None:
-            print(f"Terminating subprocess due to: {e}")
-            try:
-                os.killpg(os.getpgid(process.pid), 15)  # SIGTERM to process group
-            except Exception:
-                process.terminate()
-            try:
-                process.wait(timeout=5)  # Wait up to 5 seconds for graceful termination
-            except subprocess.TimeoutExpired:
-                try:
-                    os.killpg(os.getpgid(process.pid), 9)  # SIGKILL to process group
-                except Exception:
-                    process.kill()  # Force kill if killpg fails
-        raise  # Re-raise the exception so Gradio knows the event was cancelled
 
 
 #def generation_with_input_config_factory(max_duration):