fix: Prevent infinite hangs in coder agent and implement timeouts for LLM API calls and interactive tools

assets/agents/coder/graph.yaml

@@ -31,7 +31,7 @@ settings:
   max_loop_iterations: 20
   log_state_snapshots: true
   validate_before_run: true
-  timeout: 1800
+  timeout: 14400
 
 initial_state:
   project_dir: ''
@@ -90,6 +90,7 @@ nodes:
       Project directory: {{project_dir}}
     prompt: '{{initial_prompt}}'
     tools: []
+    timeout: 300
     output_schema:
       type: object
       properties:
@@ -254,6 +255,7 @@ nodes:
       - fs_patch
       - execute_command
     max_iterations: 100
+    timeout: 1800
     state_updates:
       last_node_output: '{{output}}'
     fallback: end_failure
@@ -327,6 +329,7 @@ nodes:
       - fs_ls
       - execute_command
     max_iterations: 15
+    timeout: 600
     output_schema:
       type: object
       properties:

config.example.yaml

@@ -292,6 +292,7 @@ clients:
   #   extra:
   #     proxy: socks5://127.0.0.1:1080                # Set proxy
   #     connect_timeout: 10                           # Set timeout in seconds for connect to api
+  #     read_timeout: 300                             # Set timeout in seconds for a read stall (no bytes received); 0 disables (default: 300)
 
   # See https://platform.openai.com/docs/quickstart
   - type: openai

src/client/common.rs

@@ -57,12 +57,16 @@ pub trait Client: Sync + Send {
         let mut builder = ReqwestClient::builder();
         let extra = self.extra_config();
         let timeout = extra.and_then(|v| v.connect_timeout).unwrap_or(10);
+        let read_timeout = extra.and_then(|v| v.read_timeout).unwrap_or(300);
         if let Some(proxy) = extra.and_then(|v| v.proxy.as_deref()) {
             builder = set_proxy(builder, proxy)?;
         }
         if let Some(user_agent) = self.app_config().user_agent.as_ref() {
             builder = builder.user_agent(user_agent);
         }
+        if read_timeout > 0 {
+            builder = builder.read_timeout(Duration::from_secs(read_timeout));
+        }
         let client = builder
             .connect_timeout(Duration::from_secs(timeout))
             .build()
@@ -261,6 +265,7 @@ impl Default for ClientConfig {
 pub struct ExtraConfig {
     pub proxy: Option<String>,
     pub connect_timeout: Option<u64>,
+    pub read_timeout: Option<u64>,
 }
 
 #[derive(Debug, Clone, Deserialize, Default)]

src/client/stream.rs

@@ -430,10 +430,7 @@ mod tests {
         assert!(error_message.contains("test_function_loop"));
     }
 
-    fn new_handler() -> (
-        SseHandler,
-        tokio::sync::mpsc::UnboundedReceiver<SseEvent>,
-    ) {
+    fn new_handler() -> (SseHandler, tokio::sync::mpsc::UnboundedReceiver<SseEvent>) {
         let (sender, receiver) = tokio::sync::mpsc::unbounded_channel();
         let abort_signal = crate::utils::create_abort_signal();
         (SseHandler::new(sender, abort_signal), receiver)

src/config/mcp_factory.rs

@@ -103,9 +103,7 @@ impl McpFactory {
         }
 
         let (auth, auth_reason) = resolve_http_auth(name, spec).await;
-        let handle = spawn_mcp_server(spec, log_path, auth)
-            .await
-            .map_err(|e| {
+        let handle = spawn_mcp_server(spec, log_path, auth).await.map_err(|e| {
             if is_auth_required_error(&e) {
                 e.context(McpAuthRequired {
                     server: name.to_string(),

src/function/mod.rs

@@ -29,16 +29,17 @@ use rust_embed::Embed;
 use serde::{Deserialize, Serialize};
 use serde_json::{Value, json};
 use skill::SKILL_FUNCTION_PREFIX;
-use std::collections::VecDeque;
 use std::ffi::OsStr;
 use std::fs::File;
 use std::io::{Read, Write};
 use std::sync::atomic::Ordering;
+use std::{collections::VecDeque, thread};
 use std::{
     collections::{HashMap, HashSet},
     env, fs, io,
     path::{Path, PathBuf},
     process::{Command, Stdio},
+    time::{Duration, Instant},
 };
 use strum_macros::AsRefStr;
 use supervisor::SUPERVISOR_FUNCTION_PREFIX;
@@ -1456,6 +1457,7 @@ pub fn run_llm_function(
     let mut child = Command::new(&cmd_name)
         .args(&cmd_args)
         .envs(envs)
+        .stdin(Stdio::null())
         .stdout(Stdio::piped())
         .stderr(Stdio::piped())
         .spawn()
@@ -1464,7 +1466,7 @@ pub fn run_llm_function(
     let stdout = child.stdout.take().expect("Failed to capture stdout");
     let stderr = child.stderr.take().expect("Failed to capture stderr");
 
-    let stdout_thread = std::thread::spawn(move || {
+    let stdout_thread = thread::spawn(move || {
         let mut buffer = [0; 1024];
         let mut reader = stdout;
         let mut out = io::stdout();
@@ -1491,7 +1493,7 @@ pub fn run_llm_function(
         buf
     });
 
-    let stderr_thread = std::thread::spawn(move || {
+    let stderr_thread = thread::spawn(move || {
         let mut buffer = [0; 1024];
         let mut reader = stderr;
         let mut err = io::stderr();
@@ -1518,9 +1520,39 @@ pub fn run_llm_function(
         buf
     });
 
-    let status = child
-        .wait()
-        .map_err(|err| anyhow!("Unable to run {command_name}, {err}"))?;
+    let timeout_secs = env::var("COYOTE_TOOL_TIMEOUT")
+        .ok()
+        .and_then(|v| v.parse::<u64>().ok())
+        .unwrap_or(1800);
+    let deadline = (timeout_secs > 0).then(|| Instant::now() + Duration::from_secs(timeout_secs));
+    let status = loop {
+        match child.try_wait() {
+            Ok(Some(status)) => break status,
+            Ok(None) => {}
+            Err(err) => bail!("Unable to run {command_name}, {err}"),
+        }
+        if let Some(deadline) = deadline
+            && Instant::now() >= deadline
+        {
+            let _ = child.kill();
+            let _ = child.wait();
+            drop(stdout_thread);
+            drop(stderr_thread);
+            let tool_error_message = format!(
+                "Tool call '{command_name}' timed out after {timeout_secs}s and was killed (set COYOTE_TOOL_TIMEOUT to adjust; 0 = unlimited)"
+            );
+            eprintln!(
+                "{}",
+                muted_warning_text(&format!("⚠️ {tool_error_message} ⚠️"))
+            );
+            let error_json = json!({"tool_call_error": tool_error_message});
+
+            debug!("Tool call error: {error_json:?}");
+
+            return Ok(Some(error_json.to_string()));
+        }
+        thread::sleep(Duration::from_millis(100));
+    };
     let stdout_bytes = stdout_thread.join().unwrap_or_default();
     let stderr_bytes = stderr_thread.join().unwrap_or_default();
 

src/graph/executor.rs

@@ -250,7 +250,30 @@ impl GraphExecutor {
                 branch_tasks.push(task);
             }
 
-            let joined = join_all(branch_tasks).await;
+            let joined = match graph_timeout {
+                Some(t) => {
+                    let remaining = t.saturating_sub(start.elapsed());
+                    let abort_handles: Vec<_> = branch_tasks
+                        .iter()
+                        .map(|task| task.abort_handle())
+                        .collect();
+                    match tokio::time::timeout(remaining, join_all(branch_tasks)).await {
+                        Ok(joined) => joined,
+                        Err(_) => {
+                            for handle in abort_handles {
+                                handle.abort();
+                            }
+                            bail!(
+                                "Graph '{}' timed out after {}s during super-step with frontier {:?}",
+                                graph.name,
+                                t.as_secs(),
+                                sorted_frontier(&frontier)
+                            );
+                        }
+                    }
+                }
+                None => join_all(branch_tasks).await,
+            };
 
             let mut branch_writes: Vec<BranchWrites> = Vec::new();
             let mut next_frontier: HashSet<String> = HashSet::new();
@@ -793,4 +816,44 @@ nodes:
             "error should list both End nodes: {err}"
         );
     }
+
+    #[tokio::test]
+    async fn graph_timeout_interrupts_in_flight_super_step() {
+        if !cmd_available("bash") {
+            eprintln!("skipping: bash not available");
+            return;
+        }
+        let ws = TestWorkspace::new();
+        ws.write_script("sleeper.sh", "#!/bin/bash\nsleep 10\necho '{}'\n");
+
+        let yaml = r#"
+name: inflight_timeout_test
+start: sleeper
+settings:
+  timeout: 1
+nodes:
+  sleeper:
+    type: script
+    script: sleeper.sh
+    state_updates: {}
+    next: done
+  done:
+    type: end
+    output: "done"
+"#;
+        let graph: Graph = serde_yaml::from_str(yaml).unwrap();
+        let mut ctx = make_ctx();
+        let abort = create_abort_signal();
+        let result = GraphExecutor::new(graph, &ws.dir)
+            .execute(&mut ctx, abort)
+            .await;
+
+        assert!(result.is_err(), "expected in-flight timeout to error");
+        let err = format!("{:#}", result.unwrap_err());
+        assert!(
+            err.contains("timed out after 1s during super-step"),
+            "error should report during-super-step timeout: {err}"
+        );
+        assert!(err.contains("sleeper"), "error should name frontier: {err}");
+    }
 }

src/graph/script.rs

@@ -54,6 +54,7 @@ impl ScriptExecutor {
         let mut cmd = build_command(language, &script_path)?;
         cmd.stdout(Stdio::piped());
         cmd.stderr(Stdio::piped());
+        cmd.kill_on_drop(true);
         cmd.envs(&self.extra_envs);
         cmd.env("AUTO_CONFIRM", "true");
         match &state_repr {