fix: canonicalize prefix paths before comparison to handle symlinked venvs (Fixes #358)

crates/pet-telemetry/src/lib.rs

@@ -39,10 +39,21 @@ pub fn report_inaccuracies_identified_after_resolving(
         executable_not_in_symlinks = false;
     }
 
-    let mut invalid_prefix = env.prefix.clone().unwrap_or_default() != resolved.prefix.clone()?;
-    if env.prefix.clone().is_none() {
-        invalid_prefix = false;
-    }
+    let invalid_prefix = if let Some(ref env_prefix) = env.prefix {
+        let resolved_prefix = resolved.prefix.clone()?;
+        // Canonicalize both paths to handle symlinks — a venv prefix like
+        // /usr/local/venvs/myvenv may be a symlink to /usr/local/venvs/versioned/myvenv-1.0.51,
+        // and sys.prefix returns the resolved target. Without this, the comparison
+        // produces a false positive "Prefix is incorrect" warning. (See #358)
+        // Wrap in norm_case to handle Windows UNC prefix (`\\?\`) from canonicalize.
+        let env_canonical =
+            norm_case(std::fs::canonicalize(env_prefix).unwrap_or(env_prefix.clone()));
+        let resolved_canonical =
+            norm_case(std::fs::canonicalize(&resolved_prefix).unwrap_or(resolved_prefix));
+        env_canonical != resolved_canonical
+    } else {
+        false
+    };
 
     let mut invalid_arch = env.arch.clone() != resolved.arch.clone();
     if env.arch.clone().is_none() {

crates/pet/src/jsonrpc.rs

@@ -115,23 +115,35 @@ pub fn handle_configure(context: Arc<Context>, id: u32, params: Value) {
         Ok(configure_options) => {
             // Start in a new thread, we can have multiple requests.
             thread::spawn(move || {
-                let mut cfg = context.configuration.write().unwrap();
-                // Expand glob patterns in workspace_directories
-                cfg.workspace_directories = configure_options.workspace_directories.map(|dirs| {
+                info!("Received configure request");
+                let now = SystemTime::now();
+
+                // Expand glob patterns before acquiring the write lock so we
+                // don't block readers/writers while traversing the filesystem.
+                let workspace_directories = configure_options.workspace_directories.map(|dirs| {
+                    trace!("Expanding workspace directory patterns: {:?}", dirs);
                     expand_glob_patterns(&dirs)
                         .into_iter()
                         .filter(|p| p.is_dir())
                         .collect()
                 });
-                cfg.conda_executable = configure_options.conda_executable;
-                // Expand glob patterns in environment_directories
-                cfg.environment_directories =
+                let environment_directories =
                     configure_options.environment_directories.map(|dirs| {
+                        trace!("Expanding environment directory patterns: {:?}", dirs);
                         expand_glob_patterns(&dirs)
                             .into_iter()
                             .filter(|p| p.is_dir())
                             .collect()
                     });
+                trace!(
+                    "Glob expansion completed in {:?}",
+                    now.elapsed().unwrap_or_default()
+                );
+
+                let mut cfg = context.configuration.write().unwrap();
+                cfg.workspace_directories = workspace_directories;
+                cfg.conda_executable = configure_options.conda_executable;
+                cfg.environment_directories = environment_directories;
                 cfg.pipenv_executable = configure_options.pipenv_executable;
                 cfg.poetry_executable = configure_options.poetry_executable;
                 // We will not support changing the cache directories once set.
@@ -146,6 +158,10 @@ pub fn handle_configure(context: Arc<Context>, id: u32, params: Value) {
                 for locator in context.locators.iter() {
                     locator.configure(&config);
                 }
+                info!(
+                    "Configure completed in {:?}",
+                    now.elapsed().unwrap_or_default()
+                );
                 send_reply(id, None::<()>);
             });
         }