Include configured src directories when resolving graphs (#22451)

## Summary

This PR augments the detected source paths with the user-configured
`src` when computing roots for `ruff analyze graph`.

Cargo.lock

@@ -2928,6 +2928,7 @@ dependencies = [
  "filetime",
  "globwalk",
  "ignore",
+ "indexmap",
  "indoc",
  "insta",
  "insta-cmd",

crates/ruff/Cargo.toml

@@ -48,6 +48,7 @@ colored = { workspace = true }
 filetime = { workspace = true }
 globwalk = { workspace = true }
 ignore = { workspace = true }
+indexmap = { workspace = true }
 is-macro = { workspace = true }
 itertools = { workspace = true }
 jiff = { workspace = true }

crates/ruff/src/commands/analyze_graph.rs

@@ -2,6 +2,7 @@ use crate::args::{AnalyzeGraphArgs, ConfigArguments};
 use crate::resolve::resolve;
 use crate::{ExitStatus, resolve_default_files};
 use anyhow::Result;
+use indexmap::IndexSet;
 use log::{debug, warn};
 use path_absolutize::CWD;
 use ruff_db::system::{SystemPath, SystemPathBuf};
@@ -11,7 +12,7 @@ use ruff_linter::source_kind::SourceKind;
 use ruff_linter::{warn_user, warn_user_once};
 use ruff_python_ast::{PySourceType, SourceType};
 use ruff_workspace::resolver::{ResolvedFile, match_exclusion, python_files_in_path};
-use rustc_hash::FxHashMap;
+use rustc_hash::{FxBuildHasher, FxHashMap};
 use std::io::Write;
 use std::path::{Path, PathBuf};
 use std::sync::{Arc, Mutex};
@@ -59,17 +60,34 @@ pub(crate) fn analyze_graph(
         })
         .collect::<FxHashMap<_, _>>();
 
-    // Create a database from the source roots.
-    let src_roots = package_roots
-        .values()
-        .filter_map(|package| package.as_deref())
-        .filter_map(|package| package.parent())
-        .map(Path::to_path_buf)
-        .filter_map(|path| SystemPathBuf::from_path_buf(path).ok())
-        .collect();
+    // Create a database from the source roots, combining configured `src` paths with detected
+    // package roots. Configured paths are added first so they take precedence, and duplicates
+    // are removed.
+    let mut src_roots: IndexSet<SystemPathBuf, FxBuildHasher> = IndexSet::default();
+
+    // Add configured `src` paths first (for precedence), filtering to only include existing
+    // directories.
+    src_roots.extend(
+        pyproject_config
+            .settings
+            .linter
+            .src
+            .iter()
+            .filter(|path| path.is_dir())
+            .filter_map(|path| SystemPathBuf::from_path_buf(path.clone()).ok()),
+    );
+
+    // Add detected package roots.
+    src_roots.extend(
+        package_roots
+            .values()
+            .filter_map(|package| package.as_deref())
+            .filter_map(|path| path.parent())
+            .filter_map(|path| SystemPathBuf::from_path_buf(path.to_path_buf()).ok()),
+    );
 
     let db = ModuleDb::from_src_roots(
-        src_roots,
+        src_roots.into_iter().collect(),
         pyproject_config
             .settings
             .analyze

crates/ruff/tests/analyze_graph.rs

@@ -714,6 +714,121 @@ fn notebook_basic() -> Result<()> {
     Ok(())
 }
 
+/// Test that the `src` configuration option is respected.
+///
+/// This is useful for monorepos where there are multiple source directories that need to be
+/// included in the module resolution search path.
+#[test]
+fn src_option() -> Result<()> {
+    let tempdir = TempDir::new()?;
+    let root = ChildPath::new(tempdir.path());
+
+    // Create a lib directory with a package.
+    root.child("lib")
+        .child("mylib")
+        .child("__init__.py")
+        .write_str("def helper(): pass")?;
+
+    // Create an app directory with a file that imports from mylib.
+    root.child("app").child("__init__.py").write_str("")?;
+    root.child("app")
+        .child("main.py")
+        .write_str("from mylib import helper")?;
+
+    // Without src configured, the import from mylib won't resolve.
+    insta::with_settings!({
+        filters => INSTA_FILTERS.to_vec(),
+    }, {
+        assert_cmd_snapshot!(command().arg("app").current_dir(&root), @r#"
+        success: true
+        exit_code: 0
+        ----- stdout -----
+        {
+          "app/__init__.py": [],
+          "app/main.py": []
+        }
+
+        ----- stderr -----
+        "#);
+    });
+
+    // With src = ["lib"], the import should resolve.
+    root.child("ruff.toml").write_str(indoc::indoc! {r#"
+        src = ["lib"]
+    "#})?;
+
+    insta::with_settings!({
+        filters => INSTA_FILTERS.to_vec(),
+    }, {
+        assert_cmd_snapshot!(command().arg("app").current_dir(&root), @r#"
+        success: true
+        exit_code: 0
+        ----- stdout -----
+        {
+          "app/__init__.py": [],
+          "app/main.py": [
+            "lib/mylib/__init__.py"
+          ]
+        }
+
+        ----- stderr -----
+        "#);
+    });
+
+    Ok(())
+}
+
+/// Test that glob patterns in `src` are expanded.
+#[test]
+fn src_glob_expansion() -> Result<()> {
+    let tempdir = TempDir::new()?;
+    let root = ChildPath::new(tempdir.path());
+
+    // Create multiple lib directories with packages.
+    root.child("libs")
+        .child("lib_a")
+        .child("pkg_a")
+        .child("__init__.py")
+        .write_str("def func_a(): pass")?;
+    root.child("libs")
+        .child("lib_b")
+        .child("pkg_b")
+        .child("__init__.py")
+        .write_str("def func_b(): pass")?;
+
+    // Create an app that imports from both packages.
+    root.child("app").child("__init__.py").write_str("")?;
+    root.child("app")
+        .child("main.py")
+        .write_str("from pkg_a import func_a\nfrom pkg_b import func_b")?;
+
+    // Use a glob pattern to include all lib directories.
+    root.child("ruff.toml").write_str(indoc::indoc! {r#"
+        src = ["libs/*"]
+    "#})?;
+
+    insta::with_settings!({
+        filters => INSTA_FILTERS.to_vec(),
+    }, {
+        assert_cmd_snapshot!(command().arg("app").current_dir(&root), @r#"
+        success: true
+        exit_code: 0
+        ----- stdout -----
+        {
+          "app/__init__.py": [],
+          "app/main.py": [
+            "libs/lib_a/pkg_a/__init__.py",
+            "libs/lib_b/pkg_b/__init__.py"
+          ]
+        }
+
+        ----- stderr -----
+        "#);
+    });
+
+    Ok(())
+}
+
 #[test]
 fn notebook_with_magic() -> Result<()> {
     let tempdir = TempDir::new()?;