From 636e69e1efdb83531b1b1411df162fcdfbae7e38 Mon Sep 17 00:00:00 2001
From: jorenham <jhammudoglu@gmail.com>
Date: Thu, 21 May 2026 16:10:12 +0200
Subject: [PATCH] Fix inherited stub method.counts in `pyrefly coverage report`

---
 pyrefly/lib/commands/report.rs                | 90 ++++++++++++++++++-
 .../stub_inherited_methods.expected.json      | 63 +++++++++++++
 .../test_files/stub_inherited_methods.py      | 14 +++
 .../test_files/stub_inherited_methods.pyi     |  9 ++
 4 files changed, 173 insertions(+), 3 deletions(-)
 create mode 100644 pyrefly/lib/test/report/test_files/stub_inherited_methods.expected.json
 create mode 100644 pyrefly/lib/test/report/test_files/stub_inherited_methods.py
 create mode 100644 pyrefly/lib/test/report/test_files/stub_inherited_methods.pyi

diff --git a/pyrefly/lib/commands/report.rs b/pyrefly/lib/commands/report.rs
index 444f54d0cc..9c1ee6d23c 100644
--- a/pyrefly/lib/commands/report.rs
+++ b/pyrefly/lib/commands/report.rs
@@ -24,7 +24,7 @@ use pyrefly_python::module_path::ModuleStyle;
 use pyrefly_python::nesting_context::NestingContext;
 use pyrefly_python::short_identifier::ShortIdentifier;
 use pyrefly_types::callable::PropertyRole;
-use pyrefly_types::class::ClassDefIndex;
+use pyrefly_types::class::{ClassDefIndex, ClassType};
 use pyrefly_types::types::Type;
 use pyrefly_util::forgetter::Forgetter;
 use pyrefly_util::includes::Includes;
@@ -1690,6 +1690,60 @@ impl ReportArgs {
             .collect()
     }
 
+    /// `module.Cls.member` names for each public class, including MRO-inherited ones.
+    fn collect_class_members(
+        module: &Module,
+        bindings: &Bindings,
+        answers: &Answers,
+        transaction: &Transaction,
+        handle: &Handle,
+        tco_classes: &SmallSet<Idx<KeyClass>>,
+    ) -> SmallSet<String> {
+        let fqname_prefix = if module.name() != ModuleName::unknown() {
+            format!("{}.", module.name())
+        } else {
+            String::new()
+        };
+
+        let mut members = SmallSet::new();
+        for idx in bindings.keys::<KeyClass>() {
+            if tco_classes.contains(&idx) {
+                continue;
+            }
+            let BindingClass::ClassDef(binding) = bindings.get(idx) else {
+                continue;
+            };
+            if Self::has_function_ancestor(&binding.parent) {
+                continue;
+            }
+            let Some(cls) = answers.get_idx(idx).and_then(|r| r.0.clone()) else {
+                continue;
+            };
+
+            let qname = Self::class_qualified_name(module, &binding.parent, &binding.def.name);
+            let fqname = format!("{fqname_prefix}{qname}");
+
+            let mro = answers
+                .get_idx(bindings.key_to_idx(&KeyClassMro(cls.index())))
+                .unwrap_or_else(|| Arc::new(ClassMro::Cyclic));
+            let mro: &[_] = match mro.as_ref() {
+                ClassMro::Resolved(a) => a,
+                ClassMro::Cyclic => &[],
+            };
+            for obj in std::iter::once(&cls).chain(mro.iter().map(ClassType::class_object)) {
+                if obj.module_name().as_str() == "builtins" {
+                    continue;
+                }
+                if let Some(fields) = transaction.get_class_fields(handle, obj) {
+                    for name in fields.names() {
+                        members.insert(format!("{fqname}.{name}"));
+                    }
+                }
+            }
+        }
+        members
+    }
+
     /// When a `.pyi` stub only covers a subset of a `.py` file's public
     /// symbols, add the uncovered symbols from the `.py` so that completeness
     /// metrics reflect the full module interface.
@@ -1700,11 +1754,14 @@ impl ReportArgs {
         py_functions: Vec<Function>,
         py_variables: Vec<Variable>,
         py_classes: Vec<ReportClass>,
+        stub_class_members: &SmallSet<String>,
     ) {
         let stub_func_names: SmallSet<String> =
             stub_functions.iter().map(|f| f.name.clone()).collect();
         for py_func in py_functions {
-            if !stub_func_names.contains(&py_func.name) {
+            if !stub_func_names.contains(&py_func.name)
+                && !stub_class_members.contains(&py_func.name)
+            {
                 stub_functions.push(py_func);
             }
         }
@@ -1712,7 +1769,8 @@ impl ReportArgs {
         let stub_var_names: SmallSet<String> =
             stub_variables.iter().map(|v| v.name.clone()).collect();
         for py_var in py_variables {
-            if !stub_var_names.contains(&py_var.name) {
+            if !stub_var_names.contains(&py_var.name) && !stub_class_members.contains(&py_var.name)
+            {
                 stub_variables.push(py_var);
             }
         }
@@ -2005,6 +2063,14 @@ impl ReportArgs {
                         &py_answers,
                         &py_tco_classes,
                     ));
+                    let stub_class_members = Self::collect_class_members(
+                        &module,
+                        &bindings,
+                        &answers,
+                        transaction,
+                        handle,
+                        &tco_classes,
+                    );
                     Self::merge_uncovered_py_symbols(
                         &mut functions,
                         &mut variables,
@@ -2012,6 +2078,7 @@ impl ReportArgs {
                         py_functions,
                         py_variables,
                         py_classes,
+                        &stub_class_members,
                     );
                 }
 
@@ -2283,6 +2350,14 @@ mod tests {
         ));
 
         // Merge uncovered symbols from .py into the stub report
+        let stub_class_members = ReportArgs::collect_class_members(
+            &module,
+            &bindings,
+            &answers,
+            &pyi_txn,
+            &pyi_handle,
+            &tco_classes,
+        );
         ReportArgs::merge_uncovered_py_symbols(
             &mut functions,
             &mut variables,
@@ -2290,6 +2365,7 @@ mod tests {
             py_functions,
             py_variables,
             py_classes,
+            &stub_class_members,
         );
 
         ReportArgs::build_module_report(
@@ -2354,6 +2430,14 @@ mod tests {
         compare_snapshot("partial_stub.expected.json", &report);
     }
 
+    /// gh-3519: don't double-count methods whose stub coverage is inherited.
+    #[test]
+    fn test_report_inherited_method_via_stub() {
+        let report =
+            build_stub_module_report("stub_inherited_methods.pyi", "stub_inherited_methods.py");
+        compare_snapshot("stub_inherited_methods.expected.json", &report);
+    }
+
     /// Stubs-only packages: .py discovered via site-package-path, merged like co-located stubs.
     #[test]
     fn test_report_external_stub_merge() {
diff --git a/pyrefly/lib/test/report/test_files/stub_inherited_methods.expected.json b/pyrefly/lib/test/report/test_files/stub_inherited_methods.expected.json
new file mode 100644
index 0000000000..71acabaa27
--- /dev/null
+++ b/pyrefly/lib/test/report/test_files/stub_inherited_methods.expected.json
@@ -0,0 +1,63 @@
+{
+  "name": "test",
+  "path": "test.pyi",
+  "names": [
+    "test.Base.m",
+    "test.Base",
+    "test.Sub"
+  ],
+  "line_count": 10,
+  "symbol_reports": [
+    {
+      "kind": "function",
+      "name": "test.Base.m",
+      "n_typable": 2,
+      "n_typed": 2,
+      "n_any": 0,
+      "n_untyped": 0,
+      "location": {
+        "line": 7,
+        "column": 5
+      }
+    },
+    {
+      "kind": "class",
+      "name": "test.Base",
+      "n_typable": 0,
+      "n_typed": 0,
+      "n_any": 0,
+      "n_untyped": 0,
+      "location": {
+        "line": 6,
+        "column": 1
+      }
+    },
+    {
+      "kind": "class",
+      "name": "test.Sub",
+      "n_typable": 0,
+      "n_typed": 0,
+      "n_any": 0,
+      "n_untyped": 0,
+      "location": {
+        "line": 9,
+        "column": 1
+      }
+    }
+  ],
+  "type_ignores": [],
+  "n_typable": 2,
+  "n_typed": 2,
+  "n_any": 0,
+  "n_untyped": 0,
+  "coverage": 100.0,
+  "strict_coverage": 100.0,
+  "n_functions": 0,
+  "n_methods": 1,
+  "n_function_params": 0,
+  "n_method_params": 1,
+  "n_classes": 2,
+  "n_attrs": 0,
+  "n_properties": 0,
+  "n_type_ignores": 0
+}
diff --git a/pyrefly/lib/test/report/test_files/stub_inherited_methods.py b/pyrefly/lib/test/report/test_files/stub_inherited_methods.py
new file mode 100644
index 0000000000..e1f45b868a
--- /dev/null
+++ b/pyrefly/lib/test/report/test_files/stub_inherited_methods.py
@@ -0,0 +1,14 @@
+# Copyright (c) Meta Platforms, Inc. and affiliates.
+#
+# This source code is licensed under the MIT license found in the
+# LICENSE file in the root directory of this source tree.
+
+
+class Base:
+    def m(self, x):
+        return None
+
+
+class Sub(Base):
+    def m(self, x):
+        return None
diff --git a/pyrefly/lib/test/report/test_files/stub_inherited_methods.pyi b/pyrefly/lib/test/report/test_files/stub_inherited_methods.pyi
new file mode 100644
index 0000000000..3efe9afe97
--- /dev/null
+++ b/pyrefly/lib/test/report/test_files/stub_inherited_methods.pyi
@@ -0,0 +1,9 @@
+# Copyright (c) Meta Platforms, Inc. and affiliates.
+#
+# This source code is licensed under the MIT license found in the
+# LICENSE file in the root directory of this source tree.
+
+class Base:
+    def m(self, x: int) -> None: ...
+
+class Sub(Base): ...