From 8aee87b6fd8cbedd87d1dc0286c9a71f0013cd2d Mon Sep 17 00:00:00 2001
From: Vivek Dasari <vivek.dasari@benchling.com>
Date: Tue, 15 Jul 2025 22:32:01 -0700
Subject: [PATCH 1/3] deps-to-remove clone of deps

---
 gazelle/python/kinds.go   |  2 ++
 gazelle/python/resolve.go |  4 ++++
 gazelle/python/target.go  | 17 +++++++++++++++++
 3 files changed, 23 insertions(+)

diff --git a/gazelle/python/kinds.go b/gazelle/python/kinds.go
index 83da53edbd..b370118dcd 100644
--- a/gazelle/python/kinds.go
+++ b/gazelle/python/kinds.go
@@ -60,10 +60,12 @@ var pyKinds = map[string]rule.KindInfo{
 		SubstituteAttrs: map[string]bool{},
 		MergeableAttrs: map[string]bool{
 			"srcs": true,
+			"deps_to_remove": true,
 		},
 		ResolveAttrs: map[string]bool{
 			"deps": true,
 			"pyi_deps": true,
+			"deps_to_remove": true,
 		},
 	},
 	pyTestKind: {
diff --git a/gazelle/python/resolve.go b/gazelle/python/resolve.go
index 0dd80841d4..9d6deb4a3d 100644
--- a/gazelle/python/resolve.go
+++ b/gazelle/python/resolve.go
@@ -39,6 +39,8 @@ const (
 	// resolvedDepsKey is the attribute key used to pass dependencies that don't
 	// need to be resolved by the dependency resolver in the Resolver step.
 	resolvedDepsKey = "_gazelle_python_resolved_deps"
+	// depsToRemoveKey is the attribute key used to store the deps_to_remove list
+	depsToRemoveKey = "_gazelle_python_deps_to_remove"
 )
 
 // Resolver satisfies the resolve.Resolver interface. It resolves dependencies
@@ -356,6 +358,7 @@ func (py *Resolver) Resolve(
 	if cfg.GeneratePyiDeps() {
 		if !deps.Empty() {
 			r.SetAttr("deps", convertDependencySetToExpr(deps))
+			r.SetAttr("deps_to_remove", convertDependencySetToExpr(deps))
 		}
 		if !pyiDeps.Empty() {
 			r.SetAttr("pyi_deps", convertDependencySetToExpr(pyiDeps))
@@ -368,6 +371,7 @@ func (py *Resolver) Resolve(
 
 		if !combinedDeps.Empty() {
 			r.SetAttr("deps", convertDependencySetToExpr(combinedDeps))
+			r.SetAttr("deps_to_remove", convertDependencySetToExpr(combinedDeps))
 		}
 	}
 }
diff --git a/gazelle/python/target.go b/gazelle/python/target.go
index 3b7f464335..8729fdcf95 100644
--- a/gazelle/python/target.go
+++ b/gazelle/python/target.go
@@ -33,6 +33,7 @@ type targetBuilder struct {
 	siblingSrcs       *treeset.Set
 	deps              *treeset.Set
 	resolvedDeps      *treeset.Set
+	depsToRemove      *treeset.Set
 	visibility        *treeset.Set
 	main              *string
 	imports           []string
@@ -50,6 +51,7 @@ func newTargetBuilder(kind, name, pythonProjectRoot, bzlPackage string, siblingS
 		siblingSrcs:       siblingSrcs,
 		deps:              treeset.NewWith(moduleComparator),
 		resolvedDeps:      treeset.NewWith(godsutils.StringComparator),
+		depsToRemove:      treeset.NewWith(godsutils.StringComparator),
 		visibility:        treeset.NewWith(godsutils.StringComparator),
 	}
 }
@@ -100,6 +102,20 @@ func (t *targetBuilder) addResolvedDependencies(deps []string) *targetBuilder {
 	return t
 }
 
+// addDepToRemove adds a single dependency to be removed to the target.
+func (t *targetBuilder) addDepToRemove(dep string) *targetBuilder {
+	t.depsToRemove.Add(dep)
+	return t
+}
+
+// addDepsToRemove adds multiple dependencies to be removed to the target.
+func (t *targetBuilder) addDepsToRemove(deps []string) *targetBuilder {
+	for _, dep := range deps {
+		t.addDepToRemove(dep)
+	}
+	return t
+}
+
 // addVisibility adds visibility labels to the target.
 func (t *targetBuilder) addVisibility(visibility []string) *targetBuilder {
 	for _, item := range visibility {
@@ -161,5 +177,6 @@ func (t *targetBuilder) build() *rule.Rule {
 		r.SetAttr("testonly", true)
 	}
 	r.SetPrivateAttr(resolvedDepsKey, t.resolvedDeps)
+	r.SetPrivateAttr(depsToRemoveKey, t.depsToRemove)
 	return r
 }

From 4b0d59426b9e49eac39c03ad44272fbaab598dbd Mon Sep 17 00:00:00 2001
From: Vivek Dasari <vivek.dasari@benchling.com>
Date: Wed, 16 Jul 2025 07:38:51 -0700
Subject: [PATCH 2/3] correctly only add deps_to_remove

---
 gazelle/python/language.go                    |   6 +-
 gazelle/python/resolve.go                     | 191 +++++++++++++++++-
 gazelle/python/target.go                      |   4 +
 .../BUILD.in                                  |   1 +
 .../BUILD.out                                 |  35 ++++
 .../MODULE.bazel                              |   6 +
 .../README.md                                 |  28 +++
 .../WORKSPACE                                 |   1 +
 .../__init__.py                               |  15 ++
 .../application.py                            |  30 +++
 .../deps-order.txt                            |   7 +
 .../foundation.py                             |  27 +++
 .../middleware.py                             |  25 +++
 .../test.yaml                                 |  15 ++
 .../deps_to_remove_with_order/BUILD.in        |   1 +
 .../deps_to_remove_with_order/BUILD.out       |  32 +++
 .../deps_to_remove_with_order/README.md       |  26 +++
 .../deps_to_remove_with_order/WORKSPACE       |   1 +
 .../deps_to_remove_with_order/__init__.py     |  15 ++
 .../deps_to_remove_with_order/core.py         |  23 +++
 .../deps_to_remove_with_order/deps-order.txt  |   3 +
 .../deps_to_remove_with_order/high_level.py   |  30 +++
 .../deps_to_remove_with_order/test.yaml       |  15 ++
 .../deps_to_remove_with_order/utils.py        |  27 +++
 24 files changed, 560 insertions(+), 4 deletions(-)
 create mode 100644 gazelle/python/testdata/deps_to_remove_ordering_violation/BUILD.in
 create mode 100644 gazelle/python/testdata/deps_to_remove_ordering_violation/BUILD.out
 create mode 100644 gazelle/python/testdata/deps_to_remove_ordering_violation/MODULE.bazel
 create mode 100644 gazelle/python/testdata/deps_to_remove_ordering_violation/README.md
 create mode 100644 gazelle/python/testdata/deps_to_remove_ordering_violation/WORKSPACE
 create mode 100644 gazelle/python/testdata/deps_to_remove_ordering_violation/__init__.py
 create mode 100644 gazelle/python/testdata/deps_to_remove_ordering_violation/application.py
 create mode 100644 gazelle/python/testdata/deps_to_remove_ordering_violation/deps-order.txt
 create mode 100644 gazelle/python/testdata/deps_to_remove_ordering_violation/foundation.py
 create mode 100644 gazelle/python/testdata/deps_to_remove_ordering_violation/middleware.py
 create mode 100644 gazelle/python/testdata/deps_to_remove_ordering_violation/test.yaml
 create mode 100644 gazelle/python/testdata/deps_to_remove_with_order/BUILD.in
 create mode 100644 gazelle/python/testdata/deps_to_remove_with_order/BUILD.out
 create mode 100644 gazelle/python/testdata/deps_to_remove_with_order/README.md
 create mode 100644 gazelle/python/testdata/deps_to_remove_with_order/WORKSPACE
 create mode 100644 gazelle/python/testdata/deps_to_remove_with_order/__init__.py
 create mode 100644 gazelle/python/testdata/deps_to_remove_with_order/core.py
 create mode 100644 gazelle/python/testdata/deps_to_remove_with_order/deps-order.txt
 create mode 100644 gazelle/python/testdata/deps_to_remove_with_order/high_level.py
 create mode 100644 gazelle/python/testdata/deps_to_remove_with_order/test.yaml
 create mode 100644 gazelle/python/testdata/deps_to_remove_with_order/utils.py

diff --git a/gazelle/python/language.go b/gazelle/python/language.go
index 56eb97b043..cab4fb2392 100644
--- a/gazelle/python/language.go
+++ b/gazelle/python/language.go
@@ -28,5 +28,9 @@ type Python struct {
 // NewLanguage initializes a new Python that satisfies the language.Language
 // interface. This is the entrypoint for the extension initialization.
 func NewLanguage() language.Language {
-	return &Python{}
+	return &Python{
+		Resolver: Resolver{
+			depsOrderResolver: NewDepsOrderResolver(),
+		},
+	}
 }
diff --git a/gazelle/python/resolve.go b/gazelle/python/resolve.go
index 9d6deb4a3d..125e573827 100644
--- a/gazelle/python/resolve.go
+++ b/gazelle/python/resolve.go
@@ -15,6 +15,7 @@
 package python
 
 import (
+	"bufio"
 	"fmt"
 	"log"
 	"os"
@@ -41,11 +42,133 @@ const (
 	resolvedDepsKey = "_gazelle_python_resolved_deps"
 	// depsToRemoveKey is the attribute key used to store the deps_to_remove list
 	depsToRemoveKey = "_gazelle_python_deps_to_remove"
+	// srcsForOrderingKey is the attribute key used to store source files for ordering constraints
+	srcsForOrderingKey = "_gazelle_python_srcs_for_ordering"
+	// depsOrderFilename is the name of the file that contains the dependency order
+	depsOrderFilename = "deps-order.txt"
 )
 
+// DepsOrderResolver holds the dependency order information parsed from deps-order.txt
+type DepsOrderResolver struct {
+	fileToIndex    map[string]int
+	loaded         bool
+	// importToSrcs maps import names to their source files (pkg-relative paths)
+	importToSrcs   map[string][]string
+}
+
+// NewDepsOrderResolver creates a new DepsOrderResolver
+func NewDepsOrderResolver() *DepsOrderResolver {
+	return &DepsOrderResolver{
+		fileToIndex:  make(map[string]int),
+		loaded:       false,
+		importToSrcs: make(map[string][]string),
+	}
+}
+
+// LoadDepsOrder loads the deps-order.txt file from the repository root
+func (d *DepsOrderResolver) LoadDepsOrder(repoRoot string) error {
+	if d.loaded {
+		return nil
+	}
+
+	depsOrderPath := filepath.Join(repoRoot, depsOrderFilename)
+	file, err := os.Open(depsOrderPath)
+	if err != nil {
+		if os.IsNotExist(err) {
+			// File doesn't exist, which is fine - we just won't use deps ordering
+			d.loaded = true
+			return nil
+		}
+		return fmt.Errorf("failed to open %s: %v", depsOrderFilename, err)
+	}
+	defer file.Close()
+
+	scanner := bufio.NewScanner(file)
+	index := 0
+	for scanner.Scan() {
+		line := strings.TrimSpace(scanner.Text())
+		if line == "" || strings.HasPrefix(line, "#") {
+			continue // Skip empty lines and comments
+		}
+		d.fileToIndex[line] = index
+		index++
+	}
+
+	if err := scanner.Err(); err != nil {
+		return fmt.Errorf("failed to read %s: %v", depsOrderFilename, err)
+	}
+
+	d.loaded = true
+	return nil
+}
+
+// GetAverageIndex calculates the average index for a set of source files
+func (d *DepsOrderResolver) GetAverageIndex(srcs []string) float64 {
+	if len(d.fileToIndex) == 0 {
+		return 0 // No ordering file, return 0
+	}
+
+	totalIndex := 0
+	validSrcs := 0
+	for _, src := range srcs {
+		// Try both the full path and just the filename
+		filename := filepath.Base(src)
+		if index, exists := d.fileToIndex[src]; exists {
+			totalIndex += index
+			validSrcs++
+		} else if index, exists := d.fileToIndex[filename]; exists {
+			totalIndex += index
+			validSrcs++
+		}
+	}
+
+	if validSrcs == 0 {
+		return float64(len(d.fileToIndex)) // Files not in order get max index
+	}
+
+	return float64(totalIndex) / float64(validSrcs)
+}
+
+// ShouldAddToDepsToRemove returns true if the dependency should be added to deps_to_remove based on ordering constraints
+func (d *DepsOrderResolver) ShouldAddToDepsToRemove(currentTargetSrcs []string, depTargetSrcs []string) bool {
+	if len(d.fileToIndex) == 0 {
+		return false // No ordering constraints
+	}
+
+	currentAvg := d.GetAverageIndex(currentTargetSrcs)
+	depAvg := d.GetAverageIndex(depTargetSrcs)
+
+	// If current target has lower average index than dependency, the dependency should be removed
+	return currentAvg < depAvg
+}
+
+// RegisterImportSources registers the mapping between import specs and their source files
+func (d *DepsOrderResolver) RegisterImportSources(importSpecs []resolve.ImportSpec, pkgPath string, srcs []string) {
+	// Convert sources to repo-relative paths
+	repoRelativeSrcs := make([]string, 0, len(srcs))
+	for _, src := range srcs {
+		repoRelativeSrcs = append(repoRelativeSrcs, filepath.Join(pkgPath, src))
+	}
+	
+	// Register each import spec
+	for _, spec := range importSpecs {
+		d.importToSrcs[spec.Imp] = repoRelativeSrcs
+	}
+}
+
+// getSourcesForImport gets the source files for a given import name using the registered mappings
+func (d *DepsOrderResolver) getSourcesForImport(importName string) []string {
+	if srcs, ok := d.importToSrcs[importName]; ok {
+		return srcs
+	}
+	return []string{}
+}
+
 // Resolver satisfies the resolve.Resolver interface. It resolves dependencies
 // in rules generated by this extension.
-type Resolver struct{}
+type Resolver struct{
+	depsOrderResolver *DepsOrderResolver
+}
 
 // Name returns the name of the language. This is the prefix of the kinds of
 // rules generated. E.g. py_library and py_binary.
@@ -78,6 +201,10 @@ func (py *Resolver) Imports(c *config.Config, r *rule.Rule, f *rule.File) []reso
 	if len(provides) == 0 {
 		return nil
 	}
+	
+	// Register the import-to-source mappings for dependency ordering
+	py.depsOrderResolver.RegisterImportSources(provides, f.Pkg, srcs)
+	
 	return provides
 }
 
@@ -327,6 +454,22 @@ func (py *Resolver) Resolve(
 						}
 						matchLabel := filteredMatches[0].Label.Rel(from.Repo, from.Pkg)
 						dep := matchLabel.String()
+						
+						// Register the mapping from dependency label to its source files
+						// This allows us to look up source files during deps_to_remove creation
+						match := filteredMatches[0]
+						depSrcsPaths := make([]string, 0)
+						// Try to infer source file from the import name
+						if strings.Contains(moduleName, ".") {
+							parts := strings.Split(moduleName, ".")
+							srcFile := parts[len(parts)-1] + ".py"
+							depSrcsPaths = append(depSrcsPaths, filepath.Join(match.Label.Pkg, srcFile))
+						} else {
+							srcFile := moduleName + ".py"
+							depSrcsPaths = append(depSrcsPaths, filepath.Join(match.Label.Pkg, srcFile))
+						}
+						py.depsOrderResolver.importToSrcs[dep] = depSrcsPaths
+						
 						addDependency(dep, mod.TypeCheckingOnly, deps, pyiDeps)
 						if explainDependency == dep {
 							log.Printf("Explaining dependency (%s): "+
@@ -355,10 +498,49 @@ func (py *Resolver) Resolve(
 
 	addResolvedDeps(r, deps)
 
+	// Load deps order constraints if available
+	err := py.depsOrderResolver.LoadDepsOrder(c.RepoRoot)
+	if err != nil {
+		log.Printf("Warning: failed to load deps-order.txt: %v", err)
+	}
+
+	// Get current rule's sources for ordering comparison
+	currentSrcs := r.AttrStrings("srcs")
+	// Convert relative paths to paths relative to repo root
+	currentSrcsPaths := make([]string, 0, len(currentSrcs))
+	for _, src := range currentSrcs {
+		currentSrcsPaths = append(currentSrcsPaths, filepath.Join(from.Pkg, src))
+	}
+
+	// Function to create deps_to_remove based on ordering constraints
+	createDepsToRemove := func(allDeps *treeset.Set) *treeset.Set {
+		depsToRemove := treeset.NewWith(godsutils.StringComparator)
+		
+		// If we have ordering constraints, check each dependency
+		if len(py.depsOrderResolver.fileToIndex) > 0 {
+			allDeps.Each(func(_ int, dep interface{}) {
+				depLabel := dep.(string)
+				
+				// Get the source files for this dependency using the registered mappings
+				depSrcs := py.depsOrderResolver.getSourcesForImport(depLabel)
+				
+				// Check if this dependency should be added to deps_to_remove based on ordering
+				if py.depsOrderResolver.ShouldAddToDepsToRemove(currentSrcsPaths, depSrcs) {
+					depsToRemove.Add(dep)
+				}
+			})
+		}
+		
+		return depsToRemove
+	}
+
 	if cfg.GeneratePyiDeps() {
 		if !deps.Empty() {
 			r.SetAttr("deps", convertDependencySetToExpr(deps))
-			r.SetAttr("deps_to_remove", convertDependencySetToExpr(deps))
+			depsToRemove := createDepsToRemove(deps)
+			if !depsToRemove.Empty() {
+				r.SetAttr("deps_to_remove", convertDependencySetToExpr(depsToRemove))
+			}
 		}
 		if !pyiDeps.Empty() {
 			r.SetAttr("pyi_deps", convertDependencySetToExpr(pyiDeps))
@@ -371,7 +553,10 @@ func (py *Resolver) Resolve(
 
 		if !combinedDeps.Empty() {
 			r.SetAttr("deps", convertDependencySetToExpr(combinedDeps))
-			r.SetAttr("deps_to_remove", convertDependencySetToExpr(combinedDeps))
+			depsToRemove := createDepsToRemove(combinedDeps)
+			if !depsToRemove.Empty() {
+				r.SetAttr("deps_to_remove", convertDependencySetToExpr(depsToRemove))
+			}
 		}
 	}
 }
diff --git a/gazelle/python/target.go b/gazelle/python/target.go
index 8729fdcf95..260debd1f2 100644
--- a/gazelle/python/target.go
+++ b/gazelle/python/target.go
@@ -178,5 +178,9 @@ func (t *targetBuilder) build() *rule.Rule {
 	}
 	r.SetPrivateAttr(resolvedDepsKey, t.resolvedDeps)
 	r.SetPrivateAttr(depsToRemoveKey, t.depsToRemove)
+	// Store source files for ordering constraints
+	if !t.srcs.Empty() {
+		r.SetPrivateAttr(srcsForOrderingKey, t.srcs)
+	}
 	return r
 }
diff --git a/gazelle/python/testdata/deps_to_remove_ordering_violation/BUILD.in b/gazelle/python/testdata/deps_to_remove_ordering_violation/BUILD.in
new file mode 100644
index 0000000000..af2c2cea4b
--- /dev/null
+++ b/gazelle/python/testdata/deps_to_remove_ordering_violation/BUILD.in
@@ -0,0 +1 @@
+# gazelle:python_generation_mode file
diff --git a/gazelle/python/testdata/deps_to_remove_ordering_violation/BUILD.out b/gazelle/python/testdata/deps_to_remove_ordering_violation/BUILD.out
new file mode 100644
index 0000000000..44c5fe0b56
--- /dev/null
+++ b/gazelle/python/testdata/deps_to_remove_ordering_violation/BUILD.out
@@ -0,0 +1,35 @@
+load("@rules_python//python:defs.bzl", "py_library")
+
+# gazelle:python_generation_mode file
+
+py_library(
+    name = "__init__",
+    srcs = ["__init__.py"],
+    visibility = ["//:__subpackages__"],
+)
+
+py_library(
+    name = "application",
+    srcs = ["application.py"],
+    visibility = ["//:__subpackages__"],
+    deps = [
+        ":foundation",
+        ":middleware",
+    ],
+)
+
+py_library(
+    name = "foundation",
+    srcs = ["foundation.py"],
+    deps_to_remove = [":middleware"],
+    visibility = ["//:__subpackages__"],
+    deps = [":middleware"],
+)
+
+py_library(
+    name = "middleware",
+    srcs = ["middleware.py"],
+    deps_to_remove = [":application"],
+    visibility = ["//:__subpackages__"],
+    deps = [":application"],
+)
diff --git a/gazelle/python/testdata/deps_to_remove_ordering_violation/MODULE.bazel b/gazelle/python/testdata/deps_to_remove_ordering_violation/MODULE.bazel
new file mode 100644
index 0000000000..00bb18361f
--- /dev/null
+++ b/gazelle/python/testdata/deps_to_remove_ordering_violation/MODULE.bazel
@@ -0,0 +1,6 @@
+###############################################################################
+# Bazel now uses Bzlmod by default to manage external dependencies.
+# Please consider migrating your external dependencies from WORKSPACE to MODULE.bazel.
+#
+# For more details, please check https://github.com/bazelbuild/bazel/issues/18958
+###############################################################################
diff --git a/gazelle/python/testdata/deps_to_remove_ordering_violation/README.md b/gazelle/python/testdata/deps_to_remove_ordering_violation/README.md
new file mode 100644
index 0000000000..c2b752e48e
--- /dev/null
+++ b/gazelle/python/testdata/deps_to_remove_ordering_violation/README.md
@@ -0,0 +1,28 @@
+# Test case for deps_to_remove with ordering violations
+
+This test case verifies that the `deps_to_remove` attribute is correctly populated
+when there are dependency ordering violations defined in `deps-order.txt`.
+
+## Test scenario:
+
+1. **deps-order.txt** defines the following order:
+   - `foundation.py` (index 0) - foundational code
+   - `middleware.py` (index 1) - middle layer
+   - `application.py` (index 2) - application layer
+
+2. **Dependencies**:
+   - `application.py` imports `middleware` and `foundation` (valid - higher depending on lower)
+   - `middleware.py` imports `application` (INVALID - lower depending on higher)
+   - `foundation.py` imports `middleware` (INVALID - lower depending on higher)
+
+3. **Expected behavior**:
+   - All dependencies should appear in `deps`
+   - Violating dependencies should also appear in `deps_to_remove`:
+     - `middleware`'s dependency on `application` should be in `deps_to_remove`
+     - `foundation`'s dependency on `middleware` should be in `deps_to_remove`
+
+## Files:
+- `foundation.py` - foundational functionality (illegally depends on middleware)
+- `middleware.py` - middle layer (illegally depends on application)
+- `application.py` - application layer
+- `deps-order.txt` - defines allowed dependency order
diff --git a/gazelle/python/testdata/deps_to_remove_ordering_violation/WORKSPACE b/gazelle/python/testdata/deps_to_remove_ordering_violation/WORKSPACE
new file mode 100644
index 0000000000..e2025846c0
--- /dev/null
+++ b/gazelle/python/testdata/deps_to_remove_ordering_violation/WORKSPACE
@@ -0,0 +1 @@
+workspace(name = "deps_to_remove_ordering_violation_test")
\ No newline at end of file
diff --git a/gazelle/python/testdata/deps_to_remove_ordering_violation/__init__.py b/gazelle/python/testdata/deps_to_remove_ordering_violation/__init__.py
new file mode 100644
index 0000000000..3e68ab20ae
--- /dev/null
+++ b/gazelle/python/testdata/deps_to_remove_ordering_violation/__init__.py
@@ -0,0 +1,15 @@
+# Copyright 2023 The Bazel Authors. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+# Empty init file for test package
\ No newline at end of file
diff --git a/gazelle/python/testdata/deps_to_remove_ordering_violation/application.py b/gazelle/python/testdata/deps_to_remove_ordering_violation/application.py
new file mode 100644
index 0000000000..b47512f007
--- /dev/null
+++ b/gazelle/python/testdata/deps_to_remove_ordering_violation/application.py
@@ -0,0 +1,30 @@
+# Copyright 2023 The Bazel Authors. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Application layer - depends on middleware and foundation (valid)."""
+
+import foundation
+import middleware
+
+def app_function():
+    """Application function using both foundation and middleware."""
+    return f"app: {foundation.foundation_function()} + {middleware.middleware_function()}"
+
+def get_app_data():
+    """Get application data."""
+    return {
+        "app": True,
+        "foundation": foundation.get_foundation_data(),
+        "middleware": middleware.process_data()
+    }
\ No newline at end of file
diff --git a/gazelle/python/testdata/deps_to_remove_ordering_violation/deps-order.txt b/gazelle/python/testdata/deps_to_remove_ordering_violation/deps-order.txt
new file mode 100644
index 0000000000..4472cd3266
--- /dev/null
+++ b/gazelle/python/testdata/deps_to_remove_ordering_violation/deps-order.txt
@@ -0,0 +1,7 @@
+# Dependency ordering constraints
+# Files listed earlier can be depended upon by files listed later
+# but not vice versa
+
+foundation.py
+middleware.py
+application.py
\ No newline at end of file
diff --git a/gazelle/python/testdata/deps_to_remove_ordering_violation/foundation.py b/gazelle/python/testdata/deps_to_remove_ordering_violation/foundation.py
new file mode 100644
index 0000000000..a66ba7e70b
--- /dev/null
+++ b/gazelle/python/testdata/deps_to_remove_ordering_violation/foundation.py
@@ -0,0 +1,27 @@
+# Copyright 2023 The Bazel Authors. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Foundation layer - ILLEGALLY depends on middleware (ordering violation)."""
+
+import middleware  # This violates ordering constraints!
+
+
+def foundation_function():
+    """Foundation function that uses middleware."""
+    return f"foundation: {middleware.middleware_function()}"
+
+
+def get_foundation_data():
+    """Get foundation data."""
+    return {"foundation": True, "data": middleware.process_data()}
diff --git a/gazelle/python/testdata/deps_to_remove_ordering_violation/middleware.py b/gazelle/python/testdata/deps_to_remove_ordering_violation/middleware.py
new file mode 100644
index 0000000000..13c5e2c3e9
--- /dev/null
+++ b/gazelle/python/testdata/deps_to_remove_ordering_violation/middleware.py
@@ -0,0 +1,25 @@
+# Copyright 2023 The Bazel Authors. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Middleware layer - ILLEGALLY depends on application (ordering violation)."""
+
+import application  # This violates ordering constraints!
+
+def middleware_function():
+    """Middleware function that illegally uses application layer."""
+    return f"middleware: {application.app_function()}"
+
+def process_data():
+    """Process data using application layer (violation)."""
+    return application.get_app_data()
\ No newline at end of file
diff --git a/gazelle/python/testdata/deps_to_remove_ordering_violation/test.yaml b/gazelle/python/testdata/deps_to_remove_ordering_violation/test.yaml
new file mode 100644
index 0000000000..fcea77710f
--- /dev/null
+++ b/gazelle/python/testdata/deps_to_remove_ordering_violation/test.yaml
@@ -0,0 +1,15 @@
+# Copyright 2023 The Bazel Authors. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+---
diff --git a/gazelle/python/testdata/deps_to_remove_with_order/BUILD.in b/gazelle/python/testdata/deps_to_remove_with_order/BUILD.in
new file mode 100644
index 0000000000..af2c2cea4b
--- /dev/null
+++ b/gazelle/python/testdata/deps_to_remove_with_order/BUILD.in
@@ -0,0 +1 @@
+# gazelle:python_generation_mode file
diff --git a/gazelle/python/testdata/deps_to_remove_with_order/BUILD.out b/gazelle/python/testdata/deps_to_remove_with_order/BUILD.out
new file mode 100644
index 0000000000..d90c9b35a4
--- /dev/null
+++ b/gazelle/python/testdata/deps_to_remove_with_order/BUILD.out
@@ -0,0 +1,32 @@
+load("@rules_python//python:defs.bzl", "py_library")
+
+# gazelle:python_generation_mode file
+
+py_library(
+    name = "__init__",
+    srcs = ["__init__.py"],
+    visibility = ["//:__subpackages__"],
+)
+
+py_library(
+    name = "core",
+    srcs = ["core.py"],
+    visibility = ["//:__subpackages__"],
+)
+
+py_library(
+    name = "high_level",
+    srcs = ["high_level.py"],
+    visibility = ["//:__subpackages__"],
+    deps = [
+        ":core",
+        ":utils",
+    ],
+)
+
+py_library(
+    name = "utils",
+    srcs = ["utils.py"],
+    visibility = ["//:__subpackages__"],
+    deps = [":core"],
+)
diff --git a/gazelle/python/testdata/deps_to_remove_with_order/README.md b/gazelle/python/testdata/deps_to_remove_with_order/README.md
new file mode 100644
index 0000000000..2290f70d71
--- /dev/null
+++ b/gazelle/python/testdata/deps_to_remove_with_order/README.md
@@ -0,0 +1,26 @@
+# Test case for deps_to_remove with deps-order.txt
+
+This test case verifies that the `deps_to_remove` attribute is correctly populated
+based on the dependency ordering constraints defined in `deps-order.txt`.
+
+## Test scenario:
+
+1. **deps-order.txt** defines the following order:
+   - `core.py` (index 0) - foundational code
+   - `utils.py` (index 1) - utility functions  
+   - `high_level.py` (index 2) - high-level functionality
+
+2. **Dependencies**:
+   - `high_level.py` imports `core` and `utils` (valid - higher index depending on lower)
+   - `utils.py` imports `core` (valid - higher index depending on lower)
+   - `core.py` imports nothing (valid - no dependencies)
+
+3. **Expected behavior**:
+   - All dependencies should appear in `deps` 
+   - No dependencies should appear in `deps_to_remove` (all are valid)
+
+## Files:
+- `core.py` - basic functionality
+- `utils.py` - depends on core
+- `high_level.py` - depends on both core and utils
+- `deps-order.txt` - defines allowed dependency order
\ No newline at end of file
diff --git a/gazelle/python/testdata/deps_to_remove_with_order/WORKSPACE b/gazelle/python/testdata/deps_to_remove_with_order/WORKSPACE
new file mode 100644
index 0000000000..e9c57a5fb8
--- /dev/null
+++ b/gazelle/python/testdata/deps_to_remove_with_order/WORKSPACE
@@ -0,0 +1 @@
+workspace(name = "deps_to_remove_with_order_test")
\ No newline at end of file
diff --git a/gazelle/python/testdata/deps_to_remove_with_order/__init__.py b/gazelle/python/testdata/deps_to_remove_with_order/__init__.py
new file mode 100644
index 0000000000..3e68ab20ae
--- /dev/null
+++ b/gazelle/python/testdata/deps_to_remove_with_order/__init__.py
@@ -0,0 +1,15 @@
+# Copyright 2023 The Bazel Authors. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+# Empty init file for test package
\ No newline at end of file
diff --git a/gazelle/python/testdata/deps_to_remove_with_order/core.py b/gazelle/python/testdata/deps_to_remove_with_order/core.py
new file mode 100644
index 0000000000..3058784620
--- /dev/null
+++ b/gazelle/python/testdata/deps_to_remove_with_order/core.py
@@ -0,0 +1,23 @@
+# Copyright 2023 The Bazel Authors. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Core foundational functionality - no dependencies."""
+
+def core_function():
+    """Basic core function."""
+    return "core functionality"
+
+def get_core_value():
+    """Get a core value."""
+    return 42
\ No newline at end of file
diff --git a/gazelle/python/testdata/deps_to_remove_with_order/deps-order.txt b/gazelle/python/testdata/deps_to_remove_with_order/deps-order.txt
new file mode 100644
index 0000000000..07b49b5245
--- /dev/null
+++ b/gazelle/python/testdata/deps_to_remove_with_order/deps-order.txt
@@ -0,0 +1,3 @@
+core.py
+utils.py
+high_level.py
diff --git a/gazelle/python/testdata/deps_to_remove_with_order/high_level.py b/gazelle/python/testdata/deps_to_remove_with_order/high_level.py
new file mode 100644
index 0000000000..b6ff8eca5e
--- /dev/null
+++ b/gazelle/python/testdata/deps_to_remove_with_order/high_level.py
@@ -0,0 +1,30 @@
+# Copyright 2023 The Bazel Authors. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""High-level functionality - depends on both core and utils."""
+
+import core
+import utils
+
+def high_level_operation():
+    """High-level operation using both core and utils."""
+    core_result = core.core_function()
+    utils_result = utils.utility_function()
+    return f"High level: {core_result} + {utils_result}"
+
+def process_data():
+    """Process data using all available functionality."""
+    value = core.get_core_value()
+    formatted = utils.format_output(value)
+    return f"Processed: {formatted}"
\ No newline at end of file
diff --git a/gazelle/python/testdata/deps_to_remove_with_order/test.yaml b/gazelle/python/testdata/deps_to_remove_with_order/test.yaml
new file mode 100644
index 0000000000..fcea77710f
--- /dev/null
+++ b/gazelle/python/testdata/deps_to_remove_with_order/test.yaml
@@ -0,0 +1,15 @@
+# Copyright 2023 The Bazel Authors. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+---
diff --git a/gazelle/python/testdata/deps_to_remove_with_order/utils.py b/gazelle/python/testdata/deps_to_remove_with_order/utils.py
new file mode 100644
index 0000000000..360c2bb05e
--- /dev/null
+++ b/gazelle/python/testdata/deps_to_remove_with_order/utils.py
@@ -0,0 +1,27 @@
+# Copyright 2023 The Bazel Authors. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Utility functions - depends on core."""
+
+import core
+
+def utility_function():
+    """Utility function that uses core functionality."""
+    base_value = core.get_core_value()
+    return f"utility result: {base_value * 2}"
+
+def format_output(value):
+    """Format output using core function."""
+    core_result = core.core_function()
+    return f"{core_result} -> {value}"
\ No newline at end of file

From 46377ad2cb474846b8fc49573a8b738c98320d34 Mon Sep 17 00:00:00 2001
From: Vivek Dasari <vivek.dasari@benchling.com>
Date: Wed, 16 Jul 2025 10:16:35 -0700
Subject: [PATCH 3/3] use median instead of average

---
 SUMMARY.md                | 188 ++++++++++++++++++++++++++++++++++++++
 gazelle/python/resolve.go |  36 +++++---
 2 files changed, 210 insertions(+), 14 deletions(-)
 create mode 100644 SUMMARY.md

diff --git a/SUMMARY.md b/SUMMARY.md
new file mode 100644
index 0000000000..f9eb9d5263
--- /dev/null
+++ b/SUMMARY.md
@@ -0,0 +1,188 @@
+# Implementation Summary: `deps_to_remove` Feature for Gazelle Python Extension
+
+## Overview
+
+This document summarizes the implementation of the `deps_to_remove` feature for `py_library` targets in the Gazelle Python extension. The feature allows automatic generation of a `deps_to_remove` attribute that contains dependencies violating ordering constraints defined in a `deps-order.txt` file.
+
+## Feature Requirements
+
+- **All dependencies** must be included in the `deps` attribute (normal behavior)
+- **Violating dependencies** must also be included in the `deps_to_remove` attribute
+- **Dependency ordering** is defined by a `deps-order.txt` file at the repository root
+- **Files listed earlier** in `deps-order.txt` can be depended upon by files listed later, but not vice versa
+
+## Implementation Details
+
+### 1. Attribute Support (`kinds.go`)
+
+**File**: `/workspaces/rules_python/gazelle/python/kinds.go`
+
+Added `deps_to_remove` attribute support to `pyLibraryKind`:
+```go
+MergeableAttrs: map[string]bool{
+    "srcs": true,
+    "deps_to_remove": true,
+},
+ResolveAttrs: map[string]bool{
+    "deps": true,
+    "pyi_deps": true,
+    "deps_to_remove": true,
+},
+```
+
+### 2. Target Builder Enhancement (`target.go`)
+
+**File**: `/workspaces/rules_python/gazelle/python/target.go`
+
+- Added `depsToRemove` field to `targetBuilder` struct
+- Added helper methods: `addDepToRemove()`, `addDepsToRemove()`
+- Updated `build()` method to store source files for ordering constraints
+
+### 3. Dependency Order Resolution (`resolve.go`)
+
+**File**: `/workspaces/rules_python/gazelle/python/resolve.go`
+
+#### Core Components:
+
+**DepsOrderResolver Structure:**
+```go
+type DepsOrderResolver struct {
+    fileToIndex    map[string]int     // File to ordering index mapping
+    loaded         bool               // Loading state
+    importToSrcs   map[string][]string // Import to source files mapping
+}
+```
+
+**Key Methods:**
+- `LoadDepsOrder()` - Parses `deps-order.txt` file
+- `GetMedianIndex()` - Calculates median ordering index for source files
+- `ShouldAddToDepsToRemove()` - Determines if dependency violates ordering
+- `RegisterImportSources()` - Maps import specs to source files
+
+#### Dependency Processing Logic:
+
+1. **During Import Registration**: Map import specs to their source files
+2. **During Dependency Resolution**: Register dependency labels to source files
+3. **During Rule Finalization**: Apply ordering constraints to create `deps_to_remove`
+
+### 4. Language Integration (`language.go`)
+
+**File**: `/workspaces/rules_python/gazelle/python/language.go`
+
+Updated `NewLanguage()` to initialize the resolver with `DepsOrderResolver`:
+```go
+return &Python{
+    Resolver: Resolver{
+        depsOrderResolver: NewDepsOrderResolver(),
+    },
+}
+```
+
+## Algorithm Details
+
+### Ordering Constraint Logic
+
+1. **File Indexing**: Each file in `deps-order.txt` gets an index (0, 1, 2, ...)
+2. **Median Calculation**: For targets with multiple sources, calculate median index
+3. **Violation Detection**: If `currentTargetIndex < dependencyTargetIndex`, it's a violation
+4. **Attribute Population**: Violating dependencies are added to both `deps` and `deps_to_remove`
+
+### Path Matching Strategy
+
+The implementation handles path matching flexibly:
+- Tries exact path matches first (`pkg/file.py`)
+- Falls back to filename matches (`file.py`)
+- Supports both repo-relative and package-relative paths
+
+## Test Coverage
+
+### Test Case 1: Valid Dependencies (`deps_to_remove_with_order`)
+
+**Files**: `core.py` → `utils.py` → `high_level.py`
+
+**Scenario**: All dependencies follow correct ordering
+- `utils.py` depends on `core.py` ✅ (valid: index 1 → index 0)
+- `high_level.py` depends on both ✅ (valid: index 2 → index 0,1)
+
+**Expected Result**: No `deps_to_remove` attributes (all dependencies are valid)
+
+### Test Case 2: Ordering Violations (`deps_to_remove_ordering_violation`)
+
+**Files**: `foundation.py` → `middleware.py` → `application.py`
+
+**Scenario**: Contains dependency ordering violations
+- `foundation.py` depends on `middleware.py` ❌ (violation: index 0 → index 1)
+- `middleware.py` depends on `application.py` ❌ (violation: index 1 → index 2)
+
+**Expected Result**:
+- `foundation` target: `deps_to_remove = [":middleware"]`
+- `middleware` target: `deps_to_remove = [":application"]`
+
+## File Structure
+
+```
+gazelle/python/
+├── kinds.go                 # Attribute definitions
+├── target.go               # Target building logic
+├── resolve.go              # Dependency resolution & ordering
+├── language.go             # Language initialization
+└── testdata/
+    ├── deps_to_remove_with_order/           # Valid dependencies test
+    │   ├── deps-order.txt
+    │   ├── core.py, utils.py, high_level.py
+    │   ├── BUILD.in, BUILD.out
+    │   └── test.yaml
+    └── deps_to_remove_ordering_violation/   # Violation test
+        ├── deps-order.txt
+        ├── foundation.py, middleware.py, application.py
+        ├── BUILD.in, BUILD.out
+        └── test.yaml
+```
+
+## Usage
+
+### 1. Create `deps-order.txt` at repository root:
+```
+# Comments are supported
+core/base.py
+utils/helpers.py
+features/advanced.py
+```
+
+### 2. Run Gazelle:
+```bash
+bazel run //:gazelle
+```
+
+### 3. Generated BUILD files will include `deps_to_remove`:
+```python
+py_library(
+    name = "advanced",
+    srcs = ["advanced.py"],
+    deps = [
+        "//core:base",      # Valid dependency
+        "//utils:helpers",  # Valid dependency
+    ],
+    # deps_to_remove is empty - no violations
+)
+
+py_library(
+    name = "helpers",
+    srcs = ["helpers.py"],
+    deps = ["//features:advanced"],        # Invalid dependency
+    deps_to_remove = ["//features:advanced"],  # Marked for removal
+)
+```
+
+## Benefits
+
+1. **Automated Detection**: Automatically identifies dependency ordering violations
+2. **Build Compatibility**: All dependencies remain in `deps` for build correctness
+3. **Tooling Integration**: `deps_to_remove` can be used by linters, analyzers, etc.
+4. **Flexible Configuration**: Simple text file configuration
+5. **Backward Compatible**: No `deps-order.txt` means no constraints applied
+
+
+---
+
+This implementation provides a robust foundation for dependency ordering enforcement in Python projects using Bazel and Gazelle.
diff --git a/gazelle/python/resolve.go b/gazelle/python/resolve.go
index 125e573827..957e108391 100644
--- a/gazelle/python/resolve.go
+++ b/gazelle/python/resolve.go
@@ -20,6 +20,7 @@ import (
 	"log"
 	"os"
 	"path/filepath"
+	"sort"
 	"strings"
 
 	"github.com/bazelbuild/bazel-gazelle/config"
@@ -102,31 +103,38 @@ func (d *DepsOrderResolver) LoadDepsOrder(repoRoot string) error {
 	return nil
 }
 
-// GetAverageIndex calculates the average index for a set of source files
-func (d *DepsOrderResolver) GetAverageIndex(srcs []string) float64 {
+// GetMedianIndex calculates the median index for a set of source files
+func (d *DepsOrderResolver) GetMedianIndex(srcs []string) float64 {
 	if len(d.fileToIndex) == 0 {
 		return 0 // No ordering file, return 0
 	}
 
-	totalIndex := 0
-	validSrcs := 0
+	var indices []int
 	for _, src := range srcs {
 		// Try both the full path and just the filename
 		filename := filepath.Base(src)
 		if index, exists := d.fileToIndex[src]; exists {
-			totalIndex += index
-			validSrcs++
+			indices = append(indices, index)
 		} else if index, exists := d.fileToIndex[filename]; exists {
-			totalIndex += index
-			validSrcs++
+			indices = append(indices, index)
 		}
 	}
 
-	if validSrcs == 0 {
+	if len(indices) == 0 {
 		return float64(len(d.fileToIndex)) // Files not in order get max index
 	}
 
-	return float64(totalIndex) / float64(validSrcs)
+	// Sort indices to find median
+	sort.Ints(indices)
+	n := len(indices)
+	
+	if n%2 == 0 {
+		// Even number of elements: average of two middle elements
+		return float64(indices[n/2-1]+indices[n/2]) / 2.0
+	} else {
+		// Odd number of elements: middle element
+		return float64(indices[n/2])
+	}
 }
 
 // ShouldAddToDepsToRemove returns true if the dependency should be added to deps_to_remove based on ordering constraints
@@ -135,11 +143,11 @@ func (d *DepsOrderResolver) ShouldAddToDepsToRemove(currentTargetSrcs []string,
 		return false // No ordering constraints
 	}
 
-	currentAvg := d.GetAverageIndex(currentTargetSrcs)
-	depAvg := d.GetAverageIndex(depTargetSrcs)
+	currentMedian := d.GetMedianIndex(currentTargetSrcs)
+	depMedian := d.GetMedianIndex(depTargetSrcs)
 
-	// If current target has lower average index than dependency, the dependency should be removed
-	return currentAvg < depAvg
+	// If current target has lower median index than dependency, the dependency should be removed
+	return currentMedian < depMedian
 }
 
 // RegisterImportSources registers the mapping between import specs and their source files