From adb096693fd9f84348e13166b94d7c79d5bb804d Mon Sep 17 00:00:00 2001
From: Andrew Nichols <andrew@frenata.net>
Date: Thu, 29 Jan 2026 18:15:24 -0500
Subject: [PATCH 1/2] feat: add failing test to demonstrate divergent repo vs
 workspace problems

---
 tests/test_cli.py               |  9 +++++-
 tests/test_complex_scenarios.py | 50 +++++++++++++++++++++++++--------
 tests/test_config.py            |  8 ++++--
 tests/test_config_patterns.py   | 16 ++++++++---
 tests/test_formatters.py        | 36 +++++++++++-------------
 tests/test_git.py               |  2 ++
 tests/test_graph_discovery.py   |  6 ++--
 7 files changed, 87 insertions(+), 40 deletions(-)

diff --git a/tests/test_cli.py b/tests/test_cli.py
index 332395f..1014ef2 100755
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -12,6 +12,13 @@ def test_smoke_cli_graph():
 
 
 def test_smoke_cli_analyze():
-    sys.argv = ["bough", "analyze", "--workspace", "tests/fixtures/sample-workspace"]
+    sys.argv = [
+        "bough",
+        "analyze",
+        "--workspace",
+        "tests/fixtures/sample-workspace",
+        "--repo",
+        "tests/fixtures/sample-workspace",
+    ]
     with pytest.raises(SystemExit, match="0"):
         cli.main()
diff --git a/tests/test_complex_scenarios.py b/tests/test_complex_scenarios.py
index 7dbdf1f..9c992a5 100644
--- a/tests/test_complex_scenarios.py
+++ b/tests/test_complex_scenarios.py
@@ -23,6 +23,7 @@ def create_workspace_structure(base_path: Path, structure: dict):
         "project": {"name": "test-workspace", "version": "0.1.0"},
     }
 
+    base_path.mkdir(parents=True, exist_ok=True)
     with open(base_path / "pyproject.toml", "wb") as f:
         tomli_w.dump(root_config, f)
 
@@ -105,7 +106,7 @@ def test_deep_dependency_chain_core_change(mock_repo_class, tmp_path):
 """)
 
     # Test the public interface
-    analyzer = BoughAnalyzer.from_workspace(tmp_path, config_path)
+    analyzer = BoughAnalyzer.from_workspace(tmp_path, tmp_path, config_path)
     affected, _ = analyzer.find_affected()
 
     # Core change should transitively affect all buildable packages
@@ -133,7 +134,7 @@ def test_diamond_dependency_pattern(mock_repo_class, tmp_path):
   - "*.md"
 """)
 
-    analyzer = BoughAnalyzer.from_workspace(tmp_path, config_path)
+    analyzer = BoughAnalyzer.from_workspace(tmp_path, tmp_path, config_path)
     affected, _ = analyzer.find_affected()
 
     # Base change should affect top through both left and right paths
@@ -171,14 +172,14 @@ def test_layered_architecture_isolation(mock_repo_class, tmp_path):
 
     # Test 1: Change in models affects all apps
     mock_repo_class.return_value = mock_git_changes(["data/models/user.py"])
-    analyzer = BoughAnalyzer.from_workspace(tmp_path, config_path)
+    analyzer = BoughAnalyzer.from_workspace(tmp_path, tmp_path, config_path)
     affected, _ = analyzer.find_affected()
 
     assert affected == {"rest-api", "graphql-api", "worker"}
 
     # Test 2: Change in middleware only affects APIs that use it
     mock_repo_class.return_value = mock_git_changes(["api/middleware/auth.py"])
-    analyzer = BoughAnalyzer.from_workspace(tmp_path, config_path)
+    analyzer = BoughAnalyzer.from_workspace(tmp_path, tmp_path, config_path)
     affected, _ = analyzer.find_affected()
 
     assert affected == {"rest-api", "graphql-api"}
@@ -230,7 +231,7 @@ def test_microservices_shared_library_impact(mock_repo_class, tmp_path):
 
     # Test 1: Change in proto affects everything
     mock_repo_class.return_value = mock_git_changes(["shared/proto/user.proto"])
-    analyzer = BoughAnalyzer.from_workspace(tmp_path, config_path)
+    analyzer = BoughAnalyzer.from_workspace(tmp_path, tmp_path, config_path)
     affected, _ = analyzer.find_affected()
 
     expected = {
@@ -245,7 +246,7 @@ def test_microservices_shared_library_impact(mock_repo_class, tmp_path):
 
     # Test 2: Change in events only affects services that use events
     mock_repo_class.return_value = mock_git_changes(["shared/events/order_created.py"])
-    analyzer = BoughAnalyzer.from_workspace(tmp_path, config_path)
+    analyzer = BoughAnalyzer.from_workspace(tmp_path, tmp_path, config_path)
     affected, _ = analyzer.find_affected()
 
     expected = {"user-service", "order-service", "notification-service"}
@@ -276,7 +277,7 @@ def test_isolated_packages_no_unnecessary_rebuilds(mock_repo_class, tmp_path):
     mock_repo_class.return_value = mock_git_changes(
         ["tools/standalone-b/standalone_b.py"],
     )
-    analyzer = BoughAnalyzer.from_workspace(tmp_path, config_path)
+    analyzer = BoughAnalyzer.from_workspace(tmp_path, tmp_path, config_path)
     affected, _ = analyzer.find_affected()
 
     assert affected == {"standalone-b"}
@@ -285,7 +286,7 @@ def test_isolated_packages_no_unnecessary_rebuilds(mock_repo_class, tmp_path):
     mock_repo_class.return_value = mock_git_changes(
         ["tools/standalone-a/standalone_a.py"],
     )
-    analyzer = BoughAnalyzer.from_workspace(tmp_path, config_path)
+    analyzer = BoughAnalyzer.from_workspace(tmp_path, tmp_path, config_path)
     affected, _ = analyzer.find_affected()
 
     assert affected == {"standalone-a", "main"}
@@ -313,7 +314,7 @@ def test_root_file_affects_all_buildable_packages(mock_repo_class, tmp_path):
 
     # Root pyproject.toml change should affect all buildable packages
     mock_repo_class.return_value = mock_git_changes(["pyproject.toml"])
-    analyzer = BoughAnalyzer.from_workspace(tmp_path, config_path)
+    analyzer = BoughAnalyzer.from_workspace(tmp_path, tmp_path, config_path)
     affected, _ = analyzer.find_affected()
 
     assert affected == {"web", "api"}  # Only buildable packages
@@ -343,7 +344,7 @@ def test_ignored_files_trigger_no_rebuilds(mock_repo_class, tmp_path):
     mock_repo_class.return_value = mock_git_changes(
         ["README.md", "docs/api.md", "CHANGELOG.txt"],
     )
-    analyzer = BoughAnalyzer.from_workspace(tmp_path, config_path)
+    analyzer = BoughAnalyzer.from_workspace(tmp_path, tmp_path, config_path)
     affected, _ = analyzer.find_affected()
 
     assert affected == set()
@@ -376,8 +377,35 @@ def test_complex_buildable_patterns(mock_repo_class, tmp_path):
 
     # Change common library to affect everything
     mock_repo_class.return_value = mock_git_changes(["libs/common/common.py"])
-    analyzer = BoughAnalyzer.from_workspace(tmp_path, config_path)
+    analyzer = BoughAnalyzer.from_workspace(tmp_path, tmp_path, config_path)
     affected, _ = analyzer.find_affected()
 
     # Should only include packages matching buildable patterns
     assert affected == {"user-service", "api-gateway", "web"}
+
+
+@patch("git.Repo")
+def test_divergent_git_vs_workspace_roots(mock_repo_class, tmp_path):
+    """Test that root file changes affect all buildable packages."""
+    structure = {
+        "libs/utils": {"dependencies": []},
+        "apps/web": {"dependencies": ["utils"]},
+        "apps/api": {"dependencies": ["utils"]},
+        "tools/cli": {"dependencies": []},
+    }
+
+    create_workspace_structure(tmp_path / "src", structure)
+
+    config_path = tmp_path / ".bough.yml"
+    config_path.write_text("""
+buildable:
+  - "apps/*"
+ignore:
+  - "*.md"
+""")
+
+    mock_repo_class.return_value = mock_git_changes(["src/apps/web/foo"])
+    analyzer = BoughAnalyzer.from_workspace(tmp_path, tmp_path / "src", config_path)
+    affected, _ = analyzer.find_affected()
+
+    assert affected == {"web"}
diff --git a/tests/test_config.py b/tests/test_config.py
index 2eb2e15..e0ebdfe 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -75,7 +75,9 @@ def test_analyzer_loads_config(sample_workspace, tmp_path):
   - "docs/**"
 """)
 
-    analyzer = BoughAnalyzer.from_workspace(sample_workspace, config_path)
+    analyzer = BoughAnalyzer.from_workspace(
+        sample_workspace, sample_workspace, config_path
+    )
 
     # Should have loaded config from .bough.yml in the workspace
     assert analyzer.config is not None
@@ -94,7 +96,9 @@ def test_analyzer_custom_config_path(sample_workspace, tmp_path):
   - "*.tmp"
 """)
 
-    analyzer = BoughAnalyzer.from_workspace(sample_workspace, config_path=custom_config)
+    analyzer = BoughAnalyzer.from_workspace(
+        sample_workspace, sample_workspace, config_path=custom_config
+    )
 
     assert analyzer.config.buildable == ["services/*"]
     assert analyzer.config.ignore == ["*.log", "*.tmp"]
diff --git a/tests/test_config_patterns.py b/tests/test_config_patterns.py
index 5b4af59..2515605 100644
--- a/tests/test_config_patterns.py
+++ b/tests/test_config_patterns.py
@@ -16,7 +16,9 @@ def test_custom_buildable_patterns_filter_correctly(sample_workspace, tmp_path):
   - "*.md"
 """)
 
-    analyzer = BoughAnalyzer.from_workspace(sample_workspace, config_path)
+    analyzer = BoughAnalyzer.from_workspace(
+        sample_workspace, sample_workspace, config_path
+    )
 
     # Modify a file that affects everything
 
@@ -54,7 +56,9 @@ def test_multiple_buildable_patterns(sample_workspace, tmp_path):
   - "*.md"
 """)
 
-    analyzer = BoughAnalyzer.from_workspace(sample_workspace, config_path)
+    analyzer = BoughAnalyzer.from_workspace(
+        sample_workspace, sample_workspace, config_path
+    )
 
     repo = git.Repo.init(sample_workspace)
     with repo.config_writer() as config:
@@ -91,7 +95,9 @@ def test_custom_ignore_patterns_work(sample_workspace, tmp_path):
   - "docs/**"
 """)
 
-    analyzer = BoughAnalyzer.from_workspace(sample_workspace, config_path)
+    analyzer = BoughAnalyzer.from_workspace(
+        sample_workspace, sample_workspace, config_path
+    )
 
     repo = git.Repo.init(sample_workspace)
     with repo.config_writer() as config:
@@ -125,7 +131,9 @@ def test_nested_ignore_patterns(sample_workspace, tmp_path):
   - "docs/**"
 """)
 
-    analyzer = BoughAnalyzer.from_workspace(sample_workspace, config_path)
+    analyzer = BoughAnalyzer.from_workspace(
+        sample_workspace, sample_workspace, config_path
+    )
 
     repo = git.Repo.init(sample_workspace)
     with repo.config_writer() as config:
diff --git a/tests/test_formatters.py b/tests/test_formatters.py
index 7de1022..db59eb1 100644
--- a/tests/test_formatters.py
+++ b/tests/test_formatters.py
@@ -1,25 +1,26 @@
-from hypothesis import given, strategies as st
-from unittest.mock import Mock
-from pathlib import Path
 import json
+from pathlib import Path
+from unittest.mock import Mock
+
+from hypothesis import given
+from hypothesis import strategies as st
+
 import bough.formatters as sut
 
 package_name = st.text(
-    min_size=1, 
-    max_size=20,
-    alphabet=st.characters(blacklist_characters='\n\r')
+    min_size=1, max_size=20, alphabet=st.characters(blacklist_characters="\n\r")
 )
 
 packages = st.sets(package_name, min_size=1)
 files = st.sets(package_name, min_size=1)
 
+
 @given(packages)
 def test_github_matrix_always_valid_json(package_names):
     """GitHub matrix output must always be valid JSON."""
     analyzer = Mock()
     analyzer.packages = {
-        name: Mock(directory=Path(f"/root/{name}"))
-        for name in package_names
+        name: Mock(directory=Path(f"/root/{name}")) for name in package_names
     }
     analyzer.workspace_root = Path("/root")
 
@@ -35,8 +36,7 @@ def test_quiet_output_has_correct_line_count(package_names):
     """Quiet mode outputs exactly one line per package."""
     analyzer = Mock()
     analyzer.packages = {
-        name: Mock(directory=Path(f"/root/{name}"))
-        for name in package_names
+        name: Mock(directory=Path(f"/root/{name}")) for name in package_names
     }
 
     result = sut.quiet(analyzer, package_names)
@@ -49,8 +49,7 @@ def test_human_readable_contains_all_packages(packages, files):
     """All package names must appear in human readable output."""
     analyzer = Mock()
     analyzer.packages = {
-        name: Mock(directory=Path(f"/root/{name}"))
-        for name in packages
+        name: Mock(directory=Path(f"/root/{name}")) for name in packages
     }
     analyzer.workspace_root = Path("/root")
 
@@ -60,7 +59,6 @@ def test_human_readable_contains_all_packages(packages, files):
         assert pkg in result
 
 
-
 @st.composite
 def package_graph(draw):
     """Generate a set of packages with dependencies referencing each other."""
@@ -72,22 +70,20 @@ def package_graph(draw):
     for name in names:
         deps = draw(st.sets(st.sampled_from(names), max_size=3)) - {name}
         is_buildable = draw(st.booleans())
-        packages.append({
-            "name": name,
-            "dependencies": deps,
-            "is_buildable": is_buildable
-        })
+        packages.append(
+            {"name": name, "dependencies": deps, "is_buildable": is_buildable}
+        )
 
     return packages
 
+
 @given(package_graph())
 def test_dependency_graph_contains_all_packages(packages):
     """All package names must appear in dependency graph output."""
     analyzer = Mock()
     analyzer.packages = {
         pkg["name"]: Mock(
-            directory=Path(f"/root/{pkg['name']}"),
-            dependencies=pkg["dependencies"]
+            directory=Path(f"/root/{pkg['name']}"), dependencies=pkg["dependencies"]
         )
         for pkg in packages
     }
diff --git a/tests/test_git.py b/tests/test_git.py
index 2e8b43b..0d7387e 100644
--- a/tests/test_git.py
+++ b/tests/test_git.py
@@ -1,7 +1,9 @@
 import tempfile
 from pathlib import Path
+
 import git
 import pytest
+
 import bough.git as sut
 
 
diff --git a/tests/test_graph_discovery.py b/tests/test_graph_discovery.py
index 5cd29ab..d41d5bd 100644
--- a/tests/test_graph_discovery.py
+++ b/tests/test_graph_discovery.py
@@ -7,7 +7,9 @@
 
 
 def test_dependency_graph_discovery(sample_workspace, empty_config):
-    analyzer = BoughAnalyzer.from_workspace(sample_workspace, empty_config)
+    analyzer = BoughAnalyzer.from_workspace(
+        sample_workspace, sample_workspace, empty_config
+    )
 
     # Verify packages were discovered
     expected_packages = {"auth", "database", "shared", "api", "web"}
@@ -80,7 +82,7 @@ def test_git_change_detection(
     repo.git.add(".")
     repo.index.commit(f"Update {changed_file}")
 
-    analyzer = BoughAnalyzer.from_workspace(git_workspace, empty_config)
+    analyzer = BoughAnalyzer.from_workspace(git_workspace, git_workspace, empty_config)
 
     # This should detect what changed and find affected packages
     affected, _ = analyzer.find_affected()

From 045b8dc82f024603d97abeb62ab6ecbc2ad1347a Mon Sep 17 00:00:00 2001
From: Andrew Nichols <andrew@frenata.net>
Date: Thu, 29 Jan 2026 18:03:05 -0500
Subject: [PATCH 2/2] feat: allow for a divergence between the git repo root
 and the uv workspace root

---
 bough/analyzer.py |  13 +-
 bough/cli.py      |   8 +-
 uv.lock           | 374 +++++++++++++++++++++++-----------------------
 3 files changed, 203 insertions(+), 192 deletions(-)

diff --git a/bough/analyzer.py b/bough/analyzer.py
index c680510..bc69c7f 100644
--- a/bough/analyzer.py
+++ b/bough/analyzer.py
@@ -39,10 +39,12 @@ class BoughAnalyzer:
 
     def __init__(
         self,
+        repo_root: Path,
         workspace_root: Path,
         config: "BoughConfig",
         packages: dict[str, Package] | None = None,
     ) -> None:
+        self.repo_root = repo_root
         self.workspace_root = workspace_root
         logger.debug(f"Initializing analyzer for workspace: {workspace_root}")
         self.config = config
@@ -54,10 +56,12 @@ def __init__(
         logger.debug(f"Discovered {len(self.packages)} packages")
 
     @classmethod
-    def from_workspace(cls, workspace_root: Path, config_path: Path) -> "BoughAnalyzer":
+    def from_workspace(
+        cls, repo_root: Path, workspace_root: Path, config_path: Path
+    ) -> "BoughAnalyzer":
         """Create analyzer by discovering packages from workspace."""
         config = load_config(config_path)
-        return cls(workspace_root, config)
+        return cls(repo_root, workspace_root, config)
 
     def _discover_packages(self) -> None:
         root_pyproject = self.workspace_root / "pyproject.toml"
@@ -159,8 +163,9 @@ def _find_direct_packages(
         changed_files: set[str],
     ) -> set[str]:
         directly_affected = set()
+        strip_prefix = self.workspace_root.relative_to(self.repo_root)
         for file_path in changed_files:
-            file_path_obj = Path(file_path)
+            file_path_obj = Path(file_path).relative_to(strip_prefix)
 
             if self._matches_patterns(file_path, self.config.ignore):
                 logger.debug(f"Ignoring file {file_path} (matches ignore patterns)")
@@ -210,7 +215,7 @@ def find_affected(
         """Return the affected packages and files."""
         logger.debug(f"Analyzing changes from {base_commit} to HEAD")
 
-        files = find_changed_files(self.workspace_root, base_commit)
+        files = find_changed_files(self.repo_root, base_commit)
         all_affected = self._find_transitive_packages(self._find_direct_packages(files))
 
         if selection != "buildable":
diff --git a/bough/cli.py b/bough/cli.py
index 45314b4..51d95f6 100644
--- a/bough/cli.py
+++ b/bough/cli.py
@@ -23,6 +23,12 @@ def main() -> None:
         default=Path.cwd(),
         help="Path to workspace root (default: current directory)",
     )
+    default_parser.add_argument(
+        "--repo",
+        type=Path,
+        default=Path.cwd(),
+        help="Path to git repository root (default: current directory)",
+    )
     default_parser.add_argument(
         "--verbose",
         "-v",
@@ -74,7 +80,7 @@ def main() -> None:
     config_path = args.config or args.workspace / ".bough.yaml"
 
     try:
-        analyzer = BoughAnalyzer.from_workspace(args.workspace, config_path)
+        analyzer = BoughAnalyzer.from_workspace(args.repo, args.workspace, config_path)
 
         if args.command == "graph":
             output = fmt.dependency_graph(analyzer)
diff --git a/uv.lock b/uv.lock
index 53021a7..ceee40b 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1,27 +1,27 @@
 version = 1
+revision = 3
 requires-python = ">=3.12"
 
 [[package]]
 name = "asttokens"
 version = "3.0.0"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/4a/e7/82da0a03e7ba5141f05cce0d302e6eed121ae055e0456ca228bf693984bc/asttokens-3.0.0.tar.gz", hash = "sha256:0dcd8baa8d62b0c1d118b399b2ddba3c4aff271d0d7a9e0d4c1681c79035bbc7", size = 61978 }
+sdist = { url = "https://files.pythonhosted.org/packages/4a/e7/82da0a03e7ba5141f05cce0d302e6eed121ae055e0456ca228bf693984bc/asttokens-3.0.0.tar.gz", hash = "sha256:0dcd8baa8d62b0c1d118b399b2ddba3c4aff271d0d7a9e0d4c1681c79035bbc7", size = 61978, upload-time = "2024-11-30T04:30:14.439Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/25/8a/c46dcc25341b5bce5472c718902eb3d38600a903b14fa6aeecef3f21a46f/asttokens-3.0.0-py3-none-any.whl", hash = "sha256:e3078351a059199dd5138cb1c706e6430c05eff2ff136af5eb4790f9d28932e2", size = 26918 },
+    { url = "https://files.pythonhosted.org/packages/25/8a/c46dcc25341b5bce5472c718902eb3d38600a903b14fa6aeecef3f21a46f/asttokens-3.0.0-py3-none-any.whl", hash = "sha256:e3078351a059199dd5138cb1c706e6430c05eff2ff136af5eb4790f9d28932e2", size = 26918, upload-time = "2024-11-30T04:30:10.946Z" },
 ]
 
 [[package]]
 name = "attrs"
 version = "25.4.0"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/6b/5c/685e6633917e101e5dcb62b9dd76946cbb57c26e133bae9e0cd36033c0a9/attrs-25.4.0.tar.gz", hash = "sha256:16d5969b87f0859ef33a48b35d55ac1be6e42ae49d5e853b597db70c35c57e11", size = 934251 }
+sdist = { url = "https://files.pythonhosted.org/packages/6b/5c/685e6633917e101e5dcb62b9dd76946cbb57c26e133bae9e0cd36033c0a9/attrs-25.4.0.tar.gz", hash = "sha256:16d5969b87f0859ef33a48b35d55ac1be6e42ae49d5e853b597db70c35c57e11", size = 934251, upload-time = "2025-10-06T13:54:44.725Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/3a/2a/7cc015f5b9f5db42b7d48157e23356022889fc354a2813c15934b7cb5c0e/attrs-25.4.0-py3-none-any.whl", hash = "sha256:adcf7e2a1fb3b36ac48d97835bb6d8ade15b8dcce26aba8bf1d14847b57a3373", size = 67615 },
+    { url = "https://files.pythonhosted.org/packages/3a/2a/7cc015f5b9f5db42b7d48157e23356022889fc354a2813c15934b7cb5c0e/attrs-25.4.0-py3-none-any.whl", hash = "sha256:adcf7e2a1fb3b36ac48d97835bb6d8ade15b8dcce26aba8bf1d14847b57a3373", size = 67615, upload-time = "2025-10-06T13:54:43.17Z" },
 ]
 
 [[package]]
 name = "bough"
-version = "0.2.2.dev6+g5444609bb.d20251102"
 source = { editable = "." }
 dependencies = [
     { name = "gitpython" },
@@ -62,101 +62,101 @@ dev = [
 name = "colorama"
 version = "0.4.6"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/d8/53/6f443c9a4a8358a93a6792e2acffb9d9d5cb0a5cfd8802644b7b1c9a02e4/colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44", size = 27697 }
+sdist = { url = "https://files.pythonhosted.org/packages/d8/53/6f443c9a4a8358a93a6792e2acffb9d9d5cb0a5cfd8802644b7b1c9a02e4/colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44", size = 27697, upload-time = "2022-10-25T02:36:22.414Z" }
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