Fix path inclusion behavior

integration_tests/base_test.py

@@ -47,7 +47,7 @@ def check_dependencies_after(self):
 
 class BaseIntegrationTest(DependencyTestMixin, CleanRepoMixin):
     codemod = NotImplementedError
-    code_path = NotImplementedError
+    code_path: str = NotImplementedError
     original_code = NotImplementedError
     expected_new_code = NotImplementedError
     output_path = "test-codetf.txt"
@@ -77,13 +77,14 @@ def setup_method(self):
             ) from exc
 
     def _assert_run_fields(self, run, output_path):
+        code_path = os.path.relpath(self.code_path, SAMPLES_DIR)
         assert run["vendor"] == "pixee"
         assert run["tool"] == "codemodder-python"
         assert run["version"] == __version__
         assert run["elapsed"] != ""
         assert (
             run["commandLine"]
-            == f"codemodder {SAMPLES_DIR} --output {output_path} --codemod-include={self.codemod_instance.name} --path-include={self.code_path}"
+            == f'codemodder {SAMPLES_DIR} --output {output_path} --codemod-include={self.codemod_instance.name} --path-include={code_path} --path-exclude=""'
         )
         assert run["directory"] == os.path.abspath(SAMPLES_DIR)
         assert run["sarifs"] == []
@@ -149,14 +150,15 @@ def test_file_rewritten(self):
         Mocks won't work when making a subprocess call so make sure to delete all
         output files
         """
-
+        code_path = os.path.relpath(self.code_path, SAMPLES_DIR)
         command = [
             "codemodder",
             SAMPLES_DIR,
             "--output",
             self.output_path,
             f"--codemod-include={self.codemod_instance.name}",
-            f"--path-include={self.code_path}",
+            f"--path-include={code_path}",
+            '--path-exclude=""',
         ]
 
         self.check_code_before()

integration_tests/test_multiple_codemods.py

@@ -28,7 +28,8 @@ def test_two_codemods(self, codemods, tmpdir):
             str(codetf_path),
             f"--codemod-include={codemods}",
             "--path-include",
-            f"**/{source_file_name}",
+            f"{source_file_name}",
+            '--path-exclude=""',
         ]
 
         completed_process = subprocess.run(

src/codemodder/code_directory.py

@@ -6,21 +6,23 @@
 
 DEFAULT_INCLUDED_PATHS = ["**.py", "**/*.py"]
 DEFAULT_EXCLUDED_PATHS = [
-    "**/test/**",
-    "**/tests/**",
-    "**/conftest.py",
-    "**/build/**",
-    "**/dist/**",
-    "**/venv/**",
-    "**/.venv/**",
-    "**/.tox/**",
-    "**/.nox/**",
-    "**/.eggs/**",
-    "**/.git/**",
-    "**/.mypy_cache/**",
-    "**/.pytest_cache/**",
-    "**/.hypothesis/**",
-    "**/.coverage*",
+    # TODO: test code should eventually only be excluded on a per-codemod basis
+    # Some codemods represent fixes that should be applied to test code
+    "test/**",
+    "tests/**",
+    "conftest.py",
+    "build/**",
+    "dist/**",
+    "venv/**",
+    ".venv/**",
+    ".tox/**",
+    ".nox/**",
+    ".eggs/**",
+    ".git/**",
+    ".mypy_cache/**",
+    ".pytest_cache/**",
+    ".hypothesis/**",
+    ".coverage*",
 ]
 
 
@@ -64,7 +66,10 @@ def match_files(
     :return: list of <pathlib.PosixPath> files found within (including recursively) the parent directory
     that match the criteria of both exclude and include patterns.
     """
-    all_files = [str(path) for path in Path(parent_path).rglob("*")]
+    all_files = [
+        str(Path(path).relative_to(parent_path))
+        for path in Path(parent_path).rglob("*")
+    ]
     included_files = set(
         filter_files(
             all_files,
@@ -82,5 +87,5 @@ def match_files(
     return [
         path
         for p in sorted(list(included_files - excluded_files))
-        if (path := Path(p)).is_file() and path.suffix == ".py"
+        if (path := Path(parent_path).joinpath(p)).is_file() and path.suffix == ".py"
     ]

src/codemodder/codemodder.py

@@ -154,6 +154,7 @@ def run(original_args) -> int:
 
     log_section("startup")
     logger.info("codemodder: python/%s", __version__)
+    logger.info("command: %s %s", Path(sys.argv[0]).name, " ".join(original_args))
 
     repo_manager = PythonRepoManager(Path(argv.directory))
     context = CodemodExecutionContext(

tests/test_code_directory.py

@@ -42,7 +42,7 @@ def test_all_py_files_match(self, dir_structure):
 
     def test_match_excluded(self, dir_structure):
         expected = ["empty_for_testing.py", "insecure_random.py"]
-        files = match_files(dir_structure, ["**/tests/**", "*request.py"])
+        files = match_files(dir_structure, ["tests/**", "*request.py"])
         self._assert_expected(files, expected)
 
     def test_match_included_file_with_line(self, dir_structure):
@@ -53,7 +53,7 @@ def test_match_included_file_with_line(self, dir_structure):
     def test_match_excluded_line(self, dir_structure):
         expected = ["empty_for_testing.py", "insecure_random.py", "make_request.py"]
         files = match_files(
-            dir_structure, exclude_paths=["**/tests/**", "**/insecure_random.py:2"]
+            dir_structure, exclude_paths=["tests/**", "**/insecure_random.py:2"]
         )
         self._assert_expected(files, expected)
 
@@ -65,26 +65,26 @@ def test_match_included_line_and_glob(self, dir_structure):
     def test_match_excluded_line_and_glob(self, dir_structure):
         expected = ["empty_for_testing.py", "insecure_random.py", "make_request.py"]
         files = match_files(
-            dir_structure, exclude_paths=["**/tests/**", "**/insecure*.py:3"]
+            dir_structure, exclude_paths=["tests/**", "**/insecure*.py:3"]
         )
         self._assert_expected(files, expected)
 
     def test_match_excluded_dir_incorrect_glob(self, dir_structure):
         incorrect_glob = "more_samples"
         expected = ["empty_for_testing.py", "insecure_random.py", "make_request.py"]
-        files = match_files(dir_structure, ["**/tests/**", incorrect_glob])
+        files = match_files(dir_structure, ["tests/**", incorrect_glob])
         self._assert_expected(files, expected)
 
     def test_match_excluded_dir_correct_glob(self, dir_structure):
         correct_globs = ["**/more_samples/**", "*/more_samples/*"]
         for correct_glob in correct_globs:
             expected = ["insecure_random.py", "make_request.py"]
-            files = match_files(dir_structure, ["**/tests/**", correct_glob])
+            files = match_files(dir_structure, ["tests/**", correct_glob])
             self._assert_expected(files, expected)
 
     def test_match_excluded_multiple(self, dir_structure):
         expected = ["insecure_random.py"]
-        files = match_files(dir_structure, ["**/tests/**", "*request.py", "*empty*"])
+        files = match_files(dir_structure, ["tests/**", "*request.py", "*empty*"])
         self._assert_expected(files, expected)
 
     def test_match_included(self, dir_structure):
@@ -96,15 +96,15 @@ def test_match_excluded_precedence_over_included(self, dir_structure):
         expected = ["empty_for_testing.py", "insecure_random.py"]
         files = match_files(
             dir_structure,
-            exclude_paths=["**/tests/**", "*request.py"],
+            exclude_paths=["tests/**", "*request.py"],
             include_paths=["*request.py", "*empty*.py", "*random.py"],
         )
         self._assert_expected(files, expected)
 
     def test_test_directory_not_excluded(self, dir_structure):
         expected = ["test_insecure_random.py", "test_make_request.py"]
         files = match_files(
-            dir_structure, exclude_paths=["**/samples/**", "**/more_samples/**"]
+            dir_structure, exclude_paths=["samples/**", "**/more_samples/**"]
         )
         self._assert_expected(files, expected)
 
@@ -120,7 +120,7 @@ def test_include_test_overridden_by_default_excludes(self, mocker):
             "codemodder.code_directory.Path.is_file",
             return_value=True,
         )
-        files = match_files(Path("."), include_paths=["**/tests/**"])
+        files = match_files(Path("."), include_paths=["tests/**"])
         self._assert_expected(files, [])
 
     def test_include_test_without_default_includes(self, mocker):