Separate pyproject.toml location from root argument (#244)

* feat(cli): expose `config` argument

* tests: duplicate `run_within_dir` method

* feat: use root to determine files to find

* test(cli): add tests for src directory

deptry/cli.py

@@ -8,7 +8,7 @@
 from deptry.compat import metadata
 from deptry.config import read_configuration_from_pyproject_toml
 from deptry.core import Core
-from deptry.utils import PYPROJECT_TOML_PATH, run_within_dir
+from deptry.utils import PYPROJECT_TOML_PATH
 
 
 class CommaSeparatedTupleParamType(click.ParamType):
@@ -186,7 +186,6 @@ def display_deptry_version(ctx: click.Context, _param: click.Parameter, value: b
     help="Path to the pyproject.toml file to read configuration from.",
     default=PYPROJECT_TOML_PATH,
     expose_value=False,
-    hidden=True,
 )
 def deptry(
     root: Path,
@@ -212,20 +211,20 @@ def deptry(
 
     """
 
-    with run_within_dir(root):
-        Core(
-            ignore_obsolete=ignore_obsolete,
-            ignore_missing=ignore_missing,
-            ignore_transitive=ignore_transitive,
-            ignore_misplaced_dev=ignore_misplaced_dev,
-            exclude=exclude,
-            extend_exclude=extend_exclude,
-            ignore_notebooks=ignore_notebooks,
-            skip_obsolete=skip_obsolete,
-            skip_missing=skip_missing,
-            skip_transitive=skip_transitive,
-            skip_misplaced_dev=skip_misplaced_dev,
-            requirements_txt=requirements_txt,
-            requirements_txt_dev=requirements_txt_dev,
-            json_output=json_output,
-        ).run()
+    Core(
+        root=root,
+        ignore_obsolete=ignore_obsolete,
+        ignore_missing=ignore_missing,
+        ignore_transitive=ignore_transitive,
+        ignore_misplaced_dev=ignore_misplaced_dev,
+        exclude=exclude,
+        extend_exclude=extend_exclude,
+        ignore_notebooks=ignore_notebooks,
+        skip_obsolete=skip_obsolete,
+        skip_missing=skip_missing,
+        skip_transitive=skip_transitive,
+        skip_misplaced_dev=skip_misplaced_dev,
+        requirements_txt=requirements_txt,
+        requirements_txt_dev=requirements_txt_dev,
+        json_output=json_output,
+    ).run()

deptry/core.py

@@ -26,6 +26,7 @@
 
 @dataclass
 class Core:
+    root: Path
     ignore_obsolete: tuple[str, ...]
     ignore_missing: tuple[str, ...]
     ignore_transitive: tuple[str, ...]
@@ -49,7 +50,7 @@ def run(self) -> None:
 
         all_python_files = PythonFileFinder(
             exclude=self.exclude + self.extend_exclude, ignore_notebooks=self.ignore_notebooks
-        ).get_all_python_files_in(Path("."))
+        ).get_all_python_files_in(self.root)
 
         local_modules = self._get_local_modules()
 
@@ -96,10 +97,9 @@ def _get_dependencies(self, dependency_management_format: DependencyManagementFo
             return RequirementsTxtDependencyGetter(self.requirements_txt, self.requirements_txt_dev).get()
         raise ValueError("Incorrect dependency manage format. Only poetry, pdm and requirements.txt are supported.")
 
-    @staticmethod
-    def _get_local_modules() -> set[str]:
-        directories = [f for f in os.listdir() if Path(f).is_dir()]
-        return {subdir for subdir in directories if "__init__.py" in os.listdir(subdir)}
+    def _get_local_modules(self) -> set[str]:
+        directories = [f for f in os.scandir(self.root) if f.is_dir()]
+        return {subdirectory.name for subdirectory in directories if "__init__.py" in os.listdir(subdirectory)}
 
     def _log_config(self) -> None:
         logging.debug("Running with the following configuration:")

deptry/utils.py

@@ -2,9 +2,8 @@
 
 import os
 import sys
-from contextlib import contextmanager
 from pathlib import Path
-from typing import Any, Generator
+from typing import Any
 
 if sys.version_info >= (3, 11):
     import tomllib
@@ -14,27 +13,6 @@
 PYPROJECT_TOML_PATH = "./pyproject.toml"
 
 
-@contextmanager
-def run_within_dir(path: Path) -> Generator[None, None, None]:
-    """
-    Utility function to run some code within a directory, and change back to the current directory afterwards.
-
-    Example usage:
-
-    ```
-    with run_within_dir(directory):
-        some_code()
-    ```
-
-    """
-    oldpwd = os.getcwd()
-    os.chdir(path)
-    try:
-        yield
-    finally:
-        os.chdir(oldpwd)
-
-
 def load_pyproject_toml(pyproject_toml_path: str = PYPROJECT_TOML_PATH) -> dict[str, Any]:
     try:
         with Path(pyproject_toml_path).open("rb") as pyproject_file:

tests/cli/test_cli.py

@@ -7,7 +7,7 @@
 import pytest
 from _pytest.tmpdir import TempPathFactory
 
-from deptry.utils import run_within_dir
+from tests.utils import run_within_dir
 
 
 @pytest.fixture(scope="session")

tests/cli/test_cli_pdm.py

@@ -6,7 +6,7 @@
 import pytest
 from _pytest.tmpdir import TempPathFactory
 
-from deptry.utils import run_within_dir
+from tests.utils import run_within_dir
 
 
 @pytest.fixture(scope="session")

tests/cli/test_cli_pep_621.py

@@ -6,7 +6,7 @@
 import pytest
 from _pytest.tmpdir import TempPathFactory
 
-from deptry.utils import run_within_dir
+from tests.utils import run_within_dir
 
 
 @pytest.fixture(scope="session")

tests/cli/test_cli_requirements_txt.py

@@ -6,7 +6,7 @@
 import pytest
 from _pytest.tmpdir import TempPathFactory
 
-from deptry.utils import run_within_dir
+from tests.utils import run_within_dir
 
 
 @pytest.fixture(scope="session")

tests/cli/test_cli_src_directory.py

@@ -0,0 +1,28 @@
+import shlex
+import shutil
+import subprocess
+from pathlib import Path
+
+import pytest
+from _pytest.tmpdir import TempPathFactory
+
+from tests.utils import run_within_dir
+
+
+@pytest.fixture(scope="session")
+def pep_621_dir_with_src_directory(tmp_path_factory: TempPathFactory) -> Path:
+    tmp_path_proj = tmp_path_factory.getbasetemp() / "project_with_src_directory"
+    shutil.copytree("tests/data/project_with_src_directory", str(tmp_path_proj))
+    with run_within_dir(tmp_path_proj):
+        assert subprocess.check_call(shlex.split("pip install .")) == 0
+    return tmp_path_proj
+
+
+def test_cli_with_src_directory(pep_621_dir_with_src_directory: Path) -> None:
+    with run_within_dir(pep_621_dir_with_src_directory):
+        result = subprocess.run(shlex.split("deptry src"), capture_output=True, text=True)
+        assert result.returncode == 1
+        assert (
+            "The project contains obsolete dependencies:\n\n\tisort\n\tmypy\n\tpytest\n\trequests\n\n" in result.stderr
+        )
+        assert "There are dependencies missing from the project's list of dependencies:\n\n\twhite\n\n" in result.stderr

tests/data/project_with_src_directory/pyproject.toml

@@ -0,0 +1,30 @@
+[project]
+# PEP 621 project metadata
+# See https://www.python.org/dev/peps/pep-0621/
+name = "foo"
+version = "1.2.3"
+requires-python = ">=3.7"
+dependencies = [
+    "toml",
+    "urllib3>=1.26.12",
+    "isort>=5.10.1",
+    "click>=8.1.3",
+    "requests>=2.28.1",
+    "pkginfo>=1.8.3",
+]
+
+[project.optional-dependencies]
+dev = [
+    "black==22.10.0",
+    "mypy==0.982",
+]
+test = [
+  "pytest==7.2.0",
+]
+
+[build-system]
+requires = ["setuptools>=61.0.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.deptry]
+ignore_obsolete = ["pkginfo"]

tests/data/project_with_src_directory/src/project_with_src_directory/bar.py

@@ -0,0 +1 @@
+from project_with_src_directory.foo import a_local_method

tests/data/project_with_src_directory/src/project_with_src_directory/foo.py

@@ -0,0 +1,11 @@
+from os import chdir, walk
+from pathlib import Path
+
+import black
+import click
+import white as w
+from urllib3 import contrib
+
+
+def a_local_method():
+    ...

tests/data/project_with_src_directory/src/project_with_src_directory/notebook.ipynb

@@ -0,0 +1,37 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "9f4924ec-2200-4801-9d49-d4833651cbc4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import click\n",
+    "from urllib3 import contrib\n",
+    "import toml"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.11"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

tests/dependency_getter/test_pdm.py

@@ -1,7 +1,7 @@
 from pathlib import Path
 
 from deptry.dependency_getter.pdm import PDMDependencyGetter
-from deptry.utils import run_within_dir
+from tests.utils import run_within_dir
 
 
 def test_dependency_getter(tmp_path: Path) -> None:

tests/dependency_getter/test_pep_621.py

@@ -1,7 +1,7 @@
 from pathlib import Path
 
 from deptry.dependency_getter.pep_621 import PEP621DependencyGetter
-from deptry.utils import run_within_dir
+from tests.utils import run_within_dir
 
 
 def test_dependency_getter(tmp_path: Path) -> None:

tests/dependency_getter/test_poetry.py

@@ -1,7 +1,7 @@
 from pathlib import Path
 
 from deptry.dependency_getter.poetry import PoetryDependencyGetter
-from deptry.utils import run_within_dir
+from tests.utils import run_within_dir
 
 
 def test_dependency_getter(tmp_path: Path) -> None:

tests/dependency_getter/test_requirements_txt.py

@@ -1,7 +1,7 @@
 from pathlib import Path
 
 from deptry.dependency_getter.requirements_txt import RequirementsTxtDependencyGetter
-from deptry.utils import run_within_dir
+from tests.utils import run_within_dir
 
 
 def test_parse_requirements_txt(tmp_path: Path) -> None:

tests/imports/test_extract.py

@@ -9,7 +9,7 @@
 from _pytest.logging import LogCaptureFixture
 
 from deptry.imports.extract import get_imported_modules_for_list_of_files, get_imported_modules_from_file
-from deptry.utils import run_within_dir
+from tests.utils import run_within_dir
 
 
 def test_import_parser_py() -> None:

tests/test_config.py

@@ -5,7 +5,7 @@
 from _pytest.logging import LogCaptureFixture
 
 from deptry.config import read_configuration_from_pyproject_toml
-from deptry.utils import run_within_dir
+from tests.utils import run_within_dir
 
 
 def test_read_configuration_from_pyproject_toml_exists(tmp_path: Path) -> None:

tests/test_dependency_specification_detector.py

@@ -4,7 +4,7 @@
 import pytest
 
 from deptry.dependency_specification_detector import DependencyManagementFormat, DependencySpecificationDetector
-from deptry.utils import run_within_dir
+from tests.utils import run_within_dir
 
 
 def test_poetry(tmp_path: Path) -> None:

tests/test_json_writer.py

@@ -2,7 +2,7 @@
 from pathlib import Path
 
 from deptry.json_writer import JsonWriter
-from deptry.utils import run_within_dir
+from tests.utils import run_within_dir
 
 
 def test_simple(tmp_path: Path) -> None:

tests/test_python_file_finder.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 
 from deptry.python_file_finder import PythonFileFinder
-from deptry.utils import run_within_dir
+from tests.utils import run_within_dir
 
 
 def create_files_from_list_of_dicts(paths: list[dict[str, str]]) -> None:

tests/utils.py

@@ -0,0 +1,25 @@
+import os
+from contextlib import contextmanager
+from pathlib import Path
+from typing import Generator
+
+
+@contextmanager
+def run_within_dir(path: Path) -> Generator[None, None, None]:
+    """
+    Utility function to run some code within a directory, and change back to the current directory afterwards.
+
+    Example usage:
+
+    ```
+    with run_within_dir(directory):
+        some_code()
+    ```
+
+    """
+    oldpwd = os.getcwd()
+    os.chdir(path)
+    try:
+        yield
+    finally:
+        os.chdir(oldpwd)