Add deprecation messages for namespace_packages.

The docs in
https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
and
https://packaging.python.org/en/latest/guides/packaging-namespace-packages/
suggest that this field is deprecated.

setuptools/config/_apply_pyprojecttoml.py

@@ -16,6 +16,8 @@
 from typing import (TYPE_CHECKING, Any, Callable, Dict, List, Optional, Set, Tuple,
                     Type, Union)
 
+from setuptools._deprecation_warning import SetuptoolsDeprecationWarning
+
 if TYPE_CHECKING:
     from setuptools._importlib import metadata  # noqa
     from setuptools.dist import Distribution  # noqa
@@ -75,6 +77,12 @@ def _apply_tool_table(dist: "Distribution", config: dict, filename: _Path):
 
     for field, value in tool_table.items():
         norm_key = json_compatible_key(field)
+
+        if norm_key in TOOL_TABLE_DEPRECATIONS:
+            suggestion = TOOL_TABLE_DEPRECATIONS[norm_key]
+            msg = f"The parameter `{norm_key}` is deprecated, {suggestion}"
+            warnings.warn(msg, SetuptoolsDeprecationWarning)
+
         norm_key = TOOL_TABLE_RENAMES.get(norm_key, norm_key)
         _set_config(dist, norm_key, value)
 
@@ -319,6 +327,9 @@ def _acessor(obj):
 }
 
 TOOL_TABLE_RENAMES = {"script_files": "scripts"}
+TOOL_TABLE_DEPRECATIONS = {
+    "namespace_packages": "consider using implicit namespaces instead (PEP 420)."
+}
 
 SETUPTOOLS_PATCHES = {"long_description_content_type", "project_urls",
                       "provides_extras", "license_file", "license_files"}

setuptools/config/setupcfg.py

@@ -12,6 +12,7 @@
 from distutils.errors import DistutilsOptionError, DistutilsFileError
 from setuptools.extern.packaging.version import Version, InvalidVersion
 from setuptools.extern.packaging.specifiers import SpecifierSet
+from setuptools._deprecation_warning import SetuptoolsDeprecationWarning
 
 from . import expand
 
@@ -507,7 +508,7 @@ def parsers(self):
                 parse_list,
                 "The requires parameter is deprecated, please use "
                 "install_requires for runtime dependencies.",
-                DeprecationWarning,
+                SetuptoolsDeprecationWarning,
             ),
             'obsoletes': parse_list,
             'classifiers': self._get_parser_compound(parse_file, parse_list),
@@ -516,7 +517,7 @@ def parsers(self):
                 exclude_files_parser('license_file'),
                 "The license_file parameter is deprecated, "
                 "use license_files instead.",
-                DeprecationWarning,
+                SetuptoolsDeprecationWarning,
             ),
             'license_files': parse_list,
             'description': parse_file,
@@ -584,7 +585,12 @@ def parsers(self):
             'scripts': parse_list,
             'eager_resources': parse_list,
             'dependency_links': parse_list,
-            'namespace_packages': parse_list,
+            'namespace_packages': self._deprecated_config_handler(
+                parse_list,
+                "The namespace_packages parameter is deprecated, "
+                "consider using implicit namespaces instead (PEP 420).",
+                SetuptoolsDeprecationWarning,
+            ),
             'install_requires': parse_list_semicolon,
             'setup_requires': parse_list_semicolon,
             'tests_require': parse_list_semicolon,

setuptools/dist.py

@@ -270,6 +270,11 @@ def check_nsp(dist, attr, value):
                 nsp,
                 parent,
             )
+        msg = (
+            "The namespace_packages parameter is deprecated, "
+            "consider using implicit namespaces instead (PEP 420).",
+        )
+        warnings.warn(msg, SetuptoolsDeprecationWarning)
 
 
 def check_extras(dist, attr, value):

setuptools/tests/config/test_apply_pyprojecttoml.py

@@ -6,6 +6,7 @@
 import io
 import re
 import tarfile
+from inspect import cleandoc
 from pathlib import Path
 from unittest.mock import Mock
 from zipfile import ZipFile
@@ -14,6 +15,7 @@
 from ini2toml.api import Translator
 
 import setuptools  # noqa ensure monkey patch to metadata
+from setuptools._deprecation_warning import SetuptoolsDeprecationWarning
 from setuptools.dist import Distribution
 from setuptools.config import setupcfg, pyprojecttoml
 from setuptools.config import expand
@@ -211,6 +213,21 @@ def test_license_and_license_files(tmp_path):
     assert dist.metadata.license == "LicenseRef-Proprietary\n"
 
 
+class TestDeprecatedFields:
+    def test_namespace_packages(self, tmp_path):
+        pyproject = tmp_path / "pyproject.toml"
+        config = """
+        [project]
+        name = "myproj"
+        version = "42"
+        [tool.setuptools]
+        namespace-packages = ["myproj.pkg"]
+        """
+        pyproject.write_text(cleandoc(config), encoding="utf-8")
+        with pytest.warns(SetuptoolsDeprecationWarning, match="namespace_packages"):
+            pyprojecttoml.apply_configuration(makedist(tmp_path), pyproject)
+
+
 class TestPresetField:
     def pyproject(self, tmp_path, dynamic, extra_content=""):
         content = f"[project]\nname = 'proj'\ndynamic = {dynamic!r}\n"

setuptools/tests/config/test_setupcfg.py

@@ -7,6 +7,7 @@
 import pytest
 
 from distutils.errors import DistutilsOptionError, DistutilsFileError
+from setuptools._deprecation_warning import SetuptoolsDeprecationWarning
 from setuptools.dist import Distribution, _Distribution
 from setuptools.config.setupcfg import ConfigHandler, read_configuration
 from ..textwrap import DALS
@@ -409,7 +410,7 @@ def test_deprecated_config_handlers(self, tmpdir):
             'requires = some, requirement\n',
         )
 
-        with pytest.deprecated_call():
+        with pytest.warns(SetuptoolsDeprecationWarning, match="requires"):
             with get_dist(tmpdir) as dist:
                 metadata = dist.metadata
 
@@ -518,7 +519,8 @@ def test_basic(self, tmpdir):
             'python_requires = >=1.0, !=2.8\n'
             'py_modules = module1, module2\n',
         )
-        with get_dist(tmpdir) as dist:
+        deprec = pytest.warns(SetuptoolsDeprecationWarning, match="namespace_packages")
+        with deprec, get_dist(tmpdir) as dist:
             assert dist.zip_safe
             assert dist.include_package_data
             assert dist.package_dir == {'': 'src', 'b': 'c'}
@@ -572,7 +574,8 @@ def test_multiline(self, tmpdir):
             '  http://some.com/here/1\n'
             '  http://some.com/there/2\n',
         )
-        with get_dist(tmpdir) as dist:
+        deprec = pytest.warns(SetuptoolsDeprecationWarning, match="namespace_packages")
+        with deprec, get_dist(tmpdir) as dist:
             assert dist.package_dir == {'': 'src', 'b': 'c'}
             assert dist.packages == ['pack_a', 'pack_b.subpack']
             assert dist.namespace_packages == ['pack1', 'pack2']