Files are usually missing from a Python wheel for one of two reasons: the build backend did not discover the Python package or module, or it did not include the non-Python files the package needs at runtime. With setuptools, fix discovery to match your project’s layout, declare standalone modules with py_modules, and add runtime resources using package-data rules. Then clear stale build artifacts, rebuild, and inspect the wheel itself.
First identify what kind of file is missing
Package discovery and file inclusion solve different problems. A package finder selects Python packages; it does not automatically make every file in the source tree part of the wheel.
- A package directory is missing: Check the finder’s search root, include and exclude filters, package mapping, and whether the package is under
src/. Also determine whether it is a regular package or an implicit namespace package. - A standalone
.pymodule is missing: Declare its module name, without the.pysuffix, usingpy_modules. A top-level module is not the same thing as a package. - A non-Python file inside a package is missing: Add a
package_datapattern, or enableinclude_package_dataand ensure the intended file is supplied throughMANIFEST.inor an enabled version-control-system plugin. - A file outside a package is missing:
include_package_dataincludes package-directory files in the wheel by default, not arbitrary files elsewhere in the project. Consider moving runtime resources into the package. Setuptools also providesdata_filesfor some files installed outside packages, though its documentation describes that option as mostly useful for files used by other programs. - A file appears in the source distribution but not the wheel: That can be expected for tests, documentation, examples, and other development or build material. If the application needs the file at runtime, configure it as package data and rebuild.
Confirm which build backend is in use
Read pyproject.toml, especially its [build-system] table, before changing settings. Projects may use setuptools, Hatch, Flit, PDM, Poetry, or another backend, and their configuration options are not interchangeable. The examples below are for setuptools; the PyPA packaging guide explains the broader project-packaging context.
Make package discovery match your layout
For a src-layout
If the package lives at src/mypkg/, configure the finder to search src. For example:
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[tool.setuptools.packages.find]
where = ["src"]For legacy setup.py configuration, the corresponding mapping is package_dir={"": "src"}. The search root and package mapping must reflect the actual tree; a finder aimed at the project root will not correctly discover packages located only under src/.
For flat layouts, namespaces, or unusual package trees
Setuptools’ automatic flat-layout finder excludes certain names and refuses ambiguous distributions with multiple top-level packages by default. Configure discovery explicitly if you intentionally have several top-level packages, reserved package names, or nested packages that need special inclusion or exclusion rules. The PyPA guide documents controls such as find_packages(include=['sample', 'sample.*']).
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In pyproject.toml, tool.setuptools.packages.find considers implicit namespace packages by default. Set namespaces = false only when you do not intend to use implicit namespace packages:
[tool.setuptools.packages.find]
where = ["src"]
namespaces = falseFor an intentionally namespace-based package, leave namespace scanning enabled and check that the finder includes the relevant directories.
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Include runtime data files deliberately
Use package-data patterns for files inside packages
For a setuptools project with files such as JSON or text resources inside src/mypkg/, an explicit configuration can look like this:
[tool.setuptools.package-data]
mypkg = ["*.json", "*.txt"]Replace mypkg and the patterns with the actual package name and required files. Explicit package_data rules do not require MANIFEST.in or a VCS plugin. Patterns do not match dotfiles unless the pattern explicitly begins with a dot; use / as the separator in nested path globs on every platform.
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Use manifest or VCS-based inclusion when appropriate
include_package_data can include package files listed by MANIFEST.in or collected by an enabled VCS plugin. In setuptools 61.0.0 and later, its default is true for pyproject.toml configuration. The default remains false in setup.cfg and setup.py for backwards compatibility. Set the choice explicitly when predictable selection matters.
A manifest is not a wheel inclusion rule by itself: the PyPA guide to distributing packages with setuptools states that “MANIFEST.in does not affect binary distributions such as wheels.” It affects the source distribution. If you rely on manifest or VCS-driven files, check that they are in the source distribution and that the setuptools wheel configuration includes them.
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Understand why the sdist and wheel differ
A source distribution (sdist) can contain tests, documentation, and files needed to build the project. A wheel contains files prepared for installation into the target Python environment. Seeing a file in an sdist therefore does not prove it will be in the wheel. The PyPA wheel specification describes the archive as containing files installed into purelib or platlib—commonly site-packages—along with .dist-info metadata. The wheel does not contain setup.py or setup.cfg.
Rebuild and inspect the wheel
- Check the backend: Verify that
[build-system]inpyproject.tomlselects the backend whose settings you are editing. - Compare configuration with the source tree: Confirm the package path, finder root, and package mapping. Add standalone modules to
py_modulesseparately from package discovery. - Add only needed runtime-file patterns: Use package-data rules or the appropriate
include_package_dataworkflow. Do not assume a broad source-distribution manifest puts files in the wheel. - Remove stale outputs after changing configuration or the file tree: Clear
build,dist, and*.egg-info. The setuptools data-files documentation also warns that*.egg-info/SOURCES.txtcan act as a cache after package-data changes. - Build and inspect: Run
python3 -m build --wheel source-tree-directory, replacingsource-tree-directorywith the project directory. A.whlis a ZIP-format archive; inspect it and verify that the expected importable paths and runtime resources are present before publishing.
For a setuptools project, the relevant references are the setuptools data-files documentation and setuptools package-discovery documentation. If your project uses another backend, follow that backend’s own inclusion rules instead.
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