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You have to include data inside your package directory (project_name/data). pip purposefully makes it difficult to install anything outside the package install directory for security reasons.
Yup, you need it in the inner directory alongside __init__.py - this is the importable module that will get installed. We don't want to install random .../site-packages/data directories.
Other Python packaging tools provide a way to install files to other locations - setuptools calls this data_files. It's not currently supported in Flit, because I think the situations where you actually need it are limited, and Flit is focused on the simple cases. See #358 for discussion over whether that should be added.
When creating a build for a simple project layout like the following:
project_name
---init.py
--- main.py
--- module1.py
--- database.db
--- samplefile.csv
Source dist will include data directory alongside project_name dir but wheel will only include project_name dir
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