[python] What is the best project structure for a Python application?

Non-python data is best bundled inside your Python modules using the package_data support in setuptools. One thing I strongly recommend is using namespace packages to create shared namespaces which multiple projects can use -- much like the Java convention of putting packages in com.yourcompany.yourproject (and being able to have a shared com.yourcompany.utils namespace).

Re branching and merging, if you use a good enough source control system it will handle merges even through renames; Bazaar is particularly good at this.

Contrary to some other answers here, I'm +1 on having a src directory top-level (with doc and test directories alongside). Specific conventions for documentation directory trees will vary depending on what you're using; Sphinx, for instance, has its own conventions which its quickstart tool supports.

Please, please leverage setuptools and pkg_resources; this makes it much easier for other projects to rely on specific versions of your code (and for multiple versions to be simultaneously installed with different non-code files, if you're using package_data).

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