Fix py.typed usage for namespace packages

[DanielYang59]

• Fix py.typed marker file placement to close The current py.typed setup does not seem ideal #3413:

  For namespace packages (see PEP 420), the py.typed file should be in the submodules of the namespace, to avoid conflicts and for clarity.

• Add a test for py.typed files, verify the original reported issue is gone (Skipping analyzing "pymatgen.io.vasp.inputs": module is installed, but missing library stubs or py.typed marker [import])
• Double check config of analysis / ext / io, are they meant to be namespace packages as well?

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Looks like some sub-modules (analysis / ext / io) are implicit namespace packages as well (no __init__.py)? i.e. pymatgen is namespace package, so do pymatgen.ext/pymatgen.analysis/pymatgen.io. Not sure if this is intended, AFAIK sharing the pymatgen namespace is sufficient to support pymatgen-analysis-defects/analysis/diffusion, pymatgen-io-validation?

Also quote Anthony Sottile:

imo a namespace package is just always a bad idea -- you're better to use a plugin system -- here's an example of how to set one up: https://youtu.be/fY3Y_xPKWNA

>>> import pymatgen
>>> pymatgen
<module 'pymatgen' (namespace) from ['/home/yang/developer/pymatgen/src/pymatgen']>

>>> import pymatgen.io
>>> pymatgen.io
<module 'pymatgen.io' (namespace) from ['/home/yang/developer/pymatgen/src/pymatgen/io']>
>>> import pymatgen.ext
>>> pymatgen.ext
<module 'pymatgen.ext' (namespace) from ['/home/yang/developer/pymatgen/src/pymatgen/ext']>
>>> import pymatgen.analysis
>>> pymatgen.analysis
<module 'pymatgen.analysis' (namespace) from ['/home/yang/developer/pymatgen/src/pymatgen/analysis']>

https://github.com/materialsproject/pymatgen/tree/master/src/pymatgen/ext
https://github.com/materialsproject/pymatgen/tree/master/src/pymatgen/io
https://github.com/materialsproject/pymatgen/tree/master/src/pymatgen/analysis

[DanielYang59]

I believe dao.py is already included in sdist and bdist (not just this branch, but from PyPI)

[DanielYang59]

Still I would prefer closing this and let maintainers take over, esp. around the migration from namespace system to entry points.