Refactor source tree layout

Relates to #75 (closed).

• Migrate package to src directory
• Migrate tests to tests directory and update pytest configuration
• Fix various pipelines and CI containers

(pyproject.toml migration was moved to !364 (merged))

requested review from @holzer

assigned to @da15siwa

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• 1c79772f - fix format and dependencies. remove distutils from Cython extension module.

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• 425b9d3f - reintegrated quicktests

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marked the checklist item Clean up package data files & manifest as completed

marked the checklist item Clean up package data files & manifest as incomplete

marked the checklist item Remove quicktest action from setup.py and realize quicktests some other way as completed

Actually, I think we should change the source tree right away. Is there a good reason to wait for this?

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• f7411ab1 - add package_data, clean up MANIFEST.in

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marked the checklist item Clean up package data files & manifest as completed

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• b53718a9 - clean up Cython extensions

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@holzer I've run into some problems concerning our single Cython extension module (pystencils.boundaries.createindexlistcython). Building it conditionally on the user's machine through the use_cython package variant does not work, and I'm not sure it ever worked. For Cython to be available, it needs to be specified as a build dependency, instead of a project dependency. The discovery code in the old setup.py seems not to work since unless Cython is specified as a build dependency, it cannot be imported by the setup script.

Right now I don't see any way to build the extension module conditionally. So there's two options: Either always build it - but then we will either have to provide platform-specific wheels, or the users will always face significantly increased install times, even if in 99% of cases they don't even use that extension module. Or remove it, and accept slower runtimes of this particular piece of code.

Personally, I'd opt for removing it.

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• b53718a9...4e579214 - 2 commits from branch pycodegen:master
• 5578214a - Merge branch 'master' into refactor_packaging

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• f37f76aa - removed Cython for the moment
• a4e4e6a3 - remove pre-built Cython extensions

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• 1d855213 - introduce src layout

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• 11bb21c1 - renamed tests directory

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changed title from Draft: Refactor packaging to Draft: Refactor source tree layout