chore: move pipelines out of api package

[ltalirz]

pipelines used by the API package still belong in amorphouspy, since they can be used by users of the python package as well.

[codecov]

Codecov Report

❌ Patch coverage is 66.04478% with 91 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
...api/src/amorphouspy_api/visualization/viscosity.py	8.33%	33 Missing ⚠️
amorphouspy/src/amorphouspy/pipelines/viscosity.py	46.15%	28 Missing ⚠️
amorphouspy_api/src/amorphouspy_api/pipeline.py	72.44%	27 Missing ⚠️
...ouspy_api/src/amorphouspy_api/visualization/cte.py	40.00%	3 Missing ⚠️

📢 Thoughts on this report? Let us know!

[ltalirz]

@Atilaac this would be the rough outline

At this point, the "pipelines" (except for the top-level pipeline) are still python functions themselves; this will change once I reactivate #174 and the viscosity pipeline will actually become an executorlib workflow.

Some of the current "pipelines" may also move into the code outside the pipelines folder (e.g. the code for extracting the equilibration frames

[ltalirz]

now that the pipeline code moves in to the amorphouspy package, I will need to add tests for it before I can merge the PR ;-)