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cucapra / pollen

generating hardware accelerators for pangenomic graph queries
MIT License
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Try setting up CI #142

Closed sampsyo closed 7 months ago

sampsyo commented 9 months ago

A totally not ready, experimental approach to #53. Nothing to see here yet.

sampsyo commented 8 months ago

One note as this starts to take shape: so far, this only runs the tests for slow-odgi. It should eventually also run the tests for the data generator and the new tests for the parser added in #136.

sampsyo commented 7 months ago

I think this is ready to go (i.e., we can merge if @anshumanmohan & @susan-garry approve)! The point is to make sure our tests that are currently pass keep passing, and we don't accidentally break some tests without noticing (which has happened a few times!). It will also hopefully give us some confidence to do some refactoring, and even changing the test setup, because we'll get feedback if we do anything wrong.

This CI setup tests only two things: slow_odgi (using odgi itself as the differential testing basis) and the Pollen DSL parser (which has RON snapshots of parsed ASTs checked in). It does not cover pollen_data_gen (whose testing setup relies on a baseline that uses odgi's Python bindings, our use of which is going away soon anyway, so it didn't seem worth it).

The only tricky part of this CI setup was running odgi, without compiling it from source (which would be real slow). What I ended up doing was using a preexisting Docker container for odgi. So whenever our tests would invoke a real odgi binary, they instead do docker run odgi.

sampsyo commented 7 months ago

Excellent; merging this now!