Add support for SampleData[Sequences]

[wasade]

Fixes #49.

I wasn't sure how to add a test to this, and I didn't see a comparable test in q2-vsearch for the different input type. But happy to implement a test if recommended.

[thermokarst]

Sorry @wasade for letting this sit for so long - I was traveling last week, but am back in the office now.

[thermokarst]

This looks great to me! I am "requesting changes" here though, because this change wont work until we define a new transformer in q2-types that will let us do the reverse transformation defined here (QIIME1DemuxDirFmt -> SingleLanePerSampleSingleEndFastqDirFmt). @wasade, would you be able to cut a PR for that? I opened an issue here: qiime2/q2-types#176

[thermokarst]

For posterity, here is the error when running right now (without that transformer in place):

Plugin error from deblur:

  No transformation from <class 'qiime2.plugin.model.directory_format.QIIME1DemuxDirFmt'> to <class 'q2_types.per_sample_sequences._format.SingleLanePerSampleSingleEndFastqDirFmt'>

[ebolyen]

... and transforming to that format isn't possible since there are no quality scores 😞

So this is another situation where we really need typing.Union as it would let you do the obvious thing for the view annotation: typing.Union[QIIME1DemuxFormat, SingleLanePerSampleSingleEndFastqDirFmt] and then do an isinstance check inside the method (like a normal ad-hoc polymorphic python function).

Until then, we'd need to create a custom union-object (like what is used in demux summarize), but then you need to define transformers from everything to that, which really defeats the point of having transformers at all.

I think this situation has come up at least 2 or 3 times before this, so maybe it's time to just fix it for real and implement typing.Union?

[thermokarst]

We discussed out-of-band and will hold off on merging this PR until we have some kind of Union option in place.

[ebolyen]

It seems like 2020.1 might be a good time for Python 3.7 (letting us use type.Union in a multiprocessing env).

I will optimistically add this to our list...

[thermokarst]

Pushing this off to 2020.5, at the earliest.

[lizgehret]

Hey @ebolyen now that we do have typing.Union available, is this something we should get merged?

[Oddant1]

Pushing this off to 2020.5, at the earliest.

At the earliest. . . Following up on @lizgehret, @ebolyen that issue qiime2/q2-types#176 Matt mentioned is still open, is this actually fine now, and should that issue actually be closed? The issue is related to creating a transformer between the two formats, but if I'm understanding the conversation correctly with typing.Union we shouldn't even need that transformer, and that transformer isn't possible anyway.