add test for 2D CLI

[martinschorb]

this addresses #127

Test fails to demonstrate the issue. WIP

[martinschorb]

Is it OK if we just choose ome.zarr as default? I guess by now, that would be my call.

Or will it break some older scripts that assume bdv.n5 to be in there as default for all eternity?

[martinschorb]

Maybe this would then justify an increase in version number (minor only). What do you think @constantinpape ?

[constantinpape]

I agree @martinschorb. We should switch the default and then bump the minor version.

[martinschorb]

looks like there are a bunch of tests relying on the default.
Will look into it and try to fix them.

[constantinpape]

The changes look good now. But the default data format should also be changed for other functions, e.g. https://github.com/mobie/mobie-utils-python/blob/master/mobie/segmentation.py#L20.

But we can also do this in a separate PR and merge this one now.

[martinschorb]

I found that this test is full of explicit bdv.n5 calls. https://github.com/mobie/mobie-utils-python/blob/master/test/metadata/test_source_metadata.py

But I don't fully understand the way these tests work and if the format plays a role at all for them.

[constantinpape]

I found that this test is full of explicit bdv.n5 calls.

The reason is that this test checks for the json validation of the source field and has some specific settings for bdv.n5, see
https://github.com/mobie/mobie-utils-python/blob/master/test/metadata/test_source_metadata.py#L19-L22

I think we can leave this test as it is.

[constantinpape]

I have updated the remaining places where the default file format was still bdv.n5. I will look into the failing tests later.

[constantinpape]

Just fyi @martinschorb, there is some additional logic needed to support ome.zarr for all the scripts. This is in principle not a problem, but I am not 100% sure when I have time to implement it. If you think we should get this out as soon as possible we can also skip this and do the update already. (This is only for some rather obscure functionality, so I think it would not affect any users.)

[martinschorb]

I am totally fine with some functionality being restricted to (legacy) file formats.
For the sorresponding tests, I would just explicitely specify the format.