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sgkit-dev / sgkit

Scalable genetics toolkit
https://sgkit-dev.github.io/sgkit
Apache License 2.0
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Change in Xarray repr is causing doctest failures #1204

Closed tomwhite closed 4 months ago

tomwhite commented 4 months ago

Tests are failing with 

__________________ [doctest] sgkit.window.window_by_position ___________________
163     >>> ds["variant_position"] = (["variants"], np.array([1, 4, 6, 8, 12, 1, 21, 25, 40, 55]))
164     >>> ds.variant_contig.values
165     array([0, 0, 0, 0, 0, 1, 1, 1, 1, 1])
166     >>> ds.variant_position.values
167     array([ 1,  4,  6,  8, 12,  1, 21, 25, 40, 55])
168 
169     >>> # Contiguous equally-spaced windows, each 10 base pairs in size
170     >>> # and using offset to start windows at 1
171     >>> ds_w1 = sg.window_by_position(ds, size=10, offset=1, merge=False)
172     >>> ds_w1
Differences (unified diff with -expected +actual):
    @@ -1,7 +1,7 @@
    -<xarray.Dataset>
    +<xarray.Dataset> Size: 192B
     Dimensions:        (windows: 8)
     Dimensions without coordinates: windows
     Data variables:
    -    window_contig  (windows) int64 0 0 1 1 1 1 1 1
    -    window_start   (windows) int64 0 4 5 6 6 8 9 9
    -    window_stop    (windows) int64 4 5 6 6 8 9 9 10
    +    window_contig  (windows) int64 64B 0 0 1 1 1 1 1 1
    +    window_start   (windows) int64 64B 0 4 5 6 6 8 9 9
    +    window_stop    (windows) int64 64B 4 5 6 6 8 9 9 10

This is due to https://github.com/pydata/xarray/issues/8690.