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Fix channel str support #221

Merged
merged 11 commits into from
May 17, 2024
Merged

Fix channel str support #221

merged 11 commits into from
May 17, 2024

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berombau
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@berombau berombau commented Mar 5, 2024

These test cases did not work:

    def test_plot_can_render_a_single_channel_str_from_image(self, sdata_blobs_str: SpatialData):
        sdata_blobs_str.pl.render_images(elements="blobs_image", channel="c1").pl.show()

    def test_plot_can_render_a_single_channel_str_from_multiscale_image(self, sdata_blobs_str: SpatialData):
        sdata_blobs_str.pl.render_images(elements="blobs_multiscale_image", channel="c1").pl.show()

    def test_plot_can_render_two_channels_str_from_image(self, sdata_blobs_str: SpatialData):
        sdata_blobs_str.pl.render_images(elements="blobs_image", channel=["c1", "c2"]).pl.show()

    def test_plot_can_render_two_channels_str_from_multiscale_image(self, sdata_blobs_str: SpatialData):
        sdata_blobs_str.pl.render_images(elements="blobs_multiscale_image", channel=["c1", "c2"]).pl.show()

I added the tests and the two fixes needed to make them pass. Reported by @thienthu.
The problem with buggy channel string support is usually creating a new Image2DModel with the data but not also the string labels via a c_coords parameter (see src/spatialdata_plot/pl/utils.py:1247).

@codecov-commenter
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 77.70%. Comparing base (ac062d8) to head (b5f8902).

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #221   +/-   ##
=======================================
  Coverage   77.70%   77.70%           
=======================================
  Files          11       11           
  Lines        1722     1722           
=======================================
  Hits         1338     1338           
  Misses        384      384           
Files Coverage Δ
src/spatialdata_plot/pl/render.py 94.61% <100.00%> (ø)
src/spatialdata_plot/pl/utils.py 66.70% <100.00%> (ø)

@timtreis
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Should now all be fixed, it's failing because the codecov retry limit is reached for now. Will try again in a bit and then merge. Thanks for the work @berombau!

@timtreis timtreis merged commit b51099e into scverse:main May 17, 2024
3 of 5 checks passed
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3 participants