Vitessce config generator

[flying-sheep]

Fixes https://github.com/theislab/ehrdata-datasets/issues/10

Rendered docs

[codecov]

Codecov Report

Attention: Patch coverage is 82.35294% with 6 lines in your changes missing coverage. Please review.

Project coverage is 34.48%. Comparing base (4160406) to head (59da27f).
Report is 17 commits behind head on main.

Files with missing lines	Patch %	Lines
src/ehrdata/pl/vitessce.py	80.00%	6 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##             main      #40       +/-   ##
===========================================
+ Coverage   15.36%   34.48%   +19.11%     
===========================================
  Files          12       18        +6     
  Lines         501      635      +134     
===========================================
+ Hits           77      219      +142     
+ Misses        424      416        -8     

Files with missing lines	Coverage Δ
src/ehrdata/pl/__init__.py	100.00% <100.00%> (ø)
src/ehrdata/pl/vitessce.py	80.00% <80.00%> (ø)

[flying-sheep]

OK, finally done.

Tests are slow, because the newest published generate-tiff-offsets depends on a pinned version of tifffile. Newer versions of scikit-image want newer tifffile versions, so the dependency resolver needs to backtrack until it finds scikit-image 0.21 or so, which is slow.

It’s fixed on main (hms-dbmi/generate-tiff-offsets#6), @ilan-gold is on it (pypi/support#4878) and will release a new generate-tiff-offsets version soonish

[eroell]

Awesome, this works on the latest notebooks where we demonstrate this as it should.
Thanks!