Issues when reproducing the Main Guide

[wgmao]

Thank you for your help resolving the earlier issue #161. I have updated bento toolkit to the latest version 2.1.4.post2 and I tried to run through the main guide tutorial (https://bento-tools.readthedocs.io/en/latest/tutorial_gallery/Main_Guide.html) as a start. It went pretty well for the first half of the tutorial but failed at the step calling the flux function.

res = 0.1
bt.tl.flux(sdata, method="radius", res=res, recompute=True)

The function stuck unless you interrupted, and it didn't quite finish. The error message can be found below.

Traceback (most recent call last): File "<string>", line 1, in <module> 
File "~/miniconda3/envs/Bento/lib/python3.10/multiprocessing/spawn.py", line 116, in spawn_main exitcode = _main(fd, parent_sentinel) 
File "~/miniconda3/envs/Bento/lib/python3.10/multiprocessing/spawn.py", line 125, in _main prepare(preparation_data) 
File "~/miniconda3/envs/Bento/lib/python3.10/multiprocessing/spawn.py", line 236, in prepare _fixup_main_from_path(data['init_main_from_path']) 
File "~/miniconda3/envs/Bento/lib/python3.10/multiprocessing/spawn.py", line 287, in _fixup_main_from_path main_content = runpy.run_path(main_path, 
File "~/miniconda3/envs/Bento/lib/python3.10/runpy.py", line 289, in run_path return _run_module_code(code, init_globals, run_name, 
File "~/miniconda3/envs/Bento/lib/python3.10/runpy.py", line 96, in _run_module_code _run_code(code, mod_globals, init_globals, 
File "~/miniconda3/envs/Bento/lib/python3.10/runpy.py", line 86, in _run_code exec(code, run_globals) File "~/subcellular/bento_toy.py", line 62, in <module> bt.pl.flux(sdata_crop, res=res, ax=ax) 
File "~/miniconda3/envs/Bento/lib/python3.10/site-packages/bento/plotting/_utils.py", line 34, in wrapper plot_func(*args, **kwds) 
File "~/miniconda3/envs/Bento/lib/python3.10/site-packages/bento/plotting/_utils.py", line 63, in wrapper plot_func(*args, **kwds) File "~/miniconda3/envs/Bento/lib/python3.10/site-packages/bento/plotting/_plotting.py", line 437, in flux _raster( 
File "~/miniconda3/envs/Bento/lib/python3.10/site-packages/bento/plotting/_layers.py", line 104, in _raster points = get_points(sdata, points_key=points_key, astype="pandas", sync=True) 
File "~/miniconda3/envs/Bento/lib/python3.10/site-packages/bento/_utils.py", line 100, in get_points raise ValueError(f"Points key {points_key} not found in sdata.points") 
ValueError: Points key cell_boundaries_raster not found in sdata.points

I debugged a little bit and sdata.points.keys() only included transcripts without cell_boundaries_raster inside the function at certain points, though the input sdata to the bt.tl.flux function indeed includes both transcripts and cell_boundaries_raster.

[ckmah]

Thank you for reporting the bug @wgmao, that's not good! I will take a look.