Bug encountered while running "sheet_from_cell_centers" function on points generated using from "sheet_from_cell_centers"

[sniffo]

Hi there, went back to a project I started a while back with cylindrical tissues. The code used to work fine but am now encountering an error while trying to generate a cylindrical tissue. I have included the traceback as well, seems to be an issue with the __setitem__(self, key, value) function in pandas.

The code I am trying to run:

points = hexa_cylinder(30, 10, 5, noise = 0, capped = True)
 sheet = tyssue.generation.shapes.sheet_from_cell_centers(points)

Traceback:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
/tmp/ipykernel_266938/1420852574.py in <module>
----> 1 sheet = tyssue.generation.shapes.sheet_from_cell_centers(points)

~/anaconda3/envs/hearttyssue/lib/python3.9/site-packages/tyssue/generation/shapes.py in sheet_from_cell_centers(points, noise, interp_s)
    376     eptm_ = Epithelium("v", dsets)
    377 
--> 378     eptm_ = single_cell(eptm_, 0)
    379 
    380     eptm = get_outer_sheet(eptm_)

~/anaconda3/envs/hearttyssue/lib/python3.9/site-packages/tyssue/utils/utils.py in single_cell(eptm, cell, copy)
    204     """
    205     edges = eptm.edge_df[eptm.edge_df["cell"] == cell].index
--> 206     return get_sub_eptm(eptm, edges, copy)
    207 
    208 

~/anaconda3/envs/hearttyssue/lib/python3.9/site-packages/tyssue/utils/utils.py in get_sub_eptm(eptm, edges, copy)
    179         sub_eptm.datasets["edge"]["cell_o"] = edge_df["cell"]
    180 
--> 181     sub_eptm.datasets["vert"]["srce_o"] = set(edge_df["srce"])
    182     sub_eptm.datasets["face"]["face_o"] = set(edge_df["face"])
    183     if "cell" in eptm.datasets:

~/anaconda3/envs/hearttyssue/lib/python3.9/site-packages/pandas/core/frame.py in __setitem__(self, key, value)
   3610         else:
   3611             # set column
-> 3612             self._set_item(key, value)
   3613 
   3614     def _setitem_slice(self, key: slice, value):

~/anaconda3/envs/hearttyssue/lib/python3.9/site-packages/pandas/core/frame.py in _set_item(self, key, value)
   3782         ensure homogeneity.
   3783         """
-> 3784         value = self._sanitize_column(value)
   3785 
   3786         if (

~/anaconda3/envs/hearttyssue/lib/python3.9/site-packages/pandas/core/frame.py in _sanitize_column(self, value)
   4508         if is_list_like(value):
   4509             com.require_length_match(value, self.index)
-> 4510         return sanitize_array(value, self.index, copy=True, allow_2d=True)
   4511 
   4512     @property

~/anaconda3/envs/hearttyssue/lib/python3.9/site-packages/pandas/core/construction.py in sanitize_array(data, index, dtype, copy, raise_cast_failure, allow_2d)
    557         if isinstance(data, (set, frozenset)):
    558             # Raise only for unordered sets, e.g., not for dict_keys
--> 559             raise TypeError(f"'{type(data).__name__}' type is unordered")
    560 
    561         # materialize e.g. generators, convert e.g. tuples, abc.ValueView

TypeError: 'set' type is unordered

Python Version: 3.9.7
Tyssue Version: 0.8.1
Pandas Version: 1.3.4

I am currently trying to work out a fix, but thought it would be useful for all to know.

[glyg]

Hi @sniffo thanks for the bug report - I actually fixed the issue in the zarr branch (see PR #248), I'll merge the branch today, although the work is not complete, and you can install from source then

You can see the fix here

Things are a bit hectic right now, but hopefully I'll have more time for tyssue in january

Best

Guillaume

[sniffo]

Hi Guillaume,

The fix seems to work! I simply edited the source file within my conda env. Thanks for the prompt response!