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kephale / napari-tyssue

This is a napari plugin that supports the 3D tissue simulator, tyssue
BSD 3-Clause "New" or "Revised" License
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TypeError: 'set' type is unordered #3

Closed haesleinhuepf closed 1 year ago

haesleinhuepf commented 2 years ago

Hi @kephale ,

I just installed napari-tyssue for the first time and attempted to play with it. After starting up napari, I clicked on Plugins > napari-tyssue > napari-tyssue Invagiation and hit the Start Simulation button. The Napari window remains empty and this error pops up:

collision solver could not be imported You may need to install CGAL and re-install tyssue
C++ extension are not available for this version
C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\tyssue\utils\utils.py:161: FutureWarning: Passing a set as an indexer is deprecated and will raise in a future version. Use a list instead.!
C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\tyssue\utils\utils.py:162: FutureWarning: Passing a set as an indexer is deprecated and will raise in a future version. Use a list instead.!
C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\tyssue\utils\utils.py:164: FutureWarning: Passing a set as an indexer is deprecated and will raise in a future version. Use a list instead.!
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
File ~\mambaforge\envs\bio39\lib\threading.py:980, in Thread._bootstrap_inner(self=<Thread(Thread-2, started 13292)>)
    977     _sys.setprofile(_profile_hook)
    979 try:
--> 980     self.run()
        self = <Thread(Thread-2, started 13292)>
    981 except:
    982     self._invoke_excepthook(self)

File ~\mambaforge\envs\bio39\lib\threading.py:917, in Thread.run(self=<Thread(Thread-2, started 13292)>)
    915 try:
    916     if self._target:
--> 917         self._target(*self._args, **self._kwargs)
        self = <Thread(Thread-2, started 13292)>
    918 finally:
    919     # Avoid a refcycle if the thread is running a function with
    920     # an argument that has a member that points to the thread.
    921     del self._target, self._args, self._kwargs

File ~\mambaforge\envs\bio39\lib\site-packages\napari_tyssue\invagination.py:148, in InvaginationWidget.start_simulation(self=<napari_tyssue.invagination.InvaginationWidget object>)
    146 def start_simulation(self):
--> 148     sheet = ellipsoid_sheet(*self.specs["settings"]["abc"], 13)
        self.specs = {'vert': {'height': 0, 'basal_shift': 0, 'delta_rho': 30, 'vitelline_K': 280.0, 'radial_tension': 0}, 'face': {'contractility': 1.12, 'prefered_area': 22, 'area_elasticity': 1, 'surface_tension': 10.0}, 'edge': {'line_tension': 0.0}, 'settings': {'abc': [12, 12, 21.0], 'geometry': 'cylindrical', 'height_axis': 'z', 'vitelline_space': 0.2, 'threshold_length': 0.001}}
        self = <napari_tyssue.invagination.InvaginationWidget object at 0x000002A1F8269940>
        self.specs["settings"]["abc"] = [12, 12, 21.0]
        self.specs["settings"] = {'abc': [12, 12, 21.0], 'geometry': 'cylindrical', 'height_axis': 'z', 'vitelline_space': 0.2, 'threshold_length': 0.001}
    149     print(f"The sheet has {sheet.Nf} vertices")
    150     sheet.update_specs(self.specs)

File ~\mambaforge\envs\bio39\lib\site-packages\tyssue\generation\shapes.py:280, in ellipsoid_sheet(a=12, b=12, c=21.0, n_zs=13, **kwargs={})
    257 """Creates an ellipsoidal apical mesh.
    258
    259 Parameters
   (...)
    276
    277 """
    278 centers = get_ellipsoid_centers(a, b, c, n_zs, **kwargs)
--> 280 eptm = sheet_from_cell_centers(centers)
        centers = <class 'numpy.ndarray'> (184, 3) float64
    281 eptm.settings["abc"] = [a, b, c]
    282 EllipsoidGeometry.update_all(eptm)

File ~\mambaforge\envs\bio39\lib\site-packages\tyssue\generation\shapes.py:378, in sheet_from_cell_centers(points=<class 'numpy.ndarray'> (184, 3) float64, noise=0, interp_s=0.0001)
    375 dsets = from_3d_voronoi(vor3D)
    376 eptm_ = Epithelium("v", dsets)
--> 378 eptm_ = single_cell(eptm_, 0)
        eptm_ = <tyssue.core.objects.Epithelium object at 0x000002A1FF58EB20>
    380 eptm = get_outer_sheet(eptm_)
    381 eptm.reset_index()

File ~\mambaforge\envs\bio39\lib\site-packages\tyssue\utils\utils.py:203, in single_cell(eptm=<tyssue.core.objects.Epithelium object>, cell=0, copy=False)
    189 """
    190 Define epithelium instance for all element to a define cell.
    191
   (...)
    200 sub_etpm: class:'Epithelium' instance corresponding to the cell
    201 """
    202 edges = eptm.edge_df[eptm.edge_df["cell"] == cell].index
--> 203 return get_sub_eptm(eptm, edges, copy)
        edges = Int64Index([   0, 1048, 1046, 1952, 1044, 1042, 1954, 1040, 1956, 1038,
            ...
             594, 2082, 2056,  596, 2070,  672,  670,  620, 2080,  622],
           dtype='int64', name='edge', length=1088)
        eptm = <tyssue.core.objects.Epithelium object at 0x000002A1FF58EB20>
        copy = False

File ~\mambaforge\envs\bio39\lib\site-packages\tyssue\utils\utils.py:178, in get_sub_eptm(eptm=<tyssue.core.objects.Epithelium object>, edges=Int64Index([   0, 1048, 1046, 1952, 1044, 1042, ...         dtype='int64', name='edge', length=1088), copy=False)
    175 if "cell" in eptm.datasets:
    176     sub_eptm.datasets["edge"]["cell_o"] = edge_df["cell"]
--> 178 sub_eptm.datasets["vert"]["srce_o"] = set(edge_df["srce"])
        edge_df =       srce  trgt  face   dx   dy   dz   nx   ny   nz  ...  sub_vol   ux   uy   uz  edge_o  srce_o  trgt_o  face_o  cell_o
edge                                                  ...                                                               
0      265   266     0  0.0  0.0  0.0  0.0  0.0  1.0  ...      0.0  0.0  0.0  0.0       0     265     266       0       0
1048   312   183    86  0.0  0.0  0.0  0.0  0.0  1.0  ...      0.0  0.0  0.0  0.0    1048     312     183      86       0
1046   313   312    86  0.0  0.0  0.0  0.0  0.0  1.0  ...      0.0  0.0  0.0  0.0    1046     313     312      86       0
1952   163   290   162  0.0  0.0  0.0  0.0  0.0  1.0  ...      0.0  0.0  0.0  0.0    1952     163     290     162       0
1044   313   308    85  0.0  0.0  0.0  0.0  0.0  1.0  ...      0.0  0.0  0.0  0.0    1044     313     308      85       0
...    ...   ...   ...  ...  ...  ...  ...  ...  ...  ...      ...  ...  ...  ...     ...     ...     ...     ...     ...
672    260   264    55  0.0  0.0  0.0  0.0  0.0  1.0  ...      0.0  0.0  0.0  0.0     672     260     264      55       0
670    255   257    54  0.0  0.0  0.0  0.0  0.0  1.0  ...      0.0  0.0  0.0  0.0     670     255     257      54       0
620    345   273    50  0.0  0.0  0.0  0.0  0.0  1.0  ...      0.0  0.0  0.0  0.0     620     345     273      50       0
2080   116   263   174  0.0  0.0  0.0  0.0  0.0  1.0  ...      0.0  0.0  0.0  0.0    2080     116     263     174       0
622    273   274    50  0.0  0.0  0.0  0.0  0.0  1.0  ...      0.0  0.0  0.0  0.0     622     273     274      50       0

[1088 rows x 33 columns]
        sub_eptm = <tyssue.core.objects.Epithelium object at 0x000002A1FF5F7670>
        sub_eptm.datasets["vert"] =              x         y         z  is_active  rho  height  basal_shift
vert
0    -0.282037 -0.058243  0.014139          1  0.0     0.0          4.0
1     0.282037 -0.058243  0.014139          1  0.0     0.0          4.0
2    -0.147297 -0.159968 -0.186780          1  0.0     0.0          4.0
3     0.147297 -0.159968 -0.186780          1  0.0     0.0          4.0
4     0.060467 -0.214078  0.184146          1  0.0     0.0          4.0
...        ...       ...       ...        ...  ...     ...          ...
357   0.145120 -0.138533  0.206654          1  0.0     0.0          4.0
358   0.153748 -0.101686  0.219516          1  0.0     0.0          4.0
359   0.127815 -0.063622  0.248699          1  0.0     0.0          4.0
360   0.058587 -0.145571  0.242919          1  0.0     0.0          4.0
361   0.054321 -0.101626  0.264899          1  0.0     0.0          4.0

[362 rows x 7 columns]
        sub_eptm.datasets = {'edge':       srce  trgt  face   dx   dy   dz   nx   ny   nz  ...  sub_vol   ux   uy   uz  edge_o  srce_o  trgt_o  face_o  cell_o
edge                                                  ...                                                               
0      265   266     0  0.0  0.0  0.0  0.0  0.0  1.0  ...      0.0  0.0  0.0  0.0       0     265     266       0       0
1048   312   183    86  0.0  0.0  0.0  0.0  0.0  1.0  ...      0.0  0.0  0.0  0.0    1048     312     183      86       0
1046   313   312    86  0.0  0.0  0.0  0.0  0.0  1.0  ...      0.0  0.0  0.0  0.0    1046     313     312      86       0
1952   163   290   162  0.0  0.0  0.0  0.0  0.0  1.0  ...      0.0  0.0  0.0  0.0    1952     163     290     162       0
1044   313   308    85  0.0  0.0  0.0  0.0  0.0  1.0  ...      0.0  0.0  0.0  0.0    1044     313     308      85       0
...    ...   ...   ...  ...  ...  ...  ...  ...  ...  ...      ...  ...  ...  ...     ...     ...     ...     ...     ...
672    260   264    55  0.0  0.0  0.0  0.0  0.0  1.0  ...      0.0  0.0  0.0  0.0     672     260     264      55       0
670    255   257    54  0.0  0.0  0.0  0.0  0.0  1.0  ...      0.0  0.0  0.0  0.0     670     255     257      54       0
620    345   273    50  0.0  0.0  0.0  0.0  0.0  1.0  ...      0.0  0.0  0.0  0.0     620     345     273      50       0
2080   116   263   174  0.0  0.0  0.0  0.0  0.0  1.0  ...      0.0  0.0  0.0  0.0    2080     116     263     174       0
622    273   274    50  0.0  0.0  0.0  0.0  0.0  1.0  ...      0.0  0.0  0.0  0.0     622     273     274      50       0

[1088 rows x 33 columns], 'vert':              x         y         z  is_active  rho  height  basal_shift
vert
0    -0.282037 -0.058243  0.014139          1  0.0     0.0          4.0
1     0.282037 -0.058243  0.014139          1  0.0     0.0          4.0
2    -0.147297 -0.159968 -0.186780          1  0.0     0.0          4.0
3     0.147297 -0.159968 -0.186780          1  0.0     0.0          4.0
4     0.060467 -0.214078  0.184146          1  0.0     0.0          4.0
...        ...       ...       ...        ...  ...     ...          ...
357   0.145120 -0.138533  0.206654          1  0.0     0.0          4.0
358   0.153748 -0.101686  0.219516          1  0.0     0.0          4.0
359   0.127815 -0.063622  0.248699          1  0.0     0.0          4.0
360   0.058587 -0.145571  0.242919          1  0.0     0.0          4.0
361   0.054321 -0.101626  0.264899          1  0.0     0.0          4.0

[362 rows x 7 columns], 'face':         x    y    z  num_sides  area  perimeter  is_alive  id
face
0     0.0  0.0  0.0          6   1.0        1.0         1   0
1     0.0  0.0  0.0          6   1.0        1.0         1   0
2     0.0  0.0  0.0          6   1.0        1.0         1   0
3     0.0  0.0  0.0          6   1.0        1.0         1   0
4     0.0  0.0  0.0          6   1.0        1.0         1   0
...   ...  ...  ...        ...   ...        ...       ...  ..
179   0.0  0.0  0.0          6   1.0        1.0         1   0
180   0.0  0.0  0.0          6   1.0        1.0         1   0
181   0.0  0.0  0.0          6   1.0        1.0         1   0
182   0.0  0.0  0.0          6   1.0        1.0         1   0
183   0.0  0.0  0.0          6   1.0        1.0         1   0

[184 rows x 8 columns], 'cell':         x    y    z  area  vol  num_faces  is_alive  id
cell
0     0.0  0.0  0.0   0.0  0.0          6         1   0}
    179 sub_eptm.datasets["face"]["face_o"] = set(edge_df["face"])
    180 if "cell" in eptm.datasets:

File ~\mambaforge\envs\bio39\lib\site-packages\pandas\core\frame.py:3977, in DataFrame.__setitem__(self=             x         y         z  is_active  r... 0.0     0.0          4.0

[362 rows x 7 columns], key='srce_o', value={0, 1, 2, 3, 4, 5, ...})
   3974     self._setitem_array([key], value)
   3975 else:
   3976     # set column
-> 3977     self._set_item(key, value)
        key = 'srce_o'
        self =              x         y         z  is_active  rho  height  basal_shift
vert
0    -0.282037 -0.058243  0.014139          1  0.0     0.0          4.0
1     0.282037 -0.058243  0.014139          1  0.0     0.0          4.0
2    -0.147297 -0.159968 -0.186780          1  0.0     0.0          4.0
3     0.147297 -0.159968 -0.186780          1  0.0     0.0          4.0
4     0.060467 -0.214078  0.184146          1  0.0     0.0          4.0
...        ...       ...       ...        ...  ...     ...          ...
357   0.145120 -0.138533  0.206654          1  0.0     0.0          4.0
358   0.153748 -0.101686  0.219516          1  0.0     0.0          4.0
359   0.127815 -0.063622  0.248699          1  0.0     0.0          4.0
360   0.058587 -0.145571  0.242919          1  0.0     0.0          4.0
361   0.054321 -0.101626  0.264899          1  0.0     0.0          4.0

[362 rows x 7 columns]
        value = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361}

File ~\mambaforge\envs\bio39\lib\site-packages\pandas\core\frame.py:4171, in DataFrame._set_item(self=             x         y         z  is_active  r... 0.0     0.0          4.0

[362 rows x 7 columns], key='srce_o', value={0, 1, 2, 3, 4, 5, ...})
   4161 def _set_item(self, key, value) -> None:
   4162     """
   4163     Add series to DataFrame in specified column.
   4164
   (...)
   4169     ensure homogeneity.
   4170     """
-> 4171     value = self._sanitize_column(value)
        value = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361}
        self =              x         y         z  is_active  rho  height  basal_shift
vert
0    -0.282037 -0.058243  0.014139          1  0.0     0.0          4.0
1     0.282037 -0.058243  0.014139          1  0.0     0.0          4.0
2    -0.147297 -0.159968 -0.186780          1  0.0     0.0          4.0
3     0.147297 -0.159968 -0.186780          1  0.0     0.0          4.0
4     0.060467 -0.214078  0.184146          1  0.0     0.0          4.0
...        ...       ...       ...        ...  ...     ...          ...
357   0.145120 -0.138533  0.206654          1  0.0     0.0          4.0
358   0.153748 -0.101686  0.219516          1  0.0     0.0          4.0
359   0.127815 -0.063622  0.248699          1  0.0     0.0          4.0
360   0.058587 -0.145571  0.242919          1  0.0     0.0          4.0
361   0.054321 -0.101626  0.264899          1  0.0     0.0          4.0

[362 rows x 7 columns]
   4173     if (
   4174         key in self.columns
   4175         and value.ndim == 1
   4176         and not is_extension_array_dtype(value)
   4177     ):
   4178         # broadcast across multiple columns if necessary
   4179         if not self.columns.is_unique or isinstance(self.columns, MultiIndex):

File ~\mambaforge\envs\bio39\lib\site-packages\pandas\core\frame.py:4905, in DataFrame._sanitize_column(self=             x         y         z  is_active  r... 0.0     0.0          4.0

[362 rows x 7 columns], value={0, 1, 2, 3, 4, 5, ...})
   4903 if is_list_like(value):
   4904     com.require_length_match(value, self.index)
-> 4905 return sanitize_array(value, self.index, copy=True, allow_2d=True)
        value = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361}
        self =              x         y         z  is_active  rho  height  basal_shift
vert
0    -0.282037 -0.058243  0.014139          1  0.0     0.0          4.0
1     0.282037 -0.058243  0.014139          1  0.0     0.0          4.0
2    -0.147297 -0.159968 -0.186780          1  0.0     0.0          4.0
3     0.147297 -0.159968 -0.186780          1  0.0     0.0          4.0
4     0.060467 -0.214078  0.184146          1  0.0     0.0          4.0
...        ...       ...       ...        ...  ...     ...          ...
357   0.145120 -0.138533  0.206654          1  0.0     0.0          4.0
358   0.153748 -0.101686  0.219516          1  0.0     0.0          4.0
359   0.127815 -0.063622  0.248699          1  0.0     0.0          4.0
360   0.058587 -0.145571  0.242919          1  0.0     0.0          4.0
361   0.054321 -0.101626  0.264899          1  0.0     0.0          4.0

[362 rows x 7 columns]

File ~\mambaforge\envs\bio39\lib\site-packages\pandas\core\construction.py:611, in sanitize_array(data={0, 1, 2, 3, 4, 5, ...}, index=Int64Index([  0,   1,   2,   3,   4,   5,   6,  ...          dtype='int64', name='vert', length=362), dtype=None, copy=True, raise_cast_failure=True, allow_2d=True)
    608 else:
    609     if isinstance(data, (set, frozenset)):
    610         # Raise only for unordered sets, e.g., not for dict_keys
--> 611         raise TypeError(f"'{type(data).__name__}' type is unordered")
        data = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361}
        type(data) = <class 'set'>
    613     # materialize e.g. generators, convert e.g. tuples, abc.ValueView
    614     if hasattr(data, "__array__"):
    615         # e.g. dask array GH#38645

TypeError: 'set' type is unordered

This is my conda list:

# packages in environment at C:\Users\haase\mambaforge\envs\bio39:
#
# Name                    Version                   Build  Channel
alabaster                 0.7.12                     py_0    conda-forge
anyio                     3.6.2              pyhd8ed1ab_0    conda-forge
aom                       3.5.0                h63175ca_0    conda-forge
apoc-backend              0.10.0             pyhd8ed1ab_0    conda-forge
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py39ha55989b_3    conda-forge
arrow                     1.2.3                    pypi_0    pypi
asciitree                 0.3.3                      py_2    conda-forge
asttokens                 2.1.0              pyhd8ed1ab_0    conda-forge
attrs                     22.1.0             pyh71513ae_1    conda-forge
autopep8                  2.0.0              pyhd8ed1ab_0    conda-forge
babel                     2.11.0             pyhd8ed1ab_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.11.1             pyha770c72_0    conda-forge
binaryornot               0.4.4                    pypi_0    pypi
bleach                    5.0.1              pyhd8ed1ab_0    conda-forge
blosc                     1.21.1               h74325e0_3    conda-forge
bokeh                     2.4.3              pyhd8ed1ab_3    conda-forge
brotli                    1.0.9                hcfcfb64_8    conda-forge
brotli-bin                1.0.9                hcfcfb64_8    conda-forge
brotlipy                  0.7.0           py39ha55989b_1005    conda-forge
bzip2                     1.0.8                h8ffe710_4    conda-forge
c-blosc2                  2.4.3                h183a6f4_0    conda-forge
ca-certificates           2022.9.24            h5b45459_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachey                    0.2.1              pyh9f0ad1d_0    conda-forge
certifi                   2022.9.24          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1           py39h68f70e3_2    conda-forge
cfitsio                   4.1.0                h5a969a9_0    conda-forge
chardet                   5.0.0                    pypi_0    pypi
charls                    2.3.4                h39d44d4_0    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
click                     8.1.3           win_pyhd8ed1ab_2    conda-forge
click-default-group       1.2.2              pyhd8ed1ab_1    conda-forge
cloudpickle               2.2.0              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
commonmark                0.9.1                      py_0    conda-forge
contourpy                 1.0.6            py39h1f6ef14_0    conda-forge
control                   0.9.2              pyhd8ed1ab_0    conda-forge
cookiecutter              2.1.1                    pypi_0    pypi
cryptography              38.0.3           py39h58e9bdb_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cytoolz                   0.12.0           py39ha55989b_1    conda-forge
czifile                   2019.7.2           pyh9f0ad1d_0    conda-forge
dask                      2022.10.2          pyhd8ed1ab_0    conda-forge
dask-core                 2022.10.2          pyhd8ed1ab_0    conda-forge
dataclasses               0.8                pyhc8e2a94_3    conda-forge
dav1d                     1.0.0                h8ffe710_1    conda-forge
debugpy                   1.6.3            py39h99910a6_1    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
deprecated                1.2.13             pyh6c4a22f_0    conda-forge
devbio-napari             0.8.0            win_h08f2357_0    conda-forge
distributed               2022.10.2          pyhd8ed1ab_0    conda-forge
docstring_parser          0.13               pyhd8ed1ab_0    conda-forge
docutils                  0.19             py39hcbf5309_1    conda-forge
eigen                     3.4.0                h2d74725_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
exceptiongroup            1.0.1              pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                h1537add_0    conda-forge
fasteners                 0.17.3             pyhd8ed1ab_0    conda-forge
ffmpeg                    5.1.2           gpl_h6a9407d_103    conda-forge
fftw                      3.3.10          nompi_h38027f0_105    conda-forge
finesse                   3.0a3            py39h1cfdcae_2    conda-forge
flit-core                 3.8.0              pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.1               hbde0cde_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.38.0           py39ha55989b_1    conda-forge
freetype                  2.12.1               h546665d_0    conda-forge
freetype-py               2.3.0              pyhd8ed1ab_0    conda-forge
fsspec                    2022.10.0          pyhd8ed1ab_0    conda-forge
funcsigs                  1.0.2                      py_3    conda-forge
future                    0.18.2             pyhd8ed1ab_6    conda-forge
gettext                   0.21.1               h5728263_0    conda-forge
giflib                    5.2.1                h8d14728_2    conda-forge
git                       2.38.1               h57928b3_1    conda-forge
glib                      2.74.1               h12be248_1    conda-forge
glib-tools                2.74.1               h12be248_1    conda-forge
gst-plugins-base          1.21.1               h001b923_1    conda-forge
gstreamer                 1.21.1               h6b5321d_1    conda-forge
h5py                      3.7.0           nompi_py39hbc6f334_102    conda-forge
hdbscan                   0.8.29           py39hc266a54_1    conda-forge
hdf5                      1.12.2          nompi_h2a0e4a3_100    conda-forge
heapdict                  1.0.1                      py_0    conda-forge
hsluv                     5.0.2              pyh44b312d_0    conda-forge
icu                       70.1                 h0e60522_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
imagecodecs               2022.9.26        py39h414dd1e_3    conda-forge
imagecodecs-lite          2019.12.3        py39hc266a54_6    conda-forge
imageio                   2.22.0             pyhfa7a67d_0    conda-forge
imageio-ffmpeg            0.4.7              pyhd8ed1ab_0    conda-forge
imagesize                 1.4.1              pyhd8ed1ab_0    conda-forge
importlib-metadata        5.0.0              pyha770c72_1    conda-forge
importlib_resources       5.10.0             pyhd8ed1ab_0    conda-forge
iniconfig                 1.1.1              pyh9f0ad1d_0    conda-forge
intel-openmp              2022.1.0          h57928b3_3787    conda-forge
invagination              0.0.2                    pypi_0    pypi
ipycanvas                 0.13.1             pyhd8ed1ab_0    conda-forge
ipyevents                 2.0.1              pyhd8ed1ab_0    conda-forge
ipykernel                 6.17.0             pyh025b116_0    conda-forge
ipython                   8.6.0              pyh08f2357_1    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                8.0.2              pyhd8ed1ab_1    conda-forge
jedi                      0.18.1             pyhd8ed1ab_2    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jinja2-time               0.2.0                    pypi_0    pypi
joblib                    1.2.0              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   h8ffe710_2    conda-forge
json5                     0.9.5              pyh9f0ad1d_0    conda-forge
jsonschema                4.17.0             pyhd8ed1ab_0    conda-forge
jupyter                   1.0.0            py39hcbf5309_7    conda-forge
jupyter_client            7.3.4              pyhd8ed1ab_0    conda-forge
jupyter_console           6.4.4              pyhd8ed1ab_0    conda-forge
jupyter_core              4.11.2           py39hcbf5309_0    conda-forge
jupyter_server            1.23.0             pyhd8ed1ab_0    conda-forge
jupyterlab                3.5.0              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_server         2.16.2             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.3              pyhd8ed1ab_0    conda-forge
jupytext                  1.14.0             pyheef035f_0    conda-forge
jxrlib                    1.1                  h8ffe710_2    conda-forge
khronos-opencl-icd-loader 2022.09.30           h64bf75a_2    conda-forge
kiwisolver                1.4.4            py39h1f6ef14_1    conda-forge
krb5                      1.19.3               h1176d77_0    conda-forge
lcms2                     2.14                 h90d422f_0    conda-forge
lerc                      4.0.0                h63175ca_0    conda-forge
libaec                    1.0.6                h39d44d4_0    conda-forge
libavif                   0.11.1               h8f5c5bc_0    conda-forge
libblas                   3.9.0              16_win64_mkl    conda-forge
libbrotlicommon           1.0.9                hcfcfb64_8    conda-forge
libbrotlidec              1.0.9                hcfcfb64_8    conda-forge
libbrotlienc              1.0.9                hcfcfb64_8    conda-forge
libcblas                  3.9.0              16_win64_mkl    conda-forge
libclang                  15.0.4          default_h77d9078_0    conda-forge
libclang13                15.0.4          default_h77d9078_0    conda-forge
libcurl                   7.86.0               heaf79c2_1    conda-forge
libdeflate                1.14                 hcfcfb64_0    conda-forge
libffi                    3.4.2                h8ffe710_5    conda-forge
libflang                  11.0.1          h0e60522_20210131    conda-forge
libglib                   2.74.1               he8f3873_1    conda-forge
libiconv                  1.17                 h8ffe710_0    conda-forge
libitk                    5.2.1                h6e1890f_6    conda-forge
libitk-devel              5.2.1                h002f227_6    conda-forge
liblapack                 3.9.0              16_win64_mkl    conda-forge
liblapacke                3.9.0              16_win64_mkl    conda-forge
libogg                    1.3.4                h8ffe710_1    conda-forge
libpng                    1.6.38               h19919ed_0    conda-forge
libsodium                 1.0.18               h8d14728_1    conda-forge
libsqlite                 3.39.4               hcfcfb64_0    conda-forge
libssh2                   1.10.0               h680486a_3    conda-forge
libtiff                   4.4.0                h8e97e67_4    conda-forge
libvorbis                 1.3.7                h0e60522_0    conda-forge
libwebp-base              1.2.4                h8ffe710_0    conda-forge
libxcb                    1.13              hcd874cb_1004    conda-forge
libxml2                   2.10.3               hc3477c8_0    conda-forge
libzlib                   1.2.13               hcfcfb64_4    conda-forge
libzopfli                 1.0.3                h0e60522_0    conda-forge
llvm-openmp               11.0.1               h2d74725_0    conda-forge
llvmlite                  0.39.1           py39hd28a505_1    conda-forge
locket                    1.0.0              pyhd8ed1ab_0    conda-forge
loguru                    0.6.0            py39hcbf5309_2    conda-forge
lz4                       4.0.2            py39hf617134_0    conda-forge
lz4-c                     1.9.3                h8ffe710_1    conda-forge
m2w64-gcc-libgfortran     5.3.0                         6    conda-forge
m2w64-gcc-libs            5.3.0                         7    conda-forge
m2w64-gcc-libs-core       5.3.0                         7    conda-forge
m2w64-gmp                 6.1.0                         2    conda-forge
m2w64-libwinpthread-git   5.0.0.4634.697f757               2    conda-forge
magicgui                  0.6.0              pyhd8ed1ab_0    conda-forge
mako                      1.2.3              pyhd8ed1ab_0    conda-forge
markdown-it-py            2.1.0              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.1            py39ha55989b_2    conda-forge
matplotlib-base           3.6.2            py39haf65ace_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mdit-py-plugins           0.3.1              pyhd8ed1ab_0    conda-forge
mdurl                     0.1.0              pyhd8ed1ab_0    conda-forge
mistune                   2.0.4              pyhd8ed1ab_0    conda-forge
mkl                       2022.1.0           h6a75c08_874    conda-forge
more-itertools            9.0.0              pyhd8ed1ab_0    conda-forge
mpmath                    1.2.1              pyhd8ed1ab_0    conda-forge
msgpack-python            1.0.4            py39h1f6ef14_1    conda-forge
msys2-conda-epoch         20160418                      1    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
napari                    0.4.16          pyh275ddea_0_pyqt    conda-forge
napari-3d-ortho-viewer    0.0.1              pyhd8ed1ab_0    conda-forge
napari-accelerated-pixel-and-object-classification 0.10.2             pyhd8ed1ab_0    conda-forge
napari-animation          0.0.3              pyhd8ed1ab_0    conda-forge
napari-assistant          0.4.1                     dev_0    <develop>
napari-assistant-plugin-generator 0.1.0                     dev_0    <develop>
napari-blob-detection     0.0.2              pyhd8ed1ab_0    conda-forge
napari-brightness-contrast 0.1.8              pyhd8ed1ab_0    conda-forge
napari-clusters-plotter   0.5.2              pyhd8ed1ab_0    conda-forge
napari-console            0.0.6              pyhd8ed1ab_0    conda-forge
napari-crop               0.1.6              pyhd8ed1ab_0    conda-forge
napari-curtain            0.1.1              pyhd8ed1ab_0    conda-forge
napari-czifile2           0.2.7              pyhd8ed1ab_0    conda-forge
napari-folder-browser     0.1.3              pyhd8ed1ab_0    conda-forge
napari-layer-details-display 0.1.4              pyhd8ed1ab_0    conda-forge
napari-mouse-controls     0.1.3              pyhd8ed1ab_0    conda-forge
napari-plot-profile       0.2.2              pyhd8ed1ab_0    conda-forge
napari-plugin-engine      0.2.0              pyhd8ed1ab_2    conda-forge
napari-plugin-search      0.1.3              pyhd8ed1ab_0    conda-forge
napari-pyclesperanto-assistant 0.21.0             pyhd8ed1ab_0    conda-forge
napari-pystackreg         0.1.1              pyhd8ed1ab_0    conda-forge
napari-roi                0.1.7              pyhd8ed1ab_0    conda-forge
napari-segment-blobs-and-things-with-membranes 0.3.3              pyhd8ed1ab_0    conda-forge
napari-simpleitk-image-processing 0.4.4              pyhd8ed1ab_0    conda-forge
napari-skimage-regionprops 0.5.6              pyhd8ed1ab_0    conda-forge
napari-svg                0.1.6              pyhd8ed1ab_0    conda-forge
napari-tabu               0.1.5              pyhd8ed1ab_0    conda-forge
napari-time-slicer        0.4.9              pyhd8ed1ab_1    conda-forge
napari-tools-menu         0.1.17             pyhd8ed1ab_0    conda-forge
napari-tyssue             0.0.1                    pypi_0    pypi
napari-workflow-inspector 0.2.2              pyhd8ed1ab_0    conda-forge
napari-workflow-optimizer 0.1.4              pyhd8ed1ab_0    conda-forge
napari-workflows          0.2.6              pyhd8ed1ab_0    conda-forge
nbclassic                 0.4.8              pyhd8ed1ab_0    conda-forge
nbclient                  0.7.0              pyhd8ed1ab_0    conda-forge
nbconvert                 7.2.3              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.2.3              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.2.3              pyhd8ed1ab_0    conda-forge
nbformat                  5.7.0              pyhd8ed1ab_0    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
networkx                  2.8.8              pyhd8ed1ab_0    conda-forge
notebook                  6.5.2              pyha770c72_1    conda-forge
notebook-shim             0.2.2              pyhd8ed1ab_0    conda-forge
npe2                      0.6.1              pyhd8ed1ab_1    conda-forge
numba                     0.56.3           py39h99ae161_0    conda-forge
numcodecs                 0.10.2           py39h415ef7b_0    conda-forge
numexpr                   2.8.4                    pypi_0    pypi
numpy                     1.23.4           py39hbccbffa_1    conda-forge
numpydoc                  1.5.0              pyhd8ed1ab_0    conda-forge
openh264                  2.3.1                h63175ca_1    conda-forge
openjpeg                  2.5.0                hc9384bd_1    conda-forge
openssl                   1.1.1s               hcfcfb64_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandas                    1.5.1            py39h2ba5b7c_1    conda-forge
pandoc                    2.19.2               h57928b3_1    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
partd                     1.3.0              pyhd8ed1ab_0    conda-forge
pcre2                     10.40                h17e33f8_0    conda-forge
pep517                    0.12.0             pyhd8ed1ab_3    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.2.0            py39h595c93f_3    conda-forge
pint                      0.20.1             pyhd8ed1ab_0    conda-forge
pip                       22.3.1             pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
platformdirs              2.5.2              pyhd8ed1ab_1    conda-forge
platymatch                0.0.3              pyhd8ed1ab_0    conda-forge
pluggy                    1.0.0              pyhd8ed1ab_5    conda-forge
ply                       3.11                       py_1    conda-forge
pooch                     1.6.0              pyhd8ed1ab_0    conda-forge
prometheus_client         0.15.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.32             pyha770c72_0    conda-forge
prompt_toolkit            3.0.32               hd8ed1ab_0    conda-forge
psutil                    5.9.4            py39ha55989b_0    conda-forge
psygnal                   0.6.0            py39h1f6ef14_0    conda-forge
pthread-stubs             0.4               hcd874cb_1001    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pyclesperanto-prototype   0.19.4             pyhd8ed1ab_0    conda-forge
pycodestyle               2.9.1              pyhd8ed1ab_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pydantic                  1.10.2           py39ha55989b_1    conda-forge
pygments                  2.13.0             pyhd8ed1ab_0    conda-forge
pynndescent               0.5.8              pyh1a96a4e_0    conda-forge
pyopencl                  2022.2.4         py39he9b43b8_1    conda-forge
pyopengl                  3.1.6              pyhd8ed1ab_1    conda-forge
pyopenssl                 22.1.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyperclip                 1.8.2              pyhd8ed1ab_2    conda-forge
pyqt                      5.15.7           py39hb77abff_2    conda-forge
pyqt5-sip                 12.11.0          py39h99910a6_2    conda-forge
pyqtgraph                 0.13.1             pyhd8ed1ab_1    conda-forge
pyrsistent                0.19.2           py39ha55989b_0    conda-forge
pysocks                   1.7.1              pyh0701188_6    conda-forge
pyspellchecker            0.7.0              pyhd8ed1ab_0    conda-forge
pystackreg                0.2.7            py39h2ba5b7c_1    conda-forge
pytest                    7.2.0              pyhd8ed1ab_2    conda-forge
python                    3.9.13          h9a09f29_0_cpython    conda-forge
python-build              0.9.0              pyhd8ed1ab_0    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.2             pyhd8ed1ab_0    conda-forge
python-slugify            6.1.2                    pypi_0    pypi
python_abi                3.9                      2_cp39    conda-forge
pytomlpp                  1.0.11           py39h1f6ef14_1    conda-forge
pytools                   2022.1.12          pyhd8ed1ab_0    conda-forge
pytz                      2022.6             pyhd8ed1ab_0    conda-forge
pywavelets                1.3.0            py39hc266a54_2    conda-forge
pywin32                   304              py39h99910a6_2    conda-forge
pywinpty                  2.0.9            py39h99910a6_0    conda-forge
pyyaml                    6.0              py39ha55989b_5    conda-forge
pyzmq                     24.0.1           py39hea35a22_1    conda-forge
qt-main                   5.15.6               h9c3277a_1    conda-forge
qtconsole                 5.4.0              pyhd8ed1ab_0    conda-forge
qtconsole-base            5.4.0              pyha770c72_0    conda-forge
qtpy                      2.3.0              pyhd8ed1ab_0    conda-forge
quantities                0.13.0                   pypi_0    pypi
redlionfish               0.8              py39hcbf5309_2    conda-forge
reikna                    0.7.6              pyh6c4a22f_0    conda-forge
requests                  2.28.1             pyhd8ed1ab_1    conda-forge
rich                      12.6.0             pyhd8ed1ab_0    conda-forge
scikit-image              0.19.3           py39h2ba5b7c_2    conda-forge
scikit-learn              1.1.3            py39h6fe01c0_1    conda-forge
scipy                     1.9.3            py39hfbf2dce_1    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                65.5.1             pyhd8ed1ab_0    conda-forge
shellingham               1.5.0              pyhd8ed1ab_0    conda-forge
simpleitk                 2.1.1.1          py39h138a4a7_1    conda-forge
sip                       6.7.4            py39h99910a6_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sly                       0.4                pyhd8ed1ab_0    conda-forge
slycot                    0.5.0.0          py39h73a3b6d_2    conda-forge
snappy                    1.1.9                hfb803bf_2    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
snowballstemmer           2.2.0              pyhd8ed1ab_0    conda-forge
sortedcontainers          2.4.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
sphinx                    5.3.0              pyhd8ed1ab_0    conda-forge
sphinxcontrib-applehelp   1.0.2                      py_0    conda-forge
sphinxcontrib-devhelp     1.0.2                      py_0    conda-forge
sphinxcontrib-htmlhelp    2.0.0              pyhd8ed1ab_0    conda-forge
sphinxcontrib-jsmath      1.0.1                      py_0    conda-forge
sphinxcontrib-qthelp      1.0.3                      py_0    conda-forge
sphinxcontrib-serializinghtml 1.1.5              pyhd8ed1ab_2    conda-forge
sqlite                    3.39.4               hcfcfb64_0    conda-forge
stack_data                0.6.0              pyhd8ed1ab_0    conda-forge
stackview                 0.3.5              pyhd8ed1ab_0    conda-forge
suitesparse               5.4.0                h5d0cbe0_1    conda-forge
superqt                   0.3.8              pyhd8ed1ab_0    conda-forge
svt-av1                   1.3.0                h63175ca_0    conda-forge
sympy                     1.11.1           py39hcbf5309_2    conda-forge
tables                    3.7.0                    pypi_0    pypi
tabulate                  0.9.0              pyhd8ed1ab_1    conda-forge
tbb                       2021.6.0             h91493d7_1    conda-forge
tbb-devel                 2021.6.0             h91493d7_1    conda-forge
tblib                     1.7.0              pyhd8ed1ab_0    conda-forge
terminado                 0.17.0             pyh08f2357_0    conda-forge
text-unidecode            1.3                      pypi_0    pypi
the-segmentation-game     0.2.0              pyhd8ed1ab_0    conda-forge
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tifffile                  2022.10.10         pyhd8ed1ab_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h8ffe710_0    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
tornado                   6.1              py39hb82d6ee_3    conda-forge
tqdm                      4.64.1             pyhd8ed1ab_0    conda-forge
traitlets                 5.5.0              pyhd8ed1ab_0    conda-forge
transforms3d              0.4.1              pyhd8ed1ab_0    conda-forge
typer                     0.7.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.4.0                hd8ed1ab_0    conda-forge
typing_extensions         4.4.0              pyha770c72_0    conda-forge
tyssue                    0.8.0                    pypi_0    pypi
tzdata                    2022f                h191b570_0    conda-forge
ucrt                      10.0.22621.0         h57928b3_0    conda-forge
umap-learn                0.5.3            py39hcbf5309_0    conda-forge
unicodedata2              15.0.0           py39ha55989b_0    conda-forge
urllib3                   1.26.11            pyhd8ed1ab_0    conda-forge
vc                        14.3                 h3d8a991_9    conda-forge
vispy                     0.10.0           py39h5d4886f_0    conda-forge
vs2015_runtime            14.32.31332          h1d6e394_9    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.4.2              pyhd8ed1ab_0    conda-forge
wheel                     0.38.2             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.3              pyhd8ed1ab_0    conda-forge
win32_setctime            1.1.0              pyhd8ed1ab_0    conda-forge
win_inet_pton             1.1.0              pyhd8ed1ab_6    conda-forge
winpty                    0.4.3                         4    conda-forge
wrapt                     1.14.1           py39ha55989b_1    conda-forge
x264                      1!164.3095           h8ffe710_2    conda-forge
x265                      3.5                  h2d74725_3    conda-forge
xorg-libxau               1.0.9                hcd874cb_0    conda-forge
xorg-libxdmcp             1.1.3                hcd874cb_0    conda-forge
xz                        5.2.6                h8d14728_0    conda-forge
yaml                      0.2.5                h8ffe710_2    conda-forge
zarr                      2.13.3             pyhd8ed1ab_0    conda-forge
zeromq                    4.3.4                h0e60522_1    conda-forge
zfp                       1.0.0                h63175ca_3    conda-forge
zict                      2.2.0              pyhd8ed1ab_0    conda-forge
zipp                      3.10.0             pyhd8ed1ab_0    conda-forge
zlib-ng                   2.0.6                h8ffe710_0    conda-forge
zstd                      1.5.2                h7755175_4    conda-forge

Maybe, some dependency has a wrong version?

Thanks!

Best, Robert

kephale commented 2 years ago

Arg, yeah I didnt communicate it well, but the invagination simulation requires some components that can only be installed via conda. I probably should do a module check and give a warning.

haesleinhuepf commented 2 years ago

Ah, I see! Consider updating the installation instructions:

You are better off using conda. You will need pytables, and ideally CGAL.

For example, I don't know what CGAL is 😉

kephale commented 2 years ago

Yeah, will do.

BTW, definitely poke me if you have use cases, I enjoy playing with this code.