bug: Flopy is crashing on function using shapefiles

[edesousa-intera]

Getting error messages in various flopy shapefile-related functions such as Gridgen(add_refinement_features) and Grid Intersect.
I believe it may be related to updated Shapely and/or PyShp libraries, but couldn't pin down the error.

Using GridIntersect returns an error message:

Code:
ix = GridIntersect(vtx_grid, method='vertex', rtree=True)

Error message:

---

TypeError Traceback (most recent call last)
~\AppData\Local\Temp\ipykernel_15016\2427717357.py in
1 # Selection for Alluvium cells
----> 2 ix = GridIntersect(vtx_grid, method='vertex', rtree=True)

c:\Anaconda3\lib\site-packages\flopy\utils\gridintersect.py in init(self, mfgrid, method, rtree)
172 if self.method == "vertex":
173 # build arrays of geoms and cellids
--> 174 self.geoms, self.cellids = self._get_gridshapes()
175
176 # build STR-tree if specified

c:\Anaconda3\lib\site-packages\flopy\utils\gridintersect.py in _vtx_grid_to_geoms_cellids(self)
421 points.append(
422 (
--> 423 self.mfgrid._vertices[iv][1],
424 self.mfgrid._vertices[iv][2],
425 )

TypeError: list indices must be integers or slices, not NoneType

[dbrakenhoff]

The error you post seems to indicate variable iv is None. This error is not related to the shapely or pyshp versions as far as I can tell. I don't know enough to know what's going wrong, but for some reason the entries in icverts in your grid are None.

Gridintersect loops through this dataset for each cell to obtain the vertices and construct shapely geometries:

vtx_grid._cell2d[('icvert_0', 'icvert_1', 'icvert_2', 'icvert_3', 'icvert_4', 'icvert_5')]

Where the no. of icvert_# columns it checks is determined by vtx_grid._cell2d["ncvert"].

Are you mixing different geometries, e.g. rectangles and triangles, in your grid? If so, I don't think we handle that case correctly and this is a bug we need to address. Otherwise, there's something odd about your grid...?

As for the errors related to Gridgen, you'll need to post those so we can take a look at those. This GridIntersect error is probably not related.

[langevin-usgs]

Hey @edesousa-intera, can you try and reproduce your error with a very simple example, and post the files here? I don't think we have enough to go on with your description.

Will transfer this to a discussion.

[edesousa-intera]

Hi Chris,

Thanks for the quick reply and my apologies, the error message I sent was due to a problem unrelated to the shapefile function, so please ignore it.

I'm still have problems with gridgen class with the add_refinement_features function (something to do with bounding box), but let me do some more testing and I'll put the details here soon.