BlueBrain / BlueBrain/VessMorphoVis

CLI Bugs

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Dominant language
Python
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Description

Hey,
first of all thanks for this great library, it's a big help.
I wanted to report some bugs I encountered when using the CLI to reconstruct a mesh.

- The _tessellation-level_ option is called _tessellation-ratio_ in the code. This fails when _arguments.tessellation_ratio_ is called
https://github.com/BlueBrain/VessMorphoVis/blob/90446383cef5caa4f9a8d8613a4a9a04c293fdf6/vmv/options/vessmorphovis_options.py#L171
Quickfixing this by changing the line to _arguments.tessellation_level_ allows the program to continue, but setting the tessellation to another value than 1.0 will cause a _TypeError: Converting py args to operator properties: : keyword "apply_as" unrecognized_ in the mesh builder.

- vmv.file does not have a function _read_morphology_from_file_
https://github.com/BlueBrain/VessMorphoVis/blob/90446383cef5caa4f9a8d8613a4a9a04c293fdf6/vmv/interface/cli/mesh_reconstruction.py#L298

- _only cli_options.mesh.export_obj_ is used to determine if _vmv.file.export_mesh_object_ should be called, this ignores for example export-vascular-mesh-stl
https://github.com/BlueBrain/VessMorphoVis/blob/90446383cef5caa4f9a8d8613a4a9a04c293fdf6/vmv/interface/cli/mesh_reconstruction.py#L112

- _vmv.file.export_mesh_object_ gets wrong arguments
https://github.com/BlueBrain/VessMorphoVis/blob/90446383cef5caa4f9a8d8613a4a9a04c293fdf6/vmv/interface/cli/mesh_reconstruction.py#L113-L116

- Even when _mesh_objects_ from _vmv.scene.get_list_of_meshes_in_scene()_ is just one mesh, it's still a list object
https://github.com/BlueBrain/VessMorphoVis/blob/90446383cef5caa4f9a8d8613a4a9a04c293fdf6/vmv/interface/cli/mesh_reconstruction.py#L100-L109
I just fixed it by setting mesh_object = mesh_objects[0] when len(mesh_objects) == 1

When these points were fixed, everything worked as expected.
If you have any questions I can provide more accurate descriptions.

Contributor guide

Open the contributing guide

Research direction

Start in vmv/interface/cli/mesh_reconstruction.py at the referenced lines, then inspect vmv/options/vessmorphovis_options.py and the vmv.file functions involved in mesh loading and export. Reproduce CLI mesh reconstruction and trace each reported argument, export-condition, missing-function, and mesh-list failure. Done means all listed CLI paths complete successfully with the requested tessellation and export options.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
cli
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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