Installing in conda env, reinstalls VTK

[demacdo]

Hi, not sure if this is an issue with my install method or not, but any help would be appreciated.

I'm trying to install pymeshfix in an existing conda environment in which PyVista is working fine. But in this environment, my VTK is sourced from the channel vmtk (http://www.vmtk.org/) rather than conda-forge.

When I try to install pymeshfix in this environment, it doesn't detect the existing VTK installation. I get a "Requirement already satisfied" message for pyvista, but "Collecting vtk" for VTK.

Here's how I'm creating the env:
conda create -n vmtk -c vmtk -c conda-forge python=3.6 itk vtk vmtk pyvista
Followed by:
pip install pymeshfix

I've tried creating a conda env from scratch with just PyVista, and then pip install pymeshfix works without any issues. Again, I'm not sure if this is expected behaviour and maybe I'm doing something unwise with my installation.

Thanks!

[akaszynski]

Could you please post your ``pyvista.Report()here prior to runningpymeshfix`?

Also, one thing you might try is creating an env.yml and then install from that file and include both the conda and pip dependencies in that single file. We do this already for our own conda testing:

name: pyvista-env
channels:
  - conda-forge
dependencies:
  - python>=3.5
  - numpy
  - vtk
  - scooby>=0.5.1
  - meshio>=4.0.3, <5.0
  - matplotlib
  - transforms3d==0.3.1
  - appdirs
  - pyqt
  - imageio>=2.5.0
  - imageio-ffmpeg
  - colorcet
  - cmocean
  - itkwidgets>=0.25.2
  - tqdm
  - pytest
  - pytest-cov
  - pytest-qt
  - codecov
  - hypothesis>=5.8.0
  - pip
  - trimesh
  - rtree
  - pyembree
  - panel
  - ipygany
  - pip:
      - pytest-memprof
      - ipyvtk-simple>=0.1.2

[demacdo]

Thanks! Running pv.Report() from my original env gives the following:

---

Date: Sat Apr 03 14:21:54 2021 EDT

            OS : Darwin
        CPU(s) : 8
       Machine : x86_64
  Architecture : 64bit
   Environment : IPython
    GPU Vendor : NVIDIA Corporation
  GPU Renderer : NVIDIA GeForce GTX 680MX OpenGL Engine
   GPU Version : 4.1 NVIDIA-12.0.24 355.11.10.50.10.103

Python 3.6.1 | packaged by conda-forge | (default, May 23 2017, 14:31:56)
[GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)]

       pyvista : 0.29.0
           vtk : 8.1.0
         numpy : 1.13.0
       imageio : 2.9.0
       appdirs : 1.4.4
        scooby : 0.5.6
        meshio : unknown
    matplotlib : 3.1.0
       IPython : 7.16.1
         scipy : 1.2.1

---

I also tried creating from a new env from an env.yml file, as follows, but it again seems to install VTK 9 from pip alongside the VTK 8 from conda. Running pv.Report() from this env gives me an error:

Error:

Corrupt value: 0x0
python(86705,0x10b5825c0) malloc: *** set a breakpoint in malloc_error_break to debug
Abort trap: 6

Env:

name: vmtk_02
channels:
  - vmtk
  - conda-forge
dependencies:
  - ipython
  - itk
  - matplotlib
  - meshio
  - numpy
  - pip
  - python=3.6
  - pyvista
  - scipy
  - vmtk=1.4
  - vtk=8.1
  - pip:
    - pymeshfix