ml4h install: vtk module is pinned to a version not supported in py3.8

[amygdala]

I tried doing an ml4h install as follows: pip install git+https://github.com/broadinstitute/ml4h.git
I got the following error. It looks like the vtk module is pinned to a too-old version that has since been removed. I am happy to put in a PR to fix this, if someone will let me know what version it should be changed to.

pip install -U git+https://github.com/broadinstitute/ml4h.git
Collecting git+https://github.com/broadinstitute/ml4h.git
  Cloning https://github.com/broadinstitute/ml4h.git to /private/var/folders/ff/j2rj0tmn4870zbchzfgv7bnc004l5y/T/pip-req-build-98i6y9uf
  Running command git clone -q https://github.com/broadinstitute/ml4h.git /private/var/folders/ff/j2rj0tmn4870zbchzfgv7bnc004l5y/T/pip-req-build-98i6y9uf
  Resolved https://github.com/broadinstitute/ml4h.git to commit 54dd1aec236a79a4fd647f98f6b6c40f08496fb8
Collecting ml4ht@ git+https://github.com/broadinstitute/torch_ml4h
  Cloning https://github.com/broadinstitute/torch_ml4h to /private/var/folders/ff/j2rj0tmn4870zbchzfgv7bnc004l5y/T/pip-install-tayn5rfn/ml4ht_5b27838f4da5433d9fb41d57d981383e
  Running command git clone -q https://github.com/broadinstitute/torch_ml4h /private/var/folders/ff/j2rj0tmn4870zbchzfgv7bnc004l5y/T/pip-install-tayn5rfn/ml4ht_5b27838f4da5433d9fb41d57d981383e
  Resolved https://github.com/broadinstitute/torch_ml4h to commit 19f415eeabefb85753c7c2d5b43d2a79448d08df
Collecting pydot==1.2.4
...<lines omitted>...
  Using cached scikit_image-0.18.2-cp38-cp38-macosx_10_9_x86_64.whl (12.8 MB)
Collecting biosppy
  Using cached biosppy-0.7.3.tar.gz (85 kB)
ERROR: Could not find a version that satisfies the requirement vtk==8.1.2 (from ml4h) (from versions: 9.0.0, 9.0.1, 9.0.2, 9.0.3, 9.0.20210612.dev0, 9.0.20210626.dev0, 9.0.20210707.dev0, 9.0.20210708.dev0, 9.0.20210709.dev0, 9.0.20210710.dev0, 9.0.20210717.dev0)
ERROR: No matching distribution found for vtk==8.1.2

cc @deflaux as fyi

[paolodi]

Thanks for reporting the issue! I cannot reproduce it on pip 21.2.3 (python 3.6). vtk 8.1.2 should be still accessible in the PyPI registry. Do you observe the error for a newer version of Python?

Moving to vtk>=9.0.0 would probably be fine if that unblocks you. We can fix eventual compatibility issues in the mesh generation code at a later stage.

[amygdala]

Oh, interesting. I'm using pip 21.2.3 too, but running python 3.8. It looks like it's successfully loaded with py3.7 too, so it must be a 3.8 issue.

[paolodi]

Understood! I guess it's up to you then. If having vtk==9.0.0 (and Python 3.8) makes it easier for you, please feel free to go ahead with a PR and we can deal with eventual incompatibilities later on.

[amygdala]

Thanks. I think I'll hold off on the PR for now, as I can work around the issue by instead using py 3.7, and I'd hate to break anyone unexpectedly. But we can leave the issue up for tracking.