Fix failing minimum tests

[ashnair1]

This PR fixes the cause for the minimum tests failing in #854 (and presumably any PR created after Dec 1st).

scikit-learn has officially begun deprecating sklearn to prevent malicious actors from using it. So any dependency that attempts to install sklearn would install the new sklearn package which throws an exception at certain intervals - Refer https://pypi.org/project/sklearn/ for more details.

open3d=0.11.2 was our problem package. The open3d team had switched from sklearn to scikit-learn in version 0.13.0. This PR bumps the minimum version to the same.

It seems there was a PR prepped to replace open3d with pyvista - #663. If this lands for the 0.4.0 release, this PR can be ignored.

[adamjstewart]

Good catch! Looks like we'll also need to bump our pandas min version as a result. @isaaccorley any updates on the pyvista PR?

[ashnair1]

Good catch! Looks like we'll also need to bump our pandas min version as a result. @isaaccorley any updates on the pyvista PR?

Indeed. Do you recommend that be done in a separate PR? Or shall I just include it here and change the issue title to "Fix failing min tests"?

Edit: Think I'll just go ahead and push it here since the goal is to fix the failing tests.

[ashnair1]

Really kicked the hornet's nest with this one. Will need some time to find a stable configuration.

Current constraint:

open3d 0.13.0 depends on jupyter-packaging~=0.10 and jupyter-packaging 0.10+ depends on setuptools>=46.4.0.

Seems open3d pinned jupyter-packaging~=0.10 to support Python 3.6.

[ashnair1]

Got stung a few times but things look stable now.

Summary of changes and reasons:

open3d (0.13.0) required the following packages to be updated

• setuptools (indirectly)
• pandas
• numpy
• pillow
• ipywidgets

rasterio was updated to avoid a deprecation warning caused by importing Iterable from collections.
nbconvert was pinned to reduce the resolve time. Without this, time required for running the minimum test jumped to 10 min.

[adamjstewart]

rasterio was updated to avoid a deprecation warning caused by importing Iterable from collections.

Let's silence that warning in pyproject.toml instead.

[ashnair1]

rasterio was updated to avoid a deprecation warning caused by importing Iterable from collections.

Let's silence that warning in pyproject.toml instead.

Seems like this was already added in pyproject.toml line 80

Edit: Ah nvm this was coming from rasterio.transform

[isaaccorley]

I stay up late at night regretting ever adding open3d as a dependency.

[adamjstewart]

Do you think we should push forward and merge this PR and then revert it if we get pyvista working, or is pyvista close? We could skip pyvista tests on macOS/Windows if those are too hard to test.

[isaaccorley]

If we can skip windows and mac tests then we could get pyvista in. It's just a matter of installing xvfb via apt in the github action and then running pyvista.start_xvfb() prior to the plot test.