Update code to work with recent versions of xarray, ensure tests pass

[vnmanoharan]

As of xarray v2022.06.0, arrays with a MultiIndex no longer have associated "virtual" coordinates but instead have real coordinates (https://docs.xarray.dev/en/stable/whats-new.html#v2022-06-0rc0-9-june-2022) . Some of our code had assumed that the x, y, z dimensions associated with a flattened detector schema would remain virtual, but that code broke when they became non-virtual, and the x, y, z dimensions started getting duplicated in our metadata update operations. This PR fixes this problem, allowing holopy to be used with more recent versions of xarray.

Fixes

409

411

415

Other changes:

• added environment.yml file to make it easier to setup a conda environment for developing holopy
• fixed some deprecation warnings associated with changes in scipy.ndimage
• created workaround for incompatibility of nose with unittest.expectedFailure.

test_2_colour_noise_sd (test_io.TestAccumulator) is failing, but other tests are passing. This test was failing before any changes were made.

[pep8speaks]

Hello @vnmanoharan! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! :beers:

Comment last updated at 2024-01-03 16:50:30 UTC

[vnmanoharan]

This PR now includes changes from #431 to ensure all tests pass.