Deprecation warnings

[benjaminhwilliams]

While working in xia2, I noticed a deprecation warning, so I did a little semi-automatic tidy-up. This PR does the following, based on the advice in the deprecation warnings:

• Replace dials.util.halraiser with dials.util.show_mail_on_error context manager;
• Replace dxtbx.model.experiment_list.ExperimentListDumper and dxtbx.serialize.dump with as_file method of experiment list;
• Replace dials.algorithms.indexing.index_reflections with dials.algorithms.indexing.assign_indices.AssignIndicesGlobal;
• Remove some unused imports and variables to satisfy flake8.

Any objections?

There is a corresponding PR in xia2 (xia2/xia2#325), and others to follow in dials_scratch & dxtbx.

[benjaminhwilliams]

Had to leave work before the checks finished. I'll tidy up the Flake8 problems on Monday.

[benjaminhwilliams]

@phyy-nx, I notice your 👍. Since I naturally have CCTBX as part of the DIALS build, my conversions caught lots of instances of the same sort of stuff in cctbx_project/xfel. Want me to open a corresponding PR there, or just leave it alone?

[graeme-winter]

@benjaminhwilliams humbly suggest you leave those ones to the XFEL folks, since they will have a lot of other ongoing work there so high risk of conflicts 🙂

[benjaminhwilliams]

Isn't Git fun?

[benjaminhwilliams]

The final Flake8 warning command_line/analyse_background.py:68:13: F841 local variable 'mask' is assigned to but never used will be resolved by #889.

[ndevenish]

Mostly looks good - replacing halraiser is something I've wanted to do for a long time, so very pleased to see it.

If you disagree with the #noqa thing then feel free to merge it in anyway.

[rjgildea]

Possibly outside the remit of this pull request, but since you touched this file... does the file example_experiment_data.py really need the example_ prefix, since it already is underneath the path doc/examples (the first rule of tautology club is...)?

I agree with @ndevenish's comments regarding # noqa: F841 - it would be a useful addition to the example to demonstrate printing out the objects (as it demonstrates that printing them gives some useful human-readable output).