Remove custom action methods

[melodyyzh]

Description

Removed the following methods in a branch off trunk-major after adding deprecation warnings in #1692

• _InternalCustomUpdater.update.
• _InternalCustomTuner.tune.
• _InternalCustomWriter.write.
• HDF5Log.write.

Motivation and context

Resolves #1648

How has this been tested?

Ran python tests on all the hoomd files, removed the wrap action act method in custom_operation.py to avoid the test calling the operation function and introduce error.

Change log

Removed:

* ``_InternalCustomUpdater.update``.
  (`#1699 <https://github.com/glotzerlab/hoomd-blue/pull/1699>`__).
* ``_InternalCustomTuner.tune``.
  (`#1699 <https://github.com/glotzerlab/hoomd-blue/pull/1699>`__).  
* ``_InternalCustomWriter.write``.
  (`#1699 <https://github.com/glotzerlab/hoomd-blue/pull/1699>`__).
* ``HDF5Log.write``.
  (`#1699 <https://github.com/glotzerlab/hoomd-blue/pull/1699>`__).

Checklist:

• I have reviewed the Contributor Guidelines.
• I agree with the terms of the HOOMD-blue Contributor Agreement.
• My name is on the list of contributors (sphinx-doc/credits.rst) in the pull request source branch.

[melodyyzh]

The pytest failed at test_hdf5.py because it called hdf5_writer.write(), which was removed in this PR. Based on the conversation in PR #1588 , I am thinking we can either remove this line because timestep is optional, or replace it with simulation.timestep if it has been implemented in the documation?

[joaander]

You can remove test_write_method from test_hdf5.py. There is no need to test a method that does not exist.

[tommy-waltmann]

Does the changelog need to be updated to say these methods were removed?

[joaander]

Does the changelog need to be updated to say these methods were removed?

Yes. I handle changelog updates separately from pull requests in HOOMD-blue and will add this at some point after the PR is merged.

What does need to be added to this PR is an update to migrating.rst with a Migrating to HOOMD-blue 5.0 section that notes the changes needed to user scripts.

[melodyyzh]

pre-commit.ci autofix

[shihkual]

LGTM!

[tcmoore3]

LGTM.