Migrations: Fix bug in "progress bar" logic and work around upstream memory leak

[eecavanna]

In this branch, I updated the latest migration notebook in the following ways:

1. I fixed a bug where the notebook would sometimes divide by zero (https://github.com/microbiomedata/nmdc-runtime/issues/751)
2. I worked around an upstream bug (https://github.com/linkml/linkml/issues/2395) that would result in a memory leak when serializing the validation report as a whole
3. I removed some extraneous whitespace from one of the cells

Type of change

Please delete options that are not relevant.

• [x] Bug fix (non-breaking change which fixes an issue)

How Has This Been Tested?

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration, if it is not simply make up-test && make test-run.

• [x] Many, many, many, grueling, tedious, slogging manual runs of the affected notebook cell in PyCharm

Definition of Done (DoD) Checklist:

• [x] I have performed a self-review of my code
• [x] I have commented my code, particularly in hard-to-understand areas