Fix gh actions failures

[stephprince]

Motivation

This PR will fix a couple of our current workflow failures. These changes were originally included in #2015, but I have moved into a separate PR here so that we can merge into dev before the 3.0 release.

These changes will:

• Fix the daily run_all_tests.yml workflows that are failing due to some tox environment configuration errors introduced in Remove python 3.8 support and add python 3.13 support #2007
• Fix the python 3.13 gallery test failures due to an import from a deprecated scipy dataset
• Fix the sphinx link check workflows failing due to an update to the hdmf-zarr docs

TODO

• manually trigger run_all_tests.yml workflow to check that it runs successfully

How to test the behavior?

Run the run_all_tests.yml workflow

Checklist

• Did you update CHANGELOG.md with your changes?
• Have you checked our Contributing document?
• Have you ensured the PR clearly describes the problem and the solution?
• Is your contribution compliant with our coding style? This can be checked running ruff check . && codespell from the source directory.
• Have you checked to ensure that there aren't other open Pull Requests for the same change?
• Have you included the relevant issue number using "Fix #XXX" notation where XXX is the issue number? By including "Fix #XXX" you allow GitHub to close issue #XXX when the PR is merged.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 91.69%. Comparing base (80fc386) to head (2ee7798).
Report is 1 commits behind head on dev.

Additional details and impacted files

@@           Coverage Diff           @@
##              dev    #2016   +/-   ##
=======================================
  Coverage   91.69%   91.69%           
=======================================
  Files          27       27           
  Lines        2708     2708           
  Branches      707      707           
=======================================
  Hits         2483     2483           
  Misses        149      149           
  Partials       76       76           

Flag	Coverage Δ
integration	72.82% <ø> (ø)
unit	82.64% <ø> (ø)

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