Prepare for release of PyNWB 4.2.0

[rly]

Prepare for release of PyNWB 4.2.0.

Also fixes several things found while working through the checklist, and expands the checklist itself:

• Fixed the tag filter on the "Run all tests" workflow
• Fixed some -upgraded entries in the "Run all tests" matrices
• Cleaned up and fixed errors in make_a_release.rst
• Fixed and shortened the runtime of the resources_streaming.py tutorial

Version number

The semantic-versioning checklist item flags "removes or narrows accepted input" as a breaking change. #2235 narrows TimeSeries.control_description and the other array-valued fields from Iterable to array types, so a str, set, range, or generator is no longer accepted, and it changes TimeSeries.get_timestamps from raising TypeError to raising ValueError.

4.2.0 stays a minor release because those iterables were accepted by the type check but did not produce a correct file, and get_timestamps already raised for the same input.

Before merging:

• Make sure all PRs to be included in this release have been merged to dev.
• Major and minor releases: Update the dependency version bounds in pyproject.toml and the pinned versions in environment-ros3.yml to the latest as needed. The zarr and numcodecs upper bounds in the zarr extra track hdmf-zarr's own bounds. Check hdmf-zarr's requirements before touching them rather than raising them to the latest release. (dandi is pinned to 0.78.0 and installed from conda-forge rather than PyPI, since conda-forge publishes cp314 builds for every platform the ROS3 jobs use. The defaults channel was dropped from environment-ros3.yml because every package in the environment resolves from conda-forge. Both were checked with conda env create --dry-run for linux-64, osx-arm64, and win-64.)
• Major releases: Remove the deprecated functionality slated for removal in this version. (n/a, minor release; nothing is marked for removal before PyNWB 5.0)
• Check legal file dates and information in Legal.txt, license.txt, README.rst, docs/source/conf.py, and any other locations as needed
• Update pyproject.toml as needed
• Confirm the version number matches the severity of the changes, following semantic versioning. A changelog entry that removes or narrows accepted input, changes a return type, or turns a warning into an exception is a breaking change and belongs in a major release. Two cases are exempt from that rule and may go in a minor release: input that was accepted but could not be written or read back correctly, and a change in the type of an exception that was already raised for the same input. Record the reasoning in this pull request. (See "Version number" above.)
• Update README.rst as needed
• Update src/pynwb/nwb-schema submodule as needed. Check the version number and commit SHA manually. Make sure we are using the latest release and not the latest commit on the main branch.
• Update changelog (set release date) in CHANGELOG.md and any other docs as needed
• Cross-check the changelog against git log --oneline <previous-tag>..HEAD so that every merged PR is represented.
• Confirm the release notes will be extracted from the new heading by running the awk from deploy_release.yml with hdr="## PyNWB <version>" against CHANGELOG.md and checking that the output is non-empty and stops before the previous version's heading.
• Run tests locally including gallery and validation tests, and inspect all warnings and outputs (python test.py -v -p -i -b -w -x > out.txt 2>&1). Try to remove all warnings.
• Test docs locally and inspect all warnings and outputs cd docs; make clean && make html
• Build and test-install the distributions from a clean clone (git clone --recurse-submodules into a temp directory): run python -m build, then install the .whl and the .tar.gz into separate fresh virtual environments and confirm import pynwb, that nwb-schema/core ships with the expected schema version, and that writing and validating a minimal NWBFile succeeds.
• After pushing this branch to GitHub, manually trigger the "Run all tests" GitHub Actions workflow on this branch by going to https://github.com/NeurodataWithoutBorders/pynwb/actions/workflows/run_all_tests.yml, selecting "Run workflow" on the right, selecting this branch, and clicking "Run workflow". Make sure all tests pass, and check the ROS3 streaming jobs specifically, since those need a conda environment and are not run locally. https://github.com/NeurodataWithoutBorders/pynwb/actions/runs/33644415245
• Check that the readthedocs build for this PR succeeds (see the PR check)

After merging:

1. Create release by following steps in docs/source/make_a_release.rst or use alias git pypi-release [tag] if set up
2. After the CI bot creates the new release (wait ~10 min), check the release notes on the GitHub releases page. The workflow fills them from this version's section of CHANGELOG.md, and falls back to auto-generated notes if that section is empty or its heading does not match the tag.
3. Check that the readthedocs "stable" build runs and succeeds
4. Either monitor conda-forge/pynwb-feedstock for the regro-cf-autotick-bot bot to create a PR updating the version of PyNWB to the latest PyPI release, usually within 24 hours of release, or manually create a PR updating recipe/meta.yaml with the latest version number and SHA256 retrieved from PyPI > PyNWB > Download Files > View hashes for the .tar.gz file. Re-render and update dependencies as needed.

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.14%. Comparing base (b5c3b81) to head (ff99f7d).

❗ There is a different number of reports uploaded between BASE (b5c3b81) and HEAD (ff99f7d). Click for more details.

HEAD has 5 uploads less than BASE

Flag	BASE (b5c3b81)	HEAD (ff99f7d)
unit	4	3
integration	4	0

Additional details and impacted files

@@             Coverage Diff             @@
##              dev    #2246       +/-   ##
===========================================
- Coverage   96.17%   86.14%   -10.03%     
===========================================
  Files          30       30               
  Lines        3003     3003               
  Branches      437      437               
===========================================
- Hits         2888     2587      -301     
- Misses         65      324      +259     
- Partials       50       92       +42     

Flag	Coverage Δ
integration	?
unit	86.14% <ø> (-0.27%)	⬇️

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[rly]

@oruebel This is now good to go