Prepare for release of HDMF 6.2.0

[rly]

Before merging:

• Make sure all PRs to be included in this release have been merged to dev.
• Major and minor releases: Update dependency ranges in pyproject.toml as needed.
• Update the GitHub Actions used in the workflows to their latest versions. Pin each action to a full commit SHA, except actions that publish immutable releases, which may use a version tag (see .github/zizmor.yml for the policy).
• 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
• Update README.rst as needed
• Update src/hdmf/common/hdmf-common-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
• Run tests locally including gallery tests, and inspect all warnings and outputs (pytest && python test_gallery.py). Try to remove all warnings.
• Run PyNWB tests locally including gallery and validation tests, and inspect all warnings and outputs (cd pynwb; git checkout dev; git pull; python test.py -v > out.txt 2>&1)
• Run HDMF-Zarr tests locally including gallery and validation tests, and inspect all warnings and outputs (cd hdmf-zarr; git checkout dev; git pull; pytest && python test_gallery.py)
• Test docs locally and inspect all warnings and outputs cd docs; make clean && make html
• After pushing this branch to GitHub, manually trigger the "Run all tests" GitHub Actions workflow on this branch by going to https://github.com/hdmf-dev/hdmf/actions/workflows/run_all_tests.yml, selecting "Run workflow" on the right, selecting this branch, and clicking "Run workflow". Make sure all tests pass.
• 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), verify that the release notes on the GitHub releases page include the changelog for this version
3. Check that the readthedocs "stable" build runs and succeeds
4. Either monitor conda-forge/hdmf-feedstock for the regro-cf-autotick-bot bot to create a PR updating the version of HDMF 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 > HDMF > Download Files > View hashes for the .tar.gz file. Re-render and update the dependencies as needed.

Notes on this release

Changes in this PR beyond setting the release date:

• Pointed the hdmf-common-schema submodule at the 1.10.0 release tag (e7f84f0). It was on 4508b8f, one commit past 1.9.0, which is the MeaningsTable.target change already described in the changelog.
• Moved the changelog entry for Validate quantity in GroupSpec and DatasetSpec #1521 from the 6.1.0 section into 6.2.0. That PR merged on 2026-07-06, after the 6.1.0 tag on 2026-06-25, and the entry is not in the changelog as of the 6.1.0 tag.
• Added https://nwb-users.slack.com to linkcheck_ignore in docs/source/conf.py, which was failing the "Check Sphinx links" workflow.
• Closed the HDF5IO opened by the TestWriteHDF5withZarrInput tests. Since Avoid Zarr-to-HDF5 export deadlock and make the IO finalizer non-blocking #1547 changed HDMFIO.__del__ to warn rather than close, those tests emitted a ResourceWarning under -W always.

Local test results:

• hdmf: 1965 passed, 20 skipped, 1 xfailed, 919 subtests passed. Gallery: 7 tests OK. Remaining warnings under -W always are the intentional EnumData is experimental warning and third-party deprecations from linkml-runtime and sssom.
• hdmf-zarr (dev, 5e633ff): 547 passed, 11 skipped, 1080 subtests passed. Gallery: 5 tests OK. Warnings are hdmf-zarr's own and zarr's NestedDirectoryStore deprecation.
• Sphinx make clean && make html: build succeeded, no warnings. sphinx-build -W -b linkcheck: build succeeded, no broken links.
• PyNWB (dev, 6285dd8): 763 tests, 7 failures and 1 error, all in integration.hdf5.test_misc for TestUnitsCustomWaveformUnitIO and TestUnitsWaveformTimeBeforePeakIO. These reproduce identically against the released hdmf 6.1.0, so they are a pre-existing issue on pynwb dev from Make Units.waveform_unit configurable NeurodataWithoutBorders/pynwb#2237, not a regression in this release.

CI notes:

• All PR checks pass, including check-sphinx-links (confirming the linkcheck_ignore addition), run-pynwb-tests, run-hdmf-zarr-tests, and the readthedocs build.
• "Run all tests" (32220709636): 36 of 37 jobs pass. The remaining job, windows-python3.14-ros3, hangs in "Run ros3 tests" until the 6-hour limit. That is pre-existing on dev: the nightly runs on 2026-08-17 and 2026-08-18 were both cancelled after hanging on the same job, while linux-python3.14-ros3 and macos-python3.14-ros3 finish in under two minutes. Worth a separate issue.
• Two earlier attempts at "Run all tests" failed in the python3.14-upgraded-optional jobs while installing lxml. lxml 6.1.2 was published to PyPI at 04:58:23 UTC and the jobs resolved it at 04:58:45, before the cp314 wheels finished uploading, so pip fell back to the sdist and the build failed. Unrelated to this release; the rerun after the wheels landed is green.

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.16%. Comparing base (0c730c0) to head (dabd631).

Additional details and impacted files

@@           Coverage Diff           @@
##              dev    #1562   +/-   ##
=======================================
  Coverage   93.16%   93.16%           
=======================================
  Files          41       41           
  Lines       10259    10259           
  Branches     2122     2122           
=======================================
  Hits         9558     9558           
  Misses        422      422           
  Partials      279      279           

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