Prepare 6.1.0 release

[rly]

Prepare for release of HDMF 6.1.0

Bumps the ## HDMF 6.0.3 (Upcoming) changelog heading to ## HDMF 6.1.0 (June 24, 2026). Update the date to the actual release day if it slips. Note: this release contains a breaking change (removal of the file argument from HERD.add_ref/HERD.add_ref_termset); confirm a minor bump (rather than major) is intended for the HERD API.

This PR also includes a CI fix discovered while reviewing the release infrastructure: the gallery-py310-minimum tox env no longer pins the docs dependency group to its minimum versions. It now installs the docs group at latest compatible versions, then downgrades only the project's own direct deps with --resolution lowest-direct, mirroring the equivalent fix in pynwb#2205.

It also moves the gallery, docs (Sphinx link check + Read the Docs), and coverage CI from Python 3.13 to 3.14. linkml-runtime 1.11.1 and its deps (oaklib, schemasheets) now support 3.14; verified locally by installing the full .[all] + docs stack on 3.14.4 and running test_gallery.py (all 7 examples, including the linkml/oaklib termset examples, pass). The stale # TODO: Update to 3.14 when linkml and its deps support 3.14 markers are removed.

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.
• 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.
  (Currently pinned to 1.9.0, commit 497bde3.)
• 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.
  • https://github.com/hdmf-dev/hdmf/actions/runs/28201343737
• 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), update the release notes on the
   GitHub releases page with the changelog
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.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.22%. Comparing base (14021a6) to head (3184f2b).

Additional details and impacted files

@@            Coverage Diff             @@
##              dev    #1516      +/-   ##
==========================================
- Coverage   93.22%   93.22%   -0.01%     
==========================================
  Files          41       41              
  Lines       10170    10168       -2     
  Branches     2100     2100              
==========================================
- Hits         9481     9479       -2     
  Misses        413      413              
  Partials      276      276              

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