Release 3.9.1

[mavaylon1]

Prepare for release of HDMF [version]

Before merging:

• Major and minor releases: Update package versions in requirements.txt, requirements-dev.txt,
  requirements-doc.txt, requirements-min.txt, requirements-opt.txt, environment-ros3.yml, and setup.py 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 setup.py 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
• 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)
• Run PyNWB tests locally including gallery and validation tests, and inspect all warnings and outputs
  (cd pynwb; python test.py -v > out.txt 2>&1)
• Test docs locally by going into the docs directory and running the following: make clean && make html
• Push changes to this PR and make sure all PRs to be included in this release have been merged
• Check that the readthedocs build for this PR succeeds (build latest to pull the new branch, then activate and
  build docs for new branch): https://readthedocs.org/projects/hdmf/builds/

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 "latest" and "stable" builds run and succeed
4. Update conda-forge/hdmf-feedstock with the latest version number
   and SHA256 retrieved from PyPI > HDMF > Download Files > View hashes for the .tar.gz file. Re-render as needed

[codecov]

Codecov Report

All modified lines are covered by tests ✅

Comparison is base (f0c23c3) 88.57% compared to head (a17dc0c) 88.57%.

Additional details and impacted files

@@           Coverage Diff           @@
##              dev     #955   +/-   ##
=======================================
  Coverage   88.57%   88.57%           
=======================================
  Files          45       45           
  Lines        9400     9400           
  Branches     2673     2673           
=======================================
  Hits         8326     8326           
  Misses        759      759           
  Partials      315      315           

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[mavaylon1]

Checklist

• the common schema is pointing to main, I manually did a git checkout main to verify
• @rly the pynwb tests are not passing though I don't think it is on the hdmf side.

FAILED tests/read_dandi/test_read_dandi.py::TestReadNWBDandisets::test_read_first_nwb_asset - SystemExit: 1
FAILED tests/unit/test_file.py::TestNoCacheSpec::test_simple - AssertionError: UserWarning not triggered
FAILED tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache - AssertionError: Regex didn't match: '.*UserWarning: No cached namespaces found in tests/back_compat/1\\.0\\.2_nwbfile\\.nwb\\s*warnings.warn\\(msg\\)\\s*The file tests/back_compat/1\\.0\\.2_nwbfile\\.nwb has no cached namespace information\\. Falling back to...
FAILED tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache_bad_ns - AssertionError: Regex didn't match: ".*UserWarning: No cached namespaces found in tests/back_compat/1\\.0\\.2_nwbfile\\.nwb\\s*warnings.warn\\(msg\\)\\s*The file tests/back_compat/1\\.0\\.2_nwbfile\\.nwb has no cached namespace information\\. Falling back to...```

[rly]

Looks good. Thanks!