Prepare release 3.0

[stephprince]

Prepare for release of PyNWB 3.0

TODO

• merge all PRs with breaking changes into this branch
• make pre-release 3.0.0rc1 on GitHub and PyPi for downstream testing

Before merging:

• Make sure all PRs to be included in this release have been merged to dev.
• Major and minor releases: Update package versions in requirements.txt, requirements-dev.txt,
  requirements-doc.txt, requirements-opt.txt, and environment-ros3.yml to the latest versions,
  and update dependency ranges in pyproject.toml and minimums in requirements-min.txt as needed.
  Run pip install pur && pur -r requirements-dev.txt -r requirements.txt -r requirements-opt.txt
  and manually update environment-ros3.yml.
• 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/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
• Run tests locally including gallery, validation, and streaming tests, and inspect all warnings and outputs
  (python test.py -v -p -i -b -w -r > out.txt 2>&1). Try to remove all warnings.
• 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/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.
• 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/pynwb-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 > PyNWB > Download Files > View hashes for the .tar.gz file. Re-render and update
   dependencies as needed.

[codecov]

Codecov Report

Attention: Patch coverage is 97.14286% with 6 lines in your changes missing coverage. Please review.

Project coverage is 92.69%. Comparing base (b84b04a) to head (fc2997e).

Files with missing lines	Patch %	Lines
src/pynwb/__init__.py	78.57%	2 Missing and 1 partial ⚠️
src/pynwb/file.py	89.47%	1 Missing and 1 partial ⚠️
src/pynwb/validation.py	98.55%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev    #2015      +/-   ##
==========================================
+ Coverage   91.69%   92.69%   +1.00%     
==========================================
  Files          27       28       +1     
  Lines        2708     2710       +2     
  Branches      707      709       +2     
==========================================
+ Hits         2483     2512      +29     
+ Misses        149      128      -21     
+ Partials       76       70       -6     

Flag	Coverage Δ
integration	73.35% <79.52%> (+0.53%)	⬆️
unit	83.13% <66.19%> (+0.49%)	⬆️

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[stephprince]

@rly this is ready for you to review, but should not be merged into dev until after the pre-release is published.

Since we discussed waiting at least a week after 3.0.0rc1 to make the official release, it may be best to separate out the changes to tox.ini, .github/workflows/run_all_tests.yml, and hdmf-zarr links in docs/source/conf.py into a separate PR since those are smaller, non-breaking changes.

[rly]

I'll finish the review tomorrow. This is fine but for the future, I recommend using the release-3.0.0 branch as a "staging" branch that we avoid pushing directly to, but rather make PRs to (with small exceptions like updating the changelog). That makes it 1) easier to review each new change to the branch and 2) we can merge the changes without squashing which will create one commit per PR that has been merged into this branch.

[stephprince]

This is fine but for the future, I recommend using the release-3.0.0 branch as a "staging" branch that we avoid pushing directly to, but rather make PRs to (with small exceptions like updating the changelog). That makes it 1) easier to review each new change to the branch and 2) we can merge the changes without squashing which will create one commit per PR that has been merged into this branch.

Definitely that makes sense, will do next time.