Address warnings emitted by GitHub Actions in generated project

[pkalita-lbl]

In a newly generated project several workflows produce warnings that could get cleaned up:

build-docs
The set-output command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

test (3.10)
Node.js 12 actions are deprecated. For more information see: https://github.blog/changelog/2022-09-22-github-actions-all-actions-will-begin-running-on-node16-instead-of-node12/. Please update the following actions to use Node.js 16: actions/checkout@v2, actions/setup-python@v2

test (3.9)
Node.js 12 actions are deprecated. For more information see: https://github.blog/changelog/2022-09-22-github-actions-all-actions-will-begin-running-on-node16-instead-of-node12/. Please update the following actions to use Node.js 16: actions/checkout@v2, actions/setup-python@v2

deploy
Input 'emit_telemetry' has been deprecated with message: Use of this input causes the action to do nothing. You should remove this build step from your workflow.

Build and publish Python 🐍 distributions 📦 to PyPI
Node.js 12 actions are deprecated. For more information see: https://github.blog/changelog/2022-09-22-github-actions-all-actions-will-begin-running-on-node16-instead-of-node12/. Please update the following actions to use Node.js 16: actions/checkout@v2, actions/setup-python@v2.2.2

Build and publish Python 🐍 distributions 📦 to PyPI
The set-output command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

Publish Python Package: .github#L1
ubuntu-latest workflows will use ubuntu-22.04 soon. For more details, see actions/runner-images#6399

[pkalita-lbl]

The set-output and Node.js 12 ones should just be a matter of upgrading to the latest major version of a few actions. The emit_telemetry one comes from the automatic GitHub Pages action, so it's not really under our control. And the ubuntu-latest is just informational and doesn't require any action on our end.

[pkalita-lbl]

See also: microbiomedata/nmdc-schema#513