Enable fetching of "obs4ref" data from pmp

[lewisjared]

Description

PMP requires some datasets that have been preprocessed by PCMDI into an obs4mips.

• HadISST: HadISST obs_preparation_progress#20
• NOAA-20CR: NOAA-20CR obs_preparation_progress#1

Both datasets have been checked by @dhegedus99 so we now have the appropriate licences to use these data.

Checklist

Please confirm that this pull request has done the following:

• Tests added
• Documentation added (where applicable)
• Changelog item added to changelog/

[Copilot]

Pull Request Overview

This PR enables the fetching of "obs4ref" data from PMP by incorporating the dataset into the ingestion workflow and extending the CLI. Key changes include:

• Adding an ingestion call for obs4ref data in integration tests and updating the expected providers.
• Introducing a new CLI command to fetch obs4ref data and updating related logging and testing routines.
• Removing the legacy PMP registry module.

Reviewed Changes

Copilot reviewed 9 out of 11 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
tests/integration/test_ar7_ft.py	Added ingestion for obs4ref data and updated expected metrics providers.
stubs/pooch/init.pyi	Added a stub for get_logger to support updated logging handling.
packages/ref/src/cmip_ref/testing.py	Updated the sample data fetch implementation using new registry helper.
packages/ref/src/cmip_ref/dataset_registry/init.py	Introduced the new reference data registry for non-published datasets.
packages/ref/src/cmip_ref/cli/datasets.py	Added a CLI command to fetch obs4ref data along with improved documentation.
packages/ref/src/cmip_ref/cli/_logging.py	Adjusted logging setup to clear interfering handlers from pooch logger.
packages/ref-metrics-pmp/src/cmip_ref_metrics_pmp/registry/init.py	Removed outdated PMP registry module.
docs/getting_started.md	Fixed a spelling typo in the documentation.
.github/workflows/ci-integration.yaml	Expanded CI to run the new fetch-obs4ref-data command.

Files not reviewed (2)

• packages/ref/src/cmip_ref/dataset_registry/pmp_reference.txt: Language not supported
• tests/test-data/.gitignore: Language not supported

Comments suppressed due to low confidence (2)

tests/integration/test_ar7_ft.py:67

• [nitpick] The use of 'obs4mips' as the source-type for the obs4ref data may be ambiguous. Consider aligning the source-type with the dataset name (e.g. 'obs4ref') if the ingestion logic permits to improve clarity.

invoke_cli(["datasets", "ingest", "--source-type", "obs4mips", str(sample_data_dir / ".." / "obs4ref")])

packages/ref-metrics-pmp/src/cmip_ref_metrics_pmp/registry/init.py:1

• The complete removal of the PMP registry module appears intentional; please verify that all dependencies on this module are updated to avoid broken references.

Entire file removed

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

see 2 files with indirect coverage changes

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[lewisjared]

I'm going to pull out the changes that add updates to the integration test as that is currently broken because the PMP output fails to parse. I'll make a follow PR to demonstrate that so @lee1043 can resolve, but that PR will need updated sample data (Climate-REF/ref-sample-data#24), which in turn depends on these changes ♻️

[lee1043]

Thank you for this PR!