fix: replace print() with logger.warning() in extensions catalog warnings

[Quratulain-bilal]

Problem

print(..., file=sys.stderr) is inappropriate for library code - it bypasses the logging framework and can't be silenced or redirected by consumers.

Fix

Replaced with logger.warning() for proper log management. Removed unused local sys imports.

[Copilot]

Pull request overview

Replaces direct stderr warnings with standard Python logging in the extension catalog.

Changes:

• Added a module logger.
• Migrated two catalog warnings to logger.warning().
• Removed unused local sys imports.

Show a summary per file

File	Description
src/specify_cli/extensions/__init__.py	Routes catalog warnings through logging.

Review details

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Suppressed comments (1)

src/specify_cli/extensions/init.py:3757

• Please cover the partial-fetch failure path with caplog: make one catalog raise ExtensionError, let another succeed, and assert the named warning is logged while merging continues. This is the second logging behavior changed by the PR and currently has no regression test.

                logger.warning(
                    "Could not fetch catalog '%s': %s", catalog_entry.name, e,
                )

• Files reviewed: 1/1 changed files
• Comments generated: 1
• Review effort level: Balanced

[mnriem]

Thanks — this is the right fix (stderr print in library code can't be silenced/redirected by consumers), and the caplog regression test is exactly what I want to see. Just one thing before review: please disclose any AI assistance per CONTRIBUTING. With that added, this is in good shape — and for reference, PRs like this one (focused + a real test) are much easier to prioritize than the untested atomic-write batch.

[Copilot]

🟡 Changes recommended

An unused import will fail Ruff CI, and one changed warning path lacks logging coverage.

Once you've addressed the issues Copilot identified, you can request another Copilot review.

Review details

Suppressed comments (1)

src/specify_cli/extensions/init.py:3522

• The PR changes this security warning from direct stderr output to logging, but the existing environment-variable test only checks the returned catalog entry. Add a caplog assertion for this path so a regression back to print() (or removal of the warning) is covered as well.

                    logger.warning(
                        "Using non-default extension catalog. "
                        "Only use catalogs from sources you trust.",

• Files reviewed: 2/2 changed files
• Comments generated: 1
• Review effort level: Balanced

[Quratulain-bilal]

AI Assistance Disclosure

I used AI assistance (GitHub Copilot) to identify print() calls in library code that bypass the logging framework. The refactoring was reviewed and validated by me — I verified the logger output matches the original stderr behavior and added a regression test using caplog to confirm warnings are logged at the correct level.

@mnriem I've added the AI disclosure above. This PR was developed with Copilot assistance to identify the print-to-logger migration points, and I personally reviewed the changes and wrote the caplog regression test. Ready for re-review when you have a chance.

[mnriem]

Please address Copilot feedback