Update schema dependency and update sample data files accordingly

[eecavanna]

On this branch, I made three main changes:

1. I "bumped" the schema version that the ingest script uses by default, to the latest version in the bertron-schema repository.
2. I updated the data files used by the test suite so that they comply with that schema. This involves removing the has_ prefix from some field names.
3. I pinned the schema dependency used by the API so that it matches the version that the ingest script uses by default.

I also made these minor changes:

1. I replaced an invocation of a deprecated function related to timestamp generation, with an invocation of a function that is not deprecated. Now, the pytest output will not show a warning related to the original invocation.
2. I added instructions for running the test suite from a container shell, which makes it so the pytest output appears in color, like this:
   

[Copilot]

Pull Request Overview

This PR updates the project to use a specific version of the bertron-schema dependency and ensures test data files comply with the updated schema. It also includes minor improvements to deprecation warnings and test documentation.

• Pin bertron-schema dependency to a specific commit hash instead of using the latest version
• Update JSON test data files to use new schema field names (removing "has_" prefixes)
• Replace deprecated datetime.utcnow() with datetime.now(UTC) to eliminate pytest warnings

Reviewed Changes

Copilot reviewed 6 out of 7 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
pyproject.toml	Updates bertron-schema dependency to specific commit with detailed comments
tests/data/nmdc-example.json	Updates field names to match new schema (removes "has_" prefixes)
tests/data/monet-example.json	Updates field names to match new schema (removes "has_" prefixes)
tests/data/gold-example.json	Updates field names to match new schema (removes "has_" prefixes)
mongodb/ingest_data.py	Replaces deprecated datetime function and updates schema URL to match dependency
CONTRIBUTING.md	Adds instructions for running tests in container with colored output

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[jeff-cohere]

Thanks for the helpful comments explaining how to maintain the schema dependencies, Eric!