Migration to peprs

[khoroshevskyi]

Changes:

• Adding peprs to pepdbagent, to speed up validation and pep saving

TODO:

• ❗ If this PR includes a new database schema migration, following steps are completed: Database Version Migration
• Version of pepdbagent updated in __version__.py file
• Changelog updated

[Copilot]

Pull request overview

Migrates pepdbagent from peppy to peprs for project/sample handling, updating the raw PEP dict shape and adjusting tests + fixture PEPs accordingly.

Changes:

• Replace peppy imports/usages with peprs across pepdbagent modules and tests.
• Update raw project/sample dict conventions from _config/_sample_dict to config/samples (and subsamples where applicable).
• Adjust test fixture PEP YAMLs and expectations to accommodate peprs parsing/inference behavior.

Reviewed changes

Copilot reviewed 19 out of 19 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
pepdbagent/modules/project.py	Switches project CRUD paths to peprs constants/dict shape; updates sample retrieval conversion.
pepdbagent/modules/sample.py	Returns peprs.Sample when raw=False and updates sample-name lookup key handling.
pepdbagent/modules/view.py	Updates view retrieval to return peprs projects / peprs-style raw dicts.
pepdbagent/models.py	Updates pydantic raw-project model aliases to peprs constants.
pepdbagent/utils.py	Switches SAMPLE_RAW_DICT_KEY import to peprs constant.
pepdbagent/const.py	Removes outdated peppy-const comment.
requirements/requirements-all.txt	Replaces peppy dependency with peprs.
tests/utils.py	Uses peprs.Project(...) during DB seeding; adds skip-on-parse-failure behavior.
tests/test_project.py	Updates project retrieval/serialization assertions to peprs dict shape and pandas conversion.
tests/test_updates.py	Updates update flows to use samples list and peprs.Project.from_dict.
tests/test_samples.py	Updates sample type assertions to peprs.Sample and adjusts expectations for inferred numeric types.
tests/test_project_history.py	Updates history update flows to use peprs dict shape (samples, config).
tests/data/private_test/remove/project_config.yaml	Removes a derive source entry to fit updated parsing/fixtures.
tests/data/private_test/derive/project_config.yaml	Removes a derive source entry to fit updated parsing/fixtures.
tests/data/private_test/amendments1/project_config.yaml	Removes a derive source entry to fit updated parsing/fixtures.
tests/data/namespace3/remove/project_config.yaml	Removes a derive source entry to fit updated parsing/fixtures.
tests/data/namespace3/piface/project_config.yaml	Adjusts pipeline_interfaces fixture value format.
tests/data/namespace2/derive/project_config.yaml	Removes a derive source entry to fit updated parsing/fixtures.
tests/data/namespace1/amendments1/project_config.yaml	Removes a derive source entry to fit updated parsing/fixtures.

Comments suppressed due to low confidence (1)

pepdbagent/modules/project.py:103

• The get() docstring still describes the old peppy raw-project keys (_config, _sample_dict, _subsample_dict). After migrating to peprs, the raw dict returned here uses config/samples/subsamples (via peprs.const). Please update the docstring so it matches the actual return shape.

        :return: peprs.Project object with found project or dict with unprocessed
            PEP elements: {
                name: str
                description: str
                _config: dict

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[Copilot]

Using peprs.Project.to_dict(raw=True, by_sample=True) will preserve peprs/polars-inferred column dtypes (e.g., numeric columns become ints). This appears to be a behavioral change vs the prior peppy-based behavior (tests now expect time == 0 instead of '0') and can be a breaking API change for clients expecting strings. Consider normalizing sample values to strings before persisting, or explicitly documenting this type change as part of the migration.