Prevent MP2 localizer deprecation warnings during import

[Copilot]

Import-time registry stub generation constructed the deprecated MP2 natural-orbital localizer through the public factory path, emitting Python and C++ warnings.

• Factory lifecycle

  • Added a private introspection construction path without user-facing warnings.
  • Preserved warnings for explicit qdk_mp2_natural_orbitals creation.

• Stub generation

  • Reused one unwrapped instance for type and settings inspection.

• Regression coverage

  • Verifies package import is warning-free.
  • Verifies explicit creation emits one Python warning and one C++ log message.

Original prompt

Reproduce and fix issue #572 on current main in a clean cloud environment.

Importing qdk_chemistry must not emit the MP2NaturalOrbitalLocalizer deprecation message through either Python warnings or the C++ logger. Explicitly requesting the deprecated qdk_mp2_natural_orbitals implementation must continue to emit the intended deprecation warning exactly at the user-facing creation boundary.

Find and correct the underlying registration or construction lifecycle that causes an internal import-time operation to be treated as user-requested deprecated usage. Do not solve this by suppressing, filtering, catching, redirecting, or globally disabling warnings or logging, and do not add an environment-variable escape hatch. Preserve normal deprecation behavior for explicit use.

Implement the minimum focused fix and add regression tests proving both warning-free package import and retained explicit deprecation behavior. Avoid unrelated deprecation or registry refactoring. Follow the repository instructions and skills, run the smallest relevant Python tests and configured lint checks, and use "Fixes #572" in the pull request description.

[David Williams-Young (wavefunction91)]

Copilot Pick this PR back up and finish it. Do not rebuild or reinstall qdk-chemistry, and do not run the full test suite, documentation build, or broad pre-commit set on the agent runner. Use the focused regression test already added in this PR as the local validation: python -m pytest -q python/tests/test_mp2_natural_orbital_deprecation.py. If the existing environment cannot run that test without rebuilding, do not substitute a package build; inspect the implementation and rely on the PR CI jobs for compiled validation. Confirm by source inspection that import-time registry/stub introspection uses the non-warning construction path, while explicit public factory creation still emits exactly the intended Python deprecation warning and C++ log warning. Review the diff for a minimum, principled lifecycle fix rather than warning suppression. The current workflow has a macOS failure, but its logs are unavailable until the still-running workflow completes; inspect and address it only if it is caused by this PR. Keep the PR focused on #572.

[Copilot]

Copilot Pick this PR back up and finish it. Do not rebuild or reinstall qdk-chemistry, and do not run the full test suite, documentation build, or broad pre-commit set on the agent runner. Use the fo...

Finished in 613e4a9. Source inspection confirms stub introspection uses the non-warning factory path, while public creation retains one Python warning and one C++ log warning. The requested local test could not run because pytest is absent, so I did not rebuild or install. The macOS failure was caused by the new test inheriting a disabled global logger; the test now establishes and restores warning-level logging.

[Copilot]

Pull request overview

This PR prevents MP2 natural-orbital localizer deprecation warnings from being emitted during qdk_chemistry import-time registry stub generation by introducing an internal “introspection” construction path that bypasses deprecation emission, while preserving existing deprecation behavior for explicit user creation via the public factory APIs.

Changes:

• Added an internal factory creation path (FactoryAccess / _create_for_introspection) that constructs instances without triggering deprecation warnings/logs.
• Updated registry stub generation to reuse a single introspected instance for both type and settings inspection.
• Added regression tests covering warning-free stub generation and preserved explicit deprecation behavior.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
python/tests/test_mp2_natural_orbital_deprecation.py	Adds regression tests for warning-free stub generation and one-time deprecation on explicit creation.
python/src/qdk_chemistry/algorithms/registry.py	Refactors settings inspection into a helper and adds internal introspection instance creation.
python/src/qdk_chemistry/init.py	Switches stub generation to use internal introspection construction + reused instance settings inspection.
python/src/pybind11/algorithms/factory_bindings.hpp	Exposes an internal _create_for_introspection binding that bypasses deprecation emission.
cpp/include/qdk/chemistry/algorithms/algorithm.hpp	Moves deprecation logging into public create() and adds FactoryAccess to call internal create_impl() without logging.

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[Copilot]

Pull request overview

Copilot reviewed 6 out of 6 changed files in this pull request and generated 1 comment.