Fix pip install and pysimple backend runtime

[krystophny]

Fixes pip install . failing due to invalid pyproject.toml keys and avoids clobbering the repo build/ dir by scikit-build.

Also declares f90wrap as a runtime dependency for pysimple and improves import error messages when f90wrap or _simple_backend is missing.

Test: make test (log: /tmp/simple_make_test2.log)

[qodo-code-review]

PR Compliance Guide 🔍

Below is a summary of compliance checks for this PR:

Security Compliance
⚪	Misleading import error handling Description: The ImportError handling branches on exc.name being "_simple_backend", but the code imports "simple_backend", which may mask genuine import errors and mislead users with incorrect guidance. init.py [25-36] Referred Code if getattr(exc, "name", None) == "f90wrap": raise ImportError( "f90wrap is required to import SIMPLE Python bindings. Install f90wrap." ) from exc if getattr(exc, "name", None) == "_simple_backend": raise ImportError( "Fortran extension _simple_backend failed to import. " "Rebuild SIMPLE with Python bindings enabled." ) from exc raise ImportError( "simple_backend module not found. Build SIMPLE with Python bindings enabled." ) from exc
	Misleading import error handling Description: The ImportError handling checks exc.name for "_simple_backend" while importing "simple_backend", potentially hiding the actual import failure source and causing confusing error messages. _backend.py [35-46] Referred Code if getattr(exc, "name", None) == "f90wrap": raise ImportError( "f90wrap is required to import SIMPLE Python bindings. Install f90wrap." ) from exc if getattr(exc, "name", None) == "_simple_backend": raise ImportError( "Fortran extension _simple_backend failed to import. " "Rebuild SIMPLE with Python bindings enabled." ) from exc raise ImportError( "simple_backend module not found. Build SIMPLE with Python bindings enabled." ) from exc
Ticket Compliance
🟡	🎫 #6 🔴 Make the threshold estimation for fractal dimension independent of the number of points and transparent, targeting ~1.7 for chaos classification.
🟡	🎫 #4 🔴 Add a switch to enable or disable evaluation of non-canonical z at full time-steps.
🟡	🎫 #7 🔴 Add an option to specify initial energy in simple.in.
🟡	🎫 #5 🔴 Make activation and timing of the Poincaré classifier configurable.
🟡	🎫 #10 🔴 Fix parsing of simple.in to avoid "Bad real number in item 1 of list input" error when reading cut_in_per or related input.
🟡	🎫 #8 🔴 Convert simple.in to namelist format.
🟡	🎫 #9 🔴 Change the last column in confined_fraction.dat to show number of confined particles or remove it to avoid confusion.
Codebase Duplication Compliance
⚪	Codebase context is not defined Follow the guide to enable codebase context checks.
Custom Compliance
🟢	Generic: Meaningful Naming and Self-Documenting Code Objective: Ensure all identifiers clearly express their purpose and intent, making code self-documenting Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Robust Error Handling and Edge Case Management Objective: Ensure comprehensive error handling that provides meaningful context and graceful degradation Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Secure Error Handling Objective: To prevent the leakage of sensitive system information through error messages while providing sufficient detail for internal debugging. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Secure Logging Practices Objective: To ensure logs are useful for debugging and auditing without exposing sensitive information like PII, PHI, or cardholder data. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Security-First Input Validation and Data Handling Objective: Ensure all data inputs are validated, sanitized, and handled securely to prevent vulnerabilities Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
⚪	Generic: Comprehensive Audit Trails Objective: To create a detailed and reliable record of critical system actions for security analysis and compliance. Status: No audit logs: The new error-handling paths raise ImportError with clearer messages but do not add any audit logging for these critical initialization failures, which may be desired for diagnostics. Referred Code if getattr(exc, "name", None) == "f90wrap": raise ImportError( "f90wrap is required to import SIMPLE Python bindings. Install f90wrap." ) from exc if getattr(exc, "name", None) == "_simple_backend": raise ImportError( "Fortran extension _simple_backend failed to import. " "Rebuild SIMPLE with Python bindings enabled." ) from exc raise ImportError( "simple_backend module not found. Build SIMPLE with Python bindings enabled." ) from exc Learn more about managing compliance generic rules or creating your own custom rules

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[qodo-code-review]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
General	Refactor duplicated logic into a helper Refactor the duplicated ImportError handling logic from _load_backend into a new helper function, _import_simple_backend, to centralize the logic and improve maintainability. python/pysimple/_backend.py [25-47] +def _import_simple_backend() -> ModuleType: + """Import simple_backend with detailed error handling.""" + try: + return import_module("simple_backend") + except ImportError as exc: + if getattr(exc, "name", None) == "f90wrap": + raise ImportError( + "f90wrap is required to import SIMPLE Python bindings. Install f90wrap." + ) from exc + if getattr(exc, "name", None) == "_simple_backend": + raise ImportError( + "Fortran extension _simple_backend failed to import. " + "Rebuild SIMPLE with Python bindings enabled." + ) from exc + raise ImportError( + "simple_backend module not found. Build SIMPLE with Python bindings enabled." + ) from exc + + def _load_backend() -> ModuleType: """ Lazily import the f90wrap backend. """ global _BACKEND if _BACKEND is None: - try: - _BACKEND = import_module("simple_backend") - except ImportError as exc: # pragma: no cover - exercised in test skips - if getattr(exc, "name", None) == "f90wrap": - raise ImportError( - "f90wrap is required to import SIMPLE Python bindings. Install f90wrap." - ) from exc - if getattr(exc, "name", None) == "_simple_backend": - raise ImportError( - "Fortran extension _simple_backend failed to import. " - "Rebuild SIMPLE with Python bindings enabled." - ) from exc - raise ImportError( - "simple_backend module not found. Build SIMPLE with Python bindings enabled." - ) from exc + _BACKEND = _import_simple_backend() return _BACKEND [To ensure code accuracy, apply this suggestion manually] Suggestion importance[1-10]: 7 __ Why: The suggestion correctly identifies significant code duplication introduced in the PR and proposes a sound refactoring to improve maintainability by centralizing the import logic.	Medium
	Remove duplicated import handling logic Replace the duplicated ImportError handling in init.py by importing and using the proposed _import_simple_backend helper function from the _backend module. python/pysimple/init.py [22-36] -try: - import simple_backend as _backend -except ImportError as exc: - if getattr(exc, "name", None) == "f90wrap": - raise ImportError( - "f90wrap is required to import SIMPLE Python bindings. Install f90wrap." - ) from exc - if getattr(exc, "name", None) == "_simple_backend": - raise ImportError( - "Fortran extension _simple_backend failed to import. " - "Rebuild SIMPLE with Python bindings enabled." - ) from exc - raise ImportError( - "simple_backend module not found. Build SIMPLE with Python bindings enabled." - ) from exc +from ._backend import _import_simple_backend +_backend = _import_simple_backend() + Apply / Chat Suggestion importance[1-10]: 7 __ Why: The suggestion correctly identifies duplicated import logic and proposes replacing it with a call to a centralized helper function, which improves code quality and maintainability.	Medium
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