Replace print-based diagnostics with the logging module#76
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All modules now log through named loggers under the 'pleque' hierarchy. The package root installs a NullHandler (library best practice) and gains a pleque.set_log_level() convenience helper that attaches a single stream handler for interactive use. https://claude.ai/code/session_01T8Bv18R1iJkgxQ7e4rTAKc
- Initialisation hints (mg_axis, psi_lcfs, x_points, strike_points) can now also be provided as basedata variables; explicit arguments take precedence with a logged warning (idea from MR !63 / feature/fast_forward_init). - init_method is now functional: 'full' ignores all hints, 'hints' (default) uses them to assist the recognition, and 'fast_forward' takes the axis and X-point hints as final and skips the critical-point search (with fallback to 'hints' when the required hints are missing). Unknown values raise ValueError; read_geqdsk and EquilibriaTimeSlices.get_time_slice pass the option through. - The bare except around the initialisation now catches Exception, logs the traceback, and draws the (blocking) debug plot only when the new debug_plots setting is enabled (PLEQUE_DEBUG_PLOTS=1); the same gating applies to the diagnostic plot in find_extremes. Initialisation failures no longer open matplotlib windows in headless/CI environments. - First-wall resolution extracted into _resolve_first_wall with the synthetic rectangular wall construction moved to equi_tools.synthesize_rectangular_wall; the chosen wall source is logged. - find_extremes warns when no O-point candidate is found; F'=FF'/F is guarded against division by zero. - Class and constructor docstrings now describe the actual initialisation sequence, including where it deliberately differs from the thesis-chapter description (1D profile splines built after the critical-point search; LCFS found by marching squares + downhill refinement, not by field-line tracing). https://claude.ai/code/session_01T8Bv18R1iJkgxQ7e4rTAKc
- New tests/test_equilibrium_init.py: synthetic-wall generation, vacuum equilibria, profile-derivative vs direct-profile equivalence, hint arguments and basedata hints (incl. duplicity warning), init_method full/hints/fast_forward consistency on bundled cases, double-null X-points, spline-order override, logging assertions, and the failure path (logged exception, no debug plot by default, debug plot with PLEQUE_DEBUG_PLOTS=1). - The synthetic analytic equilibrium builder moved from tests/test_invert_equilibrium.py to pleque.tests.utils (synthetic_dataset/synthetic_test_wall) for reuse. - tests/test_equilibria.py::test_critical placeholder replaced with real assertions for limiter and X-point configurations. https://claude.ai/code/session_01T8Bv18R1iJkgxQ7e4rTAKc
Resolve conflict in pleque/core/coordinates.py: keep the Coordinates refactor from develop (PR #75) and re-apply the named logger, converting the warning print added by the refactor to logger.warning as well. https://claude.ai/code/session_01T8Bv18R1iJkgxQ7e4rTAKc
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All modules now log through named loggers under the 'pleque' hierarchy.
The package root installs a NullHandler (library best practice) and gains
a pleque.set_log_level() convenience helper that attaches a single stream
handler for interactive use.
https://claude.ai/code/session_01T8Bv18R1iJkgxQ7e4rTAKc