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jax fortran oracle tests (#1404) Restored clubb_jax vs clubb_f2py fortran bindings tests that compare the outputs of clubb_jax functions directly to their compiled fortran counterparts. clubb_jax changes are minimal: Use hardcoded pi that matches the pi used in fortran instead of jnp.pi remove the clubb_release hardcoded path from the gases_ckd_data.py parser. 2026-10-20 14:57:07 -0500bb08268b3348ef71f7eec35eb0fb5ee4eb10197dRestore jax fortran oracle tests (#1404)addclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_mirror_lower_triangular_vs_fortran.pyaddclubb_jax/pytests/f2py_unit_test_helpers.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_hydrostatic_vs_fortran.pyeditclubb_python_api/f2py_fortran_wrappers/skx_module_wrapper.F90addclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_responder_params_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_binormal_moments_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_w_up_in_cloud_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_cholesky_corr_mtx_approx_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_setter_var_params_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_clip_variance_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_skx_func_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_Nc_Ncn_eqns_vs_fortran.pyeditclubb_jax/src/CLUBB_core/advance_helper_module.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_new_pdf_main_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_advance_xp3_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_calc_ddzt_umvm_sqd_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_new_hybrid_pdf_main_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_new_pdf_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_fill_holes_mean_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_mono_flux_limiter_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_pdf_utilities_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_pdf_moment_integrals_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_ly93_pdf_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_spurious_source_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_remapping_module_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_cholesky_factor_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_adg2_driver_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_compute_gamma_skw_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_cos_solar_zen_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_T_in_K_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_sunray_sw_vs_fortran.pyedittests/run_pytests.shaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_close_luhar_pdf_vs_fortran.pyedit.agents/skills/clubb-pytests/SKILL.mdaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_advance_helper_extras_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_rcm_sat_adj_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_sponge_damp_xp23_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_mixing_length_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_calc_comp_corrs_binormal_vs_fortran.pyeditclubb_python_api/clubb_f2py.pyfaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_coefs_semiimpl_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_xpyp_term_ta_godunov_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_limits_f_x_responder_vs_fortran.pyeditclubb_python_api/clubb_python/CLUBB_core/interpolation.pyeditjenkins_tests/clubb_jax/Jenkinsfileaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_clip_skewness_vs_fortran.pyeditclubb_python_api/clubb_python/clubb_api.pyaddclubb_python_api/clubb_python/microphys.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_smooth_heaviside_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_diagnose_correlations_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_saturation_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_diagnose_xp3_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_calc_wp3_on_wp2_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_xpyp_term_ta_pdf_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_pos_definite_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_new_tsdadg_pdf_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_diagnose_upxp_vs_fortran.pyedittests/README.mdaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_clip_covar_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_mean_adv_vs_fortran.pyaddclubb_python_api/f2py_fortran_wrappers/cloud_sed_module_wrapper.F90addclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_diffusion_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_interpolation_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_luhar_3d_driver_vs_fortran.pyeditclubb_jax/src/Radiation/BUGSrad/gases_ckd_data.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_solver_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_cloud_drop_sed_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_calc_roots_vs_fortran.pyeditclubb_python_api/f2py_fortran_wrappers/interpolation_wrapper.F90addclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_grid_operators_vs_fortran.pyeditclubb_jax/README.mdaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_remapping_ppm_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_sfc_varnce_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_param_names_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_calendar_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_calculate_w_responder_params_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_compute_sigma_sqd_w_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/conftest.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_calculate_thvm_vs_fortran.pyeditclubb_python_api/clubb_python/CLUBB_core/skx_module.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_pvertinterp_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_config_flags_complete_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_luhar_params_vs_fortran.pyclubb_jax/src/CLUBB_core/fill_holes.py.agents/skills/clubb-documentation/language/SKILL.mdclubb_jax/pytests/auto_llm_generated_pytests/test_multicolumn_microphys_adapters.pyclubb_jax/src/Microphys/pdf_hydromet_microphys_wrapper.py.agents/skills/clubb-documentation/change-messages/SKILL.md82c8fdb39580f015d26f9cb021b8376696d96b7f1792549343000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comFix per-column inputs in JAX microphysics (#1407) * Align JAX microphysics with per-column Fortran inputs Pass each column’s parameters into PDF preparation and its own grid spacing into hydrometeor hole filling after the master multi-column fix. The previous scalar remapping disagreed with current Fortran from step 2. Six focused eager/JIT checks pass, covering column independence, conserved mass and derivatives. Both regressions detect the retained pre-fix adapters; full case comparisons are in progress. (cherry picked from commit 7fc8280d9ce3fe0ec51bf5e7f3cfd3a0e7c8838a) * Explain PR problems before describing their solutions Change-first PR openings make their motivation harder to follow. Use Motivation and Change to describe the problem first, then its cause and the proposed solution; align the language guidance with that order. Both documentation skills validate, and relative-link checks pass. 2026-10-20 21:22:23 -050082c8fdb39580f015d26f9cb021b8376696d96b7fFix per-column inputs in JAX microphysics (#1407)edit.agents/skills/clubb-documentation/change-messages/SKILL.mdeditclubb_jax/src/CLUBB_core/fill_holes.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_multicolumn_microphys_adapters.pyeditclubb_jax/src/Microphys/pdf_hydromet_microphys_wrapper.pyedit.agents/skills/clubb-documentation/language/SKILL.mdclubb_jax/src/CLUBB_core/parameter_indices.pyinput/parameter_and_flag_configs/coriolis_cases/atex_long_parameters.ininput/parameter_and_flag_configs/e3sm_maint32/tunable_parameters.inclubb_jax/src/CLUBB_core/model_flags.pyclubb_python_api/pytests/auto_llm_generated_pytests/test_python_port_api_coverage.pyclubb_python_api/clubb_python/CLUBB_core/mixing_length.pyinput/flag_sets/run_bindiff_w_flags_config_core_flags.jsoninput/parameter_and_flag_configs/coriolis_cases/coriolis_test_parameters.intuner/pytests/test_parameter_ranges.pysrc/CLUBB_core/mixing_length.F90src/clubb_tuner.F90input/flag_sets/config_core_flags_wo_never_supported_jax_features.jsoninput/parameter_and_flag_configs/Lscale/configurable_model_flags.insrc/CLUBB_core/model_flags.F90clubb_python_driver/advance_clubb_core.pyclubb_python_api/clubb_python/derived_types/config_flags_converter.pyclubb_python_api/f2py_fortran_wrappers/mixing_length_wrapper.F90clubb_python_driver/clubb_constants.pyclubb_jax/tests/test_loss_driver.pysrc/G_unit_test_types/pdf_parameter_tests.F90tests/run_jax_vs_fortran_cases.pysrc/SILHS/silhs_importance_sample_module.F90clubb_jax/pytests/auto_llm_generated_pytests/test_mixing_length.pysrc/CLUBB_core/parameters_tunable.F90clubb_jax/pytests/auto_llm_generated_pytests/test_param_names.pyclubb_jax/tests/run_jax_timestep_gradient_test.pyclubb_jax/src/CLUBB_core/mixing_length.pyinput/parameter_and_flag_configs/tauMatchLscale/configurable_model_flags.ininput/parameter_and_flag_configs/e3sm_maint32/maint32_defaults_report.mdclubb_jax/tests/benchmark_mixing_length.pysrc/CLUBB_core/clubb_api_module.F90utilities/clubb_settings_validation.pytests/run_python_vs_fortran_cases.pyclubb_python_api/clubb_f2py.pyfclubb_jax/README.mdinput/parameter_and_flag_configs/tauMatchLscale/tunable_parameters.indash_app/misc_tab/mixing_length_trajectories/analysis.pyclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_advance_xm_wpxp.pyinput/parameter_and_flag_configs/e3sm_maint32/configurable_model_flags.ininput/parameter_and_flag_configs/default/configurable_model_flags.indash_app/pytests/test_tune_callbacks_settings.pyinput/parameter_and_flag_configs/compatible_r8029/configurable_model_flags.inclubb_jax/src/CLUBB_core/parameters_tunable.pyinput/parameter_and_flag_configs/e3sm/configurable_model_flags.intuner/pytests/test_adam_baselines.pyinput/flag_sets/run_bindiff_w_flags_config_host_flags.json.agents/skills/clubb-testing-and-reporting/SKILL.mdclubb_jax/src/CLUBB_core/advance_clubb_core_module.pysrc/CLUBB_core/parameter_indices.F90clubb_python_api/pytests/auto_llm_generated_pytests/test_init_sequence.pyinput/parameter_and_flag_configs/e3sm/tunable_parameters.indash_app/pytests/test_run_runtime.pyclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_mixing_length_vs_fortran.pysrc/G_unit_test_types/spurious_source_test.F90clubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_mixing_length.pyinput/parameter_and_flag_configs/default/tunable_parameters.insrc/CLUBB_core/numerical_check.F90clubb_jax/src/CLUBB_core/config_flags.pyinput/parameter_and_flag_configs/coriolis_cases/ekman_parameters.insrc/CLUBB_core/advance_clubb_core_module.F90tests/pytests/test_run_clubb_conv_test.pysrc/clubb_driver.F90utilities/pytests/test_settings_rules.py.agents/skills/clubb-finalization/SKILL.mddash_app/pytests/test_callbacks_runs.pyclubb_jax/src/CLUBB_core/numerical_check.pyinput/parameter_and_flag_configs/Lscale/tunable_parameters.ininput/parameter_and_flag_configs/compatible_r8029/tunable_parameters.inclubb_python_api/f2py_fortran_wrappers/model_flags_wrapper.F90clubb_python_api/clubb_python/derived_types/config_flags.pydfa3b53697658b3f5f24cb5ae83c8e11fe0c0d651792614890000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comPort differentiable legacy mixing length and migrate its selector (#1408) * Make legacy mixing length differentiable and migrate its selector The value-dependent JAX parcel loops prevented reverse differentiation and serialized independent launches. Use fixed scans with masks, batched launch levels and per-column error state while preserving Fortran stopping rules. Port the remaining legacy/tau branches and use the configured method in driver derivative checks. Replace the logical tau switch with Lscale_method (1=legacy, 2=tau), and rename mu to Lscale_mu_entrain throughout core, bindings, inputs and validation. Keep 102 tunable parameters; coherent physics is a separate follow-up. Local GNU Debug/API build, source checks, 447 unit checks and 240 API checks pass. Integrated Jenkins validation follows this checkpoint. * Read renamed entrainment parameters in Dash trajectories Saved output now names parcel entrainment Lscale_mu_entrain. Prefer that parameter while retaining support for older files saved with mu. Update Dash test settings to use the integer mixing-length selector. The local Dash suite passes 552 checks. * Require completed tests before branch finalization Requests to finalize immediately still require applicable Jenkins jobs to finish and their results to be reviewed. Distinguish validation checkpoints from a completed handoff, and report relevant stages of baseline-failing jobs. 2026-10-21 15:34:50 -0500dfa3b53697658b3f5f24cb5ae83c8e11fe0c0d65Port differentiable legacy mixing length and migrate its selector 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Hueblerhuebler@uwm.eduThe previous commit changed flags, which will now break the BFB tests even when the bit changing message is included, so now we need to have RESOLVED:dfa3b53697658b3f5f24cb5ae83c8e11fe0c0d65 messsages or enable temporary backwards compatibility. 2026-10-21 15:41:22 -0500b2a6a9ceab12125d4a2542da4e20736039f3a744The previous commit changed flags, which will now break the BFB tests even when the bit changing message is included, so now we need to have RESOLVED:dfa3b53697658b3f5f24cb5ae83c8e11fe0c0d65 messsages or enable temporary backwards compatibility.editREADMEgithttps://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerhttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyfalse61https://carson.math.uwm.edu/jenkins/view/clubb_branch_tests/job/clubb_branch_python/61/59https://carson.math.uwm.edu/jenkins/view/clubb_branch_tests/job/clubb_branch_python/59/BRANCHorigin/mixing-length-api-jaxINCLUDE_GENERATED_PYTESTSfalseStarted by user 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