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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 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_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_calc_wp3_on_wp2_vs_fortran.pyedit.agents/skills/clubb-pytests/SKILL.mdaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_T_in_K_vs_fortran.pyeditclubb_python_api/f2py_fortran_wrappers/interpolation_wrapper.F90editclubb_python_api/f2py_fortran_wrappers/skx_module_wrapper.F90addclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_pos_definite_vs_fortran.pyeditclubb_python_api/clubb_python/CLUBB_core/skx_module.pyeditclubb_jax/src/Radiation/BUGSrad/gases_ckd_data.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_smooth_heaviside_vs_fortran.pyeditclubb_python_api/clubb_python/CLUBB_core/interpolation.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_w_up_in_cloud_vs_fortran.pyaddclubb_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_diagnose_upxp_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_hydrostatic_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_calc_roots_vs_fortran.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_Nc_Ncn_eqns_vs_fortran.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_rcm_sat_adj_vs_fortran.pyaddclubb_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_skx_func_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_param_names_vs_fortran.pyaddclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_diagnose_xp3_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.mdaddclubb_jax/pytests/auto_llm_generated_pytests/test_multicolumn_microphys_adapters.pyeditclubb_jax/src/Microphys/pdf_hydromet_microphys_wrapper.pyeditclubb_jax/src/CLUBB_core/fill_holes.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/parameter_and_flag_configs/Lscale/configurable_model_flags.ininput/flag_sets/config_core_flags_wo_never_supported_jax_features.jsonsrc/CLUBB_core/model_flags.F90clubb_python_api/clubb_python/derived_types/config_flags_converter.pyclubb_python_driver/advance_clubb_core.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.F90src/SILHS/silhs_importance_sample_module.F90tests/run_jax_vs_fortran_cases.pyclubb_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.mdutilities/clubb_settings_validation.pyclubb_jax/tests/benchmark_mixing_length.pysrc/CLUBB_core/clubb_api_module.F90tests/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.py.agents/skills/clubb-testing-and-reporting/SKILL.mdinput/flag_sets/run_bindiff_w_flags_config_host_flags.jsonclubb_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.pyclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_mixing_length.pysrc/G_unit_test_types/spurious_source_test.F90input/parameter_and_flag_configs/default/tunable_parameters.insrc/CLUBB_core/numerical_check.F90clubb_jax/src/CLUBB_core/config_flags.pysrc/CLUBB_core/advance_clubb_core_module.F90input/parameter_and_flag_configs/coriolis_cases/ekman_parameters.intests/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/clubb_python/derived_types/config_flags.pyclubb_python_api/f2py_fortran_wrappers/model_flags_wrapper.F90dfa3b53697658b3f5f24cb5ae83c8e11fe0c0d651792614890000https://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 (#1408)edit.agents/skills/clubb-testing-and-reporting/SKILL.mdeditclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_mixing_length.pyeditclubb_python_api/clubb_python/derived_types/config_flags_converter.pyeditsrc/SILHS/silhs_importance_sample_module.F90editdash_app/pytests/test_tune_callbacks_settings.pyedittuner/pytests/test_parameter_ranges.pyeditclubb_python_driver/advance_clubb_core.pyeditinput/parameter_and_flag_configs/coriolis_cases/atex_long_parameters.ineditclubb_jax/src/CLUBB_core/parameters_tunable.pyeditinput/parameter_and_flag_configs/Lscale/configurable_model_flags.ineditclubb_jax/README.mdeditclubb_python_driver/clubb_constants.pyeditclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_advance_xm_wpxp.pyedittests/run_jax_vs_fortran_cases.pyedittests/pytests/test_run_clubb_conv_test.pyeditsrc/CLUBB_core/numerical_check.F90editinput/parameter_and_flag_configs/tauMatchLscale/configurable_model_flags.ineditutilities/clubb_settings_validation.pyeditclubb_python_api/pytests/auto_llm_generated_pytests/test_init_sequence.pyeditclubb_python_api/pytests/auto_llm_generated_pytests/test_python_port_api_coverage.pyeditclubb_jax/src/CLUBB_core/numerical_check.pyeditinput/parameter_and_flag_configs/default/tunable_parameters.ineditsrc/CLUBB_core/mixing_length.F90addclubb_jax/tests/benchmark_mixing_length.pyeditinput/parameter_and_flag_configs/e3sm_maint32/tunable_parameters.ineditclubb_jax/tests/test_loss_driver.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_param_names.pyeditsrc/CLUBB_core/parameter_indices.F90editsrc/CLUBB_core/advance_clubb_core_module.F90editinput/flag_sets/config_core_flags_wo_never_supported_jax_features.jsoneditclubb_jax/src/CLUBB_core/config_flags.pyeditsrc/CLUBB_core/clubb_api_module.F90editinput/parameter_and_flag_configs/tauMatchLscale/tunable_parameters.ineditclubb_jax/src/CLUBB_core/mixing_length.pyeditinput/parameter_and_flag_configs/Lscale/tunable_parameters.ineditinput/parameter_and_flag_configs/default/configurable_model_flags.ineditclubb_python_api/clubb_python/derived_types/config_flags.pyeditinput/parameter_and_flag_configs/e3sm_maint32/configurable_model_flags.ineditsrc/clubb_tuner.F90editinput/flag_sets/run_bindiff_w_flags_config_core_flags.jsoneditinput/parameter_and_flag_configs/e3sm/configurable_model_flags.inedittuner/pytests/test_adam_baselines.pyeditsrc/clubb_driver.F90editinput/parameter_and_flag_configs/e3sm_maint32/maint32_defaults_report.mdeditsrc/CLUBB_core/parameters_tunable.F90editclubb_jax/tests/run_jax_timestep_gradient_test.pyeditclubb_python_api/clubb_python/CLUBB_core/mixing_length.pyeditdash_app/misc_tab/mixing_length_trajectories/analysis.pyeditclubb_python_api/clubb_f2py.pyfeditsrc/CLUBB_core/model_flags.F90addclubb_jax/pytests/auto_llm_generated_pytests/test_mixing_length.pyeditinput/parameter_and_flag_configs/coriolis_cases/coriolis_test_parameters.ineditsrc/G_unit_test_types/spurious_source_test.F90editclubb_jax/src/CLUBB_core/parameter_indices.pyeditclubb_jax/src/CLUBB_core/advance_clubb_core_module.pyeditinput/parameter_and_flag_configs/compatible_r8029/tunable_parameters.ineditclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_mixing_length_vs_fortran.pyedittests/run_python_vs_fortran_cases.pyeditsrc/G_unit_test_types/pdf_parameter_tests.F90editutilities/pytests/test_settings_rules.pyedit.agents/skills/clubb-finalization/SKILL.mdeditclubb_jax/src/CLUBB_core/model_flags.pyeditdash_app/pytests/test_callbacks_runs.pyeditclubb_python_api/f2py_fortran_wrappers/mixing_length_wrapper.F90editinput/flag_sets/run_bindiff_w_flags_config_host_flags.jsoneditinput/parameter_and_flag_configs/e3sm/tunable_parameters.ineditinput/parameter_and_flag_configs/coriolis_cases/ekman_parameters.ineditdash_app/pytests/test_run_runtime.pyeditclubb_python_api/f2py_fortran_wrappers/model_flags_wrapper.F90editinput/parameter_and_flag_configs/compatible_r8029/configurable_model_flags.inREADMEb2a6a9ceab12125d4a2542da4e20736039f3a7441792615282000https://carson.math.uwm.edu/jenkins/user/hueblerGunther 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 Hueblerhueblerhttps://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreplyfalseBRANCHorigin/mixing_length_fix_2Started by user agent_devagent_devagent_dev0000707168858138860.82157945794

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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. 2026-10-21 12:48:48 -0500c3e58209f1f366289b7cca342cb8a62205ae84e7Make legacy mixing length differentiable and migrate its selectoreditsrc/clubb_tuner.F90editclubb_jax/README.mdeditsrc/CLUBB_core/clubb_api_module.F90editsrc/CLUBB_core/mixing_length.F90editclubb_jax/pytests/auto_llm_generated_pytests/test_param_names.pyeditclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_mixing_length_vs_fortran.pyeditclubb_python_api/pytests/auto_llm_generated_pytests/test_python_port_api_coverage.pyeditinput/parameter_and_flag_configs/e3sm_maint32/maint32_defaults_report.mdedittuner/pytests/test_parameter_ranges.pyeditclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_mixing_length.pyeditclubb_python_driver/advance_clubb_core.pyeditsrc/CLUBB_core/advance_clubb_core_module.F90editclubb_jax/tests/run_jax_timestep_gradient_test.pyeditclubb_python_api/f2py_fortran_wrappers/mixing_length_wrapper.F90editclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_advance_xm_wpxp.pyeditsrc/G_unit_test_types/pdf_parameter_tests.F90editclubb_python_api/pytests/auto_llm_generated_pytests/test_init_sequence.pyeditinput/parameter_and_flag_configs/Lscale/tunable_parameters.inedittests/pytests/test_run_clubb_conv_test.pyeditclubb_jax/src/CLUBB_core/model_flags.pyeditinput/parameter_and_flag_configs/coriolis_cases/coriolis_test_parameters.ineditinput/parameter_and_flag_configs/tauMatchLscale/configurable_model_flags.ineditclubb_jax/src/CLUBB_core/advance_clubb_core_module.pyedittests/run_jax_vs_fortran_cases.pyeditclubb_python_api/clubb_python/derived_types/config_flags_converter.pyeditinput/parameter_and_flag_configs/e3sm/tunable_parameters.ineditclubb_jax/src/CLUBB_core/parameter_indices.pyeditclubb_jax/src/CLUBB_core/parameters_tunable.pyaddclubb_jax/tests/benchmark_mixing_length.pyeditinput/parameter_and_flag_configs/e3sm/configurable_model_flags.ineditsrc/CLUBB_core/numerical_check.F90editutilities/clubb_settings_validation.pyeditinput/flag_sets/run_bindiff_w_flags_config_core_flags.jsoneditclubb_jax/src/CLUBB_core/mixing_length.pyeditsrc/CLUBB_core/parameter_indices.F90editsrc/CLUBB_core/parameters_tunable.F90editsrc/CLUBB_core/model_flags.F90edittuner/pytests/test_adam_baselines.pyeditsrc/clubb_driver.F90editinput/flag_sets/config_core_flags_wo_never_supported_jax_features.jsonedittests/run_python_vs_fortran_cases.pyeditclubb_python_api/clubb_f2py.pyfeditutilities/pytests/test_settings_rules.pyeditinput/parameter_and_flag_configs/default/configurable_model_flags.ineditinput/flag_sets/run_bindiff_w_flags_config_host_flags.jsoneditinput/parameter_and_flag_configs/e3sm_maint32/tunable_parameters.ineditinput/parameter_and_flag_configs/tauMatchLscale/tunable_parameters.ineditinput/parameter_and_flag_configs/Lscale/configurable_model_flags.ineditsrc/G_unit_test_types/spurious_source_test.F90editinput/parameter_and_flag_configs/compatible_r8029/configurable_model_flags.ineditclubb_jax/src/CLUBB_core/numerical_check.pyeditinput/parameter_and_flag_configs/compatible_r8029/tunable_parameters.ineditclubb_python_api/clubb_python/derived_types/config_flags.pyeditclubb_jax/src/CLUBB_core/config_flags.pyeditinput/parameter_and_flag_configs/default/tunable_parameters.ineditclubb_jax/tests/test_loss_driver.pyeditclubb_python_api/clubb_python/CLUBB_core/mixing_length.pyeditinput/parameter_and_flag_configs/coriolis_cases/ekman_parameters.inaddclubb_jax/pytests/auto_llm_generated_pytests/test_mixing_length.pyeditclubb_python_driver/clubb_constants.pyeditclubb_python_api/f2py_fortran_wrappers/model_flags_wrapper.F90editinput/parameter_and_flag_configs/coriolis_cases/atex_long_parameters.ineditsrc/SILHS/silhs_importance_sample_module.F90editinput/parameter_and_flag_configs/e3sm_maint32/configurable_model_flags.indash_app/pytests/test_run_runtime.pydash_app/misc_tab/mixing_length_trajectories/analysis.pydash_app/pytests/test_tune_callbacks_settings.pydash_app/pytests/test_callbacks_runs.pyc35d6c46613a9fef38eef005d3c95b6f19eff2c21792604928000https://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerhuebler@uwm.eduRead 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. 2026-10-21 12:48:48 -0500c35d6c46613a9fef38eef005d3c95b6f19eff2c2Read renamed entrainment parameters in Dash trajectorieseditdash_app/pytests/test_tune_callbacks_settings.pyeditdash_app/misc_tab/mixing_length_trajectories/analysis.pyeditdash_app/pytests/test_run_runtime.pyeditdash_app/pytests/test_callbacks_runs.py.agents/skills/clubb-finalization/SKILL.md.agents/skills/clubb-testing-and-reporting/SKILL.md6cc78c6532ba5d69fad302a171d83ff22497b3f51792604928000https://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerhuebler@uwm.eduRequire 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 12:48:48 -05006cc78c6532ba5d69fad302a171d83ff22497b3f5Require completed tests before branch finalizationedit.agents/skills/clubb-testing-and-reporting/SKILL.mdedit.agents/skills/clubb-finalization/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.insrc/CLUBB_core/mixing_length.F90tuner/pytests/test_parameter_ranges.pysrc/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_jax/tests/test_loss_driver.pyclubb_python_driver/clubb_constants.pysrc/G_unit_test_types/pdf_parameter_tests.F90src/SILHS/silhs_importance_sample_module.F90tests/run_jax_vs_fortran_cases.pyclubb_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.mdsrc/CLUBB_core/clubb_api_module.F90utilities/clubb_settings_validation.pyclubb_jax/tests/benchmark_mixing_length.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.py.agents/skills/clubb-testing-and-reporting/SKILL.mdinput/flag_sets/run_bindiff_w_flags_config_host_flags.jsonclubb_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.pyclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_mixing_length.pysrc/G_unit_test_types/spurious_source_test.F90input/parameter_and_flag_configs/default/tunable_parameters.insrc/CLUBB_core/numerical_check.F90clubb_jax/src/CLUBB_core/config_flags.pysrc/CLUBB_core/advance_clubb_core_module.F90input/parameter_and_flag_configs/coriolis_cases/ekman_parameters.intests/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/clubb_python/derived_types/config_flags.pyclubb_python_api/f2py_fortran_wrappers/model_flags_wrapper.F90dfa3b53697658b3f5f24cb5ae83c8e11fe0c0d651792614890000https://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 (#1408)editinput/parameter_and_flag_configs/coriolis_cases/coriolis_test_parameters.inedit.agents/skills/clubb-finalization/SKILL.mdeditclubb_python_api/clubb_f2py.pyfeditclubb_python_api/pytests/auto_llm_generated_pytests/test_python_port_api_coverage.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_mixing_length.pyeditinput/parameter_and_flag_configs/coriolis_cases/atex_long_parameters.ineditclubb_jax/src/CLUBB_core/mixing_length.pyeditsrc/CLUBB_core/clubb_api_module.F90editclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_advance_xm_wpxp.pyeditinput/parameter_and_flag_configs/e3sm_maint32/tunable_parameters.ineditinput/parameter_and_flag_configs/e3sm/tunable_parameters.ineditsrc/CLUBB_core/mixing_length.F90editinput/parameter_and_flag_configs/default/tunable_parameters.ineditclubb_jax/src/CLUBB_core/config_flags.pyedittests/pytests/test_run_clubb_conv_test.pyedittests/run_python_vs_fortran_cases.pyeditclubb_jax/src/CLUBB_core/numerical_check.pyeditutilities/clubb_settings_validation.pyeditclubb_python_driver/advance_clubb_core.pyeditclubb_jax/src/CLUBB_core/model_flags.pyeditclubb_python_api/clubb_python/derived_types/config_flags_converter.pyeditclubb_jax/pytests/auto_llm_generated_pytests/f2py_unit_tests/test_mixing_length_vs_fortran.pyeditinput/parameter_and_flag_configs/e3sm/configurable_model_flags.ineditinput/parameter_and_flag_configs/compatible_r8029/tunable_parameters.ineditclubb_jax/src/CLUBB_core/advance_clubb_core_module.pyeditsrc/CLUBB_core/parameters_tunable.F90editclubb_python_api/f2py_fortran_wrappers/mixing_length_wrapper.F90editclubb_jax/README.mdeditinput/parameter_and_flag_configs/compatible_r8029/configurable_model_flags.ineditinput/parameter_and_flag_configs/e3sm_maint32/configurable_model_flags.ineditsrc/G_unit_test_types/pdf_parameter_tests.F90edit.agents/skills/clubb-testing-and-reporting/SKILL.mdeditclubb_python_api/clubb_python/derived_types/config_flags.pyeditinput/parameter_and_flag_configs/tauMatchLscale/configurable_model_flags.ineditsrc/SILHS/silhs_importance_sample_module.F90editsrc/clubb_tuner.F90edittuner/pytests/test_adam_baselines.pyeditclubb_jax/tests/test_loss_driver.pyeditdash_app/pytests/test_tune_callbacks_settings.pyeditutilities/pytests/test_settings_rules.pyeditclubb_jax/src/CLUBB_core/parameters_tunable.pyeditinput/flag_sets/config_core_flags_wo_never_supported_jax_features.jsoneditclubb_jax/tests/run_jax_timestep_gradient_test.pyeditclubb_python_api/f2py_fortran_wrappers/model_flags_wrapper.F90editinput/parameter_and_flag_configs/tauMatchLscale/tunable_parameters.ineditclubb_jax/pytests/auto_llm_generated_pytests/test_param_names.pyeditdash_app/misc_tab/mixing_length_trajectories/analysis.pyaddclubb_jax/tests/benchmark_mixing_length.pyeditinput/flag_sets/run_bindiff_w_flags_config_host_flags.jsoneditsrc/clubb_driver.F90editinput/flag_sets/run_bindiff_w_flags_config_core_flags.jsoneditsrc/CLUBB_core/parameter_indices.F90editinput/parameter_and_flag_configs/Lscale/configurable_model_flags.inedittests/run_jax_vs_fortran_cases.pyeditinput/parameter_and_flag_configs/default/configurable_model_flags.ineditclubb_python_api/pytests/auto_llm_generated_pytests/test_call_tree_mixing_length.pyeditsrc/G_unit_test_types/spurious_source_test.F90editinput/parameter_and_flag_configs/Lscale/tunable_parameters.ineditsrc/CLUBB_core/advance_clubb_core_module.F90edittuner/pytests/test_parameter_ranges.pyeditinput/parameter_and_flag_configs/e3sm_maint32/maint32_defaults_report.mdeditdash_app/pytests/test_run_runtime.pyeditinput/parameter_and_flag_configs/coriolis_cases/ekman_parameters.ineditsrc/CLUBB_core/model_flags.F90editclubb_python_api/clubb_python/CLUBB_core/mixing_length.pyeditsrc/CLUBB_core/numerical_check.F90editclubb_python_api/pytests/auto_llm_generated_pytests/test_init_sequence.pyeditdash_app/pytests/test_callbacks_runs.pyeditclubb_jax/src/CLUBB_core/parameter_indices.pyeditclubb_python_driver/clubb_constants.pyREADMEb2a6a9ceab12125d4a2542da4e20736039f3a7441792615282000https://carson.math.uwm.edu/jenkins/user/hueblerGunther 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.editREADMEinput/parameter_and_flag_configs/Lscale/configurable_model_flags.ininput/parameter_and_flag_configs/e3sm_maint32/configurable_model_flags.ininput/parameter_and_flag_configs/compatible_r8029/configurable_model_flags.ininput/parameter_and_flag_configs/default/configurable_model_flags.ininput/parameter_and_flag_configs/e3sm/configurable_model_flags.ininput/parameter_and_flag_configs/tauMatchLscale/configurable_model_flags.inad4278602c33012277b039d69fff03a0c8d425571792615380000https://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerhuebler@uwm.eduRemove inline mixing-length selector comments Remove the method enumeration from the six model-flag namelists. Preserve selector values and existing assignment spacing. 2026-10-21 15:43:00 -0500ad4278602c33012277b039d69fff03a0c8d42557Remove inline mixing-length selector commentseditinput/parameter_and_flag_configs/Lscale/configurable_model_flags.ineditinput/parameter_and_flag_configs/e3sm_maint32/configurable_model_flags.ineditinput/parameter_and_flag_configs/default/configurable_model_flags.ineditinput/parameter_and_flag_configs/compatible_r8029/configurable_model_flags.ineditinput/parameter_and_flag_configs/e3sm/configurable_model_flags.ineditinput/parameter_and_flag_configs/tauMatchLscale/configurable_model_flags.indoc/figures/coherence_survival_distance.pngdoc/figures/coherence_work_barrier.pngdoc/coherence_mixing_length.md3045bd3a9835b5e8f57e41064be719147b6d11931792617435000https://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerhuebler@uwm.eduClarify the coherent mixing-length method note The probability and barrier notation was harder to follow than necessary. Apply the documentation review, remove stale launch-energy descriptions, and add sketches of the running barrier and expected travel distance. 2026-10-21 16:17:15 -05003045bd3a9835b5e8f57e41064be719147b6d1193Clarify the coherent mixing-length method noteadddoc/figures/coherence_work_barrier.pngadddoc/figures/coherence_survival_distance.pngeditdoc/coherence_mixing_length.mdgithttps://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerhttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyfalse42https://carson.math.uwm.edu/jenkins/job/clubb_branch_jax/42/40https://carson.math.uwm.edu/jenkins/job/clubb_branch_jax/40/