Started by an SCM change674feb2438c46510eaadecd3e0c3bdede3df2939ac1feb2438c46510eaadecd3e0c3bdede3df2939ac1refs/remotes/origin/masterfeb2438c46510eaadecd3e0c3bdede3df2939ac1feb2438c46510eaadecd3e0c3bdede3df2939ac1refs/remotes/origin/masterfeb2438c46510eaadecd3e0c3bdede3df2939ac1feb2438c46510eaadecd3e0c3bdede3df2939ac1refs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#6742145329442141clubb_BFB_gfortran_test #674674false6749807SUCCESS1791188947592http://carson.math.uwm.edu/jenkins/job/clubb_BFB_gfortran_test/674/- clubb_jax/AGENTS.mdLLM_prompts/script_cli_conventions.mdLLM_prompts/update_python_api_and_drivers.mdLLM_prompts/jenkins_workflow.mdLLM_prompts/dash_app_workflow.mdLLM_prompts/port_underlying_fortran_to_other_languages.mdLLM_prompts/numerical_regression_workflow.md.agents/skills/clubb-jax-port/SKILL.mdLLM_prompts/README.mdAGENTS.md.agents/skills/clubb-script-cli/SKILL.mdLLM_prompts/fortran_column_refactor.mdLLM_prompts/SHORTCUTS.mdLLM_prompts/update_host_models_after_clubb_changes.mdLLM_prompts/jax_porting_workflow.mdd1c3f80378f8621f388662593c7e5a47f1847b351791138711000http://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comImprove agent workflow discovery and completion evidence (#1375)
This is just a rework of out LLM shortcuts. I had chatgpt go through a bunch of sessions and investigate my inefficiencies in my workflow (like how often I have to ask for corrections for things that were already instructions in these shortcuts), and had it rework our shortcuts.
The things done seem to make sense - they're a little shorter and more concise, broken up a bit better, include some extra things. Hard to say if any of it's effective though - hopefully I'll notice an improvement with things
2026-10-04 13:31:51 -0500d1c3f80378f8621f388662593c7e5a47f1847b35Improve agent workflow discovery and completion evidence (#1375)addLLM_prompts/README.mdeditAGENTS.mdaddLLM_prompts/script_cli_conventions.mdaddLLM_prompts/numerical_regression_workflow.mdeditLLM_prompts/update_python_api_and_drivers.mdeditLLM_prompts/update_host_models_after_clubb_changes.mdaddLLM_prompts/fortran_column_refactor.mdadd.agents/skills/clubb-script-cli/SKILL.mdeditLLM_prompts/SHORTCUTS.mdeditLLM_prompts/dash_app_workflow.mdaddLLM_prompts/jax_porting_workflow.mdaddLLM_prompts/jenkins_workflow.mdeditLLM_prompts/port_underlying_fortran_to_other_languages.mdaddclubb_jax/AGENTS.mdadd.agents/skills/clubb-jax-port/SKILL.md
- clubb_jax/src/Microphys/cloud_sed_module.pyclubb_jax/src/CLUBB_core/precipitation_fraction.pyclubb_jax/tests/test_silhs_fortran_oracle.pyclubb_jax/tests/test_microphysics_port_structure.pyclubb_jax/tests/test_silhs_sampling.pyclubb_jax/src/Microphys/ice_dfsn_module.pyclubb_jax/src/Microphys/KK_microphys_module.pyclubb_jax/src/SILHS/est_kessler_microphys_module.pyclubb_jax/src/SILHS/latin_hypercube_arrays.pyclubb_jax/src/SILHS/silhs_api_module.pyclubb_jax/src/SILHS/lh_microphys_var_covar_module.pyclubb_jax/src/Microphys/estimate_scm_microphys_module.pyclubb_jax/tests/test_silhs_driver.pyclubb_jax/JAX_CONVERSION_PLAN.mdclubb_jax/tests/test_silhs_diagnostics.pytests/run_jax_vs_fortran_cases.pyclubb_jax/src/CLUBB_core/fill_holes.pyclubb_jax/src/clubb_case_initalization.pyclubb_jax/tests/test_microphysics_error_paths.pyclubb_jax/src/Input_fields/corr_varnce_input_reader.pysrc/SILHS/latin_hypercube_driver_module.F90clubb_jax/tests/test_microphysics_integration.pyclubb_jax/README.mdclubb_jax/src/SILHS/__init__.pyclubb_jax/src/SILHS/parameters_silhs.pyclubb_jax/src/Microphys/advance_microphys_module.pytests/pytests/test_jax_compare_forwarding.pyclubb_jax/src/CLUBB_core/setup_clubb_pdf_params.pyclubb_jax/src/Microphys/gfdl_activation.pyclubb_jax/src/SILHS/latin_hypercube_driver_module.pyclubb_jax/src/Microphys/microphys_driver.pyclubb_jax/src/CLUBB_core/jax_stats.pyclubb_jax/src/Microphys/lh_microphys_driver_module.pyclubb_jax/src/Microphys/silhs_category_variance_module.pyLLM_prompts/SHORTCUTS.mdclubb_jax/tests/test_silhs_port_structure.pyLLM_prompts/update_host_models_after_clubb_changes.mdsrc/SILHS/parameters_silhs.F90clubb_jax/tests/test_microphysics_host_errors.pyclubb_jax/src/Microphys/parameters_microphys.pyclubb_jax/src/SILHS/math_utilities.pyclubb_jax/src/SILHS/silhs_importance_sample_module.pyclubb_jax/src/SILHS/generate_uniform_sample_module.pysrc/Microphys/microphys_init_cleanup.F90clubb_jax/src/Microphys/pdf_hydromet_microphys_wrapper.pyclubb_jax/src/Microphys/morrison_microphys_module.pysrc/SILHS/generate_uniform_sample_module.F90clubb_jax/src/SILHS/transform_to_pdf_module.pyclubb_jax/SILHS_PORT_NOTES.mdclubb_jax/src/Microphys/microphys_init_cleanup.pyclubb_jax/src/CLUBB_core/stats_clubb_utilities.pyclubb_jax/src/Microphys/mixed_moment_PDF_integrals.pyclubb_jax/src/advance_clubb_to_end.pyclubb_jax/src/Microphys/coamps_microphys_driver_module.pyf51ab963e7cde71123d3afd8f77d077a35cf211f1791158488000http://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comJax silhs (#1372)
Adding silhs to jax.
To avoid randomness issues I added a silhs flag, l_lh_deterministic_test, that causes samples and random numbers to be generated in a deterministic order that is pretty basic but seems like a fine enough sampling method for a test that only matters for comparing jax to fortran matching. This required changing the fortran to have this deterministic test sample generation.
I added 3 new silhs tests:
rico_silhs with a 60s timestep matches up to 360 timestpes (6 hours)
lba_kk_silhs (lba with kk microphys instead of defauly morrison) passes up to 270ish steps, I set test to 240 steps
lba_silhs (with morrison) passes <80, from past exploration this seems mainly due to morrison being in single precision
* Port SILHS sampling and microphysics coupling to JAX
Add native JAX Latin-hypercube sampling with explicit persistent permutation
state and case-owned initialization. Couple sampled states to KK and Morrison
microphysics in interactive and diagnostic modes, with weighted statistics,
substep averaging, and fatal-path/configuration guards.
Preserve Fortran routine structure, argument grouping, and source comments
throughout SILHS and the microphysics interface layer. Leave Fortran, MT95,
and the KK/Morrison numerical cores unchanged.
Validation: 103 focused sampling/interface/error-path checks and eight real
SILHS driver checks pass. Earlier interface/support validation and the
20-pair disabled-SILHS JAX/Fortran comparison also pass. Enabled SILHS random
stream parity is deferred to a future common-random-input comparison.
* Add deterministic SILHS comparisons and initialize JAX output grids
Add a default-off l_lh_deterministic_test flag to Fortran and JAX. Use
ordered strata and a shared four-value, binary-exact draw cycle in the
high-level LHS and overlap-pool routines, preserving sequence reuse and
leaving the native random generators unchanged. Reject independent
importance sampling and random starts in this comparison mode.
Add interactive RICO, LBA KK and native LBA Morrison configurations to the
JAX/Fortran comparison suite without relaxing the existing tolerances.
Initialize SILHS host statistics from JAX case setup so reduced statistics
files also contain Fortran's lh_zt and lh_sample_number coordinates.
Validation: Fortran build and source checks pass; 581 raw sampling values
match exactly; 59 sampler/contract/forwarding checks and 46 output/support
checks pass. RICO matches through 360 steps at 60s with standard statistics
and with reduced statistics at debug 0.
Document the remaining comparison limits: LBA KK's repeating-cycle Nrp2
difference starts at saved prefix 274, while its configured cap remains
275. Native Morrison's selected scope was verified with midpoint inputs;
the repeating-cycle comparison was not rerun after the requested stop.
* Match Fortran SILHS sampling precision and overlap
Preserve default-real rounding in inverse-normal coefficients before
promotion to the sample dtype. Apply vertical overlap to starting-level
straight Monte Carlo samples and retain source sampling failure status.
Add a live Fortran inverse-normal oracle and regressions for overlap and
the source sample-count check. Keep comparison limits and tolerances.
* Restore SILHS diagnostics and microphysics host error guards
Carry weight-limiter and Kessler diagnostic failures through compiled
returns and ErrInfo. Preserve Fortran debug guards at the host boundaries
so negative-debug tracing can retain per-column failure status.
Write ordered microphysics/SILHS settings and approximate correlations
from initialization into the standalone setup file. Keep report lifetime
and output-name resolution outside the timestep driver.
Add focused failure/report regressions and update the port notes with
repeating-input comparisons and the native Morrison compiler sensitivity.
* Document deterministic SILHS comparison patterns
Explain the ordered permutation, repeating within-stratum offsets and overlap
pool at every Fortran deterministic randomness override. Mirror the explanation
in JAX, including index phases, sequence reuse and independence from RNG state.
Executable statements are unchanged in both implementations; source/AST checks
confirm these changes only add comments.
* Use definition decorators for microphysics JIT boundaries
Move the existing PDF preparation, scheme tendency and hydrometeor transport
JIT boundaries onto their routine definitions with @partial(jax.jit, ...).
Keep the static arguments unchanged and call the source-named routines directly
from the standalone driver.
Update host injection and source-order checks for the canonical routine names.
Lightweight error/feedback fixtures still check eager and compiled routine
bodies; real standalone runs exercise the decorated entry points.
Validation: 140 focused tests; 28 passed, 2435 warnings in 453.39s (0:07:33); unchanged RICO360/LBAKK275
strict comparisons; supported whole-driver and reverse-mode tracing.
* Simplify deterministic SILHS sampling comments
Describe the repeatable-testing branches directly, with their base values and
index offsets. Show the first twelve pool entries for four columns, grouped by
sample, and use the same concise descriptions in the Fortran and JAX mirrors.
Only comments and argument documentation change; executable code is unchanged.
* Exclude E3SM from host compatibility updates
Keep the exclusion visible in shortcut discovery and the host workflow.
Treat sys_admin mappings as synchronization metadata, not the active host list.
* Shortening tests timesteps a bit and adding a space for niceness
2026-10-04 19:01:28 -0500f51ab963e7cde71123d3afd8f77d077a35cf211fJax silhs (#1372)addclubb_jax/tests/test_silhs_fortran_oracle.pyedittests/pytests/test_jax_compare_forwarding.pyeditclubb_jax/src/Microphys/silhs_category_variance_module.pyaddclubb_jax/src/SILHS/transform_to_pdf_module.pyaddclubb_jax/tests/test_silhs_sampling.pyeditclubb_jax/src/Microphys/cloud_sed_module.pyeditclubb_jax/src/clubb_case_initalization.pyaddclubb_jax/tests/test_silhs_port_structure.pyeditclubb_jax/src/Microphys/gfdl_activation.pyeditclubb_jax/tests/test_microphysics_error_paths.pyaddclubb_jax/src/SILHS/math_utilities.pyaddclubb_jax/src/SILHS/generate_uniform_sample_module.pyeditclubb_jax/src/Microphys/morrison_microphys_module.pyeditclubb_jax/src/CLUBB_core/setup_clubb_pdf_params.pyaddclubb_jax/src/SILHS/latin_hypercube_driver_module.pyaddclubb_jax/src/SILHS/est_kessler_microphys_module.pyeditclubb_jax/tests/test_microphysics_integration.pyeditclubb_jax/src/CLUBB_core/stats_clubb_utilities.pyaddclubb_jax/SILHS_PORT_NOTES.mdeditclubb_jax/src/Microphys/ice_dfsn_module.pyeditclubb_jax/src/Microphys/estimate_scm_microphys_module.pyeditclubb_jax/src/CLUBB_core/precipitation_fraction.pyeditsrc/SILHS/parameters_silhs.F90editclubb_jax/src/Input_fields/corr_varnce_input_reader.pyaddclubb_jax/tests/test_microphysics_host_errors.pyedittests/run_jax_vs_fortran_cases.pyeditclubb_jax/src/CLUBB_core/jax_stats.pyaddclubb_jax/src/SILHS/lh_microphys_var_covar_module.pyaddclubb_jax/tests/test_silhs_driver.pyeditclubb_jax/JAX_CONVERSION_PLAN.mdeditLLM_prompts/SHORTCUTS.mdeditclubb_jax/src/Microphys/coamps_microphys_driver_module.pyeditsrc/SILHS/generate_uniform_sample_module.F90editclubb_jax/src/CLUBB_core/fill_holes.pyeditclubb_jax/src/Microphys/microphys_driver.pyeditclubb_jax/tests/test_microphysics_port_structure.pyeditLLM_prompts/update_host_models_after_clubb_changes.mdeditclubb_jax/README.mdaddclubb_jax/src/SILHS/parameters_silhs.pyeditclubb_jax/src/Microphys/mixed_moment_PDF_integrals.pyeditsrc/Microphys/microphys_init_cleanup.F90editclubb_jax/src/Microphys/pdf_hydromet_microphys_wrapper.pyaddclubb_jax/src/SILHS/latin_hypercube_arrays.pyeditsrc/SILHS/latin_hypercube_driver_module.F90addclubb_jax/src/SILHS/__init__.pyaddclubb_jax/tests/test_silhs_diagnostics.pyeditclubb_jax/src/Microphys/KK_microphys_module.pyaddclubb_jax/src/SILHS/silhs_importance_sample_module.pyeditclubb_jax/src/Microphys/lh_microphys_driver_module.pyeditclubb_jax/src/Microphys/microphys_init_cleanup.pyeditclubb_jax/src/advance_clubb_to_end.pyeditclubb_jax/src/Microphys/advance_microphys_module.pyeditclubb_jax/src/Microphys/parameters_microphys.pyaddclubb_jax/src/SILHS/silhs_api_module.py
- clubb_jax/src/advance_clubb_to_end.pyclubb_jax/SILHS_PORT_NOTES.md9233e347a33c4422eaadde0503786b7f6134ebcf1791167559000http://carson.math.uwm.edu/jenkins/user/hueblerGunther Hueblerhuebler@uwm.eduClarify current SILHS comparison limits
Separate current LBA test caps from earlier longer validation runs.
Remove trailing spaces from the radiation-call blank line.
2026-10-04 21:32:39 -05009233e347a33c4422eaadde0503786b7f6134ebcfClarify current SILHS comparison limitseditclubb_jax/src/advance_clubb_to_end.pyeditclubb_jax/SILHS_PORT_NOTES.md
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pytest admission, ownership and Jenkins coverage (#1377)
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* Keep component-specific validation beside Dash and JAX
2026-10-04 22:34:54 -05009afedd80dbc4a1f64989768f1f5124eb03483513Organize pytest admission, ownership and Jenkins coverage 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- utilities/stats_json_to_namelist.pyinput/stats/READMEdash_app/run_tab/tab.pydash_app/shared/stats.py.gitignoredash_app/persistence.pydash_app/run_tab/runtime.pyinput/stats/stats.jsondash_app/run_tab/callbacks_selection.pydash_app/run_tab/stats.pydash_app/run_tab/layout.pydash_app/README.mddash_app/services/models.pydash_app/assets/33_stats_tree.jsdash_app/shared/actions.pydash_app/run_tab/discovery.pydash_app/pytests/test_stats_selection.pydash_app/DEVELOPMENT.mdutilities/pytests/test_stats_json_to_namelist.pydash_app/assets/11_tab_run_theme.cssutilities/create_case_namelist.pydash_app/pytests/test_persistence.pyfeb2438c46510eaadecd3e0c3bdede3df2939ac11791171498000http://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAdd hierarchical JSON statistics selection and Dash editor (#1378)
* Add hierarchical JSON stats selection and Dash editor
* Ignore locally saved custom stats configurations
2026-10-04 22:38:18 -0500feb2438c46510eaadecd3e0c3bdede3df2939ac1Add hierarchical JSON statistics selection and Dash editor (#1378)editdash_app/run_tab/tab.pyeditdash_app/shared/actions.pyaddutilities/stats_json_to_namelist.pyeditdash_app/README.mdeditdash_app/pytests/test_persistence.pyeditdash_app/run_tab/discovery.pyeditdash_app/run_tab/callbacks_selection.pyaddinput/stats/stats.jsonadddash_app/run_tab/stats.pyeditdash_app/run_tab/layout.pyadddash_app/shared/stats.pyeditutilities/create_case_namelist.pyeditdash_app/run_tab/runtime.pyeditdash_app/services/models.pyadddash_app/pytests/test_stats_selection.pyadddash_app/assets/33_stats_tree.jsedit.gitignoreaddutilities/pytests/test_stats_json_to_namelist.pyeditdash_app/assets/11_tab_run_theme.csseditinput/stats/READMEeditdash_app/DEVELOPMENT.mdeditdash_app/persistence.py
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