Started by an SCM change00005917585907801.0636463671598122636263635886e48f97c2a96bc78fb498c82f1ed0bb6902353496e48f97c2a96bc78fb498c82f1ed0bb690235349refs/remotes/origin/master6e48f97c2a96bc78fb498c82f1ed0bb6902353496e48f97c2a96bc78fb498c82f1ed0bb690235349refs/remotes/origin/master6e48f97c2a96bc78fb498c82f1ed0bb6902353496e48f97c2a96bc78fb498c82f1ed0bb690235349refs/remotes/origin/masterhttps://github.com/larson-group/clubb.githttp://carson.math.uwm.edu/jenkins/job/clubb_BFB_e3sm_flags_gfortran_test/lastCompletedBuild/artifacthttp://carson.math.uwm.edu/jenkins/job/clubb_BFB_e3sm_flags_gfortran_test/changeshttp://carson.math.uwm.edu/jenkins/job/clubb_BFB_e3sm_flags_gfortran_test/lastCompletedBuild/pipeline-overviewhttp://carson.math.uwm.edu/jenkins/job/clubb_BFB_e3sm_flags_gfortran_test/lastCompletedBuild/testReportfalseUpdate sys_admin RepoRun Python Testfalse#588591758486675clubb_BFB_e3sm_flags_gfortran_test #588588false58810892SUCCESS1792311367610http://carson.math.uwm.edu/jenkins/job/clubb_BFB_e3sm_flags_gfortran_test/588/- clubb_jax/pytests/auto_llm_generated_pytests/test_windm_edsclrm_scalar_indices.pyclubb_jax/src/CLUBB_core/err_info.pyclubb_jax/pytests/auto_llm_generated_pytests/test_radiation_error_diagnostics.pyclubb_jax/pytests/auto_llm_generated_pytests/test_xp2_error_diagnostics.pyclubb_jax/src/CLUBB_core/advance_windm_edsclrm_module.pyclubb_jax/pytests/auto_llm_generated_pytests/test_jit_compile.pyclubb_jax/src/CLUBB_core/__init__.pyclubb_jax/src/CLUBB_core/numerical_check.pyclubb_jax/src/advance_clubb_to_end.pyclubb_jax/src/CLUBB_core/err_info_codes.pyclubb_jax/src/CLUBB_core/advance_xp2_xpyp_module.pyclubb_python_api/JAX_INTEROPERABILITY_PROPOSAL.mdclubb_jax/src/Radiation/radiation_module.pyaa8c2aa4037dda69d686ca97bcbbe1a8208401fd1792259885000http://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comRemove the JAX error-message code registry (#1401)
* Remove the JAX error-message code registry
Print failure details at the runtime checks that detect them. Remove the
extra reason_code field and its setters, decoder, initialization/reset
handling and exports; retain the normal per-column fatal-error status.
Update the scalar-guard assertions and add cached-call diagnostic checks.
Local CPU checks passed for the ErrInfo pytree, diagnostic output, driver
debug gates and state reset/batching behavior (65 cases across five modules).
* Correct the multiple-LHS diagnostic test's wp3 grid
Allocate synthetic wp3 on thermodynamic levels, as required by
calc_wp3_on_wp2, so the test reaches the multiple-LHS guard during tracing.
The 21 selected CPU diagnostic checks pass, covering cached-call output,
per-column fatal status and preservation of fields on the unsupported path.
* Restore the C2 explanation in the multiple-LHS diagnostic
Name C2rt, C2thl and C2rtthl when their unequal values prevent a single-LHS
solve. Keep the direct runtime print and existing fatal-status handling.
The focused CPU cached-call test passes, including the restored explanation,
quiet valid calls and preservation of incoming fields on failure.
* Revert "Restore the C2 explanation in the multiple-LHS diagnostic"
This reverts commit 170a13e2bc7af24e92d8d8bc9de9d9db601921ed.
* List single-LHS requirements in the JAX diagnostic
Print the approved static requirements after the unsupported multiple-LHS
message: explicit turbulent advection or ADG1, plus per-column equivalence
of C2thl and C2rtthl to C2rt within the relative epsilon tolerance.
The focused CPU cached-call test passes, checking the listed requirements,
quiet valid calls and preservation of incoming fields and fatal status.
2026-10-17 12:58:05 -0500aa8c2aa4037dda69d686ca97bcbbe1a8208401fdRemove the JAX error-message code registry (#1401)editclubb_jax/src/CLUBB_core/numerical_check.pyeditclubb_jax/src/CLUBB_core/err_info.pyeditclubb_jax/src/Radiation/radiation_module.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_radiation_error_diagnostics.pydeleteclubb_jax/src/CLUBB_core/err_info_codes.pyeditclubb_jax/src/CLUBB_core/advance_xp2_xpyp_module.pyeditclubb_python_api/JAX_INTEROPERABILITY_PROPOSAL.mdeditclubb_jax/src/CLUBB_core/__init__.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_jit_compile.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_xp2_error_diagnostics.pyeditclubb_jax/src/advance_clubb_to_end.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_windm_edsclrm_scalar_indices.pyeditclubb_jax/src/CLUBB_core/advance_windm_edsclrm_module.py
- .agents/skills/clubb-jax-port/SKILL.md.agents/skills/clubb-testing-and-reporting/SKILL.md.agents/skills/clubb-documentation/change-messages/SKILL.md6e48f97c2a96bc78fb498c82f1ed0bb6902353491792260807000http://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comRestrict BIT_CHANGING guidance to Fortran result changes (#1399)
Keep JAX numerical acceptance focused on agreement with the corresponding
Fortran implementation rather than preserving earlier JAX output. Clarify
the reporting rule and link it from the JAX porting workflow.
All 21 skill schemas, 112 local links and 7 heading anchors pass, along with
diff formatting. Only three skill Markdown files change.
2026-10-17 13:13:27 -05006e48f97c2a96bc78fb498c82f1ed0bb690235349Restrict BIT_CHANGING guidance to Fortran result changes (#1399)edit.agents/skills/clubb-testing-and-reporting/SKILL.mdedit.agents/skills/clubb-documentation/change-messages/SKILL.mdedit.agents/skills/clubb-jax-port/SKILL.md
githttp://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreplyfalseStarted by an SCM change00004369204359401.0176787678587c47faf30cea562966e64eedc259a5074c6cf89b1c47faf30cea562966e64eedc259a5074c6cf89b1refs/remotes/origin/masterc47faf30cea562966e64eedc259a5074c6cf89b1c47faf30cea562966e64eedc259a5074c6cf89b1refs/remotes/origin/masterc47faf30cea562966e64eedc259a5074c6cf89b1c47faf30cea562966e64eedc259a5074c6cf89b1refs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#587436920486675clubb_BFB_e3sm_flags_gfortran_test #587587false58710748SUCCESS1792224969052http://carson.math.uwm.edu/jenkins/job/clubb_BFB_e3sm_flags_gfortran_test/587/- .agents/skills/clubb-doc-language/SKILL.md.agents/skills/clubb-file-descriptions/SKILL.md.agents/skills/clubb-documentation/SKILL.mdAGENTS.md.agents/skills/clubb-change-messages/SKILL.md.agents/skills/clubb-readmes/SKILL.md.agents/skills/clubb-code-comments/SKILL.mdc179bae7435e6e90a0f796cb621d9de4690429b81792177736000http://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAdd CLUBB documentation skills (#1397)
* Add CLUBB documentation skills
Add focused guidance for READMEs, file descriptions, routine/code comments,
and plain language, with a documentation entry skill selected by AGENTS.md.
This gives agents one route to the writing rules for the current task.
Shorten the existing PR/commit guide and require BFB discussion only when a
change could plausibly affect model results or scientific output.
All 18 skill definitions and 45 local guidance links validate; git diff
--check passes.
* Require code reading and checks before finishing documentation
Route small documentation edits through the writing skills. Require agents
to inspect the implementation before drafting and check facts, coverage,
links, and comment syntax before finishing. Clarify that weak file headers
need complete descriptions in the appropriate language form.
Validation: all 18 skill schemas, 46 local guidance links, and whitespace
checks pass. The fresh-agent study uses these exact frozen guidance files.
* Clarify documentation wording and optional usage examples
Explain meaning before usage and make important ordering clear. Read the
applicable language or porting standards for documentation conventions.
Describe file interfaces independently of current callers, using callers as
optional examples. Recommend examples in file headers when useful, or beside
individual routines for collections of independent helpers.
Validation: all 18 skill schemas, 49 local guidance links, and whitespace
checks pass. These refinements have not had a new fresh-agent trial.
2026-10-16 14:08:56 -0500c179bae7435e6e90a0f796cb621d9de4690429b8Add CLUBB documentation skills (#1397)editAGENTS.mdadd.agents/skills/clubb-file-descriptions/SKILL.mdadd.agents/skills/clubb-code-comments/SKILL.mdadd.agents/skills/clubb-documentation/SKILL.mdadd.agents/skills/clubb-doc-language/SKILL.mdedit.agents/skills/clubb-change-messages/SKILL.mdadd.agents/skills/clubb-readmes/SKILL.md
- .agents/skills/clubb-column-refactor/SKILL.mdjenkins_tests/README.md.agents/skills/clubb-jenkins/test-authoring/SKILL.md.agents/skills/clubb-jenkins/SKILL.md.agents/skills/clubb-documentation/code-comments/SKILL.md.agents/skills/clubb-testing-and-reporting/SKILL.md.agents/skills/clubb-documentation/file-descriptions/SKILL.md.agents/skills/clubb-script-cli/SKILL.md.agents/skills/clubb-fortran-port/SKILL.md.agents/skills/clubb-python-api/SKILL.md.agents/skills/clubb-documentation/readmes/SKILL.md.agents/skills/clubb-numerical-diagnosis/SKILL.md.agents/skills/clubb-documentation/language/SKILL.md.agents/skills/clubb-readmes/SKILL.md.agents/skills/clubb-code-comments/SKILL.mdjenkins_tests/jenkins_api_login.py.agents/skills/clubb-jax-port/SKILL.md.agents/skills/clubb-doc-language/SKILL.md.agents/skills/clubb-file-descriptions/SKILL.md.agents/skills/clubb-host-compatibility/SKILL.md.agents/skills/clubb-documentation/SKILL.md.agents/skills/clubb-finalization/SKILL.mdAGENTS.md.agents/skills/clubb-documentation/change-messages/SKILL.md.agents/skills/clubb-pytests/SKILL.md.agents/skills/clubb-change-messages/SKILL.mdeb23a4c1b51706cad0060c28d8c5ead8da595e1c1792199605000http://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAdd Jenkins workflows and branch finalization guidance (#1396)
* Set up Jenkins API login over HTTPS
Add an interactive token login script and teach the Jenkins skill to reuse
its private local credential file or direct users through setup. This lets
each developer use their own Jenkins account without SSH access.
Ten focused regression checks and a live HTTPS login/save check passed.
BFB is not applicable: login tooling and guidance do not affect model
execution or output.
* Explain Jenkins login setup and agent use
Describe why agents use the saved login, how developers set it up, and what
the public routines and failure paths do. Apply the new documentation
guidance to the script, test comments and usage documentation.
Executable Python statements are unchanged. Ten focused login checks pass.
* Remove Jenkins login pytests
Remove the provisional test file from the Jenkins login change at the
user’s request. Keep the login script and workflow guidance unchanged.
* Document Jenkins access and test authoring
Add a Jenkins README and a separate authoring skill for simple,
reproducible pipelines and coordinated live-job changes. Keep API access
in its existing skill and route both workflows from AGENTS.md.
Place the login script with the Jenkins files and update its references.
Runtime statements and the credential location are unchanged. Login help,
import, live HTTPS identity, skill validation and local links pass.
* Prefer relevant Jenkins evidence in test reports
Add shared guidance for choosing checks and explaining what their results
establish. Lead PR reports with relevant Jenkins build links, include local
checks when they add evidence, and keep unexpected failures visible.
Connect validation and change-message workflows to the shared skill.
Skill metadata and local guidance links validate; only Markdown changes.
* Keep README verification notes in change reports
Remove the authoring-history sentence from the Jenkins README and clarify
where the README skill should record example verification. Review the PR
documentation for similar notes while retaining reader-relevant setup.
Skill metadata, local links and diff formatting checks pass.
* Group related skills under their entry points
Nest documentation guides and Jenkins test authoring while preserving
skill names and workflow text. Rebase links, make shared parent guidance
explicit, and use recursive skill discovery for validation.
The Codex skill loader discovers every nested child. Recursive schema,
link and preservation checks pass.
* Clarify Jenkins test authoring scope and when to wait
Require a user request before changing Jenkins test definitions, while allowing
relevant existing branch builds during normal validation. Align pytest
integration guidance with that boundary.
Guide intermediate work toward fast meaningful checks and later review of
slow builds; weigh longer waits at final validation and report pending results.
All 20 skill schemas and 99 local guidance links validate; diff formatting
passes. No pipeline or runtime changes, or live Jenkins actions.
* Explain Jenkins permissions before promising site changes
Describe the permissions needed to read, run, create or edit jobs without
assuming a particular account. Link the guidance from authoring and setup,
and explain how to use assigned tokens or switch saved accounts.
All 20 skill schemas and 101 local guidance links pass, including the new
section anchors. Diff formatting passes; this commit changes Markdown only.
Prior live HTTPS checks confirmed creation, build and cancellation access,
read-only configuration access, and denied configuration writes.
* Add branch finalization workflow and agent PR conventions
Define merge preparation as a full branch audit followed by current validation
and a commit, push and draft-PR handoff. Pause for substantive unintended
issues the user has not accepted; allow minor cleanup without interruption.
Route finalization from AGENTS and shared testing guidance. Keep agent PRs
as drafts and sign PR comments posted through a user account with the agent name.
Codex discovers all 21 repo skills. All 21 schemas and 110 local guidance
links validate; diff formatting passes. Only agent guidance changes.
* Clarify which builds an agent may cancel
Limit cancellation to builds and queue items launched for the current task
unless the user authorizes stopping others. A shared Jenkins username does
not establish ownership. Wrap the nearby setup and authoring text.
Final branch audit found no substantive blockers. Login smoke checks passed
for live HTTPS authentication, private credential replacement and failure
preservation without changing the user credential file. All 21 skill schemas,
110 local links and 5 heading anchors pass; Codex discovers all 21 skills.
2026-10-16 20:13:25 -0500eb23a4c1b51706cad0060c28d8c5ead8da595e1cAdd Jenkins workflows and branch finalization guidance (#1396)add.agents/skills/clubb-finalization/SKILL.mdedit.agents/skills/clubb-jax-port/SKILL.mdadd.agents/skills/clubb-documentation/language/SKILL.mdadd.agents/skills/clubb-testing-and-reporting/SKILL.mdeditAGENTS.mdadd.agents/skills/clubb-documentation/code-comments/SKILL.mdadd.agents/skills/clubb-jenkins/test-authoring/SKILL.mddelete.agents/skills/clubb-file-descriptions/SKILL.mddelete.agents/skills/clubb-readmes/SKILL.mddelete.agents/skills/clubb-change-messages/SKILL.mdedit.agents/skills/clubb-host-compatibility/SKILL.mdadd.agents/skills/clubb-documentation/file-descriptions/SKILL.mdedit.agents/skills/clubb-numerical-diagnosis/SKILL.mddelete.agents/skills/clubb-code-comments/SKILL.mdedit.agents/skills/clubb-column-refactor/SKILL.mddelete.agents/skills/clubb-doc-language/SKILL.mdadd.agents/skills/clubb-documentation/readmes/SKILL.mdedit.agents/skills/clubb-pytests/SKILL.mdedit.agents/skills/clubb-fortran-port/SKILL.mdedit.agents/skills/clubb-python-api/SKILL.mdedit.agents/skills/clubb-documentation/SKILL.mdadd.agents/skills/clubb-documentation/change-messages/SKILL.mdedit.agents/skills/clubb-script-cli/SKILL.mdaddjenkins_tests/jenkins_api_login.pyaddjenkins_tests/README.mdedit.agents/skills/clubb-jenkins/SKILL.md
- src/Microphys/microphys_init_cleanup.F90d9e8b9588ff7b16679ca79b67fcf5382bcc723c41792209029000http://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comReset microphysics defaults when initializing another case (#1398)
Restore module and saved-local namelist defaults before reading a new case.
This prevents omitted settings from inheriting the previous case's values. This isn't an issue for any way that clubb is currently run in the codebase, but would potentially cause an issue for a future use case (this is foreshadowing).
2026-10-16 22:50:29 -0500d9e8b9588ff7b16679ca79b67fcf5382bcc723c4Reset microphysics defaults when initializing another case (#1398)editsrc/Microphys/microphys_init_cleanup.F90
- clubb_jax/src/CLUBB_core/sfc_varnce_module.pyclubb_jax/src/CLUBB_core/model_flags.pyclubb_jax/src/CLUBB_core/new_hybrid_pdf_main.pyclubb_jax/src/CLUBB_core/adg1_adg2_3d_luhar_pdf.pyclubb_jax/src/CLUBB_core/interpolation.pyclubb_jax/src/CLUBB_core/parameters_tunable.pyclubb_jax/src/CLUBB_core/precipitation_fraction.pyclubb_jax/src/CLUBB_core/advance_wp2_wp3_module.pyclubb_jax/src/CLUBB_core/setup_clubb_pdf_params.pyclubb_jax/src/CLUBB_core/advance_windm_edsclrm_module.pyclubb_jax/src/CLUBB_core/jax_stats.pyclubb_jax/src/CLUBB_core/file_functions.pyclubb_jax/src/CLUBB_core/grid_class.pyclubb_jax/src/CLUBB_core/advance_clubb_core_module.pyclubb_jax/src/CLUBB_core/advance_xm_wpxp_module.pyclubb_jax/src/CLUBB_core/advance_xp2_xpyp_module.pyclubb_jax/src/CLUBB_core/mono_flux_limiter.pyclubb_jax/src/CLUBB_core/fill_holes.pyclubb_jax/src/CLUBB_core/stats_netcdf.pyclubb_jax/src/CLUBB_core/clip_explicit.pyclubb_jax/src/CLUBB_core/mixing_length.pyclubb_jax/pytests/auto_llm_generated_pytests/test_sfc_varnce_diagnostics.pyclubb_jax/src/CLUBB_core/err_info.pyclubb_jax/src/CLUBB_core/pdf_params.pyclubb_jax/pytests/auto_llm_generated_pytests/test_core_diagnostics.pyclubb_jax/src/CLUBB_core/remapping_module.pyclubb_jax/src/CLUBB_core/sponge_layer_damping.pyclubb_jax/src/CLUBB_core/new_pdf.pyclubb_jax/src/CLUBB_core/matrix_operations.pyclubb_jax/src/CLUBB_core/pdf_closure_module.pyclubb_jax/src/CLUBB_core/pos_definite_module.pyclubb_jax/src/CLUBB_core/numerical_check.pyclubb_jax/src/CLUBB_core/matrix_solver_wrapper.pyclubb_jax/src/CLUBB_core/corr_varnce_module.pyclubb_jax/src/CLUBB_core/new_tsdadg_pdf.pyc47faf30cea562966e64eedc259a5074c6cf89b11792221315000http://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comRestore missing debug printouts in JAX core (#1390)
* Restore missing debug printouts in JAX core
The port kept many failure checks but omitted their Fortran messages, making
failed columns and solvers difficult to diagnose. Restore runtime messages,
column headers and available field dumps with the source debug gates. Record
diagnostics needing unported machinery in the skip report.
BFB is not established by the available comparisons. All 23 curated CPU
JAX/Fortran cases matched within default tolerances: absolute 1e-7 and
percentage 1e-7%, or 0.001% for the curated Morrison cases. Runs used four
columns, standard statistics and existing durations/caps. Separately, 24
starting-tree kernel comparisons found exactly equal result/state values.
The CPU JAX suite passed 787 tests, including compiled diagnostic checks;
the focused rerun passed 14. Source/diff review and git diff --check passed.
* Remove diagnostic restoration report
Remove the standalone report on intentionally skipped diagnostics. Observed
Fortran differences remain documented in the affected JAX modules.
This removes documentation only, so model/output BFB is not applicable.
Diff review, a tracked-file reference search and git diff --check passed.
Runtime tests were not rerun for this deletion.
* Identify scalar fields in solver diagnostics
The separate scalar solves all printed the same generic field label. Restore
the Fortran names sclrp2, sclrprtp and sclrpthlp so a failure identifies which
variance or covariance solve failed.
Source comparison confirms the three labels match their Fortran call sites.
Python syntax and whitespace checks passed. Jenkins validation will exercise
the published revision.
2026-10-17 02:15:15 -0500c47faf30cea562966e64eedc259a5074c6cf89b1Restore missing debug printouts in JAX core (#1390)editclubb_jax/src/CLUBB_core/grid_class.pyeditclubb_jax/src/CLUBB_core/fill_holes.pyeditclubb_jax/src/CLUBB_core/clip_explicit.pyeditclubb_jax/src/CLUBB_core/numerical_check.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_sfc_varnce_diagnostics.pyeditclubb_jax/src/CLUBB_core/adg1_adg2_3d_luhar_pdf.pyeditclubb_jax/src/CLUBB_core/advance_xm_wpxp_module.pyeditclubb_jax/src/CLUBB_core/setup_clubb_pdf_params.pyeditclubb_jax/src/CLUBB_core/pdf_closure_module.pyeditclubb_jax/src/CLUBB_core/pdf_params.pyeditclubb_jax/src/CLUBB_core/file_functions.pyeditclubb_jax/src/CLUBB_core/model_flags.pyeditclubb_jax/src/CLUBB_core/sfc_varnce_module.pyeditclubb_jax/src/CLUBB_core/remapping_module.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_core_diagnostics.pyeditclubb_jax/src/CLUBB_core/pos_definite_module.pyeditclubb_jax/src/CLUBB_core/interpolation.pyeditclubb_jax/src/CLUBB_core/advance_windm_edsclrm_module.pyeditclubb_jax/src/CLUBB_core/advance_xp2_xpyp_module.pyeditclubb_jax/src/CLUBB_core/matrix_solver_wrapper.pyeditclubb_jax/src/CLUBB_core/parameters_tunable.pyeditclubb_jax/src/CLUBB_core/precipitation_fraction.pyeditclubb_jax/src/CLUBB_core/new_pdf.pyeditclubb_jax/src/CLUBB_core/advance_wp2_wp3_module.pyeditclubb_jax/src/CLUBB_core/advance_clubb_core_module.pyeditclubb_jax/src/CLUBB_core/corr_varnce_module.pyeditclubb_jax/src/CLUBB_core/new_hybrid_pdf_main.pyeditclubb_jax/src/CLUBB_core/mixing_length.pyeditclubb_jax/src/CLUBB_core/mono_flux_limiter.pyeditclubb_jax/src/CLUBB_core/sponge_layer_damping.pyeditclubb_jax/src/CLUBB_core/stats_netcdf.pyeditclubb_jax/src/CLUBB_core/err_info.pyeditclubb_jax/src/CLUBB_core/jax_stats.pyeditclubb_jax/src/CLUBB_core/new_tsdadg_pdf.pyeditclubb_jax/src/CLUBB_core/matrix_operations.py
githttp://carson.math.uwm.edu/jenkins/user/noreplynoreplyfalse588http://carson.math.uwm.edu/jenkins/job/clubb_BFB_e3sm_flags_gfortran_test/588/586http://carson.math.uwm.edu/jenkins/job/clubb_BFB_e3sm_flags_gfortran_test/586/