Started by an SCM change00009926744298980.4366975673591999371664666467156e48f97c2a96bc78fb498c82f1ed0bb6902353496e48f97c2a96bc78fb498c82f1ed0bb690235349refs/remotes/origin/master6e48f97c2a96bc78fb498c82f1ed0bb6902353496e48f97c2a96bc78fb498c82f1ed0bb690235349refs/remotes/origin/master6e48f97c2a96bc78fb498c82f1ed0bb6902353496e48f97c2a96bc78fb498c82f1ed0bb690235349refs/remotes/origin/masterhttps://github.com/larson-group/clubb.githttps://carson.math.uwm.edu/jenkins/job/clubb_release_intel_build/715/artifacthttps://carson.math.uwm.edu/jenkins/job/clubb_release_intel_build/changeshttps://carson.math.uwm.edu/jenkins/job/clubb_release_intel_build/715/stageshttps://carson.math.uwm.edu/jenkins/job/clubb_release_intel_build/715/testReportfalseCheckout Clubb_ReleaseCompile Clubb Release Runfalse#7159926741679182clubb_release_intel_build #715715false71510948SUCCESS1792313468005https://carson.math.uwm.edu/jenkins/job/clubb_release_intel_build/715/clubb_jax/pytests/auto_llm_generated_pytests/test_windm_edsclrm_scalar_indices.pyclubb_jax/pytests/auto_llm_generated_pytests/test_radiation_error_diagnostics.pyclubb_jax/src/CLUBB_core/err_info.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/advance_clubb_to_end.pyclubb_jax/src/CLUBB_core/numerical_check.pyclubb_jax/src/CLUBB_core/err_info_codes.pyclubb_python_api/JAX_INTEROPERABILITY_PROPOSAL.mdclubb_jax/src/CLUBB_core/advance_xp2_xpyp_module.pyclubb_jax/src/Radiation/radiation_module.pyaa8c2aa4037dda69d686ca97bcbbe1a8208401fd1792259885000https://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)deleteclubb_jax/src/CLUBB_core/err_info_codes.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_radiation_error_diagnostics.pyeditclubb_jax/src/advance_clubb_to_end.pyeditclubb_jax/src/CLUBB_core/numerical_check.pyeditclubb_jax/src/Radiation/radiation_module.pyeditclubb_jax/src/CLUBB_core/__init__.pyeditclubb_jax/src/CLUBB_core/err_info.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_jit_compile.pyeditclubb_python_api/JAX_INTEROPERABILITY_PROPOSAL.mdaddclubb_jax/pytests/auto_llm_generated_pytests/test_xp2_error_diagnostics.pyeditclubb_jax/src/CLUBB_core/advance_xp2_xpyp_module.pyeditclubb_jax/src/CLUBB_core/advance_windm_edsclrm_module.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_windm_edsclrm_scalar_indices.py.agents/skills/clubb-jax-port/SKILL.md.agents/skills/clubb-testing-and-reporting/SKILL.md.agents/skills/clubb-documentation/change-messages/SKILL.md6e48f97c2a96bc78fb498c82f1ed0bb6902353491792260807000https://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.mdgithttps://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreplyfalseStarted by an SCM change0005299638700713381720.39172217221716ec5e8070d3173282a6317b067f8673a657a1eb6fec5e8070d3173282a6317b067f8673a657a1eb6frefs/remotes/origin/masterec5e8070d3173282a6317b067f8673a657a1eb6fec5e8070d3173282a6317b067f8673a657a1eb6frefs/remotes/origin/masterec5e8070d3173282a6317b067f8673a657a1eb6fec5e8070d3173282a6317b067f8673a657a1eb6frefs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#7168700711679182clubb_release_intel_build #716716false71611069SUCCESS1792399868641https://carson.math.uwm.edu/jenkins/job/clubb_release_intel_build/716/.agents/skills/clubb-bit-changing/SKILL.md.agents/skills/clubb-jax-port/SKILL.mdAGENTS.md.agents/skills/clubb-finalization/SKILL.md.agents/skills/clubb-documentation/change-messages/SKILL.md.agents/skills/clubb-testing-and-reporting/SKILL.mdccafe4f166f956eed26b91f7fdacd5600f60f5b21792344464000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comDefine when to declare bit-changing commits (#1403) * Define conservative bit-change declarations Centralize the policy around intentional Fortran numerical answer changes, with named affected BFB tests or precise untested conditions. Preserve standalone coverage and the current JAX parity boundary, keep declarations sparse, and separate answer-changing edits from preserving cleanup. Route message writing, validation and branch finalization to one owner. Skill schemas, local links, heading anchors, parser examples and manual decision scenarios were checked; no model or CI code changes. * Define the optimization level for bitwise preservation Use -O0 as the normal preservation standard. Differences confined to optimized builds do not require an answer-change declaration when -O0 is verified BFB; report known optimized-only differences and their configuration in the PR. The changed skill schema and whitespace checks pass. Inspected current debug compile flags and manually reviewed the optimized-only decision scenario; documentation only, no numerical rerun. 2026-10-18 12:27:44 -0500ccafe4f166f956eed26b91f7fdacd5600f60f5b2Define when to declare bit-changing commits (#1403)editAGENTS.mdedit.agents/skills/clubb-documentation/change-messages/SKILL.mdedit.agents/skills/clubb-jax-port/SKILL.mdadd.agents/skills/clubb-bit-changing/SKILL.mdedit.agents/skills/clubb-finalization/SKILL.mdedit.agents/skills/clubb-testing-and-reporting/SKILL.mdclubb_jax/src/clubb_standalone.pyclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyrun_scripts/README.mdutilities/clubb_case_runner.pyutilities/pytests/test_time_clubb.pytests/run_timestep_sweep.pyclubb_jax/pytests/auto_llm_generated_pytests/test_case_cache_reuse.pyclubb_python_driver/clubb_standalone.pytests/README.mdsrc/clubb_standalone.F90run_scripts/run_scm_loss.pyutilities/time_clubb.py.agents/skills/clubb-testing-and-reporting/SKILL.mdutilities/create_case_namelist.pyutilities/pytests/test_create_case_namelist.pytests/run_stats_output_consistency.pytests/run_jax_vs_fortran_cases.py.agents/skills/clubb-fortran-port/SKILL.mdclubb_jax/src/clubb_case_initalization.pyutilities/pytests/auto_llm_generated_pytests/test_timing_workers.pyutilities/README.mdtests/case_runner_lifecycle_test.pyclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.py.agents/skills/clubb-numerical-diagnosis/SKILL.mdutilities/pytests/auto_llm_generated_pytests/test_loss_cli.pytests/pytests/auto_llm_generated_pytests/test_scm_jax_driver_test.pyrun_scripts/run_scm.py.agents/skills/clubb-fortran-format/SKILL.mdAGENTS.mdclubb_jax/src/Microphys/microphys_init_cleanup.py.agents/skills/clubb-finalization/SKILL.mdjenkins_tests/clubb_driver/Jenkinsfileutilities/timing_profiles.pyclubb_jax/README.mdrun_scripts/run_tuner_job.pyutilities/pytests/auto_llm_generated_pytests/test_clubb_case_runner.pytests/run_restart_test.pyclubb_jax/src/CLUBB_core/calc_pressure.pyutilities/pytests/timing_test_inputs.pytests/run_loss_output_consistency.py4f8368a377989b649fc0ed53c26957e193d210671792350419000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAdd reusable case runners for timing (#1400) We have multiple entry points now for clubb standalone (fortran,python,jax), and there's additional logic that chooses which fortran installation to use (gfortran,ifort,nvhpc,etc). All of this has historically (~1 year) been done by run_scm.py, but we have a number of other scripts that need this same kind of logic, so instead of making run_scm.py more complicated and letting other scripts import it's pieces, we've made a `clubb_case_runner`. `clubb_case_runner` is a python object that abstracts the backend decisions. The "flow" is roughly: - high level script wants to run a clubb case some how - generates one or more case namelists (arm.in, bomex.in, etc) - creates a `clubb_case_runner` by passing it whatever runtime options (-jax/-python/-exe) the user requested - runs a case by passing this `clubb_case_runner` whatever namelists it wants to run. In addition to deduplicating runtime setting logic, this allows python scripts to create these high level `clubb_case_runner` objects and use those to do things that usually requires duplicate multiprocessesing and error code parsing logic. 2026-10-18 14:06:59 -05004f8368a377989b649fc0ed53c26957e193d21067Add reusable case runners for timing (#1400)editclubb_jax/src/clubb_standalone.pyeditrun_scripts/run_scm.pyedittests/pytests/auto_llm_generated_pytests/test_scm_jax_driver_test.pyedittests/run_stats_output_consistency.pyeditAGENTS.mdeditutilities/time_clubb.pyedit.agents/skills/clubb-numerical-diagnosis/SKILL.mdeditclubb_jax/src/Microphys/microphys_init_cleanup.pyedittests/run_jax_vs_fortran_cases.pyeditutilities/pytests/auto_llm_generated_pytests/test_loss_cli.pyeditclubb_jax/src/CLUBB_core/calc_pressure.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.pyaddutilities/pytests/timing_test_inputs.pyedittests/run_restart_test.pyaddutilities/pytests/auto_llm_generated_pytests/test_clubb_case_runner.pyaddutilities/clubb_case_runner.pyedittests/run_timestep_sweep.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyeditjenkins_tests/clubb_driver/Jenkinsfileedittests/README.mdeditutilities/timing_profiles.pyedit.agents/skills/clubb-testing-and-reporting/SKILL.mdaddutilities/pytests/auto_llm_generated_pytests/test_timing_workers.pyeditsrc/clubb_standalone.F90editutilities/README.mdedit.agents/skills/clubb-fortran-port/SKILL.mdeditutilities/pytests/test_create_case_namelist.pyedit.agents/skills/clubb-fortran-format/SKILL.mdeditclubb_python_driver/clubb_standalone.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_case_cache_reuse.pyeditutilities/pytests/test_time_clubb.pyeditclubb_jax/README.mdeditclubb_jax/src/clubb_case_initalization.pyedit.agents/skills/clubb-finalization/SKILL.mdeditrun_scripts/run_scm_loss.pyeditrun_scripts/run_tuner_job.pyeditutilities/create_case_namelist.pyeditrun_scripts/README.mdaddtests/case_runner_lifecycle_test.pyedittests/run_loss_output_consistency.pyclubb_jax/src/clubb_case_initalization.pyclubb_jax/src/clubb_standalone.pyutilities/README.mdclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.pyclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyclubb_jax/src/clubb_loss_driver.pyclubb_jax/pytests/auto_llm_generated_pytests/test_code_timer_module.pyrun_scripts/README.mdclubb_jax/view_profile.pyclubb_jax/run_jax.pyclubb_jax/pytests/auto_llm_generated_pytests/test_profile_cli.pyclubb_jax/src/CLUBB_core/code_timer_module.pyutilities/time_clubb.pyclubb_jax/src/advance_clubb_to_end.pyclubb_jax/README.mdclubb_jax/src/clubb_driver_test.pyec5e8070d3173282a6317b067f8673a657a1eb6f1792362852000https://carson.math.uwm.edu/jenkins/user/noreplynoreplynoreply@github.comAdd JAX timing and profiling (#1393) * Add JAX timing and persistent benchmark workers Write Fortran-format CPU timing summaries and optional XProf/Perfetto traces from JAX driver phases. Use synchronized persistent workers for full-case warmups and repetitions across Fortran, Python and JAX. Retain compiled JAX programs when initialization settings are unchanged. Validation: 243 focused checks and CPU case workflows passed. Repeated five-step BOMEX/RICO_SILHS numeric outputs matched fresh controls exactly. The two-column BOMEX JAX/Fortran comparison passed 1e-7 absolute and percent thresholds. BFB against the parent is not established by these comparisons. GPU and GPTL execution remain untested. * Making jax timer use wall clock time instead of cpu/process time * Keep JAX timing separate from reusable runners Move process persistence, cache reuse and Python timing adapters to the case-runner branch. Keep JAX wall-clock summaries, optional deep profiles, driver instrumentation and the parser change that reads their clock label. The timing-only shared suite and a three-step CPU BOMEX run pass. BFB against master is not established; physics expressions are unchanged. * Add reusable case runners for timing and tuning Share runtime selection and persistent standalone sessions between SCM, timing and tuning. Support namelist replacement and empty model reruns, plus parameter matrices for loss sessions. Synchronize timing cohorts and record retained-model initialization separately. Use executable loss workers for native tuning instead of requiring F2PY. Restore microphysics defaults between cases (BIT_CHANGING for sessions that previously inherited settings). Short native/CPU JAX sessions match fresh same-backend stats values exactly; broader BFB is not established. Native build, focused suites and repeated loss/tuner/timing workflows pass. * Use F2PY for reusable Fortran loss runs Run persistent Fortran loss sessions through the existing Python API. Restore the native loss standalone and remove its parameter namelist reader and result writers. Python workers pass arrays directly into F2PY; ordinary standalone persistence and JAX execution remain available. Fifteen native loss metric arrays match saved results exactly. Native and CPU JAX repeated loss/tuning workflows, tuner shutdown, the native build, 454 shared checks and four API checks pass. Broader BFB is not established. * Keep case runners persistent without retaining model state Run each ordinary request through full initialization, advancement and cleanup while keeping the process alive for in-memory JIT reuse. Remove retained-model commands, transport, timing/UI options and extra bindings. Restore tuning and loss frontends to their existing allocation-reusing APIs. The native build, 445 shared checks, 121 focused JAX checks and 85 Dash checks pass. Short native/JAX/Python reused-process stats match fresh controls exactly; tuning and synchronized timing sweeps pass. Two full 16-column JAX repeats log no new compilations. These comparisons do not establish blanket BFB. * Separate microphysics initialization fixes from case runners Move native default resets to their own branch/PR and keep the runner focused on shared runtime selection and full-case process reuse. Record the mixed-case native test's dependency on that fix. Refresh the timing base and master, and clarify runner, driver and test documentation under the current skills. The shared checks pass, including output drainage, cancellation, synchronized warmup/repetition barriers and CLI forwarding. Python AST checks confirm the remaining audit edits change only documentation. Jenkins validation follows this published checkpoint. * Complete case-runner procedure descriptions Describe the remaining changed CLI, test and profile routines under the current documentation standards. Executable Python ASTs are unchanged from f66ccf2ff, the revision running in Jenkins; existing validation still applies. * Separate JAX timing from case runner changes Keep runtime selection and process reuse independent so the case runner can merge into master before JAX timing. Shared runner/CLI/timing checks pass (445 tests, including provisional coverage). * Add JAX timing after the case runner Restore the audited wall-clock summaries and optional execution tracing on top of the independent case runner. Keep the existing implementation and review history while reversing the PR merge order. * Add a JAX profiling option and viewer commands Enable captures with -jax=profile and print commands after cleanup. Keep capture export in the timer and viewing in view_profile.py. 181 focused checks pass. CPU BOMEX captures preserve numeric stats; both viewers were verified in-browser. Large full-Python Perfetto exports can truncate; XProf retained all five tested timesteps. * Clarify JAX timing usage and cleanup Document the timer lifecycle, failure handling and Dash wall-time comparison metric. Executable Python AST is unchanged. 2026-10-18 17:34:12 -0500ec5e8070d3173282a6317b067f8673a657a1eb6fAdd JAX timing and profiling (#1393)editclubb_jax/pytests/auto_llm_generated_pytests/test_device_selection.pyeditclubb_jax/src/clubb_loss_driver.pyeditclubb_jax/README.mdaddclubb_jax/view_profile.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_code_timer_module.pyeditclubb_jax/pytests/auto_llm_generated_pytests/test_jax_cli_options.pyeditclubb_jax/src/clubb_standalone.pyeditutilities/README.mdaddclubb_jax/pytests/auto_llm_generated_pytests/test_profile_cli.pyeditclubb_jax/run_jax.pyaddclubb_jax/src/CLUBB_core/code_timer_module.pyeditclubb_jax/src/advance_clubb_to_end.pyeditclubb_jax/src/clubb_driver_test.pyeditrun_scripts/README.mdeditclubb_jax/src/clubb_case_initalization.pyeditutilities/time_clubb.pygithttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyfalse717https://carson.math.uwm.edu/jenkins/job/clubb_release_intel_build/717/715https://carson.math.uwm.edu/jenkins/job/clubb_release_intel_build/715/Started by an SCM change0000217930316558790.76180978097714c47faf30cea562966e64eedc259a5074c6cf89b1c47faf30cea562966e64eedc259a5074c6cf89b1refs/remotes/origin/masterc47faf30cea562966e64eedc259a5074c6cf89b1c47faf30cea562966e64eedc259a5074c6cf89b1refs/remotes/origin/masterc47faf30cea562966e64eedc259a5074c6cf89b1c47faf30cea562966e64eedc259a5074c6cf89b1refs/remotes/origin/masterhttps://github.com/larson-group/clubb.gitfalse#71421793031679182clubb_release_intel_build #714714false71410803SUCCESS1792227069426https://carson.math.uwm.edu/jenkins/job/clubb_release_intel_build/714/.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.mdc179bae7435e6e90a0f796cb621d9de4690429b81792177736000https://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)add.agents/skills/clubb-doc-language/SKILL.mdedit.agents/skills/clubb-change-messages/SKILL.mdadd.agents/skills/clubb-documentation/SKILL.mdadd.agents/skills/clubb-readmes/SKILL.mdeditAGENTS.mdadd.agents/skills/clubb-file-descriptions/SKILL.mdadd.agents/skills/clubb-code-comments/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-documentation/file-descriptions/SKILL.md.agents/skills/clubb-testing-and-reporting/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.mdAGENTS.md.agents/skills/clubb-finalization/SKILL.md.agents/skills/clubb-documentation/change-messages/SKILL.md.agents/skills/clubb-pytests/SKILL.md.agents/skills/clubb-change-messages/SKILL.mdeb23a4c1b51706cad0060c28d8c5ead8da595e1c1792199605000https://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)editAGENTS.mdedit.agents/skills/clubb-host-compatibility/SKILL.mdadd.agents/skills/clubb-documentation/file-descriptions/SKILL.mdadd.agents/skills/clubb-documentation/readmes/SKILL.mdedit.agents/skills/clubb-column-refactor/SKILL.mdedit.agents/skills/clubb-jax-port/SKILL.mdedit.agents/skills/clubb-jenkins/SKILL.mdedit.agents/skills/clubb-documentation/SKILL.mdedit.agents/skills/clubb-numerical-diagnosis/SKILL.mdadd.agents/skills/clubb-documentation/language/SKILL.mdaddjenkins_tests/README.mddelete.agents/skills/clubb-change-messages/SKILL.mdadd.agents/skills/clubb-documentation/code-comments/SKILL.mdedit.agents/skills/clubb-pytests/SKILL.mddelete.agents/skills/clubb-readmes/SKILL.mdadd.agents/skills/clubb-testing-and-reporting/SKILL.mdadd.agents/skills/clubb-finalization/SKILL.mdedit.agents/skills/clubb-fortran-port/SKILL.mdedit.agents/skills/clubb-python-api/SKILL.mdaddjenkins_tests/jenkins_api_login.pydelete.agents/skills/clubb-file-descriptions/SKILL.mdedit.agents/skills/clubb-script-cli/SKILL.mdadd.agents/skills/clubb-jenkins/test-authoring/SKILL.mddelete.agents/skills/clubb-doc-language/SKILL.mddelete.agents/skills/clubb-code-comments/SKILL.mdadd.agents/skills/clubb-documentation/change-messages/SKILL.mdsrc/Microphys/microphys_init_cleanup.F90d9e8b9588ff7b16679ca79b67fcf5382bcc723c41792209029000https://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.F90clubb_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/advance_clubb_core_module.pyclubb_jax/src/CLUBB_core/grid_class.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/src/CLUBB_core/err_info.pyclubb_jax/pytests/auto_llm_generated_pytests/test_sfc_varnce_diagnostics.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/pos_definite_module.pyclubb_jax/src/CLUBB_core/pdf_closure_module.pyclubb_jax/src/CLUBB_core/matrix_solver_wrapper.pyclubb_jax/src/CLUBB_core/numerical_check.pyclubb_jax/src/CLUBB_core/corr_varnce_module.pyclubb_jax/src/CLUBB_core/new_tsdadg_pdf.pyc47faf30cea562966e64eedc259a5074c6cf89b11792221315000https://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)addclubb_jax/pytests/auto_llm_generated_pytests/test_core_diagnostics.pyeditclubb_jax/src/CLUBB_core/interpolation.pyeditclubb_jax/src/CLUBB_core/pdf_params.pyeditclubb_jax/src/CLUBB_core/advance_xp2_xpyp_module.pyeditclubb_jax/src/CLUBB_core/file_functions.pyeditclubb_jax/src/CLUBB_core/matrix_operations.pyeditclubb_jax/src/CLUBB_core/mixing_length.pyeditclubb_jax/src/CLUBB_core/pos_definite_module.pyeditclubb_jax/src/CLUBB_core/matrix_solver_wrapper.pyeditclubb_jax/src/CLUBB_core/new_pdf.pyeditclubb_jax/src/CLUBB_core/advance_xm_wpxp_module.pyeditclubb_jax/src/CLUBB_core/clip_explicit.pyeditclubb_jax/src/CLUBB_core/jax_stats.pyeditclubb_jax/src/CLUBB_core/numerical_check.pyeditclubb_jax/src/CLUBB_core/model_flags.pyeditclubb_jax/src/CLUBB_core/advance_clubb_core_module.pyeditclubb_jax/src/CLUBB_core/fill_holes.pyeditclubb_jax/src/CLUBB_core/parameters_tunable.pyeditclubb_jax/src/CLUBB_core/grid_class.pyeditclubb_jax/src/CLUBB_core/precipitation_fraction.pyeditclubb_jax/src/CLUBB_core/advance_windm_edsclrm_module.pyeditclubb_jax/src/CLUBB_core/adg1_adg2_3d_luhar_pdf.pyeditclubb_jax/src/CLUBB_core/stats_netcdf.pyeditclubb_jax/src/CLUBB_core/advance_wp2_wp3_module.pyeditclubb_jax/src/CLUBB_core/mono_flux_limiter.pyeditclubb_jax/src/CLUBB_core/setup_clubb_pdf_params.pyeditclubb_jax/src/CLUBB_core/err_info.pyeditclubb_jax/src/CLUBB_core/new_hybrid_pdf_main.pyeditclubb_jax/src/CLUBB_core/sponge_layer_damping.pyeditclubb_jax/src/CLUBB_core/corr_varnce_module.pyeditclubb_jax/src/CLUBB_core/sfc_varnce_module.pyaddclubb_jax/pytests/auto_llm_generated_pytests/test_sfc_varnce_diagnostics.pyeditclubb_jax/src/CLUBB_core/pdf_closure_module.pyeditclubb_jax/src/CLUBB_core/remapping_module.pyeditclubb_jax/src/CLUBB_core/new_tsdadg_pdf.pygithttps://carson.math.uwm.edu/jenkins/user/noreplynoreplyfalse715https://carson.math.uwm.edu/jenkins/job/clubb_release_intel_build/715/713https://carson.math.uwm.edu/jenkins/job/clubb_release_intel_build/713/