Started by an SCM change Obtained jenkins_tests/clubb_dash/Jenkinsfile from git https://github.com/larson-group/clubb.git [Pipeline] Start of Pipeline [Pipeline] node Running on Jenkins in /home/jenkins/workspace/clubb_dash [Pipeline] { [Pipeline] stage [Pipeline] { (Declarative: Checkout SCM) [Pipeline] checkout The recommended git tool is: git Wiping out workspace first. Cloning the remote Git repository Cloning repository https://github.com/larson-group/clubb.git > git init /home/jenkins/workspace/clubb_dash # timeout=10 Fetching upstream changes from https://github.com/larson-group/clubb.git > git --version # timeout=10 > git --version # 'git version 2.34.1' using GIT_ASKPASS to set credentials larsongroupsysadmin github token > git fetch --tags --force --progress -- https://github.com/larson-group/clubb.git +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/larson-group/clubb.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10 Avoid second fetch > git rev-parse refs/remotes/origin/master^{commit} # timeout=10 Checking out Revision 9429ba2f18a79e7b17ef53bccc8f17af6649c3fd (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f 9429ba2f18a79e7b17ef53bccc8f17af6649c3fd # timeout=10 Commit message: "Always do idiot-proofing of flags in check_clubb_settings_api" First time build. Skipping changelog. [Pipeline] } [Pipeline] // stage [Pipeline] withEnv [Pipeline] { [Pipeline] stage [Pipeline] { (Run Dash pytests) [Pipeline] withEnv [Pipeline] { [Pipeline] sh + export PATH=/home/jenkins/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin + PATH=/home/jenkins/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin + node --version v22.23.3 + bash tests/run_pytests.sh -dash --junitxml=/home/jenkins/workspace/clubb_dash/output/tests/pytests/dash.xml --durations=10 Installing uv 0.11.32 in /home/jenkins/workspace/clubb_dash/.clubb-python-tools/bin downloading uv 0.11.32 x86_64-unknown-linux-gnu installing to /home/jenkins/workspace/clubb_dash/.clubb-python-tools/bin uv uvx everything's installed! Creating CLUBB virtualenv: /home/jenkins/workspace/clubb_dash/.venv-python Downloading cpython-3.12.13-linux-x86_64-gnu (download) (32.6MiB) Downloaded cpython-3.12.13-linux-x86_64-gnu (download) Using CPython 3.12.13 Creating virtual environment at: .venv-python Activate with: source .venv-python/bin/activate Installing dash requirements into /home/jenkins/workspace/clubb_dash/.venv-python Using Python 3.12.13 environment at: .venv-python Resolved 71 packages in 775ms Downloading pillow (6.6MiB) Downloading meson (1.1MiB) Downloading plotly (9.5MiB) Downloading numpy (16.0MiB) Downloading netcdf4 (9.7MiB) Downloading kiwisolver (1.4MiB) Downloading matplotlib (8.4MiB) Downloading cryptography (4.5MiB) Downloading pygments (1.2MiB) Downloading dash (7.6MiB) Downloading cftime (1.6MiB) Downloading scipy (33.7MiB) Downloading fonttools (5.1MiB) Downloading pydantic-core (2.1MiB) Downloaded kiwisolver Downloaded cftime Downloaded pydantic-core Downloaded meson Downloaded pygments Downloaded cryptography Downloaded fonttools Downloaded pillow Downloaded netcdf4 Downloaded matplotlib Downloaded dash Downloaded numpy Downloaded scipy Downloaded plotly Prepared 71 packages in 2.18s Installed 71 packages in 88ms + annotated-types==0.8.0 + anyio==4.15.1 + attrs==26.1.0 + blinker==1.9.0 + certifi==2026.7.22 + cffi==2.1.1 + cftime==1.6.6 + charset-normalizer==3.5.2 + click==8.5.0 + contourpy==1.4.0 + cryptography==50.0.2 + cycler==0.12.1 + dash==3.4.0 + dill==0.4.1 + diskcache==5.6.3 + flask==3.1.3 + fonttools==4.66.1 + h11==0.16.0 + httpcore==1.0.9 + httpx==0.28.1 + httpx-sse==0.4.3 + idna==3.20 + importlib-metadata==9.0.1 + iniconfig==2.3.1 + itsdangerous==2.2.0 + jinja2==3.1.6 + jsonschema==4.26.0 + jsonschema-specifications==2025.9.1 + kiwisolver==1.5.1 + markupsafe==3.0.4 + matplotlib==3.10.9 + mcp==1.30.0 + meson==1.12.1 + multiprocess==0.70.19 + narwhals==2.27.1 + nest-asyncio==1.6.0 + netcdf4==1.7.4 + ninja==1.13.2 + numpy==2.5.4 + packaging==26.3 + pillow==12.3.0 + plotly==6.9.0 + pluggy==1.6.0 + psutil==7.2.2 + pycparser==3.11 + pydantic==2.14.0 + pydantic-core==2.50.0 + pydantic-settings==2.15.0 + pygments==2.21.0 + pyjwt==2.15.1 + pyparsing==3.3.3 + pytest==9.1.1 + python-dateutil==2.9.0.post0 + python-dotenv==1.2.4 + python-multipart==0.0.32 + referencing==0.37.0 + requests==2.34.2 + retrying==1.4.2 + rpds-py==2026.9.1 + scipy==1.18.1 + setuptools==84.0.0 + six==1.17.0 + sse-starlette==3.5.0 + starlette==1.7.0 + tabulate==0.10.0 + typing-extensions==4.16.0 + typing-inspection==0.4.4 + urllib3==2.8.0 + uvicorn==0.54.0 + werkzeug==3.1.9 + zipp==4.1.1 Ready: /home/jenkins/workspace/clubb_dash/.venv-python/bin/python ============================= test session starts ============================== platform linux -- Python 3.12.13, pytest-9.1.1, pluggy-1.6.0 rootdir: /home/jenkins/workspace/clubb_dash plugins: dash-3.4.0, anyio-4.15.1 collected 552 items dash_app/pytests/test_activity.py ......... [ 1%] dash_app/pytests/test_agent_integration.py .............. [ 4%] dash_app/pytests/test_agent_plot_actions.py ........ [ 5%] dash_app/pytests/test_agent_services.py ................................ [ 11%] ................. [ 14%] dash_app/pytests/test_agent_tab_registry.py ...... [ 15%] dash_app/pytests/test_agent_tuning.py ............ [ 17%] dash_app/pytests/test_analysis.py ..... [ 18%] dash_app/pytests/test_app_startup.py .......... [ 20%] dash_app/pytests/test_atlas.py . [ 20%] dash_app/pytests/test_bivariate_heatmap.py .. [ 21%] dash_app/pytests/test_callbacks_runs.py ............ [ 23%] dash_app/pytests/test_compile_tab_build_status.py ................. [ 26%] dash_app/pytests/test_custom_plot.py ........ [ 27%] dash_app/pytests/test_dashboard_activity_labels.py . [ 27%] dash_app/pytests/test_dashboard_lifecycle.py ... [ 28%] dash_app/pytests/test_dashboard_manager.py ...... [ 29%] dash_app/pytests/test_equations.py ... [ 30%] dash_app/pytests/test_fill_holes_viewer.py .... [ 30%] dash_app/pytests/test_jax_device.py ..................... [ 34%] dash_app/pytests/test_mcp_endpoint.py ... [ 35%] dash_app/pytests/test_misc_tab.py ... [ 35%] dash_app/pytests/test_netcdf.py ...... [ 36%] dash_app/pytests/test_output_directory_picker.py ...... [ 37%] dash_app/pytests/test_output_discovery.py ....... [ 39%] dash_app/pytests/test_pane_resize.py ... [ 39%] dash_app/pytests/test_param_disclosures.py ........ [ 41%] dash_app/pytests/test_pdf_contour_plot.py ...................... [ 45%] dash_app/pytests/test_performance_polling.py ....... [ 46%] dash_app/pytests/test_persistence.py .... [ 47%] dash_app/pytests/test_plot_case_cache.py .......... [ 48%] dash_app/pytests/test_plot_extraction.py ............................... [ 54%] [ 54%] dash_app/pytests/test_plot_grid_updates.py ..... [ 55%] dash_app/pytests/test_plot_help.py ... [ 55%] dash_app/pytests/test_plot_tasks.py .......... [ 57%] dash_app/pytests/test_plot_transitions.py ............. [ 60%] dash_app/pytests/test_profile_tab.py .............................. [ 65%] dash_app/pytests/test_profiles.py ...... [ 66%] dash_app/pytests/test_pyplotgen_export.py ...... [ 67%] dash_app/pytests/test_pyplotgen_output_handler.py . [ 67%] dash_app/pytests/test_reports_tab.py ....... [ 69%] dash_app/pytests/test_run_broker_simplification.py ..................... [ 73%] [ 73%] dash_app/pytests/test_run_callbacks_settings.py .............. [ 75%] dash_app/pytests/test_run_runtime.py .......... [ 77%] dash_app/pytests/test_runtime.py .. [ 77%] dash_app/pytests/test_runtime_logging.py ..... [ 78%] dash_app/pytests/test_runtime_loss_batches.py . [ 78%] dash_app/pytests/test_sam_3d_reference.py . [ 78%] dash_app/pytests/test_scm_override.py ...... [ 80%] dash_app/pytests/test_selected_build.py ..................... [ 83%] dash_app/pytests/test_state_persistence.py ............. [ 86%] dash_app/pytests/test_stats_selection.py ............................... [ 91%] [ 91%] dash_app/pytests/test_taylor_window_display.py ..... [ 92%] dash_app/pytests/test_tunable_config_save.py ............... [ 95%] dash_app/pytests/test_tune_callbacks_settings.py ............. [ 97%] dash_app/pytests/test_tutorial_tab.py .. [ 98%] dash_app/pytests/test_two_gaussian_model.py ...... [ 99%] dash_app/pytests/test_workspace_selection.py .... [100%] =============================== warnings summary =============================== dash_app/pytests/test_atlas.py: 49 warnings /home/jenkins/workspace/clubb_dash/dash_app/pytests/test_atlas.py:39: DeprecationWarning: Setting the shape on a NumPy array has been deprecated in NumPy 2.5. As an alternative, you can create a new view using np.reshape (with copy=False if needed). w_variable[0, level] = w dash_app/pytests/test_atlas.py: 49 warnings /home/jenkins/workspace/clubb_dash/dash_app/pytests/test_atlas.py:40: DeprecationWarning: Setting the shape on a NumPy array has been deprecated in NumPy 2.5. As an alternative, you can create a new view using np.reshape (with copy=False if needed). rt_variable[0, level] = rt dash_app/pytests/test_atlas.py: 49 warnings /home/jenkins/workspace/clubb_dash/dash_app/pytests/test_atlas.py:41: DeprecationWarning: Setting the shape on a NumPy array has been deprecated in NumPy 2.5. As an alternative, you can create a new view using np.reshape (with copy=False if needed). rc_variable[0, level] = rc dash_app/pytests/test_fill_holes_viewer.py::test_analysis_reads_direct_before_after_and_hardcoded_threshold dash_app/pytests/test_fill_holes_viewer.py::test_profile_field_scale_defaults_to_log_and_can_be_linear /home/jenkins/workspace/clubb_dash/dash_app/pytests/test_fill_holes_viewer.py:43: DeprecationWarning: Setting the shape on a NumPy array has been deprecated in NumPy 2.5. As an alternative, you can create a new view using np.reshape (with copy=False if needed). before[:] = np.array([[[2.0e-4], [8.0e-4], [1.0e-4]], [[8.0e-4], [1.2e-3], [1.6e-3]]]) dash_app/pytests/test_fill_holes_viewer.py::test_analysis_reads_direct_before_after_and_hardcoded_threshold dash_app/pytests/test_fill_holes_viewer.py::test_profile_field_scale_defaults_to_log_and_can_be_linear /home/jenkins/workspace/clubb_dash/dash_app/pytests/test_fill_holes_viewer.py:45: DeprecationWarning: Setting the shape on a NumPy array has been deprecated in NumPy 2.5. As an alternative, you can create a new view using np.reshape (with copy=False if needed). after[:] = np.array([[[5.0e-4], [8.0e-4], [2.0e-4]], [[8.0e-4], [1.2e-3], [1.6e-3]]]) dash_app/pytests/test_pdf_contour_plot.py: 470 warnings /home/jenkins/workspace/clubb_dash/dash_app/pytests/test_pdf_contour_plot.py:87: DeprecationWarning: Setting the shape on a NumPy array has been deprecated in NumPy 2.5. As an alternative, you can create a new view using np.reshape (with copy=False if needed). variable[:] = np.full((time_count, height_count, 1), value) dash_app/pytests/test_plot_case_cache.py::test_hydration_keeps_saved_view_and_scans_once /home/jenkins/workspace/clubb_dash/dash_app/plot_tab/case_definitions.py:35: DeprecationWarning: ast.Str is deprecated and will be removed in Python 3.14; use ast.Constant instead legacy_str = getattr(ast, "Str", None) dash_app/pytests/test_plot_case_cache.py: 4120 warnings /home/jenkins/workspace/clubb_dash/dash_app/plot_tab/case_definitions.py:36: DeprecationWarning: ast.Str is deprecated and will be removed in Python 3.14; use ast.Constant instead if legacy_str is not None and isinstance(node, legacy_str): dash_app/pytests/test_plot_case_cache.py::test_hydration_keeps_saved_view_and_scans_once /home/jenkins/workspace/clubb_dash/dash_app/plot_tab/case_definitions.py:39: DeprecationWarning: ast.Num is deprecated and will be removed in Python 3.14; use ast.Constant instead legacy_num = getattr(ast, "Num", None) dash_app/pytests/test_plot_case_cache.py: 4120 warnings /home/jenkins/workspace/clubb_dash/dash_app/plot_tab/case_definitions.py:40: DeprecationWarning: ast.Num is deprecated and will be removed in Python 3.14; use ast.Constant instead if legacy_num is not None and isinstance(node, legacy_num): dash_app/pytests/test_plot_extraction.py: 30 warnings /home/jenkins/workspace/clubb_dash/dash_app/pytests/test_plot_extraction.py:35: DeprecationWarning: Setting the shape on a NumPy array has been deprecated in NumPy 2.5. As an alternative, you can create a new view using np.reshape (with copy=False if needed). field[:] = np.transpose(cube, [('time', 'zt', 'col').index(d) for d in dims]) dash_app/pytests/test_plot_extraction.py: 30 warnings /home/jenkins/workspace/clubb_dash/dash_app/pytests/test_plot_extraction.py:39: DeprecationWarning: Setting the shape on a NumPy array has been deprecated in NumPy 2.5. As an alternative, you can create a new view using np.reshape (with copy=False if needed). ds.createVariable('lh_nl_w', 'f8', ('col', 'subcolumn', 'zt', 'time'))[:] = subcolumns.transpose(2, 3, 1, 0) dash_app/pytests/test_plot_extraction.py: 30 warnings /home/jenkins/workspace/clubb_dash/dash_app/pytests/test_plot_extraction.py:40: DeprecationWarning: Setting the shape on a NumPy array has been deprecated in NumPy 2.5. As an alternative, you can create a new view using np.reshape (with copy=False if needed). ds.createVariable('lwp', 'f8', ('col', 'time'))[:] = cube[:, 0, :].T dash_app/pytests/test_plot_extraction.py::test_file_change_invalidates_cached_results[stats0] dash_app/pytests/test_plot_extraction.py::test_file_change_invalidates_cached_results[stats1] dash_app/pytests/test_plot_extraction.py::test_file_change_invalidates_cached_results[stats2] /home/jenkins/workspace/clubb_dash/dash_app/pytests/test_plot_extraction.py:134: DeprecationWarning: Setting the shape on a NumPy array has been deprecated in NumPy 2.5. As an alternative, you can create a new view using np.reshape (with copy=False if needed). ds.variables['field'][:] = 42.0 -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html - generated xml file: /home/jenkins/workspace/clubb_dash/output/tests/pytests/dash.xml - ============================= slowest 10 durations ============================= 1.54s call dash_app/pytests/test_plot_tasks.py::test_browser_updates_selection_immediately_and_ignores_stale_results 1.36s call dash_app/pytests/test_agent_services.py::test_mcp_stdio_discovery_and_structured_error_round_trip 1.14s call dash_app/pytests/test_agent_plot_actions.py::test_profile_png_renderer_writes_a_real_png 0.95s call dash_app/pytests/test_plot_case_cache.py::test_background_worker_snapshot_resolves_in_main_process 0.78s call dash_app/pytests/test_plot_tasks.py::test_real_worker_inspects_missing_directory_and_serializes_no_update 0.76s call dash_app/pytests/test_agent_services.py::test_mcp_exposes_closed_world_typed_tools_and_annotations 0.50s call dash_app/pytests/test_agent_services.py::test_same_case_submissions_get_distinct_durable_batch_roots 0.50s call dash_app/pytests/test_run_broker_simplification.py::test_default_new_scenario_keeps_four_reservations_and_restarts_finished_case 0.46s call dash_app/pytests/test_netcdf.py::test_shared_netcdf_consumers_import_as_dashboard_packages 0.43s call dash_app/pytests/test_pdf_contour_plot.py::test_pdf_compare_mode_builds_shared_axis_directory_panels ===================== 552 passed, 8956 warnings in 31.26s ====================== [Pipeline] } [Pipeline] // withEnv [Pipeline] } [Pipeline] // stage [Pipeline] stage [Pipeline] { (Declarative: Post Actions) [Pipeline] junit Recording test results [Checks API] No suitable checks publisher found. [Pipeline] } [Pipeline] // stage [Pipeline] } [Pipeline] // withEnv [Pipeline] } [Pipeline] // node [Pipeline] End of Pipeline Finished: SUCCESS