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 a8c952996409f8c94d6a28714171145ed7d2c2ae (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f a8c952996409f8c94d6a28714171145ed7d2c2ae # timeout=10 Commit message: "Fixed bug in cubic equation solve function. Only relevant if pdf is L… (#1387)" > git rev-list --no-walk 4292a70f53a6b6c4eab864fe27b8fd9af5d86909 # timeout=10 [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 721ms Downloading pygments (1.2MiB) Downloading matplotlib (8.4MiB) Downloading meson (1.1MiB) Downloading netcdf4 (9.7MiB) Downloading numpy (16.0MiB) Downloading cftime (1.6MiB) Downloading pydantic-core (2.1MiB) Downloading pillow (6.6MiB) Downloading cryptography (4.5MiB) Downloading scipy (33.7MiB) Downloading plotly (9.5MiB) Downloading fonttools (5.1MiB) Downloading kiwisolver (1.4MiB) Downloading dash (7.6MiB) Downloaded meson Downloaded kiwisolver Downloaded cftime Downloaded pydantic-core Downloaded pygments Downloaded fonttools Downloaded cryptography Downloaded pillow Downloaded netcdf4 Downloaded matplotlib Downloaded dash Downloaded numpy Downloaded plotly Downloaded scipy Prepared 71 packages in 2.11s Installed 71 packages in 97ms + 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==2.14.1 + pydantic-core==2.50.1 + 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==1.8.0 + 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 ============================= 1.55s call dash_app/pytests/test_plot_tasks.py::test_browser_updates_selection_immediately_and_ignores_stale_results 1.38s call dash_app/pytests/test_agent_services.py::test_mcp_stdio_discovery_and_structured_error_round_trip 1.11s call dash_app/pytests/test_agent_plot_actions.py::test_profile_png_renderer_writes_a_real_png 1.06s call dash_app/pytests/test_plot_case_cache.py::test_background_worker_snapshot_resolves_in_main_process 0.85s call dash_app/pytests/test_plot_tasks.py::test_real_worker_inspects_missing_directory_and_serializes_no_update 0.72s call dash_app/pytests/test_agent_services.py::test_mcp_exposes_closed_world_typed_tools_and_annotations 0.57s call dash_app/pytests/test_pdf_contour_plot.py::test_pdf_compare_mode_builds_shared_axis_directory_panels 0.51s call dash_app/pytests/test_run_broker_simplification.py::test_default_new_scenario_keeps_four_reservations_and_restarts_finished_case 0.51s call dash_app/pytests/test_netcdf.py::test_shared_netcdf_consumers_import_as_dashboard_packages 0.49s call dash_app/pytests/test_agent_services.py::test_same_case_submissions_get_distinct_durable_batch_roots ===================== 552 passed, 8956 warnings in 31.68s ====================== [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