Merge pull request #200 from ocefpaf/skip_ir_kernel_nb

Skip all notebooks that uses the R kernel

jupyterbook/_config.yml

@@ -85,32 +85,11 @@ repository:
 sphinx:
   config:
     linkcheck_ignore: [
-      "./data_access_notebooks/2016-10-12-fetching_data.html",
-      "./data_access_notebooks/2016-11-15-glider_data_example.html",
-      "./data_access_notebooks/2016-12-20-searching_glider_deployments.html",
-      "./data_access_notebooks/2017-03-21-ERDDAP_IOOS_Sensor_Map.html",
-      "./data_access_notebooks/2017-06-12-NCEI_RA_archive_history.html",
-      "./data_access_notebooks/2017-08-01-xtractoR.html",
-      "./data_access_notebooks/2017-09-09-hurricane_irma.html",
-      "./data_access_notebooks/2017-11-30-rerddap.html",
-      "./data_access_notebooks/2018-02-20-obis.html",
-      "./data_access_notebooks/2018-03-01-erddapy.html",
-      "./data_access_notebooks/2019-03-08-grids-temperature.html",
-      "./data_access_notebooks/2019-05-27-hurricane_gis_part02.html",
-      "./data_access_notebooks/2020-10-10-GTS.html",
-      "./data_access_notebooks/2021-10-19-multiple-erddap-search.html",
-      "./data_access_notebooks/2022-11-23_pyobis_example.html",
-      "./data_analysis_and_visualization_notebooks/2016-11-16-CF-UGRID-SGRID-conventions.html",
-      "./data_analysis_and_visualization_notebooks/2017-01-23-R-notebook.html",
-      "./data_analysis_and_visualization_notebooks/2017-03-30-octave_notebook_example.html",
-      "./data_analysis_and_visualization_notebooks/2018-12-04-grids.html",
-      "./data_analysis_and_visualization_notebooks/2020-02-14-QARTOD_ioos_qc_Water-Level-Example.html",
-      "./data_analysis_and_visualization_notebooks/2021-10-25-ERDDAP-interpolate.html",
-      "./data_management_notebooks/2017-05-14-running_compliance_checker.html",
-      "./data_management_notebooks/2017-11-01-Creating-Archives-Using-Bagit.html",
-      "./data_management_notebooks/2018-02-27-pocean-timeSeries-demo.html",
-      "./data_management_notebooks/2020-12-08-DataToDwC.html",
-      "./data_management_notebooks/2023-03-20-Reading_and_writing_zarr.html",
+      "./data_access_notebooks/.*",
+      "./data_analysis_and_visualization_notebooks/.*",
+      "./data_management_notebooks/.*",
+      "./data_analysis_and_visualization_notebooks/.*",
+      "https://www.ncei.noaa.gov/archive/accession/0282699",  # slow
       ]
     linkcheck_anchors_ignore: ["aboutPanel", "searchPanel", "!forum/ioos_tech"]
     html_show_copyright: false

pytest.ini

@@ -15,8 +15,9 @@ addopts =
     --ignore="jupyterbook/content/code_gallery/data_access_notebooks/2019-05-27-hurricane_gis_part02.ipynb"
     # Take too long to run
     --ignore="jupyterbook/content/code_gallery/data_access_notebooks/2019-03-08-grids-temperature.ipynb"
-    # Pass locally but fail upstream for unknown reasons
+    # Skipping all the notbooks with the R kernel
     --ignore="jupyterbook/content/code_gallery/data_access_notebooks/2017-08-01-xtractoR.ipynb"
     --ignore="jupyterbook/content/code_gallery/data_access_notebooks/2017-11-30-rerddap.ipynb"
     --ignore="jupyterbook/content/code_gallery/data_access_notebooks/2018-02-20-obis.ipynb"
     --ignore="jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/2017-01-23-R-notebook.ipynb"
+    --ignore="jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/2024-05-16-white_shark_water_temp.ipynb"