allow errors during notebook execution and increase timeout

.github/workflows/check-broken-link.yml

@@ -65,5 +65,5 @@ jobs:
           echo "notebook_list=${notebook_list}"
           for notebook in $(echo $notebook_list | jq -r '.[]'); do
             echo "Checking links in $notebook"
-            pytest --check-links --check-links-ignore "https://doi.org/.*/" $notebook
+            pytest --check-links --check-links-ignore "https://doi.org/.*/" "https://www.sciencedirect.com/.*" $notebook
           done

books/_config.yml

@@ -11,8 +11,8 @@ only_build_toc_files: true
 # See https://jupyterbook.org/content/execute.html
 execute:
   execute_notebooks: force
-  allow_errors: false
-  timeout: 18000
+  allow_errors: true
+  timeout: 25000
   stderr_output: error
   run_in_temp: true
   execution_show_tb: True
@@ -36,7 +36,6 @@ html:
   use_issues_button: true
   use_repository_button: true
   use_download_button: true
-  use_issues_button: true
   use_edit_page_button: true
   google_analytics_id: G-4Z9774J59Y
 

books/functional_imaging/aslprep.ipynb

@@ -31,7 +31,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {
     "colab": {
      "base_uri": "https://localhost:8080/"
@@ -56,7 +56,7 @@
     "  !chmod +x googlecolab_setup.sh\n",
     "  !./googlecolab_setup.sh\n",
     "\n",
-    "  os.environ[\"MODULEPATH\"] = ':'.join(map(str, list(map(lambda x: os.path.join(os.path.abspath('/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/'), x),os.listdir('/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/')))))\n"
+    "  os.environ[\"MODULEPATH\"] = ':'.join(map(str, list(map(lambda x: os.path.join(os.path.abspath('/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/'), x),os.listdir('/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/')))))"
    ]
   },
   {