merging 5811/5812/5813/5817/5829/5830/5833/5836 to prod

deployments/a11y/image/environment.yml

@@ -35,7 +35,7 @@ dependencies:
   - nbconvert-a11y==2023.12.6
   - nb2pdf==0.6.2
   - nbpdfexport==0.2.1
-  - jupyterlab-a11y-checker==0.1.1
+  - jupyterlab-a11y-checker==0.1.2
   # ###
   # The items below are from infra-requirements, however lab conflicts with the
   # alpha notebook.

deployments/data8/config/common.yaml

@@ -56,19 +56,19 @@ jupyterhub:
       #    - course::N::enrollment_type::teacher
       #    - course::N::enrollment_type::ta
 
-      # Data 8, Spring 2024, https://github.com/berkeley-dsep-infra/datahub/issues/5358
-      #course-staff-1532352:
+      # Data 8, Summer 2024, https://github.com/berkeley-dsep-infra/datahub/issues/5834
+      course-staff-1535365:
       #  description: Enable course staff to view and access servers.
       #  # this role provides permissions to...
-      #  scopes:
-      #    - admin-ui
-      #    - list:users!group=course::1532352
-      #    - admin:servers!group=course::1532352
-      #    - access:servers!group=course::1532352
+        scopes:
+          - admin-ui
+          - list:users!group=course::1535365
+          - admin:servers!group=course::1535365
+          - access:servers!group=course::1535365
       #  # this role will be assigned to...
-      #  groups:
-      #    - course::1532352::enrollment_type::teacher
-      #    - course::1532352::enrollment_type::ta
+        groups:
+          - course::1535365::enrollment_type::teacher
+          - course::1535365::enrollment_type::ta
 
   singleuser:
     extraFiles:

deployments/dev/config/common.yaml

@@ -71,6 +71,9 @@ jupyterhub:
         description: "A newer repo2docker-based image with a primary focus of building dashboards."
         kubespawner_override:
           image: us-central1-docker.pkg.dev/ucb-datahub-2018/user-images/dev-secondary:36280727a
+          env:
+            GH_SCOPED_CREDS_CLIENT_ID: "Iv23liFjgKFgkSBWph4C"
+            GH_SCOPED_CREDS_APP_URL: "https://github.com/apps/test-gh-scoped-creds"
       - display_name: "1524699: DataHub Infrastructure"
         slug: "1524699"
         description: "Regular image with per-course subpath."

deployments/dev/images/secondary/environment.yml

@@ -31,7 +31,6 @@ dependencies:
 - scipy==1.10.1
 - seaborn==0.12.2
 - statsmodels==0.14.0
-- tensorflow-cpu==2.12.1
 - sqlalchemy==2.0.16
 - mlxtend==0.23.0
 # Spring 2024 data 100
@@ -57,7 +56,7 @@ dependencies:
 #- otter-grader==5.5.0
 #- python-duckdb==1.0.0
 #- jupyterhub==5.0.0
-
+- quarto==1.4.550
 - pip
 - pip:
   # - -r infra-requirements.txt
@@ -73,4 +72,4 @@ dependencies:
   - ydata-profiling==4.6.4
   - otter-grader==5.4.0
   - duckdb==0.10.1
-  - duckdb_engine==0.11.2
+  - duckdb_engine==0.11.2

deployments/dev/images/secondary/install.R

@@ -1,5 +1,6 @@
-#!/usr/bin/env r
+#!/usr/bin/env R
 
+# Function to install R packages with specific versions
 class_libs_install_version <- function(class_name, class_libs) {
   print(paste("Installing packages for", class_name))
   for (i in seq(1, length(class_libs), 2)) {

deployments/publichealth/config/common.yaml

@@ -38,19 +38,19 @@ jupyterhub:
         groups:
           - course::1524699::group::all-admins
 
-      # PHW 142, Spring 2024, #5368
-      #course-staff-1532521:
-      #  description: Enable course staff to view and access servers.
+      # PHW 142, Fall 2024, #5831
+      course-staff-1535789:
+        # description: Enable course staff to view and access servers.
         # this role provides permissions to...
-      #  scopes:
-      #    - admin-ui
-      #    - list:users!group=course::1532521
-      #    - admin:servers!group=course::1532521
-      #    - access:servers!group=course::1532521
+        scopes:
+          - admin-ui
+          - list:users!group=course::1535789
+          - admin:servers!group=course::1535789
+          - access:servers!group=course::1535789
         # this role will be assigned to...
-      #  groups:
-      #    - course::1532521::enrollment_type::teacher
-      #    - course::1532521::enrollment_type::ta
+        groups:
+          - course::1535789::enrollment_type::teacher
+          - course::1535789::enrollment_type::ta
 
     extraConfig:
       # Use 1x-<title> in `common.yaml` extraConfig values.

hub/values.yaml

@@ -85,6 +85,14 @@ jupyterhub:
           HistoryManager:
             # We do not need to keep around history for IPython, and especially not on NFS
             enabled: false
+      jupyter_server_config.json:
+        mountPath: /usr/local/etc/jupyter/jupyter_server_config.json
+        data:
+          # Allow JupyterLab to show the 'View -> Show Hidden Files' option
+          # in the menu. Defaults are not changed.
+          # https://github.com/jupyterlab/jupyterlab/issues/11304#issuecomment-945466766
+          ContentsManager:
+            allow_hidden: true
       culling-config:
         mountPath: /etc/jupyter/jupyter_notebook_config.json
         data: