Add content to advanced customization and nbgrader and minor changes to other

mittler-works · mittler-works · commit a2340e912c02 · 2025-10-28T15:16:38.000+01:00
diff --git a/learning-pathways/jupyter-based-teaching.md b/learning-pathways/jupyter-based-teaching.md
@@ -33,15 +33,11 @@ pathway:
       - topic: teaching
         name: jbt-featured
 
-  - section: "For teachers: Use custom Jupyter Images with JHaaS"
-    description: "Learn how to teach a course or workshop with your Jupyter customizations on JHaaS"
+  - section: "Use your customized JupyterLab for Courses"
+    description: "Learn how to teach a course or workshop with your custom JupyterLab"
     tutorials:
       - topic: teaching
         name: jbt-jhaas
-
-  - section: "For admins: Provide your Jupyter Images with Galaxy"
-    description: "Learn how to provide your custom Jupyter customizations on your Galaxy instance"
-    tutorials:
       - topic: teaching
         name: jbt-galaxy
 
diff --git a/topics/teaching/tutorials/jbt-customization-1/tutorial.md b/topics/teaching/tutorials/jbt-customization-1/tutorial.md
@@ -30,7 +30,7 @@ contributors:
 * WIP
 
 ```bash
-sudo docker run --rm -p 127.0.0.1:8888:8888 quay.io/jupyter/minimal-notebook:2025-06-23
+sudo docker run --rm -it -p 127.0.0.1:8888:8888 quay.io/jupyter/minimal-notebook:2025-06-23
 ```
 
 * Will print out a link to `http://localhost:8888/lab?token=<token>`
diff --git a/topics/teaching/tutorials/jbt-customization-2/tutorial.md b/topics/teaching/tutorials/jbt-customization-2/tutorial.md
@@ -4,7 +4,7 @@ layout: tutorial_hands_on
 title: Advanced Jupyter customization
 subtopic: practises
 draft: true
-time_estimation: 1h
+time_estimation: 90m
 questions:
   - How can I tailor Jupyter to my specific teaching needs?
 objectives:
@@ -170,12 +170,105 @@ RUN pip install jupyter_server_proxy
 
 You may install any other arbitrary server applications this way too, e.g. RStudio.
 
-# Exercise
+# Exercise 1: Persistent Data
 
 Why is the rust installation in step 1 of this tutorial problematic in case this notebook is served via JupyterHub?
 
 --> it installs rust in homedir
 
 Build a Customized JupyterLab with an available rust kernel even in JupyterHub szenario.
 
---> Dockerfile here
+```dockerfile
+FROM quay.io/jupyter/minimal-notebook:2025-06-23
+
+USER root
+RUN apt update \
+    && apt install -y build-essential \
+    && apt clean
+
+ARG RUSTUP_URL=https://sh.rustup.rs
+ARG RUSTUP_INIT=/tmp/rustup.sh
+
+ENV RUSTUP_HOME=/opt/rustup
+ENV CARGO_HOME=/opt/cargo
+ENV JUPYTER_PATH=/usr/local/share/jupyter
+ENV PATH="${PATH}:${CARGO_HOME}/bin"
+
+ADD --chmod=755 "${RUSTUP_URL}" "${RUSTUP_INIT}"
+RUN "${RUSTUP_INIT}" -v -y
+RUN cargo install --locked evcxr_jupyter
+RUN evcxr_jupyter --install
+
+RUN rm "${RUSTUP_INIT}"
+
+USER ${NB_UID}
+```
+
+# Exercise 2: Proxy Application
+
+Create a simple html page like this:
+
+```html
+<!DOCTYPE html>
+<html>
+<head>
+  <title>Hello World</title>
+  <meta charset="UTF-8" />
+</head>
+<body>
+  <h1>Hello World!</h1>
+  <p>I am served by your python server application!</p>
+</body>
+</html>
+```
+
+Include it as `index.html` in a separate folder in your container image.
+
+Create a proxy application serving this index.html file with the simple python builtin `http.server` package.
+
+Tip:
+
+```bash
+python3 -m http.server -d {path_to_dir_containing_the_html_file} {PORT}
+```
+
+
+
+Serve it via simple python 
+
+Solution:
+
+Create the index.html as explained above.
+
+Create a JupyterLab config `jupyter_lab_config.py` like this:
+
+```python
+c.ServerProxy.servers = {
+    "hello-world-server": {
+        "command": [
+          "python3",
+          "-m", "http.server",
+          "-d", "/srv/html",
+          "{port}"
+        ],
+        "launcher_entry": {
+          "enabled": True,
+          "title": "Hello World Server"
+        }
+    }
+}
+```
+
+Create a Dockerfile like this:
+
+```dockerfile
+FROM quay.io/jupyter/minimal-notebook:2025-06-23
+
+USER root
+
+COPY --chown=root:root jupyter_lab_config.py /etc/jupyter/jupyter_lab_config.py
+COPY --chown=root:root index.html /srv/html/index.html
+
+USER ${NB_UID}
+RUN pip install jupyter_server_proxy
+```
diff --git a/topics/teaching/tutorials/jbt-featured/tutorial.md b/topics/teaching/tutorials/jbt-featured/tutorial.md
@@ -4,7 +4,7 @@ layout: tutorial_hands_on
 title: Featured Jupyter customizations
 subtopic: practises
 draft: true
-time_estimation: 1h
+time_estimation: 30m
 questions:
   - Which customizations are battle-tested and recommended for teaching?
 objectives:
@@ -21,14 +21,68 @@ We present adaptions that the JLU Physics Department has been successfully using
 
 # nbgitpuller
 
+https://github.com/jupyterhub/nbgitpuller
+
+Allows a teacher to host his teaching material in a git repository.
+
+Teacher may update the repo while course is running in order to provide new exercises or to provide solutions for older exercises.
+
+nbgitpuller will will sync if either
+
+- the git puller url is opened
+- the notebook is started and git puller is configured as default url
+
 ## Install
 
+```dockerfile
+FROM quay.io/jupyter/minimal-notebook:2025-06-23
+
+RUN pip install nbgitpuller
+```
+
 ## Configuration
 
-## Usage
+Link generator: https://nbgitpuller.readthedocs.io/en/latest/link.html
+
+No special config needed, you just generate a link and call it
+
+Hint: when using nbgitpuller with a standalone JupyterLab and not JupyterHub, you need to remove the `hub/user-redirect/` part from the resulting URL!
+
+So, instead of `http://localhost:8888/hub/user-redirect/git-pull?repo=...` you should use `http://localhost:8888/git-pull?repo=...`
+
+## Use it
+
+## Exercise: create a git puller url for the igv-notebook repo
+
+From the earlier tutorial, expand the JupyterLab with igv-notebook installed: install nbgitpuller inside this JupyterLab.
+
+Then goto link generator and create a git puller link for https://github.com/igvteam/igv-notebook
+
+Configure it so the `BamFiles_Lab.ipynb` example openes automatically in the JupyterLab.
+
+solution: configure the link generator like this:
+
+| --- | --- |
+| JupyterHub URL | http://localhost:8888 |
+| Git Repository URL | https://github.com/igvteam/igv-notebook.git |
+| branch | main |
+| File to open | examples/BamFiles_Lab.ipynb |
+| Application to Open | JupyterLab |
+| Named Server to open | (leave it blank) |
+
+
+Strip off the `hub/user-redirect/` part.
+
+The link will be:
+
+http://localhost:8888/git-pull?repo=https%3A%2F%2Fgithub.com%2Figvteam%2Figv-notebook.git&urlpath=tree%2Figv-notebook.git%2Fexamples%2FBamFiles_Lab.ipynb&branch=main
+
+It should pull the repo and opens the example automatically. You should be able to run the example if you extended the igv-notebook tutorial.
 
 # nbgrader
 
+https://github.com/jupyter/nbgrader
+
 ## Install
 
 ## Configuration
@@ -42,5 +96,3 @@ We present adaptions that the JLU Physics Department has been successfully using
 # Setup Scripts
 
 ## Where to place them what to do with them
-
-(WIP)
diff --git a/topics/teaching/tutorials/jbt-galaxy/tutorial.md b/topics/teaching/tutorials/jbt-galaxy/tutorial.md
@@ -1,10 +1,10 @@
 ---
 layout: tutorial_hands_on
 
-title: Provide your custom Jupyter Image via Galaxy
+title: Provide your custom JupyterLab via Galaxy
 subtopic: practises
 draft: true
-time_estimation: 1h
+time_estimation: 15m
 questions:
   - As a Galaxy admin, how can I provide my users with a custom Notebook Server?
 objectives:
diff --git a/topics/teaching/tutorials/jbt-jhaas/tutorial.md b/topics/teaching/tutorials/jbt-jhaas/tutorial.md
@@ -1,10 +1,10 @@
 ---
 layout: tutorial_hands_on
 
-title: Teaching a course with custom Jupyter via JHaaS
+title: Provide your custom JupyterLab via JHaaS
 subtopic: practises
 draft: true
-time_estimation: 1h
+time_estimation: 15m
 questions:
   - How can I use my Jupyter customizations in a course relevant matter?
 objectives:
