Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add Jupyterlab guide and update Docker images #11

Merged
merged 6 commits into from
Apr 18, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
203 changes: 203 additions & 0 deletions JUPYTERLAB_GUIDE.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,203 @@
# JupyterLab Guide

This guide contains tips and FAQs which help to avoid common issues that arise when using JupyterLab.

# Table of Contents
### Tips
1. [Open multiple notebook tabs](#open-multiple-notebook-tabs)
2. [Check solutions or feedback](#check-solutions-or-feedback)
3. [Check memory usage](#check-memory-usage)
4. [Get a fresh copy of a notebook](#get-a-fresh-copy-of-a-notebook)
5. [View hidden files](#view-hidden-files)
6. [Clone a GitHub repo](#clone-a-github-repo)
7. [Get a copy of everything](#get-a-copy-of-everything)

### FAQs
1. [Why did I get a zero/low-mark when I submitted everything on time?](#why-did-i-get-a-zerolow-mark-when-i-submitted-everything-on-time)
2. [Why are none of my cells running?](#why-are-none-of-my-cells-running)
3. [Why does my kernel keep dying?](#why-does-my-kernel-keep-dying)
4. [Why did I get a zero on a question when all the tests passed?](#why-did-i-get-a-zero-on-a-question-when-all-the-tests-passed)
5. [Why did I get a low mark on a question when all the tests passed?](#why-did-i-get-a-low-mark-on-a-question-when-all-the-tests-passed)
6. [I made a typo in my code, can I still get marks for the question?](#i-made-a-typo-in-my-code-can-i-still-get-marks-for-the-question)
7. [I am getting a 400 (Bad Request) or 404 (Not Found) error, how do I fix it?](#i-am-getting-a-400-bad-request-or-404-not-found-error-how-do-i-fix-it)
8. [How do I get a blank worksheet or tutorial for practice?](#how-do-i-get-a-blank-worksheet-or-tutorial-for-practice)

## Tips

## Open multiple notebook tabs

When working on a notebook, you might want to have multiple tabs of the same notebook open to easily reference previous questions.

**DO NOT** open another browser tab, create another instance of JupyterLab, and open the same notebook. Doing so may overwrite the notebook you are working on with an empty or half-completed version.

Instead, use JupyterLab's built in tab functionality to create another view for the notebook.

To do so in JupyterLab, right click the tab that contains the notebook in question.

On the dropdown menu, click **New View for Notebook**:

![Alt text](images/image1.png)

This will create a split screen, showing a copy of the notebook on half of the screen.

## Check solutions or feedback

Solutions and feedback are uploaded to your home directory. This is a different directory to where assignments are stored.

To get to your home directory, open JupyterLab and then click the small grey folder icon on top of the menu to the left that shows files and folders.

![Alt text](images/image2.png)

Then that same menu should show assignment solutions and feedback. Solutions are typically released a few days after the due date, feedback is released after assignments are graded (this may take a couple weeks as tutorials are manually graded).

## Check memory usage

Student JupyterLab instances are limited to 2GB (2048MB) of memory usage, if that limit is reached by running a notebook then the kernel will be killed and cells will stop running.

To check how much memory JupyterLab is using, there is a indicator on the bottom left of the window:

![Alt text](images/image3.png)

The maximum amount of memory usage a notebook should use is around 1GB (1024MB). If you find that JupyterLab is hitting the limit very often, here are some steps you can take:

### Restart your JupyterLab server

On the top left, go to **File -> Hub Control Panel** and it will open a window with a red button with text **Stop My Server**, click the button and then click the **Log Out** button on the top right.

Close the browser tab and then open JupyterLab again from Canvas.

### Check your code

If restarting your server does not work, then there may be an issue with your code.

Run your notebook one cell at a time. If you hit a cell that causes memory usage to hit the 2GB limit, examine the code in the cell to make sure there aren't any errors e.g. running a function on unfiltered data.

## Get a fresh copy of a notebook

If you need a new copy of a notebook, for example if you accidentally deleted a grading cell or want one for practice, first rename the notebook you have in your account currently.

For example if you need a new copy of a `worksheet_wrangling.ipynb`, right-click it in the file menu and choose the **Rename** option and rename it to `worksheet_wrangling_old.ipynb`.

Then close JupyterLab and then open the assignment again on Canvas. A new copy of the assignment should be created in place of the renamed assignment.

## View hidden files

*Warning*: Only delete hidden files that you have created, other hidden files may be used by the server

To view hidden files, on the top left go to **View** and on the dropdown click **Show Hidden Files**

## Clone a GitHub repo

To clone a GitHub repo for collaborative work, follow these steps:

1. Find the HTTPS repo link from GitHub and copy it to the clipboard

![alt text](images/image5.png)

2. Go to your JupyterLab and make sure you're in the home directory by clicking the small grey folder icon on the top left of the menu that shows your files and folders

![Alt text](images/image2.png)

3. Go to the JupyterLab git extension menu by clicking its tab on the left of JupyterLab:

![alt text](images/image6.png)

4. Click "Clone a Repository" and then paste the repo link from step 1 into the box and click Clone.

![alt text](images/image7.png)

The repo should now be in your home directory in a folder titled with the name of your repo.

To get to your cloned repo, remember to navigate to the home directory as shown in step 2.

## Get a copy of everything

To get a zipped copy of all of your work at the end of term:

1. Open a terminal by clicking the terminal icon when you first open JupyterLab from the Canvas homepage or in a new JupyterLab tab.

![Alt text](images/image4.png)

2. Enter the following command into the terminal:
```
cd /home/jovyan/work/ && zip -r backupjupyterlab.zip *
```
If you received a `Disk quota exceeded` error, then there are too many files. Delete any files or folders that you don't need (especially large .csv files) and try the command again.

3. Go to your home folder [as described here](#check-solutions-or-feedback) and there should be a zip file. Right-click the file and click Download to download a copy onto your device.

## FAQs

### Why did I get a zero/low-mark when I submitted everything on time?

Make sure that you are opening another notebook tab [in the correct way](#open-multiple-notebook-tabs). If you opened another browser tab with JupyterLab, then there is a chance your notebook was overwritten.

Lastly, do not rename the assignment notebook file or any folders. The autograder relies on those names to collect submissions.

### Why are none of my cells running?

Before anything else, try restarting JupyterHub as described [here](#restart-your-jupyterlab-server).

Make sure you're using a compatible browser. We recommend Chrome, Edge, or Firefox. Also update your browser to the latest version.

Update your device's operating system to the latest version and reboot your device.

Disable any extensions to check if they are affecting JupyterLab.

Try opening JupyterLab in an incognito browser session.

### Why does my kernel keep dying?

Please read [Check memory usage](#check-memory-usage).

### Why did I get a zero on a question when all the tests passed?

You may have deleted a grading cell accidentally (grading cells are cells that contain test functions e.g. `test_3.2()`).

The autograder relies on these cells to give students marks. Creating a new cell and then copying the test function into that cell will not fix the issue.

If you do accidentally delete a grading cell, you should [get a fresh copy of the assignment notebook](#get-a-fresh-copy-of-a-notebook). Then, copy your work into the fresh notebook.

### Why did I get a low mark on a question when all the tests passed?

Some questions have hidden tests that are not shown in the student version of the assignment.

Your answer may have passed the visible tests but failed the hidden tests when it was being marked.

Examine the feedback for the question carefully to see if hidden tests were run on your code. Instructions for accessing feedback are [here](#check-solutions-or-feedback).

### I made a typo in my code, can I still get marks for the question?

We will not be making exceptions for typos in autograded coding questions.

Read the questions carefully as some questions request answers of a certain type (e.g. String).

The questions include tests that give instant feedback on your code. Run those tests frequently to ensure that you haven't made any typos.

### I am getting a 400 (Bad Request) or 404 (Not Found) error, how do I fix it?

Before continuing with the instructions below, try JupyterLab again after restarting your browser.

The errors could be due to your browser's cache and it may need to be cleared.

Instructions:

[For Edge](https://www.microsoft.com/en-us/edge/learning-center/how-to-manage-and-clear-your-cache-and-cookies?form=MA13I2)

[For Chrome](https://support.google.com/accounts/answer/32050?hl=en&co=GENIE.Platform%3DDesktop)

[For Firefox](https://support.mozilla.org/en-US/kb/how-clear-firefox-cache)

After clearing your browser's cache, restart the browser and try opening JupyterLab again.

If it still has the same error, try using Incognito or Private Browsing on your browser.

Lastly, disable any browser extensions as they could interfere with JupyterLab. Also check that your browser is updated to its latest version.

### How do I get a blank worksheet or tutorial for practice?

Follow the instructions [here](#get-a-fresh-copy-of-a-notebook) to get a blank copy of a tutorial or worksheet.




20 changes: 9 additions & 11 deletions dockerfiles/r-stat-301-grading/Dockerfile
Original file line number Diff line number Diff line change
@@ -1,17 +1,15 @@
# Copyright (c) UBC-DSCI Development Team.
# Distributed under the terms of the Modified BSD License.
FROM ubcdsci/r-stat-301:latest

LABEL maintainer="Tiffany Timbers <[email protected]>"
# TODO: For testing purposes only, change back to ubcdsci/r-stat-301:latest
FROM ubcstatit/r-stat-301-student:latest

# install the rise slides extension
RUN mamba install --quiet --yes "rise"
LABEL maintainer="Brian Kim <[email protected]>"

# install nbgrader
RUN mamba install --quiet --yes "nbgrader=0.7.1" \
&& jupyter nbextension install --sys-prefix --py nbgrader --overwrite \
&& jupyter nbextension enable --sys-prefix --py nbgrader \
&& jupyter serverextension enable --sys-prefix --py nbgrader
# install rise slides extension, nbgrader, clean cache
RUN mamba install --quiet --yes \
'nbgrader=0.8.2' && \
mamba clean --all -f -y

# Clean the cache
RUN mamba clean --all -f -y
# re-upgrade jupyter-server (mamba downgrades it)
RUN pip install --upgrade jupyter-server
114 changes: 56 additions & 58 deletions dockerfiles/r-stat-301/Dockerfile
Original file line number Diff line number Diff line change
@@ -1,67 +1,65 @@
# Copyright (c) UBC-DSCI Development Team.
# Distributed under the terms of the Modified BSD License.
FROM jupyter/r-notebook
FROM jupyter/minimal-notebook

LABEL maintainer="Tiffany Timbers <[email protected]>"
LABEL maintainer="Brian Kim <[email protected]>"

SHELL ["/bin/bash", "-o", "pipefail", "-c"]

USER root

# install vim
RUN apt-get update && apt-get install -y vim
# R pre-requisites
RUN apt-get update --yes && \
apt-get install --yes --no-install-recommends \
fonts-dejavu \
unixodbc \
unixodbc-dev \
r-cran-rodbc \
gfortran \
gcc \
vim && \
apt-get clean && rm -rf /var/lib/apt/lists/*

USER ${NB_UID}

# Change workdir to $HOME/work so config files are preserved when bind mounting
WORKDIR "${HOME}/work"

# disable warnings that pollute build logs; seems to be related to the update to python 3.11
# https://discourse.jupyter.org/t/debugger-warning-it-seems-that-frozen-modules-are-being-used-python-3-11-0/16544/12
ENV PYDEVD_DISABLE_FILE_VALIDATION=1

COPY conda-linux-64.lock /tmp/conda-linux-64.lock

RUN mamba update --quiet --file /tmp/conda-linux-64.lock && \
mamba clean --all -y -f && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}" && \
Rscript -e "install.packages('faux', repos='http://cran.us.r-project.org')" && \
Rscript -e "install.packages('moderndive', repos='http://cran.us.r-project.org')"

# Install pexpect from main branch to fix asyncio issue with jupyterlab_git
RUN pip install --ignore-installed git+https://github.com/pexpect/pexpect.git@master

# Disable the cell toolbar (which ignores metadata and students often accidentally click + delete grading cells)
RUN jupyter labextension disable @jupyterlab/cell-toolbar-extension

# Disable announcement pop-up on start
RUN jupyter labextension disable "@jupyterlab/apputils-extension:announcements"

# Configure shortcuts-extension to remove Shift-M cell merge shortcut
COPY config/shortcuts.jupyterlab-settings /home/${NB_USER}/.jupyter/lab/user-settings/\@jupyterlab/shortcuts-extension/shortcuts.jupyterlab-settings

# Copy jupyter_server_config.py which allows students to see and delete hidden files
COPY config/jupyter_server_config.py /home/${NB_USER}/.jupyter

# Copy gitconfig that sets default pull strategy to rebase
COPY config/.gitconfig /home/${NB_USER}/

# Make sure everything in the home folder is owned by NB_USER for running docker image locally.
USER root
RUN chown -R ${NB_USER} /home/${NB_USER}
USER ${NB_UID}

WORKDIR "${HOME}"

# remove the "work/" directory added in an earlier layer...
RUN rm -rf work

# Install R packages
RUN mamba install --quiet --yes \
'r-cowplot' \
'r-ggally' \
'r-gridextra' \
'r-infer' \
'r-kknn' \
'r-testthat' \
'r-rpostgres' \
'r-janitor' \
'r-mltools' \
'r-leaps' \
'r-faraway' \
'r-glmnet' \
'r-titanic' \
'r-performance' \
'r-binom' \
'r-gridgraphics' \
'r-aer' \
'r-latex2exp' \
'r-gsdesign' \
'r-car' \
'r-cardata' \
'r-mlbench' \
'r-qqplotr' \
'r-see' \
'r-boot' \
'r-caret' \
&& mamba clean --all -f -y \
&& fix-permissions "${CONDA_DIR}" \
&& fix-permissions "/home/${NB_USER}" \
&& Rscript -e "remotes::install_github('allisonhorst/[email protected]')" \
&& Rscript -e "install.packages('faux', repos='http://cran.us.r-project.org')" \
&& Rscript -e "install.packages('contextual', repos='http://cran.us.r-project.org')" \
&& Rscript -e "install.packages('ISLR', repos='http://cran.us.r-project.org')" \
&& Rscript -e "install.packages('ISLR2', repos='http://cran.us.r-project.org')" \
&& Rscript -e "install.packages('glmbb', repos='http://cran.us.r-project.org')"

# Install nbgitpuller, jupytext, jlab-git
RUN pip install git+https://github.com/data-8/nbgitpuller@c23461d4f7ce47ec4e0d2bcfc3b2fde4939b80f8 \
&& jupyter serverextension enable --sys-prefix nbgitpuller \
&& pip install jupyterlab-git \
&& pip install jupytext --upgrade \
&& jupyter labextension install @techrah/text-shortcuts \
&& jupyter lab build

# Install the extension to remove the shift+M merge shortcut
RUN mkdir -p /home/${NB_USER}/.jupyter/lab/user-settings/\@jupyterlab/shortcuts-extension
COPY rm-merge-shortcut.py /home/${NB_USER}/.jupyter/lab/user-settings/\@jupyterlab/shortcuts-extension/shortcuts.jupyterlab-settings
# Disable HEALTHCHECK for performance reasons
HEALTHCHECK NONE
Loading
Loading