diff --git a/JUPYTERLAB_GUIDE.md b/JUPYTERLAB_GUIDE.md new file mode 100644 index 0000000..62e2f42 --- /dev/null +++ b/JUPYTERLAB_GUIDE.md @@ -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? + +If you are aware of the above, then 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. + + + + diff --git a/dockerfiles/r-stat-201-grading/Dockerfile b/dockerfiles/r-stat-201-grading/Dockerfile index 308c9a6..457fed1 100644 --- a/dockerfiles/r-stat-201-grading/Dockerfile +++ b/dockerfiles/r-stat-201-grading/Dockerfile @@ -1,17 +1,15 @@ # Copyright (c) UBC-STAT Development Team. # Distributed under the terms of the Modified BSD License. -FROM ubcstat/r-stat-201:latest +# TODO: For testing purposes only, change to ubcstat/r-stat-201:latest +FROM ubcstatit/r-stat-201-student:latest -LABEL maintainer="Tiffany Timbers " +LABEL maintainer="Brian Kim " -# install the rise slides extension -RUN mamba install --quiet --yes "rise" +# install rise slides extension, nbgrader, clean cache +RUN mamba install --quiet --yes \ + 'nbgrader=0.8.2' && \ + mamba clean --all -f -y -# 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 +# re-upgrade jupyter-server (mamba downgrades it) +RUN pip install --upgrade jupyter-server -# Clean the cache -RUN mamba clean --all -f -y diff --git a/dockerfiles/r-stat-201/Dockerfile b/dockerfiles/r-stat-201/Dockerfile index 06ae7f5..e0f62f0 100644 --- a/dockerfiles/r-stat-201/Dockerfile +++ b/dockerfiles/r-stat-201/Dockerfile @@ -1,47 +1,66 @@ # 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 " +LABEL maintainer="Brian Kim " + +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 + +# Install R packages from lock file. +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 "devtools::install_github('UBC-MDS/datateachr@v0.2.1')" && \ + Rscript -e "devtools::install_github('UBC-MDS/taxyvr@0.1.0')" +# 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 global 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-memoise' \ - && mamba clean --all -f -y \ - && fix-permissions "${CONDA_DIR}" \ - && fix-permissions "/home/${NB_USER}" \ - && Rscript -e "remotes::install_github('allisonhorst/palmerpenguins@v0.1.0')" \ - && Rscript -e "install.packages('ISLR', repos='http://cran.us.r-project.org')" \ - && Rscript -e "devtools::install_github('UBC-MDS/datateachr@v0.2.1')" \ - && Rscript -e "devtools::install_github('UBC-MDS/taxyvr@0.1.0')" - -# 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 \ No newline at end of file diff --git a/dockerfiles/r-stat-201/conda-linux-64.lock b/dockerfiles/r-stat-201/conda-linux-64.lock new file mode 100644 index 0000000..914a3f4 --- /dev/null +++ b/dockerfiles/r-stat-201/conda-linux-64.lock @@ -0,0 +1,580 @@ +# Generated by conda-lock. +# platform: linux-64 +# input_hash: 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any text or binary file, +# as well as directories, +# with special handling for JSON notebook documents. +# +# Most APIs take a path argument, +# which is always an API-style unicode path, +# and always refers to a directory. +# +# - unicode, not url-escaped +# - '/'-separated +# - leading and trailing '/' will be stripped +# - if unspecified, path defaults to '', +# indicating the root path. + +## Allow access to hidden files +# Default: False +c.ContentsManager.allow_hidden = True + +#------------------------------------------------------------------------------ +# FileContentsManager(FileManagerMixin, ContentsManager) configuration +#------------------------------------------------------------------------------ +## Allow access to hidden files +# See also: ContentsManager.allow_hidden +c.FileContentsManager.allow_hidden = True + +#------------------------------------------------------------------------------ +# AsyncContentsManager(ContentsManager) configuration +#------------------------------------------------------------------------------ +## Base class for serving files and directories asynchronously. + +## Allow access to hidden files +# See also: ContentsManager.allow_hidden +c.AsyncContentsManager.allow_hidden = True + +#------------------------------------------------------------------------------ +# AsyncFileContentsManager(FileContentsManager, AsyncFileManagerMixin, AsyncContentsManager) configuration +#------------------------------------------------------------------------------ +## Allow access to hidden files +# See also: ContentsManager.allow_hidden +c.AsyncFileContentsManager.allow_hidden = True diff --git a/dockerfiles/r-stat-201/config/shortcuts.jupyterlab-settings b/dockerfiles/r-stat-201/config/shortcuts.jupyterlab-settings new file mode 100644 index 0000000..ac5a216 --- /dev/null +++ b/dockerfiles/r-stat-201/config/shortcuts.jupyterlab-settings @@ -0,0 +1,31 @@ +{ + "shortcuts": [ + { + "args": {}, + "command": "notebook:merge-cell-above", + "keys": [ + "Ctrl Backspace" + ], + "selector": ".jp-Notebook:focus", + "disabled": true + }, + { + "args": {}, + "command": "notebook:merge-cell-below", + "keys": [ + "Ctrl Shift M" + ], + "selector": ".jp-Notebook:focus", + "disabled": true + }, + { + "args": {}, + "command": "notebook:merge-cells", + "keys": [ + "Shift M" + ], + "selector": ".jp-Notebook:focus", + "disabled": true + } + ] +} diff --git a/dockerfiles/r-stat-201/environment.yml b/dockerfiles/r-stat-201/environment.yml new file mode 100644 index 0000000..9c5073e --- /dev/null +++ b/dockerfiles/r-stat-201/environment.yml @@ -0,0 +1,65 @@ +name: stat_301 +channels: + - conda-forge + - r + - nodefaults +dependencies: + - anyio=3.7.1 + - jupyterlab=3.6.6 + - jupyterlab-git + - jupyter-resource-usage<1.0.0 + - jupyterlab_rise=0.2.0 + - jupytext + - nbgitpuller + - r-aer + - r-base + - r-binom + - r-boot + - r-car + - r-cardata + - r-caret + - r-caret + - r-cowplot + - r-crayon + - r-devtools + - r-e1071 + - r-faraway + - r-forecast + - r-ggally + - r-glmbb + - r-glmnet + - r-gridextra + - r-gridgraphics + - r-gsdesign + - r-hexbin + - r-htmltools + - r-htmlwidgets + - r-infer + - r-irkernel + - r-islr + - r-islr2 + - r-janitor + - r-kknn + - r-latex2exp + - r-leaps + - r-memoise + - r-mlbench + - r-mltools + - r-nycflights13 + - r-palmerpenguins + - r-performance + - r-qqplotr + - r-randomforest + - r-rcurl + - r-rmarkdown + - r-rodbc + - r-rpostgres + - r-rsqlite + - r-see + - r-shiny + - r-stringi=1.7.12 + - r-testthat + - r-tidymodels + - r-tidyverse + - r-titanic + - unixodbc diff --git a/dockerfiles/r-stat-201/rm-merge-shortcut.py b/dockerfiles/r-stat-201/rm-merge-shortcut.py deleted file mode 100644 index 84d5356..0000000 --- a/dockerfiles/r-stat-201/rm-merge-shortcut.py +++ /dev/null @@ -1,12 +0,0 @@ -{ "shortcuts": - [ - { - "command": "notebook:merge-cells", - "keys": [ - "Shift M" - ], - "selector": ".jp-Notebook:focus", - "disabled": true - } - ] -} diff --git 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