move "accidentally deleted something" section, update readme

README.md

@@ -1,90 +1,69 @@
 # Debugging Guide
 
-# Guide to Quarto Installation & Use
+Website link: https://ds100.org/debugging-guide/
+
 ## Quarto Set-Up
 
 Begin by [installing Quarto](https://quarto.org/docs/get-started/).
 
-Texts can be authored in Quarto using JupyterLab or classic Jupyter Notebook. To start a new document, open Jupyter and create a new notebook file. 
+Texts can be authored in Quarto using VSCode, JupyterLab, or classic Jupyter Notebook. We suggest using [VSCode](https://quarto.org/docs/get-started/hello/vscode.html)
+
+## Repo Organization
+This website uses Quarto to render pages. The main index can be found in `_quarto.yml`, and subpages are organized under the `chapters` section. Each subpage has it's own folder and `.md` (markdown) file. Note that unlike the [Course Notes repo](https://github.com/DS-100/course-notes), the debugging guide rarely runs any code, so we rely on `.md` files rather than `.qmd`, saving us the trouble of converting from `.qmd` to `.ipynb` for editing, then back to `.qmd` to render the website. Instead we can make edits directly to the `.md` file. 
 
-To set up the document, create a new Raw NBConvert cell. This will be used to set document-level YAML options. The Data 100 lecture notes are generated using the following YAML settings:
+## Creating a new section
+To start a new document, create an empty folder `topic_name` and create an empty markdown file `topic_name.md`. Start each document like so: 
 
 ```
 ---
-title: "Name of the Lecture"
-execute:
-    echo: true
+title: INSERT_TOPIC_TITLE
 format:
   html:
-    code-fold: true
-    code-tools: true
     toc: true
-    toc-title: Name of the Lecture
-    page-layout: full
-    theme: [cosmo, cerulean]
+    toc-depth: 5
+    toc-location: right
+    code-fold: false
+    theme:
+      - cosmo
+      - cerulean
     callout-icon: false
-jupyter: python3
+jupyter:
+  jupytext:
+    text_representation:
+      extension: .qmd
+      format_name: quarto
+      format_version: '1.0'
+      jupytext_version: 1.16.1
+  kernelspec:
+    display_name: Python 3 (ipykernel)
+    language: python
+    name: python3
 ---
 ```
 
-Now, the notebook is ready for writing content. Quarto supports all the functionality of a standard ipynb file – code cells, markdown, and LaTeX. To begin writing lecture notes, it's a good idea to first set out the main headings of the document. These typically correspond to the title slides of each lecture ([example](https://docs.google.com/presentation/d/1FZJhOS8S1lCqZCRxbyys9rCZT0QxdY4hcmvZDskEHFI/edit#slide=id.g1150ea2fb2b_0_220)) and are written with the Markdown second headng level (`##`). Quarto will auto-populate the table of contents as these headings are created.
+Now, the notebook is ready for writing content.  In VSCode, you can activate a live preview of markdown files by clicking the button on the upper right-hand corner.
 
-To view the Quarto file, open a terminal window (either [within Jupyter](https://docs.google.com/presentation/d/1FZJhOS8S1lCqZCRxbyys9rCZT0QxdY4hcmvZDskEHFI/edit#slide=id.g1150ea2fb2b_0_220) or through your machine's terminal) and navigate to the notebook's directory. Running the command `quarto preview notebook.ipynb` will render the document and open it in a new web browser tab.
+![](md_preview.png)
 
-With the preview activated, the rendered view will update every time a change is saved in the notebook. When editing the document, it's helpful to have side-by-side views of the notebook and preview so you can watch changes in real-time.
+Note that clicking on the quarto `Preview` button does not generate a *live* preview but rather a static one. 
 
 ## Document Formatting
 
 A pdf view of how this notebook renders in Quarto can be found [here](https://drive.google.com/file/d/17ga5wvfcmvAzQ1rbnCP4kEf5bckST3--/view?usp=sharing).
 
-#### Formatting Code
-
-The `code-fold: true` option in the YAML set-up will automatically collapse all code cells in the rendered document. If a particular code cell should be uncollapsed by default (e.g. to explicitly show a `pandas` example), a cell-specific YAML option can be specified:
-
-```
-#| code-fold: false
-print("this code is now visible")
-```
-
 #### Formatting Images
 
-Inserting images in a Quarto document is similar to the standard Markdown syntax. The difference is that Quarto will insert figure captions automatically. The syntax below will insert an image with an accompanying description.
-
-```
-#![The best class at Berkeley](data.png)
-```
-
-#### Formatting Learning Outcomes
-
-Each lecture note should start with a brief list of intended student learning outcomes. These are formatted as collapsable call-out cells, which can be created in a Markdown cell using the syntax below.
-
-```
-::: {.callout-note collapse="true"}
-## Learning Outcomes
-* Gain familiarity with Quarto
-* Create your first Quarto document
-* Write A+ Data 100 lecture notes
-:::
-```
+To give you the most control when inserting images, we use html with the following format to center images/figs and control their size: 
 
-## Generating Output
-To generate the final notebook as an HTML, run the terminal command `quarto render notebook.ipynb`. The HTML will be outputted in the same directory as the notebook.
+```<center><img src = "IMAGE_NAME" width = "IMAGE_WIDTH_IN_PIXELS"></img></a></center>```
 
-# Data 100-specific items
+## Generating Output + Rendering Website
+After making edits to the `.md` files, ensure that the right documents are un-commented under `_quarto.yml`'s `chapter` section. Then, run `quarto render` to render the entire website. Push your changes to Github, and you should see the changes reflected in the [website](https://ds100.org/debugging-guide/) after a few minutes. 
 
-General commands/notes:
-  * `jupyter lab # local jupyter setup`
-  * `ipynb` -> `qmd`: `quarto convert notebook.ipynb` or `quarto convert notebook.qmd`
-  * `quarto render`: renders HTML to `docs`. Note `qmd` has to exist for rendering
-  * Edit `_quarto.yml` to include note in sidebar/table of contents
-* Quick local development:
-  * TODO: how to quickly render just one notes directory and not all notes?
 * Publish notes to GitHub pages:
   * `quarto render` everything
   * `git add`, `git commit`, `git push`
   * Can view website compilation on GitHub (look for yellow-to-green button next to commit number)
-* Common errors:
-  * `Illegal instruction: 4 ...` close jupyter lab
 
 ## Other Quarto Resources
 

_quarto.yml

@@ -27,7 +27,7 @@ format:
     theme: cosmo
     toc: true
     toc-depth: 5
-    toc-expand: 3
+    toc-expand: 3 # depth to expand index
     callout-icon: false
     number-sections: false
   pdf: default

autograder_gradescope/autograder_gradescope.md

@@ -56,11 +56,6 @@ This can happen if you “overwrite” a variable that is used in a question. Fo
 ### Why does a notebook test fail now when it passed before, and I didn’t change my code?
 You probably ran your notebook out of order. [Re-run all previous cells](https://ds100.org/debugging-guide/jupyter101/jupyter101.html#running-cells) in order, which is how your code will be graded.
 
-### I accidentally deleted something in a cell that was provided to me – how do I get it back?
-Suppose you’re working on Lab 5. One solution is to go directly to DataHub and rename your lab05 folder to something else, like lab05-old. Then, click the Lab 5 link on the course website again, and it’ll bring you to a brand-new version of Lab 5. You can then copy your work from your old Lab 5 to this new one, which should have the original version of the assignment.
-
-Alternatively, you can access this [public repo](https://github.com/DS-100/sp24-student) and navigate to a blank copy of the assignment you were working on. In the case of Lab 5 for example, the notebook would be located at `lab/lab05/lab05.ipynb`. You can then check and copy over the contents of the deleted cell into a new cell in your existing notebook. 
-
 ## Gradescope
 
 When submitting to Gradescope, there are often unexpected errors that make students lose more points than expected. Thus, it is imperative that you **stay on the submission page until the autograder finishes running**, and the results are displayed. 

docs/autograder_gradescope/autograder_gradescope.html

@@ -149,7 +149,6 @@ <h2 id="toc-title">Table of contents</h2>
   <li><a href="#im-positive-i-have-the-right-answer-but-the-test-fails.-is-there-a-mistake-in-the-test" id="toc-im-positive-i-have-the-right-answer-but-the-test-fails.-is-there-a-mistake-in-the-test" class="nav-link" data-scroll-target="#im-positive-i-have-the-right-answer-but-the-test-fails.-is-there-a-mistake-in-the-test">I’m positive I have the right answer, but the test fails. Is there a mistake in the test?</a></li>
   <li><a href="#why-does-grader.exportrun_teststrue-fail-if-all-previous-tests-passed" id="toc-why-does-grader.exportrun_teststrue-fail-if-all-previous-tests-passed" class="nav-link" data-scroll-target="#why-does-grader.exportrun_teststrue-fail-if-all-previous-tests-passed">Why does <code>grader.export(run_tests=True)</code> fail if all previous tests passed?</a></li>
   <li><a href="#why-does-a-notebook-test-fail-now-when-it-passed-before-and-i-didnt-change-my-code" id="toc-why-does-a-notebook-test-fail-now-when-it-passed-before-and-i-didnt-change-my-code" class="nav-link" data-scroll-target="#why-does-a-notebook-test-fail-now-when-it-passed-before-and-i-didnt-change-my-code">Why does a notebook test fail now when it passed before, and I didn’t change my code?</a></li>
-  <li><a href="#i-accidentally-deleted-something-in-a-cell-that-was-provided-to-me-how-do-i-get-it-back" id="toc-i-accidentally-deleted-something-in-a-cell-that-was-provided-to-me-how-do-i-get-it-back" class="nav-link" data-scroll-target="#i-accidentally-deleted-something-in-a-cell-that-was-provided-to-me-how-do-i-get-it-back">I accidentally deleted something in a cell that was provided to me – how do I get it back?</a></li>
   </ul></li>
   <li><a href="#gradescope" id="toc-gradescope" class="nav-link" data-scroll-target="#gradescope">Gradescope</a>
   <ul>
@@ -220,11 +219,6 @@ <h3 class="anchored" data-anchor-id="why-does-grader.exportrun_teststrue-fail-if
 <h3 class="anchored" data-anchor-id="why-does-a-notebook-test-fail-now-when-it-passed-before-and-i-didnt-change-my-code">Why does a notebook test fail now when it passed before, and I didn’t change my code?</h3>
 <p>You probably ran your notebook out of order. <a href="https://ds100.org/debugging-guide/jupyter101/jupyter101.html#running-cells">Re-run all previous cells</a> in order, which is how your code will be graded.</p>
 </section>
-<section id="i-accidentally-deleted-something-in-a-cell-that-was-provided-to-me-how-do-i-get-it-back" class="level3">
-<h3 class="anchored" data-anchor-id="i-accidentally-deleted-something-in-a-cell-that-was-provided-to-me-how-do-i-get-it-back">I accidentally deleted something in a cell that was provided to me – how do I get it back?</h3>
-<p>Suppose you’re working on Lab 5. One solution is to go directly to DataHub and rename your lab05 folder to something else, like lab05-old. Then, click the Lab 5 link on the course website again, and it’ll bring you to a brand-new version of Lab 5. You can then copy your work from your old Lab 5 to this new one, which should have the original version of the assignment.</p>
-<p>Alternatively, you can access this <a href="https://github.com/DS-100/sp24-student">public repo</a> and navigate to a blank copy of the assignment you were working on. In the case of Lab 5 for example, the notebook would be located at <code>lab/lab05/lab05.ipynb</code>. You can then check and copy over the contents of the deleted cell into a new cell in your existing notebook.</p>
-</section>
 </section>
 <section id="gradescope" class="level2">
 <h2 class="anchored" data-anchor-id="gradescope">Gradescope</h2>

docs/index.html

@@ -178,7 +178,7 @@ <h1 class="title">Data 100 Debugging Guide</h1>
 <h1 class="unnumbered">About</h1>
 <p>This text offers pointers for keyboard shortcuts or common mistakes that accompany the coursework in the Spring 2024 Edition of the UC Berkeley course Data 100: Principles and Techniques of Data Science.</p>
 <p>Inspiration for this guide was taken from the UC San Diego course DSC 10: Principles of Data Science and their <a href="https://dsc10.com/debugging/">debugging guide</a>.</p>
-<p>If you spot any typos or would like to suggest any changes, please email us at <strong>data100.instructors@berkeley.edu</strong></p>
+<p>If you spot any typos or would like to suggest any changes, please fill out the <a href="https://docs.google.com/forms/d/e/1FAIpQLSe0fBEJwt6aEfZxU3fh3llNk8rSWHj6Umq0km3wPqmFu0MlGA/viewform?usp=sf_link">Data 100 Content Feedback Form (Spring 2024)</a>. Note that this link will only work if you have an <span class="citation" data-cites="berkeley.edu">@berkeley.edu</span> email address. If you’re not a student at Berkeley and would like to provide feedback, please email us at <strong>data100.instructors@berkeley.edu</strong></p>
 
 
 </section>

docs/jupyter_datahub/jupyter_datahub.html

@@ -146,7 +146,10 @@ <h2 id="toc-title">Table of contents</h2>
   <li><a href="#i-cant-edit-a-cell" id="toc-i-cant-edit-a-cell" class="nav-link" data-scroll-target="#i-cant-edit-a-cell">I can’t edit a cell</a></li>
   <li><a href="#my-text-cell-looks-like-code" id="toc-my-text-cell-looks-like-code" class="nav-link" data-scroll-target="#my-text-cell-looks-like-code">My text cell looks like code</a></li>
   <li><a href="#my-text-cell-changed-to-a-code-cell-my-code-cell-changed-to-a-text-cell" id="toc-my-text-cell-changed-to-a-code-cell-my-code-cell-changed-to-a-text-cell" class="nav-link" data-scroll-target="#my-text-cell-changed-to-a-code-cell-my-code-cell-changed-to-a-text-cell">My text cell changed to a code cell / My code cell changed to a text cell</a></li>
-  <li><a href="#why-does-running-a-particular-cell-cause-my-kernel-to-die" id="toc-why-does-running-a-particular-cell-cause-my-kernel-to-die" class="nav-link" data-scroll-target="#why-does-running-a-particular-cell-cause-my-kernel-to-die">Why does running a particular cell cause my kernel to die?</a></li>
+  <li><a href="#why-does-running-a-particular-cell-cause-my-kernel-to-die" id="toc-why-does-running-a-particular-cell-cause-my-kernel-to-die" class="nav-link" data-scroll-target="#why-does-running-a-particular-cell-cause-my-kernel-to-die">Why does running a particular cell cause my kernel to die?</a>
+  <ul>
+  <li><a href="#i-accidentally-deleted-something-in-a-cell-that-was-provided-to-me-how-do-i-get-it-back" id="toc-i-accidentally-deleted-something-in-a-cell-that-was-provided-to-me-how-do-i-get-it-back" class="nav-link" data-scroll-target="#i-accidentally-deleted-something-in-a-cell-that-was-provided-to-me-how-do-i-get-it-back">I accidentally deleted something in a cell that was provided to me – how do I get it back?</a></li>
+  </ul></li>
   <li><a href="#click-here-to-download-zip-file-is-not-working" id="toc-click-here-to-download-zip-file-is-not-working" class="nav-link" data-scroll-target="#click-here-to-download-zip-file-is-not-working">“Click <u>here</u> to download zip file” is not working</a></li>
   <li><a href="#i-cant-export-my-assignment-as-a-pdf-due-to-a-latexfailed-error" id="toc-i-cant-export-my-assignment-as-a-pdf-due-to-a-latexfailed-error" class="nav-link" data-scroll-target="#i-cant-export-my-assignment-as-a-pdf-due-to-a-latexfailed-error">I can’t export my assignment as a PDF due to a <code>LatexFailed</code> error</a></li>
   </ul>
@@ -218,6 +221,11 @@ <h2 class="anchored" data-anchor-id="my-text-cell-changed-to-a-code-cell-my-code
 <section id="why-does-running-a-particular-cell-cause-my-kernel-to-die" class="level2">
 <h2 class="anchored" data-anchor-id="why-does-running-a-particular-cell-cause-my-kernel-to-die">Why does running a particular cell cause my kernel to die?</h2>
 <p>If one particular cell seems to cause your kernel to die, this is likely because the computer is trying to use more memory than it has available. For instance: your code is trying to create a gigantic array. To prevent the entire server from crashing, the kernel will “die”. This is an indication that there is a mistake in your code that you need to fix.</p>
+<section id="i-accidentally-deleted-something-in-a-cell-that-was-provided-to-me-how-do-i-get-it-back" class="level3">
+<h3 class="anchored" data-anchor-id="i-accidentally-deleted-something-in-a-cell-that-was-provided-to-me-how-do-i-get-it-back">I accidentally deleted something in a cell that was provided to me – how do I get it back?</h3>
+<p>Suppose you’re working on Lab 5. One solution is to go directly to DataHub and rename your lab05 folder to something else, like lab05-old. Then, click the Lab 5 link on the course website again, and it’ll bring you to a brand-new version of Lab 5. You can then copy your work from your old Lab 5 to this new one, which should have the original version of the assignment.</p>
+<p>Alternatively, you can access this <a href="https://github.com/DS-100/sp24-student">public repo</a> and navigate to a blank copy of the assignment you were working on. In the case of Lab 5 for example, the notebook would be located at <code>lab/lab05/lab05.ipynb</code>. You can then check and copy over the contents of the deleted cell into a new cell in your existing notebook.</p>
+</section>
 </section>
 <section id="click-here-to-download-zip-file-is-not-working" class="level2">
 <h2 class="anchored" data-anchor-id="click-here-to-download-zip-file-is-not-working">“Click <u>here</u> to download zip file” is not working</h2>