Chapter 2 Cleanup

[E-Ream]

Modeling Systems of Linear Equations

• [x] says no module named numpy, rerun to fix
• [x] many of the home activities don't correctly format equations with $ $
• [x] consider hiding some of the solutions

Gaussian Elimination

• [x] says no module named numpy, rerun to fix
• [x] issues with $ in markdowns staying as $ when published
• [x] hide solutions at bottom

LU Decomposition and Condition Number

• [x] says no module named numpy, rerun to fix
• [x] LU fact paragraph has formatting messed up with $
• [x] add more spacing below home activities for Solving Linear systems section
• [x] some formatting issues with $ in class activity blocks

Example: Mass Balances and Linear Algebra

• [x] says no module named numpy, rerun to fix
• [x] hide solution

[adowling2]

Currently, JupyterBook is configured to rerun all of the notebooks on my computer when I publish to the website. I likely forgot to install numpy. But, we could easily change it to NOT rerun the notebooks. This would just require @E-Ream and @jkeane14 to run them at the end of editing. Although this is a little more work, it would allow us to keep output that required a solution the was removed.

[adowling2]

Also, I just installed numpy on my conda environment and rerun the publish scripts. The missing module issue should be fixed. Tell me here if it was not.

[E-Ream]

@adowling2 @jkeane14 It looks like the numpy missing module issues is fixed on the published website now, so yes it worked. I'm good with changing the publish script such that it doesn't rerun the notebooks so that we can decide more specifically what cells we want to show output.

[adowling2]

Great. I updated the configuration file on main to not re-execute the notebooks.

[E-Ream]

@adowling2 I understand that we have figured out how to fix the LaTeX formatting issue for markdowns with the double $$ by adding the extra empty line above and below. However, we did not yet figure out fixing the formatting within the highlighted activity box markdowns, correct? I wanted to make sure I can fix as much as possible while going through the notebooks again.

[adowling2]

Here are some additional requests @E-Ream:

@E-Ream I accidentally posted this request to PR #21 instead of this issue. I am moving the list to here to be in the same place as your other lists.

Split Gaussian Elimination into two notebooks:

• [x] Invertible Matrix Theorem (beginning) and Mass Balance Example (end)
• [x] Gaussian Elimination
• [x] Update learning objectives accordingly
• [x] Remove "© University of Notre Dame" from the top of the notebook. (We'll automatically add this back in.)
• [x] Move "Note: " into a colored box below "Motivating Example and Gaussian Elimination" header.
• [x] Add reference to Chapter 7 in McClarren

Split LU Decomposition and Condition Number into two notebooks:

• [x] LU Decomposition
• [x] Condition Number
• [x] Update learning objectives accordingly

Prepare linear algebra in Numpy Tutorial

• [x] Review material here
• [x] Get original source file from @adowling2
• [x] Develop revision plan with @adowling2

[E-Ream]

@adowling2 Concerning the Linear Algebra Numpy Tutorial: 1) All of the pictures are referenced from a figures folder that I do not have access to, could you share that with me? 2) Would you like the two notebooks to be merged into one large tutorial or keep them separate? 3) Some of the topics discussed in the tutorial notebooks haven't been covered yet in our notebooks (i.e. Finite Difference isn't until Chap 3). Would you still like this to be in the Chap 2 folder?

[adowling2]

The images should be in this repo: https://github.com/ndcbe/CBE60499

I would like to not have any images in the new version but instead have the material typeset in the notebooks. The images were something quick for the first draft.

Let's focus on this just the first notebook for now. For the second notebook, I think we'll want to move that to the Taylor series chapter. We'll also remove content that is redundant with what we already have. (I repurposed CBE 20258 notebooks for CBE 60258.)

[adowling2]

A few more issues (after publishing draft 2):

https://ndcbe.github.io/data-and-computing/notebooks/01-publish/06-NumPy.html

• [x] Replace "NumPy Arrays" with "Getting Started with NumPy Arrays"
• [x] Remove header "Getting Started"
• [x] Promote all headers to level two headers

[adowling2]

@E-Ream A few more things to clean up:

https://ndcbe.github.io/data-and-computing/notebooks/02-publish/05-Linear-Algebra-in-Numpy.html

• [x] For all of the sections with references, use the format "Reference: ..." similar to the other pages.
• [x] On this page, all vectors and matrices should use $\mathbf{ }$ to make them bold.
• [x] Remove the ":" in the "Property" header
• [x] Promote the header "Verify our answer with linalg.solve" one level
• [x] I think the invertible matrix theorem is missing a statement before "a". My memory says it is "All of the following statements are either true or false". Please check.
• [x] Remove "Vector and Matrix Norms Definition" as a header. Promote all of the headers under it one level.

https://ndcbe.github.io/data-and-computing/notebooks/02-publish/03-LU-Factorization.html

• [x] LaTeX issues under the "LU Factorization" header.
• [x] Remove "Errors in Linear Systems" section. This is now in the subsequent notebook.
• [x] Update the "Take Home Messages" to reflect the removed content.
• [x] Remove the numbering from the take home messages, as it is not publishing correctly.
• [x] Rename the notebook "LU Decomposition"

https://ndcbe.github.io/data-and-computing/notebooks/02-publish/03b-Condition-Number.html

• [x] Make "Take Home Message" singular, remove the numbering to be consistent with the previous notebook (see above)

[adowling2]

https://ndcbe.github.io/data-and-computing/notebooks/02-publish/04-Example-Atomic-Mass-Balances.html

• [x] Reference this file: https://raw.githubusercontent.com/ndcbe/data-and-computing/main/extras/atomic-mass-balance-activity.docx