Obi preview 1 #95
Obi preview 1 #95
Conversation
|
No spelling errors! 🎉 |
|
|
|
Re-rendered previews from the latest commit:
* note not all html features will be properly displayed in the "quick preview" but it will give you a rough idea. Updated at 2025-04-29 with changes from the latest commit 7dcaf56 |
| 1. Organized these files using an organizational scheme similar to [what is described above](#example-organizational-scheme). | ||
| 1. Create folders like `plots`, `results`, and `data`. Note that `aggregated_metadata.json` and `LICENSE.TXT` also belong in the `data` folder. |
There was a problem hiding this comment.
There is a slight confusion created by the fact that the R file set does not seem to include any plots or results files and the python file set does not include any results files. So, the organization exercise doesn't follow the proposal very closely.
04-open-source-with-github.Rmd
Outdated
There was a problem hiding this comment.
I feel that there is something important missing from this chapter, specifically the issue of LICENSE. The chapter title, contents and conclusion of the excellent tutorial video for creating a github repo all imply that we are starting an "open source" project. However, without adding license, the project is public but not open source. For a new github repo (even a public one) without a license, the default copyright laws apply, meaning that the author/creators retains all rights to their source code and no one may reproduce, distribute, or create derivative works. In order to be open source it must include a license which meets the definition of open source. The end of this chapter would be a good place to introduce this idea and maybe show how easy it is to add a license in github.
|
|
||
| <img src ="https://docs.google.com/presentation/d/1LMurysUhCjZb7DVF6KS9QmJ5NBjwWVjRn40MS9f2noE/export/png?id=1LMurysUhCjZb7DVF6KS9QmJ5NBjwWVjRn40MS9f2noE&pageid=gfaa026a583_0_13" alt="In RStudio, you can create a new notebook by going to File > New File > R Notebook. Then open up this chapter’s example code folder and open the make_heatmap.R file." style="display: block; margin: auto;" /> | ||
|
|
There was a problem hiding this comment.
Note that in my browser, most of the instructions for setting up the R notebook (points 3 - 8) were hidden (under the image?) although I could see them in the source code. I am hoping they will appear when I add newlines around the code block to match formatting of python notebook section which is rendering correctly. But, this needs to be verified.
There was a problem hiding this comment.
When running the renv::snapshot() command I was prompted with a dialogue:
It looks like you've called renv::snapshot() in a project that hasn't been activated yet.
How would you like to proceed?
1: Activate the project and use the project library.
2: Do not activate the project and use the current library paths.
3: Cancel and resolve the situation another way.
I wasn't sure of the correct response. It might be good to give some guidance to learners on this topic.
| ````` | ||
| ```{r} | ||
| sessionInfo() | ||
| ``` | ||
| ````` |
There was a problem hiding this comment.
In the html of this course, this code seems to be generating not only the R-styled snippet for the sessionInfo command but also an entire example output of sessionInfo. I'm not sure but I don't think the intention is to add this sessionInfo to the Rmd file? I am guessing that the 5 back ticks are not having the intended effect here?
| @@ -185,7 +185,7 @@ Try to avoid using variable names that have no meaning like `tmp` or `x`, or `i` | |||
| > 2 Use consistent notation for naming convention. | |||
| > 3 Use standard terms. | |||
| > 4 Do not number a variable name. | |||
| > 5 When you find another way to name variable, refactor as fast as possible. | |||
| > 5 When you find another way to name a variable, refactor as fast as possible. | |||
There was a problem hiding this comment.
I'm not positive that I understand what this piece of advice is meant to convey
There was a problem hiding this comment.
I struggled with the penultimate exercise for this chapter (7.5.1). I was working off a version of the code from previous chapters (which I think should have been up to date) but it didn't quite match the "before" code I was meant to update. So, I downloaded the suggested project files (section 7.4). However, these seemed to match the "before" expectation even less well. I think they are actually the "after" solution.
| @@ -15,11 +15,11 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/1LMurysUhCjZb7DVF | |||
|
|
|||
| Documentation is an important but sometimes overlooked part of creating a reproducible analysis! There are two parts of documentation we will discuss here: 1) In notebook descriptions and 2) READMEs | |||
|
|
|||
| Both these notebook descriptions and READMEs are written in markdown -- a shorthand for html (the same as the documentation parts of your code). If you aren't familiar, markdown is such a handy tool and we encourage you to learn it (it doesn't take too long), here's a [quick guide](https://www.markdownguide.org/cheat-sheet/) to get you started. | |||
There was a problem hiding this comment.
I don't know that it is technically correct to call markdown a shorthand for html. It wasn't clear to me what point we are trying to make with the text in the parentheses. I tried to make this sentence more clear...
Purpose/implementation Section
What changes are being implemented in this Pull Request?
What was your approach?
What GitHub issue does your pull request address?
Tell potential reviewers what kind of feedback you are soliciting.
New Content Checklist
New content/chapter is in an Rmd file with this kind of format and headers.
New content/chapter contains Learning Objectives and are in the correct format.
Bookdown successfully re-renders and any new content files have been added to the _bookdown.yml.
Spell check runs successfully in Github actions style-n-check).
Any newly necessary packages that are needed have been added to the Dockerfile and image.
Images are in the correct format for rendering.
Every new image has alt text and is in a Google Slide.
Each slide is described in the notes of the slide so learners relying on a screen reader can access the content. See https://lastcallmedia.com/blog/accessible-comics for more guidance on this.
The color palette choices of the slide are contrasted in a way that is friendly to those with color vision deficiencies.
You can check this using Color Oracle.