Closed zkamvar closed 1 year ago
zkamvar
commented
1 year ago The HTML divs are allowing the authors to provide a switch between two setup possabilities.
It works in The Workbench, but I do not know about the accessibility of it. It would be better to remove the JavaScript and recode the divs as solution blocks, and attach them to a div.
zkamvar
commented
1 year ago A note about _extras/LaunchingInstances.md: This page has a lot of issues happening, the vast majority caused by kramdown's penchant for lazy continuation of markdown blocks.
In short because code blocks inside lists are not indented properly, the final </div> tag is embedded in a code block and is not properly parsed by {pegboard}. The solution is to fix all of these, but it will take a manual effort.
A lot of things such as images, code blocks, and tables are embedded in list blocks. This is fine in and of itself, but in pandoc, you exit a list block as soon as you de-indent, which happens several times for example this bash block in step 4 (written as step 3) for cyverse:
3. Open the terminal application and use 'ssh' to connect. Your command will be:
```bash
$ ssh iplantusername@your.atmosphere.ipaddress
even in GitHub's markdown it's invalid: https://github.com/datacarpentry/cloud-genomics/blob/be5780e31ae3aeeaf3158817db72b8b4ee3b19b9/_extras/LaunchingInstances.md#connect-to-atmosphere-instance#connect-to-atmosphere-instance
Another place is in the [setting up icommands section](https://github.com/datacarpentry/cloud-genomics/blob/be5780e31ae3aeeaf3158817db72b8b4ee3b19b9/_extras/LaunchingInstances.md#connect-to-atmosphere-instance#setup-icommand):
````markdown
## Setup iCommands
**Prerequisites**
* You must be connected to your Atmosphere instance
iCommands will allow you to quickly transfer data into your Atmosphere instance:
1. Initialize iCommands using the following command
```bash
$ iinitYou will then be asked to setup your account and will need to enter the following information
| Prompt | Entry |
|---|---|
| irodsHost | data.iplantcollaborative.org |
| port | 1247 |
| zone | iplant |
| irodsUserName | your iplant username |
| Current iRODS password | your iplant password |
Verify that you have connected to your iPlant Data Store; view the contents of your home directory using the following the ils command:
$ ils
anuj2054
commented
1 year ago Thank you zkamvar and Toby for the effort. When reading through all the above, it almost looks like everything has been completed. I am looking at this today and want to understand what are the outstanding things you need from me. Is there anything you still want me to fix.
zkamvar
commented
1 year ago After the transition, please be sure to replace the <div> tags with ::: discussion and ::: solution blocks, as that would be more accessible.
anuj2054
commented
1 year ago Thank you , I will make a note of that in the issues and complete them when the transition is completed.
anuj2054
commented
1 year ago @zkamvar Are ::: discussion and ::: solution, Are these HTML elements or markdown elements ?
zkamvar
commented
1 year ago
::: discussionand::: solution, Are these HTML elements or markdown elements ?
These are markdown elements. See https://github.com/carpentries/lesson-transition/issues/49#issuecomment-1523617764 for an example.
zkamvar
commented
1 year ago fixed in cb758a2fbe2d2d22aec42adbb474985d9ec4448f
tracking issues for https://github.com/datacarpentry/cloud-genomics/
_extras/LaunchingInstances.md(addressed in https://github.com/datacarpentry/cloud-genomics/pull/123)<img>tags (to be fixed in https://github.com/datacarpentry/cloud-genomics/pull/124)Details of initial build errors
```r ── Reading in lesson with pegboard ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── Error in `purrr::map()`: ℹ In index: 3. ℹ With name: /home/zhian/Documents/Carpentries/Git/carpentries/lesson-transition/datacarpentry/cloud-genomics/_episodes/03-verifying-instance.md. Caused by error in `purrr::map()`: ℹ In index: 1. Caused by error in `block[[1]]`: ! subscript out of bounds Backtrace: ▆ 1. ├─pegboard::Lesson$new(old, fix_liquid = arguments$fix_liquid) 2. │ └─pegboard (local) initialize(...) 3. │ └─pegboard:::read_jekyll_episodes(path, rmd, ...) 4. │ └─pegboard:::read_markdown_files(md_src, sandpaper = FALSE, ...) 5. │ └─purrr::map(the_episodes, Episode$new, ...) 6. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 7. │ ├─purrr:::with_indexed_errors(...) 8. │ │ └─base::withCallingHandlers(...) 9. │ ├─purrr:::call_with_cleanup(...) 10. │ └─R6 (local) .f(.x[[i]], ...) 11. │ └─pegboard (local) initialize(...) 12. │ └─purrr::map(blocks, set_ktag_block) 13. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 14. │ ├─purrr:::with_indexed_errors(...) 15. │ │ └─base::withCallingHandlers(...) 16. │ ├─purrr:::call_with_cleanup(...) 17. │ └─pegboard (local) .f(.x[[i]], ...) 18. │ └─pegboard:::get_sibling_block(tags) 19. │ └─pegboard:::are_adjacent(block[[1]], tags) 20. └─purrr (local) ``(``)
21. └─cli::cli_abort(...)
22. └─rlang::abort(...)
```