Fix broken expansion boxes by bkmgit · Pull Request #346 · datacarpentry/shell-genomics

bkmgit · 2023-07-25T14:11:03Z

Fixes #348
This is a fix for a formatting issue that prevents scp option appearing in the rendered web page. A related issue is #290

github-actions · 2023-07-25T14:11:20Z

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🤖 This automated message can help you check the rendered files in your submission for clarity. If you have any questions, please feel free to open an issue in {sandpaper}.

If you have files that automatically render output (e.g. R Markdown), then you should check for the following:

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Rendered Changes

🔍 Inspect the changes: https://github.com/datacarpentry/shell-genomics/compare/md-outputs..md-outputs-PR-346

The following changes were observed in the rendered markdown documents:

 05-writing-scripts.md | 27 ++++++++++++---------------
 md5sum.txt            |  2 +-
 2 files changed, 13 insertions(+), 16 deletions(-)

What does this mean?

If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible.

This output provides a way for you to inspect the output in a diff-friendly manner so that it's easy to see the changes that occur due to new software versions or randomisation.

⏱️ Updated at 2023-11-01 09:32:33 +0000

sstevens2

This change looks great and I think should get merged ASAP.

One note is that solution boxes not inside another fenced div current don't render correctly. You may want to look at callout with the current fix to add an empty fenced div to fix in this issue in this PR.

sstevens2 · 2023-08-16T14:32:32Z

Note, I don't think is related closely #290 which is more on sftp alternatives to scp. It will fix #348 though.

p-j-smith

Thanks @bkmgit for your first contribution! And thanks @sstevens2 for raising the issue and your review on this pr.

@bkmgit, as @sstevens2 suggested, please could you add a fenced div around your solution block to ensure it renders correctly.

Also, please could you edit your initial comment in this pr to add 'fixes #348' to it - this will link this pr to that issue and automatically close the issue once this pr is merged.

Thanks!

… instructions

p-j-smith · 2023-10-30T11:30:17Z

Looking again at this I think it would be better to use the spoiler div introduced in sandpaper 13.0 rather than solution.

Here's how it renders using the spoiler class:

I hope you don't mind @bkmgit that I pushed changes to use spoiler and update your branch with main, but as @sstevens2 said, I think it's good to get this fix merged sooner rather than later.

Thanks again for raising the issue and for your fix!

vhmcck

Hey Paul,
Thanks for doing this. It looks good on my end!
One last thing - shall we change abbreviations as you did in line 333 throughout for consistency?
I have marked the proposed changes as comments.
Cheers,
Valentina

vhmcck · 2023-10-31T01:19:00Z

-### Uploading Data to your Virtual Machine with PSCP
+### PCSP

 If you're using a Windows PC without Git Bash, we recommend you use the *PSCP* program.


vhmcck · 2023-10-31T01:19:12Z

 This program is from the same suite of tools as the PuTTY program we have been using to connect.

-1. If you haven't done so, download pscp from [http://the.earth.li/~sgtatham/putty/latest/x86/pscp.exe](https://the.earth.li/~sgtatham/putty/latest/x86/pscp.exe)
+1. If you haven't done so, download *PSCP* from [http://the.earth.li/~sgtatham/putty/latest/x86/pscp.exe](https://the.earth.li/~sgtatham/putty/latest/x86/pscp.exe)


you have not

vhmcck · 2023-10-31T01:19:55Z

@@ -388,16 +384,19 @@ $ scp dcuser@ip.address:/home/dcuser/shell_data/untrimmed_fastq/scripted_bad_rea

 Remember that in both instances, the command is run from your local machine, we've just flipped the order of the to and from parts of the command.


bkmgit · 2023-10-31T05:21:07Z

Thanks for the improvements. Sorry for delayed response. Changes seem fine.

bkmgit · 2023-10-31T05:26:36Z

scp is great for automation when you know where a file is. sftp is great when you want
to manually navigate the file system before transferring files. For most people starting
with the shell, sftp might be easier to use initially as it builds on commands they are familiar with. However, this is probably a separate change. Can make a further pull request to address this. Tools such as Globus may also be worth mentioning as scp/sftp are not great for large file transfers, though Globus is not available everywhere.

Auto-generated via {sandpaper} Source : 0119512 Branch : main Author : Benson Muite <bkmgit@users.noreply.github.com> Time : 2023-11-01 09:38:10 +0000 Message : Fix broken expansion boxes (#346) * Fix broken expansion boxes * Use 'spoiler' rather than 'solution' for the platform-specific upload instructions * Use contraction `you're` for consistency --------- Co-authored-by: Paul Smith <paul.j.smith@ucl.ac.uk>

Auto-generated via {sandpaper} Source : 89ee5db Branch : md-outputs Author : GitHub Actions <actions@github.com> Time : 2023-11-01 09:39:44 +0000 Message : markdown source builds Auto-generated via {sandpaper} Source : 0119512 Branch : main Author : Benson Muite <bkmgit@users.noreply.github.com> Time : 2023-11-01 09:38:10 +0000 Message : Fix broken expansion boxes (#346) * Fix broken expansion boxes * Use 'spoiler' rather than 'solution' for the platform-specific upload instructions * Use contraction `you're` for consistency --------- Co-authored-by: Paul Smith <paul.j.smith@ucl.ac.uk>

Fix broken expansion boxes

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github-actions bot pushed a commit that referenced this pull request Aug 7, 2023

differences for PR #346

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sstevens2 mentioned this pull request Aug 16, 2023

Transfering local to cloud drop-down menu broken #348

Closed

p-j-smith suggested changes Sep 27, 2023

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p-j-smith added 2 commits October 30, 2023 11:26

Use 'spoiler' rather than 'solution' for the platform-specific upload…

3b105a7

… instructions

Merge branch 'main' into patch-2

a5de280

github-actions bot pushed a commit that referenced this pull request Oct 30, 2023

differences for PR #346

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p-j-smith approved these changes Oct 30, 2023

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p-j-smith self-assigned this Oct 30, 2023

p-j-smith requested a review from vhmcck October 30, 2023 11:30

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p-j-smith reviewed Nov 1, 2023

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Comment thread episodes/05-writing-scripts.md Outdated

Use contraction you're for consistency

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github-actions bot pushed a commit that referenced this pull request Nov 1, 2023

differences for PR #346

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p-j-smith merged commit 0119512 into datacarpentry:main Nov 1, 2023

p-j-smith mentioned this pull request Nov 1, 2023

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Fix broken expansion boxes#346

Fix broken expansion boxes#346
p-j-smith merged 4 commits intodatacarpentry:mainfrom
bkmgit:patch-2

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		@@ -388,16 +384,19 @@ $ scp dcuser@ip.address:/home/dcuser/shell_data/untrimmed_fastq/scripted_bad_rea

		Remember that in both instances, the command is run from your local machine, we've just flipped the order of the to and from parts of the command.

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