🔄 Synced file(s) with jhudsl/AnVIL_Template

[jhudsl-robot]

Synced local file(s) with jhudsl/AnVIL_Template.

Changed files

• Synced local directory .github/workflows/ with remote directory .github/workflows/
• Synced local scripts/spell-check.R with remote scripts/spell-check.R
• Synced local scripts/url-check.R with remote scripts/url-check.R
• Created local scripts/quiz-check.R from remote scripts/quiz-check.R
• Synced local directory style-sets with remote directory style-sets
• Created local directory assets/box_images/ and copied all sub files/folders from remote directory assets/box_images/
• Synced local directory assets/AnVIL_style/ with remote directory assets/AnVIL_style/
• Created local directory assets/GDSCN_style/ and copied all sub files/folders from remote directory assets/GDSCN_style/
• Synced local scripts/anvil_repo_check.R with remote scripts/anvil_repo_check.R
• Synced local scripts/anvil_repo_table.R with remote scripts/anvil_repo_table.R

---

This PR was created automatically by the repo-file-sync-action workflow run #2974015337

[KatherineCox]

@avahoffman any idea what's going wrong here? this is breaking before it even gets to rendering

Edit: seeing the same error here: jhudsl/GDSCN_Book_Statistics_for_Genomics_Differential_Expression#20

[avahoffman]

Looks like it might be a security issue? I made a workaround that follows this issue:
This looks similar to the issue here.

Created an issue in OTTR main.. let's keep an eye on it? jhudsl/OTTR_Template#561

I created a fix here: #13 but looks like there's something else going on too. Feel free to merge the fix if you want!

[github-actions]

Re-rendered previews from the latest commit:

• See preview of Bookdown here
• See preview of Coursera/Leanpub version here
• Download the preview of .docx file

Updated at 2022-09-08 with changes from 3d7bb23

[KatherineCox]

@avahoffman I think I've got the style stuff all taken care of. Are the workflows/scripts okay to be merged into main?

[avahoffman]

@KatherineCox go for it!

[KatherineCox]

@avahoffman this was rendering fine in the PR, but when it got merged into main I'm seeing the same "can only be used inside a git repository error"
https://github.com/jhudsl/GDSCN_Book_Statistics_for_Genomics_scRNA-seq/runs/8259733991?check_suite_focus=true

[KatherineCox]

also I applied your fix to jhudsl/GDSCN_Book_Statistics_for_Genomics_Differential_Expression#20 and it successfully solved the error in the PR render there. I'm guessing it'll break if I try to merge it into main.

[avahoffman]

I imagine git config --global --add safe.directory "$GITHUB_WORKSPACE" needs to be added to ro the render-all workflow as well. Let me go ahead and put a patch in, and see if it helps.