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Hi, I get these linting errors even if I do not re...
# linting
t
Hi, I get these linting errors even if I do not remember ever editing these files. I get these errors only with the online nf-core linting tests, not locally. How to fix?
m
Try pulling these files from the upstream template branch. 
git checkout upstream/TEMPLATE -- $FILE_PATH
t
I did: 
git checkout upstream/TEMPLATE -- docs/images/nf-core-fastqrepair_logo_dark.png
but get fatal: 
invalid reference: upstream/TEMPLATE
OK sorry, I've fetched upstream/TEMPLATE and made the checkout but the files seem not to change
let me do some tests and eventually I'llupdate here. Thanks in the meantime
m
But this test is flakier then we would like, but haven't found a good solution for it yet...
👍🏻 1
t
I still have the same errors, but only linting online with actions. Local lint (
nf-core pipelines lint --release
) gives only a few warnings. I'd like to do the first release of the package. Do you suggest trying other solutions or can I go ahead?
m
Do you have a PR somewhere, I can give it a try. Alternatively, you can add them to the ignored linting tests in the .nf-core.yml file
okay, fixed it. the trick was to run the 
--fix-litnting
step on gitpod, where the image generation happens on the same system and has therefore no weird discrepancies.
t
sorry I read now. Yes and I've noticed you already fixed it.
thanks for the comments. I appreciate a lot. I am not so much familiar with github practice
I've replied to all your comments with a couple of questions to have guidance from you. Since I'd like to make the changes you have suggested. How to proceed? I merge the PR and do the changes on my branch and do another PR or is there any other way?
m
Just make the changes in the same pr
👍🏻 1
t
Thanks for the comments. I've committed in the PR and get a strange error (run marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 ) in nf-core linting comments
m
do you have a link to the error log?
t
image.png
m
hmm, probably because the linting wasn’t completed yet. it is any just an informative linting comment, nothing that important 🙂
t
ok I leave it alone, thanks
m
btw. I recommend to have pre-commit hooks installed, to avoid prettier linting errors after commiting (if you have nf-core tools installed, you just need to run 
pre-commit install
in you pipeline directory). more info https://nf-co.re/docs/contributing/code_editors_and_styling/code_formatting#running-with-pre-commit
t
oh yes, it installed prettier as a vscode plugin, but always forget to ru nit before commit.
I've installed **
m
pre-commit solves that for you 😉
this 1
t
top thanks
Sorry Matthias, I've merged the PR and still have linting errors about the images that do not match the template. For me, this is not a problem. But since I'd like to PR from dev to master to go for the first release. I would like to know if you think I can go ahead.
m
I can try to fix it again if you open the release PR. 🙂
t
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