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omnideconv / deconvExplorer

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continuous integration? #2

Closed grst closed 2 years ago

grst commented 3 years ago

Might be nice to check that the app can be started and all dependencies can be installed every time a commit is pushed.

I'm sure @federicomarini has done this before. You can also take a look at how this is implemented in omnideconv: https://github.com/omnideconv/omnideconv/blob/main/.github/workflows/R-CMD-check.yaml

federicomarini commented 3 years ago

Yup 😉 In my head this is something that would follow up another issue we do currently not have (yet), which would be packaging up. And then come the goodies with R CMD check and all the robustness associated to that process

grst commented 3 years ago

makes sense!

On Tue, 9 Nov 2021 at 16:51, Federico Marini @.***> wrote:

Yup 😉 In my head this is something that would follow up another issue we do currently not have (yet), which would be packaging up. And then come the goodies with R CMD check and all the robustness associated to that process

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czackl commented 2 years ago

A basic workflow is already set up but it can't install omnideconv from the private repo. I tried using GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} in the workflow but it can't find the repo. @grst is there a token/secret set up for the whole organization or only for the omnideconv repo? (as i have seen it been used in omnideconv)

In case this is in fact a token issue i can also send you one for adding it to the omnideconv/deconvExplorer Secrets

grst commented 2 years ago

You should be able to generate a token and add it to the secrets of deconvExplorer yourself. You can generate one in the github settings. Sending around tokens is generally a bad idea as they allow access to all private repositories of the issuer.

czackl commented 2 years ago

Yes i am aware of that :) I do not have access to the repo settings, that's the reason why i'm asking.

grst commented 2 years ago

sorry about that, made you an admin now.

On Thu, 18 Nov 2021 at 15:53, Constantin Zackl @.***> wrote:

Yes i am aware of that :) I do not have access to the repo settings, that's the reason why i'm asking.

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grst commented 2 years ago

Wow, your CI script is so much cleaner than mine. Didn't know about these R actions, I guess I need to adapt at some point.

federicomarini commented 2 years ago

I can recommend you have a look at the biocthis package (https://bioconductor.org/packages/release/bioc/html/biocthis.html) - Leo did some very nice efforts in "adapting" the tidyverse-ish GHAs to the bioc-ecosystem

That is more or less where I got the inspiration for the backbone of mine, so that I don't get too lost in all the steps.

czackl commented 2 years ago

Reopened: add docker build & server deployment