Documentation #175

dgrassellyb · 2023-12-04T17:25:09Z

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cicdguy

Amazing 🤩

bms63

ummm....whoa this is thorough!!!!!!! I will review tomorrow. 1.0 got me a little busy

dgrassellyb · 2023-12-06T09:21:26Z

I also made this cheatsheet (However some links need the documentation to be deployed)
But maybe still a bit complex to read !

Template cheatsheet.pdf

manciniedoardo

Thanks @dgrassellyb for this, this is fantastic!!

I left a few specific comments for typos and requests for clarification. I also have some comments about the front page README:

Many heading links in the readme don't work?
Full stop missing at the end of renv propagation section
Boilerplate or boilderplate? Could be a typo.
docker image build: typo in "each R version" (no "s" at the end)

I also have some general comments:

Within the navbar, for the User Guides section I would put a subsection titled "Basics" with the "Get Started", "Common structure of the workflows" and "Codespaces" sections. Then I would put another subsection titled "Invididual workflows" with all the other pages.
I would retitile "common structure" to "Common strucure of the workflows" and put it at the top of the articles.
There's also another "spell checks page" in the Articles drop down. Not sure what the difference is between the two?

vignettes/common_structure.Rmd

vignettes/cran-status.Rmd

vignettes/pkgdown.Rmd

vignettes/push-docker.Rmd

vignettes/r-cmd-checks.Rmd

manciniedoardo · 2023-12-06T09:41:23Z

vignettes/readme-render.Rmd

+
+# Render README Workflow
+
+This GitHub Actions workflow renders the README from R Markdown (`README.Rmd`) to Markdown (`README.md`). Additionally, it can format the generated Markdown using a formatter. The workflow is triggered manually (`workflow_dispatch`) and can also be invoked as a workflow call (`workflow_call`). 


Could you specify why this is required?

manciniedoardo · 2023-12-06T09:42:29Z

vignettes/spellchecks.Rmd

+
+# Spelling Workflow
+
+This GitHub Actions workflow performs spellchecking on the specified R files. The workflow is triggered manually (`workflow_dispatch`) and can also be invoked as a workflow call (`workflow_call`).


Mention somewhere the exclusion wordlist here?

manciniedoardo · 2023-12-06T09:57:00Z

Can we add a hex to the front page too? smth like below

manciniedoardo · 2023-12-06T11:16:43Z

dgrassellyb · 2023-12-06T13:25:09Z

Thanks @dgrassellyb for this, this is fantastic!!

I left a few specific comments for typos and requests for clarification. I also have some comments about the front page README:

Many heading links in the readme don't work?

Full stop missing at the end of renv propagation section

Boilerplate or boilderplate? Could be a typo.

docker image build: typo in "each R version" (no "s" at the end)

I also have some general comments:

Within the navbar, for the User Guides section I would put a subsection titled "Basics" with the "Get Started", "Common structure of the workflows" and "Codespaces" sections. Then I would put another subsection titled "Invididual workflows" with all the other pages.

I would retitile "common structure" to "Common strucure of the workflows" and put it at the top of the articles.

There's also another "spell checks page" in the Articles drop down. Not sure what the difference is between the two?

Thanks a lot for your feedbacks, I will review this ! :)

bms63 · 2023-12-06T17:14:07Z

I also made this cheatsheet (However some links need the documentation to be deployed) But maybe still a bit complex to read !

Template cheatsheet.pdf

above and beyond!!! This cheatsheet is so cool

bms63 · 2023-12-06T17:21:11Z

Just a few notes:

Musing on the README - should we just remove most of the stuff there as it is discussed more thoroughly in the vignettes.

Get Started: Could this vignette get a separate tab?

Cheatsheet: Could that be linked as a Get Started dropdown option? Like how we have it on https://pharmaverse.github.io/admiral/dev/

Lock Files and Propagation: Since we are moving away from this - wondering if this is still need to document?

bundfussr

Looks great overall.

Maybe we should structure the "Articles" menu, e.g., separate sections for workflows used in all admiral packages and workflows used in admiralci only.

vignettes/get_started.Rmd

vignettes/common_structure.Rmd

bundfussr · 2023-12-21T14:19:56Z

vignettes/pkgdown.Rmd

+
+### `multi-version-docs` Job
+
+This job, if triggered, deploys the multi-version documentation to the `gh-pages` branch. It checks for the `skip-multiversion-docs` input and `[skip docs]` in the commit message before proceeding.


Does this job also update the "Versions" menu?

vignettes/propagate.Rmd

vignettes/renv-lock.Rmd

vignettes/spellchecks.Rmd

vignettes/validation.Rmd

vignettes/common_structure.Rmd

Co-authored-by: Stefan Bundfuss <[email protected]>

dgrassellyb · 2024-02-08T18:22:28Z

@bms63 / @manciniedoardo / @cicdguy / @bundfussr : I am currently updating the doc (quite lot of changes since we removed renv !) - I just have a question about codespaces, our actual config is quite outdated (since we built it from renv dependencies) - I could work on this, but while it's not ready I was just thinking to tag the codespace section as "WIP article", what do you think ?

I guess codespaces feature is a bit low priority right ? (I am not sure if devs are really using it on admiral but let me know if I am wrong ! 🙊 )

I'd vote to keep at as a "WIP article" and get back to it later.

Ok let's do this ! it's ready to be merge now (I also pushed a fix in pkgdown to be able to push non-multi version documentation - because I guess we don't need multi version for admiralci doc !).
I also updated the cheatsheet here :
https://github.com/pharmaverse/admiralci/blob/documentation/vignettes/assets/cheatsheet.png

bms63 · 2024-02-09T01:39:19Z

Shall we just merge and publish this and do the review in an issue? Might be a little easier if we don't have to pull down and render the site??

dgrassellyb · 2024-02-09T08:18:12Z

Shall we just merge and publish this and do the review in an issue? Might be a little easier if we don't have to pull down and render the site??

I'll fork it for rendering and send you the link

* Update pkgdown.yml * [actions skip] Add/Update README.md for main * update cheatsheet * update cheatsheet * fix * fix pdf rendering * fix * fix hex * [actions skip] Add/Update README.md for main * fix rendering --------- Co-authored-by: GitHub Actions <[email protected]>

dgrassellyb · 2024-02-09T15:35:54Z

Pushed again some other fixs, here is the rendered doc from my forked repo : https://dgrassellyb.github.io/admiralci/
However .. I have an issue in r cmd checks for this PR - not sure to understand where it's coming from :

❯ checking CRAN incoming feasibility ... [1s/13s] NOTE
  Maintainer: ‘Open Source <[email protected]>’
  
  Found the following (possibly) invalid URLs:
    URL: 
      From: inst/doc/push-docker.html
      Message: Empty URL

0 errors ✔ | 0 warnings ✔ | 1 note ✖

I even updated the .Buildignore with ^inst/doc\.html$ but still get this

cicdguy · 2024-02-09T15:48:25Z

@dgrassellyb That regex looks incorrect.
Should be ^inst\/doc\/.*.html$

manciniedoardo · 2024-02-09T15:55:54Z

README.md

-reusable via the
-[`workflow_call`](https://docs.github.com/en/actions/using-workflows/reusing-workflows)
-GitHub Actions event.
+reusable via the \[`workflow_call`]\[workflow\_call] GitHub Actions


@dgrassellyb is it that I don't understand what this syntax is saying or is it a typo? Don't be afraid to tell me if it's the former 😄

Indeed since to comes from .Rmd -> .md job, I have this in the .Rmd :

reusable via the [workflow_call][workflow_call] GitHub Actions event.

ok, thanks!

bms63 · 2024-02-09T18:25:48Z

Can we minimize this image please

bms63 · 2024-02-09T18:27:17Z

Can we change the tab name to CI/CD Workflows

When I get a dozen tabs up be nice if I new which admiral to select??

bms63 · 2024-02-09T18:41:48Z

What about removing these links and just listing out our potential workflows? The one I clicked go to 404.

Can we say why this is a bad practice? can't get latest and greatest updates - encourage you to make issues to enchance our workflows.

Could we give some context on what these bullet points are leading us to?

bms63 · 2024-02-09T18:46:38Z

Possible to embed cheat sheet like we did for admiral?

Shall we remove devel references

Many thanks again!! Could be a really good reference for discussion for upcoming admiralpeds @rossfarrugia

dgrassellyb · 2024-02-12T07:47:41Z

Possible to embed cheat sheet like we did for admiral?

Shall we remove devel references

Many thanks again!! Could be a really good reference for discussion for upcoming admiralpeds @rossfarrugia

Thanks Ben I will apply some changes as you suggested (and also for your other comments above ;) )

dgrassellyb · 2024-02-12T08:14:50Z

What about removing these links and just listing out our potential workflows? The one I clicked go to 404.

Can we say why this is a bad practice? can't get latest and greatest updates - encourage you to make issues to enchance our workflows.

Could we give some context on what these bullet points are leading us to?

For the links it's not working because it's coming from my fork (if you replace on links pharmaverse by dgrassellyb it will work) - we won't have issues with links once it will be deployed in admiralci repo (non-forked one !) - I think it's nice to keep it (it's like a table of contents with redirections to detail documentation + workflows code)

pharmaverse-bot added 2 commits December 4, 2023 14:38

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dgrassellyb commented Feb 7, 2024

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Co-authored-by: Stefan Bundfuss <[email protected]>

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Co-authored-by: Stefan Bundfuss <[email protected]>

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pharmaverse-bot added 2 commits February 8, 2024 19:23

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bms63 marked this pull request as ready for review February 9, 2024 01:38

pharmaverse-bot and others added 2 commits February 9, 2024 09:39

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dgrassellyb merged commit e48e3cf into main Feb 12, 2024
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dgrassellyb deleted the documentation branch February 12, 2024 13:43

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Documentation #175

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		# Render README Workflow

		This GitHub Actions workflow renders the README from R Markdown (`README.Rmd`) to Markdown (`README.md`). Additionally, it can format the generated Markdown using a formatter. The workflow is triggered manually (`workflow_dispatch`) and can also be invoked as a workflow call (`workflow_call`).


		# Spelling Workflow

		This GitHub Actions workflow performs spellchecking on the specified R files. The workflow is triggered manually (`workflow_dispatch`) and can also be invoked as a workflow call (`workflow_call`).


		### `multi-version-docs` Job

		This job, if triggered, deploys the multi-version documentation to the `gh-pages` branch. It checks for the `skip-multiversion-docs` input and `[skip docs]` in the commit message before proceeding.

Documentation #175

Documentation #175

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