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368 convert fims to a pkgdown site #437

Merged
merged 13 commits into from
Aug 15, 2023
Merged

368 convert fims to a pkgdown site #437

merged 13 commits into from
Aug 15, 2023

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Bai-Li-NOAA
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What is the feature?

  • Set up pkgdown website for FIMS

How have you implemented the solution?

  • added .github/workflows/call-update-pkgdown.yml to automatically update the pkgdown site when there is a change in main branch.
  • added home, reference, articles, and news sections in pkgdown/_pkgdown.yml following examples from tidyverse packages (e.g., ggplot2 and dplyr)
    • home section includes links to C++ doxygen documentation page and collaborative workflow book
    • reference section includes built-in dataset and functions for package development
    • articles section includes articles that describe FIMS design and demos for developers
    • news section includes information of releases

Does the PR impact any other area of the project?

No

How to test this change

run pkgdown::build_site() locally

Developer pre-PR checklist

  • I relied on GitHub actions to 🧪 things for me while I sat on the 🛋️.

@Bai-Li-NOAA Bai-Li-NOAA linked an issue Aug 11, 2023 that may be closed by this pull request
Convert FIMS to a pkgdown site #368
Closed
@k-doering-NOAA k-doering-NOAA self-requested a review August 14, 2023 17:49
@Bai-Li-NOAA Bai-Li-NOAA marked this pull request as draft August 14, 2023 17:49
@Bai-Li-NOAA Bai-Li-NOAA removed the request for review from ChristineStawitz-NOAA August 14, 2023 17:50
@ChristineStawitz-NOAA @Bai-Li-NOAA
Update DESCRIPTION to match release number
2eb4800
@MOshima-PIFSC @Bai-Li-NOAA
resolved issues causing warnings
83ad821
@nathanvaughan-NOAA @MOshima-PIFSC
@Bai-Li-NOAA @ChristineStawitz-NOAA @k-doering-NOAA @Andrea-Havron-NOAA
Doc: demo vignette update to use fims frame method
7f72fd5 
Co-authored-by: Meg Oshima <MOshima-PIFSC@users.noreply.github.com>
Co-authored-by: Bai Li - NOAA <Bai-Li-NOAA@users.noreply.github.com>
Co-authored-by: Christine Stawitz - NOAA <ChristineStawitz-NOAA@users.noreply.github.com>
Co-authored-by: Kathryn Doering <kathryn.doering@noaa.gov>
Co-authored-by: Andrea-Havron-NOAA <Andrea-Havron-NOAA@users.noreply.github.com>
@Bai-Li-NOAA
fix: use FIMS:::m_age()
a9474f3
@Bai-Li-NOAA
fix: update survey abundance index to biomass index
f6009e0
@k-doering-NOAA @nathanvaughan-NOAA
@MOshima-PIFSC @iantaylor-NOAA @Bai-Li-NOAA
export methods from s4 class
c007105 
Co-authored-by: Nathan Vaughan <nathanvaughan-NOAA@users.noreply.github.com>
Co-authored-by: Meg Oshima <MOshima-PIFSC@users.noreply.github.com>
Co-authored-by: Ian Taylor <iantaylor-NOAA@users.noreply.github.com>
Co-authored-by: Bai Li - NOAA <Bai-Li-NOAA@users.noreply.github.com>
@ChristineStawitz-NOAA @Bai-Li-NOAA
style and docs: run devtools::document() and styler::style_pkg()
6716fc7
@Bai-Li-NOAA
doc: update functions
830b01a
@Bai-Li-NOAA Bai-Li-NOAA marked this pull request as ready for review August 14, 2023 20:56
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Instructions for code reviewer

Hello reviewer, thanks for taking the time to review this PR!

  • Please use this checklist during your review, checking off items that you have verified are complete!
  • For PRs that don't make changes to code (e.g., changes to README.md or Github actions workflows), feel free to skip over items on the checklist that are not relevant. Remember it is still important to do a thorough review.
  • Then, comment on the pull request with your review indicating where you have questions or changes need to be made before merging.
  • Remember to review every line of code you’ve been asked to review, look at the context, make sure you’re improving code health, and compliment developers on good things that they do.
  • PR reviews are a great way to learn, so feel free to share your tips and tricks. However, for optional changes (i.e., not required for merging), please include nit: (for nitpicking) before making the suggestion. For example, nit: I prefer using a data.frame() instead of a matrix because...
  • Engage with the developer when they respond to comments and check off additional boxes as they become complete so the PR can be merged in when all the tasks are fulfilled. Make it clear when this has been reached by commenting on the PR with something like This PR is now ready to be merged, no changes needed.

Checklist

  • The PR is requested to be merged into the appropriate branch (typically main)
  • The code is well-designed.
  • The functionality is good for the users of the code.
  • Any User Interface changes are sensible and look good.
  • Parallel computing remains functional.
  • The code isn’t more complex than it needs to be.
  • The developer isn’t implementing things they might need in the future but don’t know they need now.
  • Code has appropriate unit tests.
  • Tests are well-designed.
  • The developer used clear names for everything.
  • Comments are clear and useful, and mostly explain why instead of what.
  • Code is appropriately documented (doxygen and roxygen).
  • The code conforms to our style guides.

@k-doering-NOAA
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Thanks @Bai-Li-NOAA ! I can look at this first thing tomorrow.

k-doering-NOAA
k-doering-NOAA approved these changes Aug 15, 2023
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It looks great, excellent work @Bai-Li-NOAA and @timjmiller ! I was able to build the site locally.

@k-doering-NOAA k-doering-NOAA merged commit 015dd1d into main Aug 15, 2023
9 checks passed
@k-doering-NOAA k-doering-NOAA deleted the 368-convert-fims-to-a-pkgdown-site branch August 15, 2023 12:49
@k-doering-NOAA k-doering-NOAA mentioned this pull request Aug 15, 2023
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@k-doering-NOAA k-doering-NOAA k-doering-NOAA approved these changes

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Convert FIMS to a pkgdown site
6 participants
@Bai-Li-NOAA @k-doering-NOAA @timjmiller @ChristineStawitz-NOAA @MOshima-PIFSC @nathanvaughan-NOAA