Add GHA checks #11

Bai-Li-NOAA · 2025-06-24T19:23:34Z

What is the feature?

Add GHA checks

How have you implemented the solution?

call checks from {ghactions4r} for building and
updating pkgdown site, checking documentation
and style, adding a PR checklist, running R cmd
check, checking spelling
copy GHA workflows from FIMS to adding all
contributors and greetings
develop a reusable workflow update-data-r.yml
for updating data files in the package when
changes are made to the /data-raw

Does the PR impact any other area of the project, maybe another repo?

No

TO-DO:

remove changes in 965fe0b after the PR is approved

* call checks from {ghactions4r} for building and updating pkgdown site, checking documentation and style, adding a PR checklist, running R cmd check, checking spelling * copy GHA workflows from FIMS to adding all contributors and greetings * develop a reusable workflow update-data-r.yml for updating data files in the package when changes are made to the /data-raw

github-actions · 2025-06-24T19:23:43Z

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, but feel free to skip over items that are not relevant!
See the GitHub documentation for how to comment on a PR to indicate where you have questions or changes are needed before approving the PR.
Please use conventions in the guidelines for conventional commit messages for both commit messages and comments.
PR reviews are a great way to learn so feel free to share your tips and tricks. However, when suggesting changes to the PR that are optional please include nit: (for nitpicking) as the comment type. 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 the PR is approved by selecting the approved status, and potentially by commenting on the PR with something like This PR is now ready to be merged, no additional changes are needed.

Checklist

The PR is requested to be merged into the appropriate branch (typically dev).
The code is well-designed.
The functionality is good for the users of the code.
Code coverage remains high, indicating the new code is tested.
The code is commented and the comments are clear, useful, and mostly explain why instead of what.
Code is appropriately documented.

Copilot

Pull Request Overview

This PR adds GitHub Actions workflows to automate various checks including building and updating the pkgdown site, documentation updates, automated data updates, style checking, and contributor acknowledgments.

Introduces multiple GitHub Actions workflow files for tasks such as updating data files, running spell checks, and performing R CMD check.
Updates documentation files and minor code comments to improve clarity and consistency.
Includes configuration changes in pkgdown, DESCRIPTION, and the development container to support the new workflows.

Reviewed Changes

Copilot reviewed 24 out of 27 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
pkgdown/extra.css	Adds an external CSS import to support the pkgdown site style.
pkgdown/_pkgdown.yml	Configures site URL and sets Bootstrap version for the pkgdown site.
man/load_csv_ewe.Rd	Fixes a documentation typo in the parameter description.
man/get_functional_groups.Rd	Corrects the reference from “EeW” to “EwE” in the documentation.
man/ewe_nwatlantic_base.Rd	Updates the documented column count to 10 to reflect recent changes.
inst/WORDLIST	Introduces a wordlist to support spell checking.
data-raw/ewe_nwatlantic.R	Updates function calls to use the ecosystemdata namespace.
README.md	Adds a contributors section using an automated allcontributors setup.
R/load_.R	Revises inline comment text for clarity.
R/get_functional_groups.R	Updates a comment to correctly refer to the EwE model.
DESCRIPTION	Adds a language specification.
.github/workflows/*.yml	Adds multiple workflows for checks, documentation, and updates.
.devcontainer/devcontainer.json	Updates container packages to include the spelling package.
.Rbuildignore	Expands ignored paths to include new config and documentation directories.

Comments suppressed due to low confidence (1)

man/ewe_nwatlantic_base.Rd:12

Please verify that the updated documentation reflecting 10 columns accurately matches the actual structure of the data output.

10 columns:

Copilot · 2025-06-24T19:24:11Z

data-raw/ewe_nwatlantic.R

@@ -1,22 +1,22 @@
 # code to prepare `ewe_nwatlantic` datasets
-
+# TODO: remove this line after testing


Consider removing or resolving the temporary testing comment on line 2 before merging to avoid leaving development artifacts in production code.

Suggested change

# TODO: remove this line after testing

Bai-Li-NOAA · 2025-06-24T19:31:20Z

@kellijohnson-NOAA, most of the GHA workflows are using the reusable workflows provided by the {ghactions4r} package. The two newly added workflows are update-data-r.yml and call-update-data-r.yml. These workflows automatically detect changes in /data-raw, update the corresponding data files in /data, and commit the changes directly to the working branch. You can see the tested results in the commit history here (42371b9).

Bai-Li-NOAA · 2025-06-24T19:37:23Z

@k-doering-NOAA, I’ve added two workflows (update-data-r.yml and call-update-data-r.yml) to this repo. These are designed to automatically detect changes in /data-raw and update the corresponding data files in /data. The main motivation is that we occasionally forget to update the package data after modifying files in /data-raw.

This workflow will also be needed in two other NOAA-FIMS repos. Do you think this could be a candidate for a reusable workflow in the {ghactions4r} package, or would it make more sense to keep it scoped within NOAA-FIMS?

kellijohnson-NOAA · 2025-06-24T19:47:25Z

.github/workflows/greetings.yml

+        pr-message: >
+          Thank you for contributing to {ecosystemdata} and opening your first PR
+          here! We are happy to have your contributions. Please ensure that the
+          PR is made to the dev branch and let us know if you need any help!


Suggested change

PR is made to the dev branch and let us know if you need any help!

PR is made to the main branch and let us know if you need any help!

Right now, we are using the main branch for this repo rather than a dev branch.

k-doering-NOAA · 2025-06-25T23:32:19Z

@k-doering-NOAA, I’ve added two workflows (update-data-r.yml and call-update-data-r.yml) to this repo. These are designed to automatically detect changes in /data-raw and update the corresponding data files in /data. The main motivation is that we occasionally forget to update the package data after modifying files in /data-raw.

This workflow will also be needed in two other NOAA-FIMS repos. Do you think this could be a candidate for a reusable workflow in the {ghactions4r} package, or would it make more sense to keep it scoped within NOAA-FIMS?

@Bai-Li-NOAA , in my mind, this does seem in scope for ghactions4r, as it seems general enough to apply to many R packages. Do you want to submit a PR for that workflow there at some point? Or, we can open an issue for one of us to work on in the future.

Bai-Li-NOAA · 2025-06-26T12:42:46Z

@k-doering-NOAA, I can submit a PR to {ghactions4r} to add a workflow for updating data files. We can then call the workflow from NOAA-FIMS.

kellijohnson-NOAA

This looks great. I have a few questions but nothing is blocking. Additionally, all files should end with an empty line, i.e.,

It is recommended that YAML files, like other text files, end with a single newline character. This convention is rooted in the POSIX standard for text files, which defines a text file as a sequence of lines, each terminated by a newline character.

kellijohnson-NOAA · 2025-07-28T15:27:17Z

.devcontainer/devcontainer.json

 		},
 		 "ghcr.io/rocker-org/devcontainer-features/r-packages:1": {
-			"packages": "dplyr,devtools,ggplot2,jsonlite,methods,mockery,Rcpp,RcppEigen,scales,snowfall,TMB,tibble,tidyr,usethis",
+			"packages": "dplyr,devtools,ggplot2,jsonlite,methods,mockery,Rcpp,RcppEigen,scales,snowfall,spelling,TMB,tibble,tidyr,usethis",


Do we need Rcpp, RcppEigen, and TMB in this repository?

kellijohnson-NOAA · 2025-07-28T15:28:24Z

.github/workflows/call-allcontributors.yml

+name: Collect contributors
+
+on:
+  push:


Do we want to run this on every push or at some other interval like monthly?

kellijohnson-NOAA · 2025-07-28T15:32:23Z

.github/workflows/call-pr-checklist.yml

+
+            ## Checklist
+
+            - [ ] The PR is requested to be merged into the appropriate branch (typically dev).


I don't recall having a dev branch in this repo.

Suggested change

- [ ] The PR is requested to be merged into the appropriate branch (typically dev).

- [ ] The PR is requested to be merged into the appropriate branch (typically main).

kellijohnson-NOAA · 2025-07-28T15:32:43Z

.github/workflows/call-pr-checklist.yml

+            - [ ] The PR is requested to be merged into the appropriate branch (typically dev).
+            - [ ] The code is well-designed.
+            - [ ] The functionality is good for the users of the code.
+            - [ ] Code coverage remains high, indicating the new code is tested.


Do we have code coverage in this repository?

kellijohnson-NOAA · 2025-07-28T15:34:02Z

.github/workflows/call-spell-check.yml

+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main


I think will lead to two workflows on the same code so I recommend removing lines 8--10.

kellijohnson-NOAA · 2025-07-28T15:34:41Z

.github/workflows/call-update-data-r.yml

+# Update data files in /data whenever changes are made to files in /data-raw.
+# This workflow automatically commits changes directly to the working branch.


This is brilliant! I do not understand though why we are calling another file within this repository rather than just using the other file?

kellijohnson-NOAA · 2025-07-28T15:41:03Z

.github/workflows/update-data-r.yml

+          r_scripts <- list.files("data-raw", pattern = "\\.R$", full.names = TRUE)
+          if (length(r_scripts) > 0) {
+            for (script in r_scripts) {
+              system(paste("Rscript ", shQuote(script)))


I am confused 😕 why you would use a system call to run Rscript instead of just sourcing the function within R here?

kellijohnson-NOAA · 2025-07-28T15:43:32Z

data-raw/ewe_nwatlantic.R


 usethis::use_data(ewe_nwatlantic_base, overwrite = TRUE)
-usethis::use_data(ewe_nwatlantic_env, overwrite = TRUE)
+usethis::use_data(ewe_nwatlantic_env, overwrite = TRUE)


There should be a new line at the end of the file.

kellijohnson-NOAA · 2025-07-28T15:44:15Z

inst/WORDLIST

:nit: I am not sure what is best practice but I prefer that the list just be alphabetical not not sorted by capitalization first.

Bai-Li-NOAA added 3 commits June 24, 2025 17:51

add a line in ewe_nwatlantic.R for testing

965fe0b

update data from /data-raw

42371b9

Bai-Li-NOAA requested review from Copilot and kellijohnson-NOAA June 24, 2025 19:23

Bai-Li-NOAA linked an issue Jun 24, 2025 that may be closed by this pull request

[Developer Issue]: Set up GHA to detect raw data changes #8

Open

Bai-Li-NOAA linked an issue Jun 24, 2025 that may be closed by this pull request

[Developer Issue]: Add GHA workflows to check the package #3

Open

6 tasks

Copilot AI reviewed Jun 24, 2025

View reviewed changes

kellijohnson-NOAA reviewed Jun 24, 2025

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kellijohnson-NOAA approved these changes Jul 28, 2025

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Bai-Li-NOAA added 4 commits August 19, 2025 15:05

test download artifact

75dc489

trigger GHA on push and fail R CMD Check

ba41f5d

do not run on push

a0ecfa5

trigger gha on a feature branch

a552327

		@@ -1,22 +1,22 @@
		# code to prepare `ewe_nwatlantic` datasets

		# TODO: remove this line after testing

	PR is made to the dev branch and let us know if you need any help!
	PR is made to the main branch and let us know if you need any help!


		## Checklist

		- [ ] The PR is requested to be merged into the appropriate branch (typically dev).

		# Update data files in /data whenever changes are made to files in /data-raw.
		# This workflow automatically commits changes directly to the working branch.

Add GHA checks #11

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Add GHA checks #11

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Bai-Li-NOAA commented Jun 24, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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What is the feature?

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Does the PR impact any other area of the project, maybe another repo?

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github-actions bot commented Jun 24, 2025

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Bai-Li-NOAA commented Jun 24, 2025

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k-doering-NOAA commented Jun 25, 2025

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Bai-Li-NOAA commented Jun 24, 2025 •

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