Style code and document

.Rbuildignore

@@ -2,3 +2,7 @@
 ^\.Rproj\.user$
 ^data-raw$
 ^\.devcontainer$
+^\.github$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.devcontainer/devcontainer.json

@@ -13,7 +13,7 @@
 			"packages": "clang,clang-format,clang-tidy,cmake,doxygen,g++,gcc,libxt6,libxtst6,make,ninja-build"			
 		},
 		 "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",
 			"installSystemRequirements": true
 		  },
 		 // option to run rstudio. you can type rserver into the command line to

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,55 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    # Unncomment the following line once the tests are passing
+    # branches: [main]
+  pull_request:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          # This will install Git LFS and checkout the LFS objects during the checkout process.
+          lfs: true
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/call-build-pkgdown.yml

@@ -0,0 +1,16 @@
+# Checks that the pkgdown site builds for a repository, assuming that one
+# already exists, but it does not actually deploy it. See
+# call-update-pkgdown.yml for that.
+name: call-build-pkgdown
+
+on:
+  # TODO: remove push trigger once tests are passing
+  push:
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  call-workflow:
+    uses: nmfs-ost/ghactions4r/.github/workflows/build-pkgdown.yml@main

.github/workflows/call-doc-and-style-r.yml

@@ -0,0 +1,17 @@
+# Runs devtools::document() and styler::style_active_package(), then opens a
+# pull request to the branch that had changes in the push that triggered the
+# workflow.
+name: call-doc-and-style-r
+
+on:
+  push:
+    # TODO: uncomment following lines once tests are passing
+    # branches: 
+    #   - main
+  workflow_dispatch:
+
+jobs:
+  call-workflow:
+    uses: nmfs-ost/ghactions4r/.github/workflows/doc-and-style-r.yml@main
+    secrets:
+      PAT: ${{ secrets.PAT }}

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

@@ -0,0 +1,44 @@
+# Adds a comment to a newly opened PR letting reviewers know what should be
+# included in their review.
+name: Add a comment with reviewer checklist when PR opened
+
+on:
+  # TODO: remove push trigger once tests are passing
+  push:
+  pull_request:
+    types: [opened]
+
+jobs:
+  pr-checklist:
+    runs-on: ubuntu-latest
+    name: pr-checklist
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: 'Comment PR'
+        uses: actions/github-script@v0.3.0
+        if: github.event_name == 'pull_request'
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            var msg = `# 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](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/reviewing-changes-in-pull-requests/commenting-on-a-pull-request) to indicate where you have questions or changes are needed before approving the PR.
+            - Please use conventions in the [guidelines for conventional commit messages](https://www.conventionalcommits.org/) 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.
+            `
+            const { issue: { number: issue_number }, repo: { owner, repo }  } = context;
+            github.issues.createComment({ issue_number, owner, repo, body: msg });

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

@@ -0,0 +1,16 @@
+# Runs devtools::spell_check().
+name: call-spell-check
+
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    # TODO: uncomment following lines once tests are passing
+    # branches:
+    #   - main
+  workflow_dispatch:
+
+jobs:
+  call-workflow:
+    uses: nmfs-ost/ghactions4r/.github/workflows/spell-check.yml@main

.github/workflows/call-update-pkgdown.yml

@@ -0,0 +1,12 @@
+# Updates the exiting pkgdown site for a repository by deploying the changes
+# made to the pkgdown site to a branch called gh-pages.
+name: call-update-pkgdown
+
+on:
+  push:
+    # TODO: uncomment following lines once tests are passing
+    # branches: [main]
+
+jobs:
+  call-workflow:
+    uses: nmfs-ost/ghactions4r/.github/workflows/update-pkgdown.yml@main

.github/workflows/greetings.yml

@@ -0,0 +1,26 @@
+name: Greetings
+
+on: [pull_request_target, issues]
+
+jobs:
+  greeting:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+    - uses: actions/first-interaction@v1
+      with:
+        repo-token: ${{ secrets.GITHUB_TOKEN }}
+        issue-message: >
+          Thank you for contributing to ecosystemdata and opening your first issue
+          here! We are happy to have your contributions. We encourage you to
+          introduce yourself to the community on the [introduction thread in
+          our Discussions](https://github.com/orgs/NOAA-FIMS/discussions/801).
+        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!
+          Also, we encourage you to introduce yourself to the community on the
+          [introduction thread in our
+          Discussions](https://github.com/orgs/NOAA-FIMS/discussions/801).

.gitignore

@@ -48,3 +48,4 @@ po/*~
 # RStudio Connect folder
 rsconnect/
 .Rproj.user
+docs

DESCRIPTION

@@ -2,18 +2,18 @@ Package: ecosystemdata
 Title: Ecosystem database of Ecopath with Ecosim and Atlantis models
 Version: 0.1.0
 Authors@R: c(
-    person("Bai", "Li", email = "bai.li@noaa.gov", role = c("aut", "cre"),
+    person("Bai", "Li", , "bai.li@noaa.gov", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-8249-1442")),
-    person(c("Kelli", "F."), "Johnson", email = "kelli.johnson@noaa.gov",
-           role = "aut", comment = c(ORCID = "0000-0002-5149-451X"))
+    person(c("Kelli", "F."), "Johnson", , "kelli.johnson@noaa.gov", role = "aut",
+           comment = c(ORCID = "0000-0002-5149-451X"))
   )
-Description: Ecosystem database of Ecopath with Ecosim and Atlantis models.
-    The package provides functions to access and manipulate the ecosystem output
-    files from the Ecopath with Ecosim and Atlantis models.
+Description: Ecosystem database of Ecopath with Ecosim and Atlantis
+    models.  The package provides functions to access and manipulate the
+    ecosystem output files from the Ecopath with Ecosim and Atlantis
+    models.
 License: GPL (>= 3) | file LICENSE
-Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+Depends: 
+    R (>= 3.5)
 Imports:
     cli,
     dplyr,
@@ -28,6 +28,8 @@ Suggests:
     testthat (>= 3.0.0),
     usethis
 Config/testthat/edition: 3
-Depends: 
-    R (>= 3.5)
+Encoding: UTF-8
+Language: en-US
 LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2

R/ewe_nwatlantic.R

@@ -12,7 +12,7 @@
 #'     relative path. This column is helpful for understanding which EWE model
 #'     and which run the data came from.
 #'   }
-#'   \item{type}{The type refers to what data type this row is, e.g., landings, 
+#'   \item{type}{The type refers to what data type this row is, e.g., landings,
 #'     catch, biomass, weight, and mortality.
 #'   }
 #'   \item{year}{A four-digit integer specifying the year.}

R/get_functional_groups.R

@@ -4,7 +4,7 @@ utils::globalVariables(c("V1", "V2"))
 #'
 #' @description
 #' Functional group names are useful for the column names of output data from
-#' an EeW model, and thus, this function is a way to get them automatically
+#' an EwE model, and thus, this function is a way to get them automatically
 #' from the EwE output. The functional group names come from the basic
 #' estimates file.
 #'
@@ -39,12 +39,12 @@ get_functional_groups <- function(file_path) {
   out_vector <- utils::read.table(
     text = as.character(temp[-1]),
     sep = ","
-  ) |> 
+  ) |>
     # Extract non-NA rows from the first column
     dplyr::filter(!is.na(V1)) |>
     # Pull the names of the functional groups
     dplyr::pull(V2)
-  
+
   # Return a tibble with the functional groups, species, and group names
   split_functional_groups(out_vector)
 }

R/load_.R

@@ -7,7 +7,7 @@ utils::globalVariables(c("timestep", "group", "fleet", "month", "type", "year"))
 #'
 #' @param file_path The path to the CSV file containing the EwE output data.
 #' @param model_years A vector of years corresponding to the model years. TODO: this can be removed
-#' after havgina a utility function to extract model years globally from annual data
+#' after having a utility function to extract model years globally from annual data
 #' @param functional_groups A vector of names of the functional groups in the model.
 #'
 #' @export

R/use_template.R

@@ -56,4 +56,4 @@ use_testthat_template <- function(name) {
     cli::cli_abort("{path} already exists.")
   }
   invisible(TRUE)
-}
+}

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: https://NOAA-FIMS.github.io/ecosystemdata
+template:
+  bootstrap: 5
+

inst/WORDLIST

@@ -0,0 +1,14 @@
+Brito
+Buchheister
+Chagaris
+Cieri
+Ecopath
+Ecosim
+EwE
+Schueller
+bookdown
+fmars
+nwatlantic
+testthat
+tibble
+usethis

tests/testthat/test-load_model.R

@@ -26,12 +26,12 @@ model_years <- 1985:2017
 test_that("load_model() works with correct inputs", {
   ewe_model <- load_model(
     directory = base_run_dir,
-    functional_groups = functional_groups, 
+    functional_groups = functional_groups,
     type = "ewe"
   )
-  
+
   expected_colnames <- c(
-    "file_name", "type", "year", "month", "functional_group", 
+    "file_name", "type", "year", "month", "functional_group",
     "value", "species", "group", "fleet", "reference"
   )
   #' @description Test that load_model() returns correct columns.