Release 0.3.0.0

.devcontainer/devcontainer.json

@@ -13,7 +13,7 @@
 			"packages": "make,gcc,g++,cmake,clang-tidy,clang-format,clang,doxygen,ninja-build,libxtst6,libxt6"			
 		},
 		 "ghcr.io/rocker-org/devcontainer-features/r-packages:1": {
-			"packages": "RcppEigen,dplyr,ggplot2,jsonlite,magrittr,methods,Rcpp,scales,TMB,usethis,devtools",
+			"packages": "RcppEigen,dplyr,ggplot2,jsonlite,magrittr,methods,Rcpp,scales,TMB,usethis,devtools,tibble",
 			"installSystemRequirements": true
 		  },
 		 // option to run rstudio. you can type rserver into the command line to

.github/workflows/build-deploy-doxygen.yml

@@ -19,7 +19,7 @@ jobs:
 
     steps:
     - name: Get repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Installing build dependencies
       run: |

.github/workflows/build-doxygen.yml

@@ -21,7 +21,7 @@ jobs:
 
     steps:
     - name: Get repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Installing build dependencies
       run: |

.github/workflows/call-allcontributors.yml

@@ -0,0 +1,38 @@
+name: Collect contributors
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 8 * * 1'
+
+jobs:
+    run-r-script:
+        runs-on: ubuntu-latest
+        env:
+            GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+        permissions:
+            contents: write
+            pull-requests: write
+        steps:
+            - name: Checkout repository
+              uses: actions/checkout@v3
+            - name: Setup R
+              uses: r-lib/actions/setup-r@v2
+
+            - uses: r-lib/actions/setup-r-dependencies@v2
+              with:
+                packages: |
+                    gh
+                    allcontributors
+            - name: Collect contributor data
+              run: Rscript -e 'allcontributors::add_contributors(files = c("README.md"), alphabetical = FALSE)'
+            - name: Create Pull Request
+              uses: peter-evans/create-pull-request@v5
+              with:
+                commit-message: "Update contributors"
+                branch: update-contributors
+                title: "Update contributors"
+                body: "This PR updates the contributors list."
+                labels: "auto-update"
+                add-paths: |
+                  README.md

.github/workflows/call-calc-coverage.yml

@@ -5,8 +5,7 @@ name: call-calc_coverage
 on:
   workflow_dispatch:
   push:
-    branches:    
-      - main
+    on: workflow_dispatch
     paths-ignore:
       - .devcontainer
       - .github
@@ -16,9 +15,6 @@ on:
       - 'Rbuildignore'
       - '.gitignore'
       - 'man'
-  pull_request:
-    branches:
-      - main
 jobs:
   call-workflow:
     uses: nmfs-fish-tools/ghactions4r/.github/workflows/calc-coverage.yml@main

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

@@ -0,0 +1,17 @@
+# run devtools::spell_check()
+name: call-spell-check
+# on specifies the build triggers. See more info at https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
+on:
+# this workflow runs on pushing to main, pull requests to main, and manually.
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches:
+      - main
+      - dev
+  workflow_dispatch:
+jobs:
+  call-workflow:
+    uses: nmfs-fish-tools/ghactions4r/.github/workflows/spell-check.yml@main

.github/workflows/get-gtest-codecov.yml

@@ -26,7 +26,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Install Ninja
       run: sudo apt-get install ninja-build
     - uses: r-lib/actions/setup-r@v2

.github/workflows/pr-checklist.yml

@@ -10,7 +10,7 @@ jobs:
     name: pr-checklist
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: 'Comment PR'
         uses: actions/[email protected]
         if: github.event_name == 'pull_request'

.github/workflows/run-clang-format.yml

@@ -23,7 +23,7 @@ jobs:
     # Format hpp and cpp files under inst/include, src/, and test/gtest
     # We use Google style to format code.
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: DoozyX/[email protected]
       with:
         source: './inst/include ./src ./tests/gtest'

.github/workflows/run-clang-tidy.yml

@@ -19,7 +19,7 @@ jobs:
     strategy:
       fail-fast: false
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: install clang-tidy
       run: sudo apt update && sudo apt -y install clang-tidy

.github/workflows/run-googletest.yml

@@ -19,7 +19,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Install Ninja
       shell: bash
       run: ${{ runner.os == 'macOS' && 'brew install ninja' || runner.os == 'Windows' && 'choco install ninja' || 'sudo apt-get install ninja-build' }}

.gitignore

@@ -21,11 +21,6 @@
 # RStudio files
 .Rproj.user/
 
-# produced vignettes and libraries
-vignettes/*.html
-vignettes/*.pdf
-vignettes/*/libs/
-
 # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
 .httr-oauth
 
@@ -85,12 +80,14 @@ vignettes/*/libs/
 
 # IDE specific files
 *.vscode
+**/.vscode/
 
 # mac OS files
 *.DS_Store
 
-# All log file
+# All log files and json output
 *.log
+*.json
 
 #TMB tmp.def file
 src/tmp.def

CMakeLists.txt

@@ -7,7 +7,7 @@ project(FIMS
 ) # CXX is the language name
 
 # GoogleTest requires at least C++11
-set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD 17)
 
 include(FetchContent)
 

DESCRIPTION

@@ -1,45 +1,123 @@
 Package: FIMS
 Title: The Fisheries Integrated Modeling System
-Version: 0.2.0.0
+Version: 0.3.0.0
 Authors@R: c(
-    person("Christine", "Stawitz", , "[email protected]", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0003-3122-4501")),
-    person("Nathan", "Vaughan", role = "aut"),
-    person("Howard", "Townsend", role = "aut"),
-    person(c("Ian", "G."), "Taylor", role = "aut",
-           comment = c(ORCID = "0000-0002-4232-5669")),
-    person("Matthew", "Supernaw", role = "aut"),
-    person("Jane", "Sullivan", role = "aut"),
-    person("Kyle", "Shertzer", role = "aut",
-           comment = c(ORCID = "0000-0001-7196-5959")),
-    person("Megumi", "Oshima", role = "aut"),
-    person(c("Cole", "C."), "Monnahan", role = "aut",
-           comment = c(ORCID = "0000-0003-0871-6700")),
-    person(c("Timothy", "J."), "Miller", role = "aut",
-           comment = c(ORCID = "0000-0003-1411-1206")),
-    person("Richard", "Methot", role = "aut"),
-    person("Patrick", "Lynch", role = "aut",
-           comment = c(ORCID = "0000-0001-7121-6181")),
-    person("Bai", "Li", role = "aut",
-           comment = c(ORCID = "0000-0002-8249-1442")),
-    person("Huihua", "Lee", role = "aut"),
-    person(c("Christopher", "M."), "Legault", role = "aut",
-           comment = c(ORCID = "0000-0002-0328-1376")),
-    person(c("Kelli", "F."), "Johnson", role = "aut",
-           comment = c(ORCID = "0000-0002-5149-451X")),
-    person(c("James", "N."), "Ianelli", role = "aut",
-           comment = c(ORCID = "0000-0002-7170-8677")),
-    person("Alan", "Haynie", role = "aut"),
-    person(c("Andrea", "M."), "Havron", role = "aut",
-           comment = c(ORCID = "0000-0002-4080-448X")),
-    person(c("Kathryn", "L."), "Doering", role = "aut",
-           comment = c(ORCID = "0000-0002-0396-7044")),
-    person(c("Edward", "J."), "Dick", role = "aut",
-           comment = c(ORCID = "0000-0001-7681-9176")),
-    person("Jon", "Brodziak", role = "aut"),
-    person("Kristan", "Blackhart", role = "aut"),
-    person("Peter", "Kuriyama", role = "aut",
-           comment = c(ORCID = "0000-0002-6971-4015"))
+    person(
+      role = c("aut", "cre"),
+      family = "Johnson",
+      given = c("Kelli", "F."),
+      email = "[email protected]",
+      comment = c(ORCID = "0000-0002-5149-451X")
+    ),
+    person(
+      role = "aut",
+      family = "Brodziak",
+      given = c("Jon", "K.", "T."),
+      comment = c(ORCID = "0000-0001-8690-5588")
+    ),
+    person(
+      role = "aut",
+      family = "Doering",
+      given = c("Kathryn", "L."),
+      comment = c(ORCID = "0000-0002-0396-7044")
+    ),
+    person(
+      role = "aut",
+      family = "Havron",
+      given = c("Andrea", "M."),
+      comment = c(ORCID = "0000-0002-4080-448X")
+    ),
+    person(
+      role = "aut",
+      family = "Klasky",
+      given = c("Ronald"),
+      comment = c(ORCID = "0009-0004-7563-7716")
+    ),
+    person(
+      role = "aut",
+      family = "Kuriyama",
+      given = c("Peter", "T."),
+      comment = c(ORCID = "0000-0002-6971-4015")
+    ),
+    person(
+      role = "aut",
+      family = "Legault",
+      given = c("Christopher", "M."),
+      comment = c(ORCID = "0000-0002-0328-1376")
+    ),
+    person(
+      role = "aut",
+      family = "Li",
+      given = "Bai",
+      comment = c(ORCID = "0000-0002-8249-1442")
+    ),
+    person(
+      role = "aut",
+      family = "Miller",
+      given = c("Timothy", "J."),
+      comment = c(ORCID = "0000-0003-1411-1206")
+    ),
+    person(
+      role = "aut",
+      family = "Monnahan",
+      given = c("Cole", "C."),
+      comment = c(ORCID = "0000-0003-0871-6700")
+    ),
+    person(
+      role = "aut",
+      family = "Oshima",
+      given = c("Megumi", "C."),
+      comment = c(ORCID = "0009-0002-2239-1594")
+    ),
+    person(
+      role = "aut",
+      family = "Shertzer",
+      given = c("Kyle", "W."),
+      comment = c(ORCID = "0000-0001-7196-5959")
+    ),
+    person(
+      role = "aut",
+      family = "Stawitz",
+      given = c("Christine", "C."),
+      email = "[email protected]",
+      comment = c(ORCID = "0000-0003-3122-4501")
+    ),
+    person(
+      role = "aut",
+      family = "Sullivan",
+      given = c("Jane", "Y."),
+      comment = c(ORCID = "0000-0002-8094-1673")
+    ),
+    person(
+      role = "aut",
+      family = "Supernaw",
+      given = "Matthew",
+      comment = c(ORCID = "0009-0007-3681-7433")
+    ),
+    person(
+      role = "aut",
+      family = "Taylor",
+      given = c("Ian", "G."),
+      comment = c(ORCID = "0000-0002-4232-5669")
+    ),
+    person(
+      role = "aut",
+      family = "Vaughan",
+      given = c("Nathan", "R."),
+      comment = c(ORCID = "0009-0000-3054-6950")
+    ),
+    person(
+      role = "ctb",
+      family = "Blackhart",
+      given = "Kristan",
+      comment = c(ORCID = "0000-0003-4232-2510")
+    ),
+    person(
+      role = "ctb",
+      family = "Ianelli",
+      given = c("James", "N."),
+      comment = c(ORCID = "0000-0002-7170-8677")
+    )
   )
 Description: The Fisheries Integrated Modeling System is a next-generation
     framework of stock assessment models, assisting fishery managers with
@@ -54,31 +132,39 @@ License: GPL (>= 3) | file LICENSE
 URL: https://github.com/noaa-fims/fims, https://noaa-fims.github.io
 BugReports: https://github.com/noaa-fims/fims/issues
 Depends:
-    R (>= 4.0)
-Imports: 
+    R (>= 4.1.0)
+Imports:
+    cli,
     dplyr,
     ggplot2,
+    glue,
     jsonlite,
     methods,
+    purrr,
     Rcpp,
+    rlang,
     scales,
-    TMB (>= 1.8.0)
-Suggests: 
+    stats,
+    tibble,
+    TMB (>= 1.8.0),
+    utils
+Suggests:
     covr,
     knitr,
+    mockery,
     parallel,
     remotes,
     rmarkdown,
     snowfall,
     testthat (>= 3.0.0),
-    tidyverse,
+    tidyr,
     usethis,
     withr
-LinkingTo: 
+LinkingTo:
     Rcpp,
     RcppEigen,
     TMB
-VignetteBuilder: 
+VignetteBuilder:
     knitr
 Config/testthat/edition: 3
 Config/testthat/parallel: true