Merge pull request #99 from PIFSCstockassessments/FEAT-cookbook-recip…

…e-articles

Feat cookbook recipe articles

.Rbuildignore

@@ -13,4 +13,5 @@ CONTRIBUTING.md
 ^docs$
 ^pkgdown$
 ^README\.Rmd$
-^model_recipes$
+^model_recipes$
+^vignettes/articles$

.devcontainer/devcontainer.json

@@ -0,0 +1,59 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.234.0/containers/r
+{
+	"name": "R (rocker/r-ver base)",
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"image": "ghcr.io/rocker-org/devcontainer/r-ver:4.3", //commma needed if other sections are used.
+
+	// hostRequirements to set a minimum for machine type
+	//"hostRequirements": {
+	//	"cpus": 8,
+	//	"memory": "8gb",
+	//	"storage": "32gb"
+	// },
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	"features": {
+
+		// to install r packages using pak
+		// more info: https://github.com/rocker-org/devcontainer-features/blob/main/src/r-packages/README.md
+		 "ghcr.io/rocker-org/devcontainer-features/r-packages:1": {
+			"packages": "tidyverse,future,purrr,rmarkdown",
+			 "installSystemRequirements": true
+		  },
+		//to install ss3 via wget 
+		"ghcr.io/devcontainers-contrib/features/wget-apt-get:1.0.15":{
+			"-O ss3 https://github.com/nmfs-ost/ss3-source-code/releases/latest/download/ss_linux"
+		}
+	// // for quarto cli
+	     // more info: https://github.com/rocker-org/devcontainer-features/blob/main/src/quarto-cli/README.md
+	    // "ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {}
+
+		 //to use Rstudio as IDE instead of VS code
+		 //"ghcr.io/rocker-org/devcontainer-features/rstudio-server:0": {}
+	 },
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	//"postAttachCommand": {
+    //    "rstudio-start": "rserver"
+    //},
+	// Use 'postCreateCommand' to run commands after the container is created.
+	//"postCreateCommand": "echo 'options(repos = c(CRAN = \"https://cloud.r-project.org\"))' | sudo sh -c 'cat - >>\"${R_HOME}/etc/Rprofile.site\"'",
+
+	// Configure tool-specific properties.
+	 "customizations": {
+	   "vscode": {
+	 		// Set *default* container specific settings.json values on container create.
+	 		// Add the IDs of extensions you want installed when the container is created.
+	 		"extensions": [
+				 "GitHub.codespaces"
+	 		]
+	     }
+
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}
+}

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

@@ -6,7 +6,7 @@ on:
       - 'README.md'
   pull_request:
 
-name: build-ss-R-CMD-check
+name: R-CMD-check
 
 jobs:
   R-CMD-check:

.github/workflows/pkgdown.yaml

@@ -25,7 +25,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::.
+          extra-packages: any::pkgdown, local::., any::tidyverse, any::future, any::rmarkdown, any::purrr, any::furrr
           needs: website
 
       - name: Deploy package