Merge branch 'master' into final-joss-checks

.Rbuildignore

@@ -27,3 +27,4 @@ SMG.md
 ^.*.pdf$
 ^inst/paper$
 ^inst/examples$
+^\.devcontainer$

.devcontainer/Dockerfile

@@ -0,0 +1,47 @@
+# R version: latest, ... ,4.0.1 , 4.0.0
+ARG VARIANT="latest"
+FROM rocker/verse:${VARIANT}
+
+# Use the [Option] comment to specify true/false arguments that should appear in VS Code UX
+#
+# [Option] Install zsh
+ARG INSTALL_ZSH="true"
+# [Option] Upgrade OS packages to their latest versions
+ARG UPGRADE_PACKAGES="false"
+
+# Install needed packages and setup non-root user. Use a separate RUN statement to add your own dependencies.
+ARG USERNAME=vscode
+ARG USER_UID=1100
+ARG USER_GID=$USER_UID
+COPY .devcontainer/library-scripts/*.sh /tmp/library-scripts/
+RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+    && /bin/bash /tmp/library-scripts/common-debian.sh "${INSTALL_ZSH}" "${USERNAME}" "${USER_UID}" "${USER_GID}" "${UPGRADE_PACKAGES}" "true" "true" \
+    && usermod -a -G staff ${USERNAME} \
+    && apt-get -y install \
+        python3-pip \
+        libgit2-dev \
+        libcurl4-openssl-dev \
+        libssl-dev \
+        libxml2-dev \
+        libxt-dev \
+    && apt-get autoremove -y && apt-get clean -y && rm -rf /var/lib/apt/lists/* /tmp/library-scripts
+
+RUN python3 -m pip --no-cache-dir install radian pre-commit
+RUN install2.r --error --skipinstalled --repos ${CRAN} --ncpus -1 \
+        devtools \
+        languageserver \
+        precommit \
+        git2r \
+    && rm -rf /tmp/downloaded_packages
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update \
+#     && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>
+
+# install dependencies
+COPY DESCRIPTION /tmp/package/DESCRIPTION
+RUN Rscript -e "devtools::install_dev_deps('/tmp/package')"
+
+# add docthis
+RUN Rscript -e 'devtools::install_github("mdlincoln/docthis")'

.devcontainer/devcontainer.json

@@ -0,0 +1,42 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.183.0/containers/r
+{
+	"name": "covidregionaldata",
+	"build": {
+		"dockerfile": "Dockerfile",
+		// Update VARIANT to pick a specific R version: latest, ... ,4.0.1 , 4.0.0
+		"args": { "VARIANT": "latest" },
+		"context": ".."
+	},
+
+	// Set *default* container specific settings.json values on container create.
+	"settings": {
+		"r.rterm.linux": "/usr/local/bin/radian",
+		"r.bracketedPaste": true,
+		"r.sessionWatcher": true,
+		"[r]": {
+			"editor.wordSeparators": "`~!@#%$^&*()-=+[{]}\\|;:'\",<>/?"
+		}
+	},
+
+	// Add the IDs of extensions you want installed when the container is created.
+	"extensions": [
+		"ikuyadeu.r",
+		"reditorsupport.r-lsp"
+	],
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	// "postCreateCommand": "R --version",
+
+	// Uncomment to use Docker from inside the container. See https://aka.ms/vscode-remote/samples/docker-from-docker.
+	// "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind" ],
+
+	// Uncomment when using a ptrace-based debugger like C++, Go, and Rust
+	// "runArgs": [ "--cap-add=SYS_PTRACE", "--security-opt", "seccomp=unconfined" ],
+
+	// Comment out connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
+	"remoteUser": "vscode"
+}