Merge branch 'main' of github.com:UofUEpiBio/PHS7045-advanced-program…

…ming into main

Dockerfile → .devcontainer/Dockerfile

@@ -1,4 +1,4 @@
-FROM eddelbuettel/r2u:20.04
+FROM rocker/tidyverse:4.4.1
 
 RUN apt-get update && apt-get install -y --no-install-recommends \
     pandoc \
@@ -7,29 +7,32 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     gdebi-core \
     && rm -rf /var/lib/apt/lists/*
 
-RUN install.r \
-    shiny \
-    jsonlite \
-    ggplot2 \
-    htmltools \
-    remotes \
+RUN install2.r -n4 \
     renv \
-    knitr \
-    rmarkdown \
     pander \
-    quarto \
-    data.table \
-    rcpp \
-    microbenchmark \
-    reticulate \
-    bench \
     igraph \
     igraphdata \
-    netplot 
+    netplot \
+    reticulate \
+    microbenchmark \
+    bench \
+    R.utils \
+    maps
+
+RUN \
+Rscript --vanilla -e 'reticulate::install_python()' && \
+Rscript --vanilla -e 'reticulate::virtualenv_create("r-reticulate")' && \
+Rscript --vanilla -e 'reticulate::py_install("datatable")'
 
+RUN \
+Rscript --vanilla -e 'reticulate::py_install("pandas")'
 
 RUN curl -LO https://quarto.org/download/latest/quarto-linux-amd64.deb
 RUN gdebi --non-interactive quarto-linux-amd64.deb
 RUN apt-get install --no-install-recommends -y git
 
+RUN apt-get update && apt-get install -y --no-install-recommends gdb 
+
+RUN install2.r languageserver
+
 CMD ["bash"]

.devcontainer/devcontainer.json

@@ -0,0 +1,27 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/docker-existing-dockerfile
+{
+	"name": "Existing Dockerfile",
+	"build": {
+		// Sets the run context to one level up instead of the .devcontainer folder.
+		"context": "..",
+		// Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
+		"dockerfile": "Dockerfile"
+	}
+
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Uncomment the next line to run commands after the container is created.
+	// "postCreateCommand": "cat /etc/os-release",
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "devcontainer"
+}

.gitignore

@@ -2,10 +2,11 @@
 .Rhistory
 .RData
 .Ruserdata
+.DS_Store
 *_files/
 *_cache/
 libs
 *.gz
 *.docx
 *.xlsx
-_site
+_site