testing

boettiger-lab · Feb 4, 2024 · 0cd68e4 · 0cd68e4
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diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -1,53 +1,6 @@
 {
 	  "image": "ghcr.io/boettiger-lab/nasa-tops:latest",
 	  "runArgs": [ "--security-opt", "seccomp=unconfined" ],
-	  "name": "NASA TOPS Environment",
-	  // build image as a github-action and grab instead; faster.
-	  // "build": {
-	  //	"dockerfile": "Dockerfile"
-	  //},
-	  "waitFor": "onCreateCommand",
-	  "features": {
-		"ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {},
-		// Install JupyterLab and IRkernel.
-		// More info: https://github.com/rocker-org/devcontainer-templates/tree/main/src/r-ver
-		"ghcr.io/rocker-org/devcontainer-features/r-rig:1": {
-			"version": "none",
-			"installJupyterlab": true
-		}
-	  },
-	  "customizations": {
-		"codespaces": {
-			"openFiles": ["README.md"]
-		  },
-		  "vscode": {
-		  "settings": {
-			"r.rterm.linux": "/usr/local/bin/radian",
-			"r.bracketedPaste": true,
-			"r.plot.useHttpgd": true,
-			"[r]": {
-			  "editor.wordSeparators": "`~!@#%$^&*()-=+[{]}\\|;:'\",<>/?"
-			}
-		  },
-		  "extensions": [
-			"reditorsupport.r",
-			"rdebugger.r-debugger",
-			"ms-toolsai.jupyter",
-			"ms-python.python"			
-			]
-		}
-	  },
-	  // Forward the RStudio ports
-	  "forwardPorts": [8787],
-	  "portsAttributes": {
-		"8787": {
-			"label": "Rstudio",
-			"requireLocalPort": true,
-			"onAutoForward": "ignore"
-		}
-	  },
-	  // Use 'postCreateCommand' to run commands after the container is created.
-	  "postCreateCommand": "bash .devcontainer/setup.sh",
-	  "postAttachCommand": "sudo rstudio-server start &> /dev/null && bash .devcontainer/welcome.sh",
-	  "remoteUser": "rstudio"
-	}
+	  "name": "NASA TOPS Environment"
+}
+
diff --git a/.devcontainer/full-devcontainer.json b/.devcontainer/full-devcontainer.json
@@ -0,0 +1,53 @@
+{
+	  "image": "ghcr.io/boettiger-lab/nasa-tops:latest",
+	  "runArgs": [ "--security-opt", "seccomp=unconfined" ],
+	  "name": "NASA TOPS Environment",
+	  // build image as a github-action and grab instead; faster.
+	  // "build": {
+	  //	"dockerfile": "Dockerfile"
+	  //},
+	  "waitFor": "onCreateCommand",
+	  "features": {
+		"ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {},
+		// Install JupyterLab and IRkernel.
+		// More info: https://github.com/rocker-org/devcontainer-templates/tree/main/src/r-ver
+		"ghcr.io/rocker-org/devcontainer-features/r-rig:1": {
+			"version": "none",
+			"installJupyterlab": true
+		}
+	  },
+	  "customizations": {
+		"codespaces": {
+			"openFiles": ["README.md"]
+		  },
+		  "vscode": {
+		  "settings": {
+			"r.rterm.linux": "/usr/local/bin/radian",
+			"r.bracketedPaste": true,
+			"r.plot.useHttpgd": true,
+			"[r]": {
+			  "editor.wordSeparators": "`~!@#%$^&*()-=+[{]}\\|;:'\",<>/?"
+			}
+		  },
+		  "extensions": [
+			"reditorsupport.r",
+			"rdebugger.r-debugger",
+			"ms-toolsai.jupyter",
+			"ms-python.python"			
+			]
+		}
+	  },
+	  // Forward the RStudio ports
+	  "forwardPorts": [8787],
+	  "portsAttributes": {
+		"8787": {
+			"label": "Rstudio",
+			"requireLocalPort": true,
+			"onAutoForward": "ignore"
+		}
+	  },
+	  // Use 'postCreateCommand' to run commands after the container is created.
+	  "postCreateCommand": "bash .devcontainer/setup.sh",
+	  "postAttachCommand": "sudo rstudio-server start &> /dev/null && bash .devcontainer/welcome.sh",
+	  "remoteUser": "rstudio"
+	}
diff --git a/.devcontainer/jupyter-requirements.txt b/.devcontainer/jupyter-requirements.txt
@@ -25,6 +25,7 @@ jupyterlab-git
 jupyter-tensorboard-proxy 
 jupyter-resource-usage
 jupyter-vscode-proxy
+jupyter-rsession-proxy
 jupyter-book
 jupyterlab_myst
 gh-scoped-creds

diff --git a/.devcontainer/jupyterhub.Dockerfile b/.devcontainer/jupyterhub.Dockerfile
@@ -1,4 +1,4 @@
-## devcontainer-focused Rocker
+# devcontainer-focused Rocker
 FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
 
 ## latest version of geospatial libs
@@ -19,7 +19,7 @@ RUN chown ${NB_USER}:staff -R ${R_HOME}/site-library
 RUN git config --system pull.rebase false && \
     git config --system credential.helper 'cache --timeout=36000'
 
-## codeserver
+# codeserver
 RUN curl -fsSL https://code-server.dev/install.sh | sh
 
 USER rstudio
@@ -28,10 +28,10 @@ RUN usermod -s /bin/bash rstudio
 ENV PATH=$PATH:/home/rstudio/.local/bin
 
 COPY jupyter-requirements.txt jupyter-requirements.txt
-RUN python -m pip install -r jupyter-requirements.txt && rm jupyter-requirements.txt
+RUN python -m pip install --no-cache-dir -r jupyter-requirements.txt && rm jupyter-requirements.txt
 
 COPY nasa-requirements.txt requirements.txt
-RUN python -m pip install -r requirements.txt && rm requirements.txt
+RUN python -m pip install --no-cache-dir -r requirements.txt && rm requirements.txt
 
 COPY install.R install.R
 RUN Rscript install.R && rm install.R