major clean-up

* move the dev images into draft_images
* create all the devcontainer files

.devcontainer/README.md

@@ -2,5 +2,24 @@ Some notes regarding working with the nmfs-opensci jupyter lab images in codespa
 
 Many of these images include the RStudio server and jupyter-rsession-proxy. There are a number of oddies that occur when launching the RStudio server (via the button in JupyterLab)
 
-* When a Dockerfile and `"build":` or docker compose is used, the PWD is changed to `/workspaces/<reponame>` in the terminal tab of RStudio. If the image is used as-is with `"image": ` in the devcontainer.json file, this does not happen.
-* In the images, port 8888 is exposed. If `jupyter lab --ip=0.0.0.0 --port=8888 --allow-root --no-browser` is used to start Jupyter Lab, then RStudio will not launch. There is some weird re-directing of the url. Instead use
+* In RStudio, the PWD is changed to `/workspaces/<reponame>` in the terminal tab of RStudio. If the image is used as-is with `"image": ` in the devcontainer.json file, this does not happen. https://github.com/jupyterhub/jupyter-rsession-proxy/issues/145. This terminal is opened with `bash --login` so this tells it to use the right PWD `echo PWD=/home/jovyan\ncd $PWD >> ~/.bash_login`
+* In the images, port 8888 is exposed. If `jupyter lab --ip=0.0.0.0 --port=8888 --allow-root --no-browser` is used to start Jupyter Lab, then RStudio will not launch. There is some weird re-directing of the url. Instead use a different port. I use 8889
+
+Other oddities.
+
+* Rebuilding the devcontainer from a running devcontainer doesn't work because because the working directory is /home/jovyan and that does not have a devcontainer.json file.
+* If a README.md file is in the working directory (set to /home/jovyan), then that is displayed automatically with preview. If a README.md file is created and opened with 
+```
+  "customizations": {
+    "codespaces": {
+      "openFiles": [ "README.md" ],
+    },
+    "vscode": {
+      "settings": { 
+        "workbench.editorAssociations": { "*.md": "vscode.markdown.preview.editor", },
+      },
+    }
+  },
+```
+it will open in the editor not preview. My solution is to create a README.md in \home\jovyan after the container is started.
+

.devcontainer/aomlomics-jh/devcontainer.json

@@ -0,0 +1,21 @@
+{
+  "name": "aomlomics-jh",
+  "workspaceFolder": "/home/jovyan",
+  "image": "ghcr.io/nmfs-opensci/container-images/aomlomics-jh:latest",
+
+  // Ports to be forwarded from the container to the host
+  "forwardPorts": [8889],
+  "portsAttributes": {
+    "8889": {
+      "label": "Jupyter Lab",
+      "onAutoForward": "notify"
+    }
+  },
+
+  // Create a README that is automatically opened in preview mode
+  // the echo bit is to fix pwd in bash terminal in RStudio
+  "postCreateCommand": "echo '[![](https://img.shields.io/badge/Open%20Jupyter%20Lab-37a779?style=for-the-badge)](https://''-8889.app.github.dev)' > README.md && echo PWD=/home/jovyan\ncd /Users/eli.holmes/Documents/GitHub/container-images >> ~/.bash_login",
+
+  // Start Jupyter Lab
+  "postStartCommand": "jupyter lab --ip=0.0.0.0 --port=8889 --allow-root --no-browser --notebook-dir=/home/jovyan --NotebookApp.token='' --NotebookApp.password=''",
+}

.devcontainer/arcgis/devcontainer.json

@@ -0,0 +1,21 @@
+{
+  "name": "arcgis",
+  "workspaceFolder": "/home/jovyan",
+  "image": "ghcr.io/nmfs-opensci/container-images/arcgis:latest",
+
+  // Ports to be forwarded from the container to the host
+  "forwardPorts": [8889],
+  "portsAttributes": {
+    "8889": {
+      "label": "Jupyter Lab",
+      "onAutoForward": "notify"
+    }
+  },
+
+  // Create a README that is automatically opened in preview mode
+  // the echo bit is to fix pwd in bash terminal in RStudio
+  "postCreateCommand": "echo '[![](https://img.shields.io/badge/Open%20Jupyter%20Lab-37a779?style=for-the-badge)](https://''-8889.app.github.dev)' > README.md && echo PWD=/home/jovyan\ncd /Users/eli.holmes/Documents/GitHub/container-images >> ~/.bash_login",
+
+  // Start Jupyter Lab
+  "postStartCommand": "jupyter lab --ip=0.0.0.0 --port=8889 --allow-root --no-browser --notebook-dir=/home/jovyan --NotebookApp.token='' --NotebookApp.password=''",
+}

.devcontainer/cmip6-cookbook/devcontainer.json

@@ -0,0 +1,21 @@
+{
+  "name": "cmip6-cookbook",
+  "workspaceFolder": "/home/jovyan",
+  "image": "ghcr.io/nmfs-opensci/container-images/cmip6-cookbook:latest",
+
+  // Ports to be forwarded from the container to the host
+  "forwardPorts": [8889],
+  "portsAttributes": {
+    "8889": {
+      "label": "Jupyter Lab",
+      "onAutoForward": "notify"
+    }
+  },
+
+  // Create a README that is automatically opened in preview mode
+  // the echo bit is to fix pwd in bash terminal in RStudio
+  "postCreateCommand": "echo '[![](https://img.shields.io/badge/Open%20Jupyter%20Lab-37a779?style=for-the-badge)](https://''-8889.app.github.dev)' > README.md && echo PWD=/home/jovyan\ncd /Users/eli.holmes/Documents/GitHub/container-images >> ~/.bash_login",
+
+  // Start Jupyter Lab
+  "postStartCommand": "jupyter lab --ip=0.0.0.0 --port=8889 --allow-root --no-browser --notebook-dir=/home/jovyan --NotebookApp.token='' --NotebookApp.password=''",
+}

.devcontainer/coastwatch/devcontainer.json

@@ -0,0 +1,21 @@
+{
+  "name": "coastwatch",
+  "workspaceFolder": "/home/jovyan",
+  "image": "ghcr.io/nmfs-opensci/container-images/coastwatch:latest",
+
+  // Ports to be forwarded from the container to the host
+  "forwardPorts": [8889],
+  "portsAttributes": {
+    "8889": {
+      "label": "Jupyter Lab",
+      "onAutoForward": "notify"
+    }
+  },
+
+  // Create a README that is automatically opened in preview mode
+  // the echo bit is to fix pwd in bash terminal in RStudio
+  "postCreateCommand": "echo '[![](https://img.shields.io/badge/Open%20Jupyter%20Lab-37a779?style=for-the-badge)](https://''-8889.app.github.dev)' > README.md && echo PWD=/home/jovyan\ncd /Users/eli.holmes/Documents/GitHub/container-images >> ~/.bash_login",
+
+  // Start Jupyter Lab
+  "postStartCommand": "jupyter lab --ip=0.0.0.0 --port=8889 --allow-root --no-browser --notebook-dir=/home/jovyan --NotebookApp.token='' --NotebookApp.password=''",
+}

.devcontainer/codespace/devcontainer_template.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+
+# Construct the message
+message="{
+  \"name\": \"$1\",
+  \"workspaceFolder\": \"/home/jovyan\",
+  \"image\": \"ghcr.io/nmfs-opensci/container-images/$1:latest\",
+
+  // Ports to be forwarded from the container to the host
+  \"forwardPorts\": [8889],
+  \"portsAttributes\": {
+    \"8889\": {
+      \"label\": \"Jupyter Lab\",
+      \"onAutoForward\": \"notify\"
+    }
+  },
+  
+  // Create a README that is automatically opened in preview mode
+  // the echo bit is to fix pwd in bash terminal in RStudio
+  \"postCreateCommand\": \"echo '[![](https://img.shields.io/badge/Open%20Jupyter%20Lab-37a779?style=for-the-badge)](https://'${CODESPACE_NAME}'-8889.app.github.dev)' > README.md && echo PWD=/home/jovyan\ncd $PWD >> ~/.bash_login\",
+  
+  // Start Jupyter Lab
+  \"postStartCommand\": \"jupyter lab --ip=0.0.0.0 --port=8889 --allow-root --no-browser --notebook-dir=/home/jovyan --NotebookApp.token='' --NotebookApp.password=''\",
+}"
+
+echo "$message" > ./.devcontainer/$1/devcontainer.json

.devcontainer/codespace/make_devcontainers.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+# cd .devcontainer/codespace
+# chmod +x ./make_devcontainers.sh
+# ./.devcontainer/codespace/make_devcontainers.sh
+a=$(Rscript -e 'cat(here::here())')
+cd $a
+chmod +x ./.devcontainer/codespace/devcontainer_template.sh
+fils="$(ls ./images)"
+for i in $fils
+do
+   echo $i
+   mkdir ../$i
+   ./.devcontainer/codespace/devcontainer_template.sh $i
+done

.devcontainer/codespace/test.json

@@ -0,0 +1,21 @@
+{
+  "name": "vast",
+  "workspaceFolder": "/home/jovyan",
+  "image": "ghcr.io/nmfs-opensci/container-images/vast:latest",
+
+  // Ports to be forwarded from the container to the host
+  "forwardPorts": [8889],
+  "portsAttributes": {
+    "8889": {
+      "label": "Jupyter Lab",
+      "onAutoForward": "notify"
+    }
+  },
+
+  // Create a README that is automatically opened in preview mode
+  // the echo bit is to fix pwd in bash terminal in RStudio
+  "postCreateCommand": "echo '[![](https://img.shields.io/badge/Open%20Jupyter%20Lab-37a779?style=for-the-badge)](https://''-8889.app.github.dev)' > README.md && echo PWD=/home/jovyan\ncd /Users/eli.holmes/Documents/GitHub/container-images/.devcontainer/codespace >> ~/.bash_login",
+
+  // Start Jupyter Lab
+  "postStartCommand": "jupyter lab --ip=0.0.0.0 --port=8889 --allow-root --no-browser --notebook-dir=/home/jovyan --NotebookApp.token='' --NotebookApp.password=''",
+}

.devcontainer/codespace/test.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+# Construct the message
+message="{
+  \"name\": $1,
+  \"workspaceFolder\": \"/home/jovyan\",
+  \"image\": \"ghcr.io/nmfs-opensci/container-images/\"$1\":latest\",
+"

.devcontainer/echopype/devcontainer.json

@@ -0,0 +1,21 @@
+{
+  "name": "echopype",
+  "workspaceFolder": "/home/jovyan",
+  "image": "ghcr.io/nmfs-opensci/container-images/echopype:latest",
+
+  // Ports to be forwarded from the container to the host
+  "forwardPorts": [8889],
+  "portsAttributes": {
+    "8889": {
+      "label": "Jupyter Lab",
+      "onAutoForward": "notify"
+    }
+  },
+
+  // Create a README that is automatically opened in preview mode
+  // the echo bit is to fix pwd in bash terminal in RStudio
+  "postCreateCommand": "echo '[![](https://img.shields.io/badge/Open%20Jupyter%20Lab-37a779?style=for-the-badge)](https://''-8889.app.github.dev)' > README.md && echo PWD=/home/jovyan\ncd /Users/eli.holmes/Documents/GitHub/container-images >> ~/.bash_login",
+
+  // Start Jupyter Lab
+  "postStartCommand": "jupyter lab --ip=0.0.0.0 --port=8889 --allow-root --no-browser --notebook-dir=/home/jovyan --NotebookApp.token='' --NotebookApp.password=''",
+}

.devcontainer/jupyter-base-notebook/devcontainer.json

@@ -0,0 +1,21 @@
+{
+  "name": "jupyter-base-notebook",
+  "workspaceFolder": "/home/jovyan",
+  "image": "ghcr.io/nmfs-opensci/container-images/jupyter-base-notebook:latest",
+
+  // Ports to be forwarded from the container to the host
+  "forwardPorts": [8889],
+  "portsAttributes": {
+    "8889": {
+      "label": "Jupyter Lab",
+      "onAutoForward": "notify"
+    }
+  },
+
+  // Create a README that is automatically opened in preview mode
+  // the echo bit is to fix pwd in bash terminal in RStudio
+  "postCreateCommand": "echo '[![](https://img.shields.io/badge/Open%20Jupyter%20Lab-37a779?style=for-the-badge)](https://''-8889.app.github.dev)' > README.md && echo PWD=/home/jovyan\ncd /Users/eli.holmes/Documents/GitHub/container-images >> ~/.bash_login",
+
+  // Start Jupyter Lab
+  "postStartCommand": "jupyter lab --ip=0.0.0.0 --port=8889 --allow-root --no-browser --notebook-dir=/home/jovyan --NotebookApp.token='' --NotebookApp.password=''",
+}

.devcontainer/py-geospatial/devcontainer.json

@@ -0,0 +1,21 @@
+{
+  "name": "py-geospatial",
+  "workspaceFolder": "/home/jovyan",
+  "image": "ghcr.io/nmfs-opensci/container-images/py-geospatial:latest",
+
+  // Ports to be forwarded from the container to the host
+  "forwardPorts": [8889],
+  "portsAttributes": {
+    "8889": {
+      "label": "Jupyter Lab",
+      "onAutoForward": "notify"
+    }
+  },
+
+  // Create a README that is automatically opened in preview mode
+  // the echo bit is to fix pwd in bash terminal in RStudio
+  "postCreateCommand": "echo '[![](https://img.shields.io/badge/Open%20Jupyter%20Lab-37a779?style=for-the-badge)](https://''-8889.app.github.dev)' > README.md && echo PWD=/home/jovyan\ncd /Users/eli.holmes/Documents/GitHub/container-images >> ~/.bash_login",
+
+  // Start Jupyter Lab
+  "postStartCommand": "jupyter lab --ip=0.0.0.0 --port=8889 --allow-root --no-browser --notebook-dir=/home/jovyan --NotebookApp.token='' --NotebookApp.password=''",
+}

.devcontainer/py-rocket-base/devcontainer.json

@@ -1,47 +1,21 @@
 {
-  // Name of the Dev Container
-  "name": "Py-Rocket Base Codespace",
-
-  // Path to the Docker file
+  "name": "py-rocket-base",
+  "workspaceFolder": "/home/jovyan",
   "image": "ghcr.io/nmfs-opensci/container-images/py-rocket-base:latest",
 
-  // Mount a folder with the post_start.sh script to /home/jovyan/codespace
-  // Don't use /home/jovyan as that would wipe out files there
-  // We need post_start.sh in our container
-  "workspaceMount": "source=${localWorkspaceFolder}/.devcontainer/codespace,target=/home/jovyan/codespace,type=bind,consistency=delegated",
-
-  // Default workspace folder within the container
-  "workspaceFolder": "/home/jovyan/codespace",
-
-  // Required for Jupyter Lab
-  "customizations": {
-    "vscode": {
-      "extensions": [
-        "ms-toolsai.jupyter",
-        "ms-python.python",
-      ]
-    },
-  },
-
-  // Settings for the VS Code
-  "settings": {
-    "terminal.integrated.shell.linux": "/bin/bash",
-  },
-
   // Ports to be forwarded from the container to the host
   "forwardPorts": [8889],
-
-  // Attributes for the forwarded ports
   "portsAttributes": {
     "8889": {
       "label": "Jupyter Lab",
-      "onAutoForward": "openBrowser"
+      "onAutoForward": "notify"
     }
   },
-
-  // Command to run after the container starts. Runs script to add a link to the Jupyter Lab
-  "postStartCommand": "chmod +x /home/jovyan/codespace/post_start.sh && /home/jovyan/codespace/post_start.sh && rm /home/jovyan/codespace/post_start.sh &&  jupyter lab --ip=0.0.0.0 --port=8889 --allow-root --no-browser --NotebookApp.token='' --NotebookApp.password=''",
-
-  // List of extensions to be installed
-  "extensions": []
+
+  // Create a README that is automatically opened in preview mode
+  // the echo bit is to fix pwd in bash terminal in RStudio
+  "postCreateCommand": "echo '[![](https://img.shields.io/badge/Open%20Jupyter%20Lab-37a779?style=for-the-badge)](https://''-8889.app.github.dev)' > README.md && echo PWD=/home/jovyan\ncd /Users/eli.holmes/Documents/GitHub/container-images >> ~/.bash_login",
+
+  // Start Jupyter Lab
+  "postStartCommand": "jupyter lab --ip=0.0.0.0 --port=8889 --allow-root --no-browser --notebook-dir=/home/jovyan --NotebookApp.token='' --NotebookApp.password=''",
 }

.devcontainer/py-rocket-geospatial/devcontainer.json

@@ -1,44 +1,21 @@
 {
-  // Name of the Dev Container
-  "name": "Py-Rocket Geospatial Codespace",
-
-  // Path to the Docker file
+  "name": "py-rocket-geospatial",
+  "workspaceFolder": "/home/jovyan",
   "image": "ghcr.io/nmfs-opensci/container-images/py-rocket-geospatial:latest",
 
-  "workspaceMount": "source=${localWorkspaceFolder}/.devcontainer/codespace,target=/home/jovyan/codespace,type=bind,consistency=delegated",
-
-  // Default workspace folder within the container
-  "workspaceFolder": "/home/jovyan/codespace",
-
-  // Required for Jupyter Lab
-  "customizations": {
-    "vscode": {
-      "extensions": [
-        "ms-toolsai.jupyter",
-        "ms-python.python",
-      ]
-    }
-  },
-
-  // Settings for the integrated terminal
-  "settings": {
-    "terminal.integrated.shell.linux": "/bin/bash"
-  },
-
   // Ports to be forwarded from the container to the host
   "forwardPorts": [8889],
-
-  // Attributes for the forwarded ports
   "portsAttributes": {
     "8889": {
       "label": "Jupyter Lab",
-      "onAutoForward": "openPreview"
+      "onAutoForward": "notify"
     }
   },
-
-  // Command to run after the container starts. Runs script to add a link to the RStudio
-  "postStartCommand": "chmod +x /home/jovyan/codespace/post_start.sh && /home/jovyan/codespace/post_start.sh && rm /home/jovyan/codespace/post_start.sh",
-
-  // List of extensions to be installed
-  "extensions": []
+
+  // Create a README that is automatically opened in preview mode
+  // the echo bit is to fix pwd in bash terminal in RStudio
+  "postCreateCommand": "echo '[![](https://img.shields.io/badge/Open%20Jupyter%20Lab-37a779?style=for-the-badge)](https://''-8889.app.github.dev)' > README.md && echo PWD=/home/jovyan\ncd /Users/eli.holmes/Documents/GitHub/container-images >> ~/.bash_login",
+
+  // Start Jupyter Lab
+  "postStartCommand": "jupyter lab --ip=0.0.0.0 --port=8889 --allow-root --no-browser --notebook-dir=/home/jovyan --NotebookApp.token='' --NotebookApp.password=''",
 }

.devcontainer/test/devcontainer.json → .devcontainer/template_works/devcontainer.json

@@ -13,6 +13,7 @@
   },
 
   // Create a README that is automatically opened in preview mode
+  // the echo bit is to fix pwd in bash terminal in RStudio
   "postCreateCommand": "echo '[![](https://img.shields.io/badge/Open%20Jupyter%20Lab-37a779?style=for-the-badge)](https://'${CODESPACE_NAME}'-8889.app.github.dev)' > README.md && echo PWD=/home/jovyan\ncd $PWD >> ~/.bash_login",
 
   // Start Jupyter Lab

.devcontainer/template_works/junk

@@ -0,0 +1,10 @@
+  "customizations": {
+    "codespaces": {
+      "openFiles": [ "README.md" ],
+    },
+    "vscode": {
+      "settings": { 
+        "workbench.editorAssociations": { "*.md": "vscode.markdown.preview.editor", },
+      },
+    }
+  },