From cc399a2300762d89e8f7281406e10b3d51c6a3c9 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Thu, 1 Feb 2024 19:23:33 +0000
Subject: [PATCH 01/59] :see_no_evil:

---
 .devcontainer/Dockerfile                    |   32 +
 .devcontainer/devcontainer.json             |   53 +
 .devcontainer/install.R                     |   11 +
 .devcontainer/python-only-devcontainer.json |   21 +
 .devcontainer/renv.lock                     | 1553 +++++++++++++++++++
 .devcontainer/requirements.txt              |  201 +++
 .devcontainer/setup.sh                      |    6 +
 .devcontainer/welcome.sh                    |   16 +
 .github/workflows/docker-image.yml          |   24 +
 .github/workflows/quarto.yaml               |   27 +
 10 files changed, 1944 insertions(+)
 create mode 100644 .devcontainer/Dockerfile
 create mode 100644 .devcontainer/devcontainer.json
 create mode 100755 .devcontainer/install.R
 create mode 100644 .devcontainer/python-only-devcontainer.json
 create mode 100644 .devcontainer/renv.lock
 create mode 100644 .devcontainer/requirements.txt
 create mode 100755 .devcontainer/setup.sh
 create mode 100755 .devcontainer/welcome.sh
 create mode 100644 .github/workflows/docker-image.yml
 create mode 100644 .github/workflows/quarto.yaml

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
new file mode 100644
index 000000000..98264c9ac
--- /dev/null
+++ b/.devcontainer/Dockerfile
@@ -0,0 +1,32 @@
+# devcontainer-focused Rocker
+FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
+
+
+ENV NB_USER=rstudio
+ENV VIRTUAL_ENV=/opt/venv
+ENV PATH=${VIRTUAL_ENV}/bin:${PATH}
+ADD https://raw.githubusercontent.com/rocker-org/rocker-versioned2/96cdc36e3c6dcd17e7eb4b830ebd7d8147aedf51/scripts/install_python.sh install_python.sh
+RUN bash install_python.sh && rm install_python.sh
+
+
+RUN apt-get update && apt-get -y install libxt6 libzmq3-dev gh
+ADD https://raw.githubusercontent.com/rocker-org/rocker-versioned2/master/scripts/experimental/install_dev_osgeo.sh install_dev_osgeo.sh
+RUN bash install_dev_osgeo.sh && rm install_dev_osgeo.sh
+
+RUN chown -R rstudio:rstudio /opt/venv
+
+USER rstudio
+WORKDIR /home/rstudio
+RUN usermod -s /bin/bash rstudio
+
+COPY requirements.txt requirements.txt
+ENV PATH=$PATH:/home/rstudio/.local/bin
+
+RUN python -m pip install -r requirements.txt && rm requirements.txt
+COPY install.R install.R
+RUN Rscript install.R && rm install.R
+
+RUN python -m ipykernel install --user --name=nasa
+
+# some teaching preferences
+RUN git config --global pull.rebase false
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
new file mode 100644
index 000000000..e0b59ad15
--- /dev/null
+++ b/.devcontainer/devcontainer.json
@@ -0,0 +1,53 @@
+{
+	  "image": "ghcr.io/boettiger-lab/nasa-tops:latest",
+	  "runArgs": [ "--security-opt", "seccomp=unconfined" ],
+	  "name": "NASA TOPS Environment",
+	  // build image as a github-action and grab instead; faster.
+	  // "build": {
+	  //	"dockerfile": "Dockerfile"
+	  //},
+	  "waitFor": "onCreateCommand",
+	  "features": {
+		"ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {},
+		// Install JupyterLab and IRkernel.
+		// More info: https://github.com/rocker-org/devcontainer-templates/tree/main/src/r-ver
+		"ghcr.io/rocker-org/devcontainer-features/r-rig:1": {
+			"version": "none",
+			"installJupyterlab": true
+		}
+	  },
+	  "customizations": {
+		"codespaces": {
+			"openFiles": ["README.md"]
+		  },
+		  "vscode": {
+		  "settings": {
+			"r.rterm.linux": "/usr/local/bin/radian",
+			"r.bracketedPaste": true,
+			"r.plot.useHttpgd": true,
+			"[r]": {
+			  "editor.wordSeparators": "`~!@#%$^&*()-=+[{]}\\|;:'\",<>/?"
+			}
+		  },
+		  "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/install.R b/.devcontainer/install.R
new file mode 100755
index 000000000..671eff4c9
--- /dev/null
+++ b/.devcontainer/install.R
@@ -0,0 +1,11 @@
+#! /usr/local/bin/Rscript
+# install R dependencies
+
+# We could use renv.lock approach here instead, but will force re-creation of environment from scratch
+# Does not provide a good way to ensure that sf/terra/gdalcubes are installed from source while other packages can be binary
+
+install.packages(c("rstac", "spData", "earthdatalogin", "quarto"))
+remotes::install_github('r-tmap/tmap')
+
+install.packages(c("IRkernel", "languageserver", "httpgd"))
+IRkernel::installspec()
diff --git a/.devcontainer/python-only-devcontainer.json b/.devcontainer/python-only-devcontainer.json
new file mode 100644
index 000000000..b113da367
--- /dev/null
+++ b/.devcontainer/python-only-devcontainer.json
@@ -0,0 +1,21 @@
+{
+	"image": "mcr.microsoft.com/devcontainers/universal:2",
+  //  "hostRequirements": {
+  //    "cpus": 4
+  //  },
+	"waitFor": "onCreateCommand",
+	"updateContentCommand": "python3 -m pip install -r requirements.txt",
+	"postCreateCommand": "",
+	"customizations": {
+	  "codespaces": {
+		"openFiles": ["README.md"]
+	  },
+	  "vscode": {
+		"extensions": [
+		  "ms-toolsai.jupyter",
+		  "ms-python.python"
+		]
+	  }
+	}
+  }
+  
\ No newline at end of file
diff --git a/.devcontainer/renv.lock b/.devcontainer/renv.lock
new file mode 100644
index 000000000..c72df7a06
--- /dev/null
+++ b/.devcontainer/renv.lock
@@ -0,0 +1,1553 @@
+{
+  "R": {
+    "Version": "4.2.3",
+    "Repositories": [
+      {
+        "Name": "CRAN",
+        "URL": "https://packagemanager.posit.co/cran/2023-04-20"
+      }
+    ]
+  },
+  "Packages": {
+    "BH": {
+      "Package": "BH",
+      "Version": "1.81.0-1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "68122010f01c4dcfbe58ce7112f2433d"
+    },
+    "DBI": {
+      "Package": "DBI",
+      "Version": "1.1.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "b2866e62bab9378c3cc9476a1954226b"
+    },
+    "KernSmooth": {
+      "Package": "KernSmooth",
+      "Version": "2.23-20",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "stats"
+      ],
+      "Hash": "8dcfa99b14c296bc9f1fd64d52fd3ce7"
+    },
+    "MASS": {
+      "Package": "MASS",
+      "Version": "7.3-58.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "graphics",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "e02d1a0f6122fd3e634b25b433704344"
+    },
+    "Matrix": {
+      "Package": "Matrix",
+      "Version": "1.5-3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "graphics",
+        "grid",
+        "lattice",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "4006dffe49958d2dd591c17e61e60591"
+    },
+    "R6": {
+      "Package": "R6",
+      "Version": "2.5.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "470851b6d5d0ac559e9d01bb352b4021"
+    },
+    "RColorBrewer": {
+      "Package": "RColorBrewer",
+      "Version": "1.1-3",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "45f0398006e83a5b10b72a90663d8d8c"
+    },
+    "Rcpp": {
+      "Package": "Rcpp",
+      "Version": "1.0.11",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "methods",
+        "utils"
+      ],
+      "Hash": "ae6cbbe1492f4de79c45fce06f967ce8"
+    },
+    "XML": {
+      "Package": "XML",
+      "Version": "3.99-0.14",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "methods",
+        "utils"
+      ],
+      "Hash": "e5c8af79df616c135b21eaeb1dc6bc5c"
+    },
+    "abind": {
+      "Package": "abind",
+      "Version": "1.4-5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "methods",
+        "utils"
+      ],
+      "Hash": "4f57884290cc75ab22f4af9e9d4ca862"
+    },
+    "askpass": {
+      "Package": "askpass",
+      "Version": "1.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "sys"
+      ],
+      "Hash": "e8a22846fff485f0be3770c2da758713"
+    },
+    "base64enc": {
+      "Package": "base64enc",
+      "Version": "0.1-3",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "543776ae6848fde2f48ff3816d0628bc"
+    },
+    "bit": {
+      "Package": "bit",
+      "Version": "4.0.5",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "d242abec29412ce988848d0294b208fd"
+    },
+    "bit64": {
+      "Package": "bit64",
+      "Version": "4.0.5",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "bit",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "9fe98599ca456d6552421db0d6772d8f"
+    },
+    "bslib": {
+      "Package": "bslib",
+      "Version": "0.4.2",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "base64enc",
+        "cachem",
+        "grDevices",
+        "htmltools",
+        "jquerylib",
+        "jsonlite",
+        "memoise",
+        "mime",
+        "rlang",
+        "sass"
+      ],
+      "Hash": "a7fbf03946ad741129dc81098722fca1"
+    },
+    "cachem": {
+      "Package": "cachem",
+      "Version": "1.0.7",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "fastmap",
+        "rlang"
+      ],
+      "Hash": "cda74447c42f529de601fe4d4050daef"
+    },
+    "class": {
+      "Package": "class",
+      "Version": "7.3-21",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "MASS",
+        "R",
+        "stats",
+        "utils"
+      ],
+      "Hash": "8ae0d4328e2eb3a582dfd5391a3663b7"
+    },
+    "classInt": {
+      "Package": "classInt",
+      "Version": "0.4-10",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "KernSmooth",
+        "R",
+        "class",
+        "e1071",
+        "grDevices",
+        "graphics",
+        "stats"
+      ],
+      "Hash": "f5a40793b1ae463a7ffb3902a95bf864"
+    },
+    "cli": {
+      "Package": "cli",
+      "Version": "3.6.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "utils"
+      ],
+      "Hash": "89e6d8219950eac806ae0c489052048a"
+    },
+    "clipr": {
+      "Package": "clipr",
+      "Version": "0.8.0",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "utils"
+      ],
+      "Hash": "3f038e5ac7f41d4ac41ce658c85e3042"
+    },
+    "colorspace": {
+      "Package": "colorspace",
+      "Version": "2.1-0",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "graphics",
+        "methods",
+        "stats"
+      ],
+      "Hash": "f20c47fd52fae58b4e377c37bb8c335b"
+    },
+    "cpp11": {
+      "Package": "cpp11",
+      "Version": "0.4.3",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Hash": "ed588261931ee3be2c700d22e94a29ab"
+    },
+    "crayon": {
+      "Package": "crayon",
+      "Version": "1.5.2",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "grDevices",
+        "methods",
+        "utils"
+      ],
+      "Hash": "e8a1e41acf02548751f45c718d55aa6a"
+    },
+    "crosstalk": {
+      "Package": "crosstalk",
+      "Version": "1.2.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R6",
+        "htmltools",
+        "jsonlite",
+        "lazyeval"
+      ],
+      "Hash": "6aa54f69598c32177e920eb3402e8293"
+    },
+    "curl": {
+      "Package": "curl",
+      "Version": "5.0.0",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "e4f97056611e8e6b8b852d13b7400cf1"
+    },
+    "dichromat": {
+      "Package": "dichromat",
+      "Version": "2.0-0.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "stats"
+      ],
+      "Hash": "16e66f2a483e124af5fc6582d26005f7"
+    },
+    "digest": {
+      "Package": "digest",
+      "Version": "0.6.31",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "utils"
+      ],
+      "Hash": "8b708f296afd9ae69f450f9640be8990"
+    },
+    "dplyr": {
+      "Package": "dplyr",
+      "Version": "1.1.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "R6",
+        "cli",
+        "generics",
+        "glue",
+        "lifecycle",
+        "magrittr",
+        "methods",
+        "pillar",
+        "rlang",
+        "tibble",
+        "tidyselect",
+        "utils",
+        "vctrs"
+      ],
+      "Hash": "eb5742d256a0d9306d85ea68756d8187"
+    },
+    "e1071": {
+      "Package": "e1071",
+      "Version": "1.7-13",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "class",
+        "grDevices",
+        "graphics",
+        "methods",
+        "proxy",
+        "stats",
+        "utils"
+      ],
+      "Hash": "1046cb48d06cb40c2900d8878f03a0fe"
+    },
+    "earthdatalogin": {
+      "Package": "earthdatalogin",
+      "Version": "0.0.0.9000",
+      "Source": "GitHub",
+      "RemoteType": "github",
+      "RemoteHost": "api.github.com",
+      "RemoteRepo": "earthdatalogin",
+      "RemoteUsername": "boettiger-lab",
+      "RemoteRef": "HEAD",
+      "RemoteSha": "e788ce9e07f7adf75d8399b80b550271377f78ee",
+      "Requirements": [
+        "fs",
+        "httr",
+        "openssl",
+        "purrr",
+        "readr",
+        "utils"
+      ],
+      "Hash": "cdcd44cf120a815b850b643e5f85f636"
+    },
+    "ellipsis": {
+      "Package": "ellipsis",
+      "Version": "0.3.2",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "rlang"
+      ],
+      "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077"
+    },
+    "evaluate": {
+      "Package": "evaluate",
+      "Version": "0.20",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "4b68aa51edd89a0e044a66e75ae3cc6c"
+    },
+    "fansi": {
+      "Package": "fansi",
+      "Version": "1.0.4",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "utils"
+      ],
+      "Hash": "1d9e7ad3c8312a192dea7d3db0274fde"
+    },
+    "farver": {
+      "Package": "farver",
+      "Version": "2.1.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Hash": "8106d78941f34855c440ddb946b8f7a5"
+    },
+    "fastmap": {
+      "Package": "fastmap",
+      "Version": "1.1.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Hash": "f7736a18de97dea803bde0a2daaafb27"
+    },
+    "fontawesome": {
+      "Package": "fontawesome",
+      "Version": "0.5.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "htmltools",
+        "rlang"
+      ],
+      "Hash": "1e22b8cabbad1eae951a75e9f8b52378"
+    },
+    "fs": {
+      "Package": "fs",
+      "Version": "1.6.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "f4dcd23b67e33d851d2079f703e8b985"
+    },
+    "gdalcubes": {
+      "Package": "gdalcubes",
+      "Version": "0.6.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "BH",
+        "R",
+        "Rcpp",
+        "jsonlite",
+        "ncdf4"
+      ],
+      "Hash": "78c2ae3c1caeeb19635eb2ff932c4252"
+    },
+    "generics": {
+      "Package": "generics",
+      "Version": "0.1.3",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "15e9634c0fcd294799e9b2e929ed1b86"
+    },
+    "geojsonsf": {
+      "Package": "geojsonsf",
+      "Version": "2.0.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "Rcpp",
+        "geometries",
+        "jsonify",
+        "rapidjsonr",
+        "sfheaders"
+      ],
+      "Hash": "8d077646c6713838233e8710910ef92e"
+    },
+    "geometries": {
+      "Package": "geometries",
+      "Version": "0.2.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "Rcpp"
+      ],
+      "Hash": "122e8341ead01f3746dd312ecc5ffd28"
+    },
+    "ggplot2": {
+      "Package": "ggplot2",
+      "Version": "3.4.2",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "MASS",
+        "R",
+        "cli",
+        "glue",
+        "grDevices",
+        "grid",
+        "gtable",
+        "isoband",
+        "lifecycle",
+        "mgcv",
+        "rlang",
+        "scales",
+        "stats",
+        "tibble",
+        "vctrs",
+        "withr"
+      ],
+      "Hash": "3a147ee02e85a8941aad9909f1b43b7b"
+    },
+    "glue": {
+      "Package": "glue",
+      "Version": "1.6.2",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e"
+    },
+    "gridExtra": {
+      "Package": "gridExtra",
+      "Version": "2.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "grDevices",
+        "graphics",
+        "grid",
+        "gtable",
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+      "Requirements": [
+        "R",
+        "RColorBrewer",
+        "abind",
+        "classInt",
+        "grid",
+        "htmltools",
+        "htmlwidgets",
+        "leafem",
+        "leaflet",
+        "leafsync",
+        "methods",
+        "rlang",
+        "sf",
+        "stars",
+        "stats",
+        "tmaptools",
+        "units",
+        "utils",
+        "viridisLite",
+        "widgetframe"
+      ],
+      "Hash": "c65363bc002492caf754352499ce2386"
+    },
+    "tmaptools": {
+      "Package": "tmaptools",
+      "Version": "3.1-1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "RColorBrewer",
+        "XML",
+        "dichromat",
+        "grid",
+        "lwgeom",
+        "magrittr",
+        "methods",
+        "sf",
+        "stars",
+        "stats",
+        "units",
+        "viridisLite"
+      ],
+      "Hash": "dfcb77371df343b663d6668d2d63ac35"
+    },
+    "tzdb": {
+      "Package": "tzdb",
+      "Version": "0.3.0",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "cpp11"
+      ],
+      "Hash": "b2e1cbce7c903eaf23ec05c58e59fb5e"
+    },
+    "units": {
+      "Package": "units",
+      "Version": "0.8-4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "Rcpp"
+      ],
+      "Hash": "e0fbcea25008a7540c83c2c294135de0"
+    },
+    "utf8": {
+      "Package": "utf8",
+      "Version": "1.2.3",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "1fe17157424bb09c48a8b3b550c753bc"
+    },
+    "vctrs": {
+      "Package": "vctrs",
+      "Version": "0.6.2",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "cli",
+        "glue",
+        "lifecycle",
+        "rlang"
+      ],
+      "Hash": "a745bda7aff4734c17294bb41d4e4607"
+    },
+    "viridis": {
+      "Package": "viridis",
+      "Version": "0.6.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "ggplot2",
+        "gridExtra",
+        "viridisLite"
+      ],
+      "Hash": "80cd127bc8c9d3d9f0904ead9a9102f1"
+    },
+    "viridisLite": {
+      "Package": "viridisLite",
+      "Version": "0.4.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "62f4b5da3e08d8e5bcba6cac15603f70"
+    },
+    "vroom": {
+      "Package": "vroom",
+      "Version": "1.6.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "bit64",
+        "cli",
+        "cpp11",
+        "crayon",
+        "glue",
+        "hms",
+        "lifecycle",
+        "methods",
+        "progress",
+        "rlang",
+        "stats",
+        "tibble",
+        "tidyselect",
+        "tzdb",
+        "vctrs",
+        "withr"
+      ],
+      "Hash": "7015a74373b83ffaef64023f4a0f5033"
+    },
+    "widgetframe": {
+      "Package": "widgetframe",
+      "Version": "0.3.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "htmltools",
+        "htmlwidgets",
+        "magrittr",
+        "purrr",
+        "tools",
+        "utils"
+      ],
+      "Hash": "0ee89e6cb58182d39b30a5b506e04808"
+    },
+    "withr": {
+      "Package": "withr",
+      "Version": "2.5.0",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "graphics",
+        "stats"
+      ],
+      "Hash": "c0e49a9760983e81e55cdd9be92e7182"
+    },
+    "wk": {
+      "Package": "wk",
+      "Version": "0.8.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "aaf7e20556e3125a09d53453814ad339"
+    },
+    "xfun": {
+      "Package": "xfun",
+      "Version": "0.38",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "stats",
+        "tools"
+      ],
+      "Hash": "1ed71215d45e85562d3b1b29a068ccec"
+    },
+    "yaml": {
+      "Package": "yaml",
+      "Version": "2.3.7",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Hash": "0d0056cc5383fbc240ccd0cb584bf436"
+    }
+  }
+}
diff --git a/.devcontainer/requirements.txt b/.devcontainer/requirements.txt
new file mode 100644
index 000000000..03183214f
--- /dev/null
+++ b/.devcontainer/requirements.txt
@@ -0,0 +1,201 @@
+affine==2.4.0
+aiobotocore==2.9.0
+aiohttp==3.9.1
+aioitertools==0.11.0
+aiosignal==1.3.1
+annotated-types==0.6.0
+anyio==4.0.0
+argon2-cffi==23.1.0
+argon2-cffi-bindings==21.2.0
+arrow==1.2.3
+asciitree==0.3.3
+asttokens==2.4.0
+async-lru==2.0.4
+async-timeout==4.0.3
+attrs==23.1.0
+Babel==2.12.1
+backcall==0.2.0
+beautifulsoup4==4.12.2
+bleach==6.0.0
+bokeh==3.3.2
+botocore==1.33.13
+Bottleneck==1.3.7
+bounded-pool-executor==0.0.3
+cachetools==5.3.2
+certifi==2023.7.22
+cf-xarray==0.8.6
+cffi==1.15.1
+cftime==1.6.3
+charset-normalizer==3.2.0
+click==8.1.7
+click-plugins==1.1.1
+cligj==0.7.2
+cloudpickle==2.2.1
+comm==0.1.4
+contourpy==1.1.1
+cycler==0.11.0
+dask==2023.11.0
+debugpy==1.8.0
+decorator==5.1.1
+defusedxml==0.7.1
+distributed==2023.11.0
+earthaccess==0.8.2
+exceptiongroup==1.1.3
+executing==1.2.0
+fasteners==0.19
+fastjsonschema==2.18.0
+Fiona==1.9.4.post1
+flox==0.8.5
+fonttools==4.42.1
+fqdn==1.5.1
+frozenlist==1.4.1
+fsspec==2023.12.2
+geopandas==0.14.0
+geopolars==0.1.0a4
+Glances==3.4.0.3
+h5netcdf==1.3.0
+h5py==3.10.0
+idna==3.4
+importlib-metadata==6.8.0
+importlib-resources==6.1.1
+ipykernel==6.25.2
+ipython==8.15.0
+ipywidgets==8.1.1
+isoduration==20.11.0
+jedi==0.19.0
+Jinja2==3.1.2
+jmespath==1.0.1
+json5==0.9.14
+jsonpointer==2.4
+jsonschema==4.19.1
+jsonschema-specifications==2023.7.1
+jupyter==1.0.0
+jupyter-console==6.6.3
+jupyter-events==0.7.0
+jupyter-lsp==2.2.0
+jupyter_client==8.3.1
+jupyter_core==5.3.2
+jupyter_server==2.7.3
+jupyter_server_terminals==0.4.4
+jupyterlab==4.0.9
+jupyterlab-pygments==0.2.2
+jupyterlab-widgets==3.0.9
+jupyterlab_server==2.25.0
+kiwisolver==1.4.5
+llvmlite==0.41.1
+locket==1.0.0
+lxml==4.9.4
+lz4==4.3.2
+MarkupSafe==2.1.3
+matplotlib==3.8.0
+matplotlib-inline==0.1.6
+mistune==3.0.1
+msgpack==1.0.7
+multidict==6.0.4
+multimethod==1.10
+nbclient==0.8.0
+nbconvert==7.8.0
+nbformat==5.9.2
+nc-time-axis==1.4.1
+nest-asyncio==1.5.8
+netCDF4==1.6.5
+notebook==7.0.6
+notebook_shim==0.2.3
+numba==0.58.1
+numbagg==0.6.8
+numcodecs==0.12.1
+numpy==1.26.0
+numpy-groupies==0.10.2
+odc-geo==0.4.1
+odc-stac==0.3.8
+overrides==7.4.0
+packaging==23.1
+pandas==2.1.0
+pandocfilters==1.5.0
+parso==0.8.3
+partd==1.4.1
+pexpect==4.8.0
+pickleshare==0.7.5
+Pillow==10.0.1
+planetary-computer==1.0.0
+platformdirs==3.10.0
+polars==0.19.15
+pooch==1.8.0
+pqdm==0.2.0
+prometheus-client==0.17.1
+prompt-toolkit==3.0.39
+psutil==5.9.5
+ptyprocess==0.7.0
+pure-eval==0.2.2
+pyarrow==14.0.1
+pyarrow-hotfix==0.6
+pycparser==2.21
+pydantic==2.5.3
+pydantic_core==2.14.6
+Pygments==2.16.1
+pyparsing==3.1.1
+pyproj==3.6.1
+pystac==1.8.4
+pystac-client==0.7.5
+python-cmr==0.9.0
+python-dateutil==2.8.2
+python-dotenv==1.0.0
+python-json-logger==2.0.7
+pytz==2023.3.post1
+PyYAML==6.0.1
+pyzmq==25.1.1
+qtconsole==5.5.1
+QtPy==2.4.1
+radian==0.6.7
+rasterio==1.3.8
+rasterstats==0.19.0
+rchitect==0.4.2
+referencing==0.30.2
+requests==2.31.0
+rfc3339-validator==0.1.4
+rfc3986-validator==0.1.1
+rioxarray==0.15.0
+rpds-py==0.10.3
+s3fs==2023.12.2
+scipy==1.11.3
+seaborn==0.13.0
+Send2Trash==1.8.2
+shapely==2.0.1
+simplejson==3.19.2
+six==1.16.0
+sniffio==1.3.0
+snuggs==1.4.7
+sortedcontainers==2.4.0
+soupsieve==2.5
+sparse==0.14.0
+stack-data==0.6.2
+stackstac==0.5.0
+tblib==3.0.0
+terminado==0.17.1
+timebudget==0.7.1
+tinycss2==1.2.1
+tinynetrc==1.3.1
+tomli==2.0.1
+toolz==0.12.0
+tornado==6.3.3
+tqdm==4.66.1
+traitlets==5.10.1
+types-python-dateutil==2.8.19.14
+typing_extensions==4.8.0
+tzdata==2023.3
+ujson==5.8.0
+uri-template==1.3.0
+urllib3==2.0.5
+wcwidth==0.2.6
+webcolors==1.13
+webencodings==0.5.1
+websocket-client==1.6.3
+widgetsnbextension==4.0.9
+wrapt==1.16.0
+xarray==2023.8.0
+xesmf==0.8.2
+xyzservices==2023.10.1
+yarl==1.9.4
+zarr==2.16.1
+zict==3.0.0
+zipp==3.17.0
diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh
new file mode 100755
index 000000000..b89dcf16d
--- /dev/null
+++ b/.devcontainer/setup.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+sudo cp /etc/rstudio/disable_auth_rserver.conf /etc/rstudio/rserver.conf
+sudo sudo bash -c 'echo "USER=rstudio" >>/etc/environment'
+sudo /init &> /dev/null &
+
diff --git a/.devcontainer/welcome.sh b/.devcontainer/welcome.sh
new file mode 100755
index 000000000..89aab9b8c
--- /dev/null
+++ b/.devcontainer/welcome.sh
@@ -0,0 +1,16 @@
+mkdir -p ~/.local/share/rstudio/projects_settings
+export RPROJ"=$(ls ${CODESPACE_VSCODE_FOLDER}/*.Rproj)"
+echo ${RPROJ} > ~/.local/share/rstudio/projects_settings/last-project-path
+
+
+# Construct the message
+message="## [Open in RStudio](https://$CODESPACE_NAME-8787.app.github.dev)
+"
+# Echo the message to the terminal
+echo "
+👋 Welcome to Codespaces! You are on our custom image. 
+   - It includes runtimes and tools for Python & R using Jupyter, Quarto, or RStudio 
+
+🌐 Open the RStudio editor here: https://$CODESPACE_NAME-8787.app.github.dev
+   - (This may take a few seconds to load, retry if necessary)
+"
diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml
new file mode 100644
index 000000000..3fa257c41
--- /dev/null
+++ b/.github/workflows/docker-image.yml
@@ -0,0 +1,24 @@
+name: Docker Image CI
+on:
+  workflow_dispatch: null
+  push:
+    paths: ['.devcontainer/*']
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions: write-all
+    steps:
+      - uses: actions/checkout@v3
+      - name: Login to GitHub Container Registry
+        if: github.repository == 'eeholmes/earthdata-cloud-cookbook'
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{github.actor}}
+          password: ${{secrets.GITHUB_TOKEN}}
+      - name: Build the Docker image
+        if: github.repository == 'eeholmes/earthdata-cloud-cookbook'
+        run: docker build .devcontainer --tag ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:latest
+      - name: Publish
+        if: github.repository == 'eeholmes/earthdata-cloud-cookbook'
+        run: docker push ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:latest
diff --git a/.github/workflows/quarto.yaml b/.github/workflows/quarto.yaml
new file mode 100644
index 000000000..58c5eeda6
--- /dev/null
+++ b/.github/workflows/quarto.yaml
@@ -0,0 +1,27 @@
+on:
+  workflow_dispatch:
+  push:
+    branches: main
+
+name: Quarto Publish
+
+jobs:
+  build-deploy:
+    runs-on: ubuntu-latest
+    container: 
+      image: ghcr.io/eeholmes/earthdata-cloud-cookbook
+      options: --user root --security-opt seccomp=unconfined
+    permissions:
+      contents: write
+    steps:
+      - name: Quarto-inside-docker permissions
+        run: git config --system --add safe.directory '*'
+    
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+#      - name: Set up Quarto
+#        uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: Render
+        run: quarto render
\ No newline at end of file

From 39aba24d5153930af0cc11c6927e39cece7c4ed1 Mon Sep 17 00:00:00 2001
From: Carl Boettiger <cboettig@gmail.com>
Date: Thu, 1 Feb 2024 11:25:48 -0800
Subject: [PATCH 02/59] Update quarto.yaml

---
 .github/workflows/quarto.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/quarto.yaml b/.github/workflows/quarto.yaml
index 58c5eeda6..ca34a20fb 100644
--- a/.github/workflows/quarto.yaml
+++ b/.github/workflows/quarto.yaml
@@ -3,7 +3,7 @@ on:
   push:
     branches: main
 
-name: Quarto Publish
+name: Quarto Test Build
 
 jobs:
   build-deploy:
@@ -24,4 +24,4 @@ jobs:
 #        uses: quarto-dev/quarto-actions/setup@v2
 
       - name: Render
-        run: quarto render
\ No newline at end of file
+        run: quarto render

From ea7710722d904ae0fd8655ba131795740aa13c52 Mon Sep 17 00:00:00 2001
From: Carl Boettiger <cboettig@gmail.com>
Date: Thu, 1 Feb 2024 11:26:34 -0800
Subject: [PATCH 03/59] test w/o freeze

---
 .github/workflows/quarto.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/quarto.yaml b/.github/workflows/quarto.yaml
index ca34a20fb..c04c34af8 100644
--- a/.github/workflows/quarto.yaml
+++ b/.github/workflows/quarto.yaml
@@ -24,4 +24,6 @@ jobs:
 #        uses: quarto-dev/quarto-actions/setup@v2
 
       - name: Render
-        run: quarto render
+        run: |
+             rm -rf _freeze
+             quarto render

From dec7e85e98617cafdc39e96fbb0f555c7556a438 Mon Sep 17 00:00:00 2001
From: Carl Boettiger <cboettig@gmail.com>
Date: Thu, 1 Feb 2024 11:28:34 -0800
Subject: [PATCH 04/59] Update quarto.yaml

---
 .github/workflows/quarto.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/quarto.yaml b/.github/workflows/quarto.yaml
index c04c34af8..1be6967ce 100644
--- a/.github/workflows/quarto.yaml
+++ b/.github/workflows/quarto.yaml
@@ -9,7 +9,7 @@ jobs:
   build-deploy:
     runs-on: ubuntu-latest
     container: 
-      image: ghcr.io/eeholmes/earthdata-cloud-cookbook
+      image: ghcr.io/boettiger-lab/nasa-tops:latest
       options: --user root --security-opt seccomp=unconfined
     permissions:
       contents: write

From 017e846d3288b5e3bd2cd98d68196db0a6c98756 Mon Sep 17 00:00:00 2001
From: Carl Boettiger <cboettig@gmail.com>
Date: Thu, 1 Feb 2024 11:32:57 -0800
Subject: [PATCH 05/59] Update install.R

---
 .devcontainer/install.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.devcontainer/install.R b/.devcontainer/install.R
index 671eff4c9..cba5f7539 100755
--- a/.devcontainer/install.R
+++ b/.devcontainer/install.R
@@ -7,5 +7,5 @@
 install.packages(c("rstac", "spData", "earthdatalogin", "quarto"))
 remotes::install_github('r-tmap/tmap')
 
-install.packages(c("IRkernel", "languageserver", "httpgd"))
+install.packages(c("IRkernel", "languageserver", "httpgd", "aws.s3"))
 IRkernel::installspec()

From 22b91bb4c1731f34c5c8e04bed707d6fa1058e45 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Thu, 1 Feb 2024 16:01:33 -0800
Subject: [PATCH 06/59] revising image

---
 .devcontainer/Dockerfile       | 49 +++++++++++++++++++++++++---------
 .devcontainer/conda_init.sh    |  3 +++
 .devcontainer/install.R        |  8 +++---
 .devcontainer/requirements.txt |  1 +
 4 files changed, 46 insertions(+), 15 deletions(-)
 create mode 100755 .devcontainer/conda_init.sh

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index 98264c9ac..5c00d83cd 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -1,19 +1,28 @@
-# devcontainer-focused Rocker
-FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
+## devcontainer-focused Rocker
+FROM docker.io/rocker/binder:4.3
 
+USER root
 
-ENV NB_USER=rstudio
-ENV VIRTUAL_ENV=/opt/venv
-ENV PATH=${VIRTUAL_ENV}/bin:${PATH}
-ADD https://raw.githubusercontent.com/rocker-org/rocker-versioned2/96cdc36e3c6dcd17e7eb4b830ebd7d8147aedf51/scripts/install_python.sh install_python.sh
-RUN bash install_python.sh && rm install_python.sh
+## latest version of geospatial libs
+RUN /rocker_scripts/experimental/install_dev_osgeo.sh
+RUN apt-get update -qq && apt-get -y install vim
 
+# conda
+ENV CONDA_ENV=/opt/miniforge3
+ENV PATH=${PATH}:$CONDA_ENV/bin
+RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" && \
+    bash Miniforge3-$(uname)-$(uname -m).sh -b -p ${CONDA_ENV} 
 
-RUN apt-get update && apt-get -y install libxt6 libzmq3-dev gh
-ADD https://raw.githubusercontent.com/rocker-org/rocker-versioned2/master/scripts/experimental/install_dev_osgeo.sh install_dev_osgeo.sh
-RUN bash install_dev_osgeo.sh && rm install_dev_osgeo.sh
+RUN chown ${NB_USER}:staff -R ${CONDA_ENV}
 
-RUN chown -R rstudio:rstudio /opt/venv
+# podman doesn not understand group permissions
+RUN chown ${NB_USER}:staff -R ${VIRTUAL_ENV}
+RUN chown ${NB_USER}:staff -R ${R_HOME}/site-library
+
+
+
+## codeserver
+RUN curl -fsSL https://code-server.dev/install.sh | sh
 
 USER rstudio
 WORKDIR /home/rstudio
@@ -26,7 +35,23 @@ RUN python -m pip install -r requirements.txt && rm requirements.txt
 COPY install.R install.R
 RUN Rscript install.R && rm install.R
 
-RUN python -m ipykernel install --user --name=nasa
+# equivalent path to -n openscapes
+ENV MY_ENV=${CONDA_ENV}/envs/openscapes
+RUN wget https://github.com/NASA-Openscapes/corn/raw/main/ci/environment.yml && \
+    conda env create -p ${MY_ENV} -f environment.yml
 
 # some teaching preferences
 RUN git config --global pull.rebase false
+
+COPY conda_init.sh /etc/profile.d/conda_init.sh
+RUN bash -c conda_init.sh
+
+# NOTES: 
+# conda (base) just means $CONDA_ENV/bin/
+# conda (openscapes) means $MY_ENV, identically, $CONDA_ENV/envs/openscapes/bin/
+# Rather than activate it or alter path, we just get it set up as an optional kernel
+# We could easily make either the default by putting either bin path at the start of PATH 
+
+RUN $MY_ENV/bin/python -m pip install ipykernel && \
+    $MY_ENV/bin/python -m ipykernel install --sys-prefix --name=openscapes
+
diff --git a/.devcontainer/conda_init.sh b/.devcontainer/conda_init.sh
new file mode 100755
index 000000000..12ccce2db
--- /dev/null
+++ b/.devcontainer/conda_init.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+conda init &> /dev/null
+
diff --git a/.devcontainer/install.R b/.devcontainer/install.R
index cba5f7539..85481126a 100755
--- a/.devcontainer/install.R
+++ b/.devcontainer/install.R
@@ -3,9 +3,11 @@
 
 # We could use renv.lock approach here instead, but will force re-creation of environment from scratch
 # Does not provide a good way to ensure that sf/terra/gdalcubes are installed from source while other packages can be binary
-
+install.packages("pak")
 install.packages(c("rstac", "spData", "earthdatalogin", "quarto"))
-remotes::install_github('r-tmap/tmap')
+pak::pkg_install('github::r-tmap/tmap')
 
-install.packages(c("IRkernel", "languageserver", "httpgd", "aws.s3"))
+#pak::pkg_install("httpgd")
+pak::pkg_install(c("IRkernel", "languageserver"))
 IRkernel::installspec()
+
diff --git a/.devcontainer/requirements.txt b/.devcontainer/requirements.txt
index 03183214f..cd5db62ff 100644
--- a/.devcontainer/requirements.txt
+++ b/.devcontainer/requirements.txt
@@ -77,6 +77,7 @@ jupyter_client==8.3.1
 jupyter_core==5.3.2
 jupyter_server==2.7.3
 jupyter_server_terminals==0.4.4
+jupyter-vscode-proxy==0.5
 jupyterlab==4.0.9
 jupyterlab-pygments==0.2.2
 jupyterlab-widgets==3.0.9

From 65b2dcb39420c561b666942e0b9bf2ebd07a31a7 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Thu, 1 Feb 2024 16:04:25 -0800
Subject: [PATCH 07/59] fix typo

---
 .devcontainer/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index 5c00d83cd..c4dc7bea4 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -44,7 +44,7 @@ RUN wget https://github.com/NASA-Openscapes/corn/raw/main/ci/environment.yml &&
 RUN git config --global pull.rebase false
 
 COPY conda_init.sh /etc/profile.d/conda_init.sh
-RUN bash -c conda_init.sh
+RUN bash -c /etc/profile.d/conda_init.sh
 
 # NOTES: 
 # conda (base) just means $CONDA_ENV/bin/

From e9b8509ca6f17561dcfb4bc19c4ab5d44f416130 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Thu, 1 Feb 2024 16:25:36 -0800
Subject: [PATCH 08/59] conda as default

---
 .devcontainer/Dockerfile | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index c4dc7bea4..86432c9c6 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -44,7 +44,7 @@ RUN wget https://github.com/NASA-Openscapes/corn/raw/main/ci/environment.yml &&
 RUN git config --global pull.rebase false
 
 COPY conda_init.sh /etc/profile.d/conda_init.sh
-RUN bash -c /etc/profile.d/conda_init.sh
+RUN bash -c "conda init"
 
 # NOTES: 
 # conda (base) just means $CONDA_ENV/bin/
@@ -52,6 +52,8 @@ RUN bash -c /etc/profile.d/conda_init.sh
 # Rather than activate it or alter path, we just get it set up as an optional kernel
 # We could easily make either the default by putting either bin path at the start of PATH 
 
-RUN $MY_ENV/bin/python -m pip install ipykernel && \
-    $MY_ENV/bin/python -m ipykernel install --sys-prefix --name=openscapes
+RUN ${MY_ENV}/bin/python -m pip install ipykernel && \
+    ${MY_ENV}/bin/python -m ipykernel install --sys-prefix --name=openscapes
+
+ENV PATH=${MY_ENV}/bin:${PATH}
 

From a83285a58142db48a86ee7eb1fd28e78c6716046 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Thu, 1 Feb 2024 16:31:07 -0800
Subject: [PATCH 09/59] tweaks

---
 .devcontainer/Dockerfile    | 8 +++++---
 .devcontainer/conda_init.sh | 2 ++
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index 86432c9c6..82fcc3142 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -43,9 +43,6 @@ RUN wget https://github.com/NASA-Openscapes/corn/raw/main/ci/environment.yml &&
 # some teaching preferences
 RUN git config --global pull.rebase false
 
-COPY conda_init.sh /etc/profile.d/conda_init.sh
-RUN bash -c "conda init"
-
 # NOTES: 
 # conda (base) just means $CONDA_ENV/bin/
 # conda (openscapes) means $MY_ENV, identically, $CONDA_ENV/envs/openscapes/bin/
@@ -57,3 +54,8 @@ RUN ${MY_ENV}/bin/python -m pip install ipykernel && \
 
 ENV PATH=${MY_ENV}/bin:${PATH}
 
+COPY conda_init.sh /etc/profile.d/conda_init.sh
+RUN bash -c /etc/profile.d/conda_init.sh
+
+
+
diff --git a/.devcontainer/conda_init.sh b/.devcontainer/conda_init.sh
index 12ccce2db..a4af87cc9 100755
--- a/.devcontainer/conda_init.sh
+++ b/.devcontainer/conda_init.sh
@@ -1,3 +1,5 @@
 #!/bin/bash
+
 conda init &> /dev/null
+bash
 

From de2e1b026aef473b8785e61771bd6296fdcd93f1 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Thu, 1 Feb 2024 16:35:01 -0800
Subject: [PATCH 10/59] use local docker image

---
 .devcontainer/devcontainer.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index e0b59ad15..de31a31bb 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,7 +1,7 @@
 {
-	  "image": "ghcr.io/boettiger-lab/nasa-tops:latest",
+	  "image": "ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:latest",
 	  "runArgs": [ "--security-opt", "seccomp=unconfined" ],
-	  "name": "NASA TOPS Environment",
+	  "name": "NASA OpenScapes Environment",
 	  // build image as a github-action and grab instead; faster.
 	  // "build": {
 	  //	"dockerfile": "Dockerfile"

From b759cc0a31a5eb793ff83921b2f34e8ac46f8c4a Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Thu, 1 Feb 2024 16:45:04 -0800
Subject: [PATCH 11/59] not default

---
 .devcontainer/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index 82fcc3142..7b20ed69f 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -52,7 +52,7 @@ RUN git config --global pull.rebase false
 RUN ${MY_ENV}/bin/python -m pip install ipykernel && \
     ${MY_ENV}/bin/python -m ipykernel install --sys-prefix --name=openscapes
 
-ENV PATH=${MY_ENV}/bin:${PATH}
+#ENV PATH=${MY_ENV}/bin:${PATH}
 
 COPY conda_init.sh /etc/profile.d/conda_init.sh
 RUN bash -c /etc/profile.d/conda_init.sh

From 53ecd2438cf392afb426b5a262967117024e9141 Mon Sep 17 00:00:00 2001
From: Carl Boettiger <cboettig@gmail.com>
Date: Thu, 1 Feb 2024 18:00:09 -0800
Subject: [PATCH 12/59] codespaces badge

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 614ec6d0d..1fdeeab4f 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.7786710.svg)](https://zenodo.org/record/7786710) 
 
-
+[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/eeholmes/earthdata-cloud-cookbook?quickstart=1&editor=jupyter)
 
 # Hello!
 

From b8a61ee2693c77ed483cd45d76070c46e5115264 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Thu, 1 Feb 2024 18:56:48 -0800
Subject: [PATCH 13/59] simpler

---
 .devcontainer/Dockerfile       | 12 ++++--------
 .devcontainer/requirements.txt |  2 ++
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index 7b20ed69f..569fbdb9b 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -40,9 +40,6 @@ ENV MY_ENV=${CONDA_ENV}/envs/openscapes
 RUN wget https://github.com/NASA-Openscapes/corn/raw/main/ci/environment.yml && \
     conda env create -p ${MY_ENV} -f environment.yml
 
-# some teaching preferences
-RUN git config --global pull.rebase false
-
 # NOTES: 
 # conda (base) just means $CONDA_ENV/bin/
 # conda (openscapes) means $MY_ENV, identically, $CONDA_ENV/envs/openscapes/bin/
@@ -50,12 +47,11 @@ RUN git config --global pull.rebase false
 # We could easily make either the default by putting either bin path at the start of PATH 
 
 RUN ${MY_ENV}/bin/python -m pip install ipykernel && \
-    ${MY_ENV}/bin/python -m ipykernel install --sys-prefix --name=openscapes
+    ${MY_ENV}/bin/python -m ipykernel install --prefix /opt/venv --name=openscapes
 
-#ENV PATH=${MY_ENV}/bin:${PATH}
-
-COPY conda_init.sh /etc/profile.d/conda_init.sh
-RUN bash -c /etc/profile.d/conda_init.sh
 
+# some teaching preferences
+RUN git config --system pull.rebase false && \
+    git config --system credential.helper 'cache --timeout=36000'
 
 
diff --git a/.devcontainer/requirements.txt b/.devcontainer/requirements.txt
index cd5db62ff..ab9cefdb9 100644
--- a/.devcontainer/requirements.txt
+++ b/.devcontainer/requirements.txt
@@ -200,3 +200,5 @@ yarl==1.9.4
 zarr==2.16.1
 zict==3.0.0
 zipp==3.17.0
+gh-scoped-creds
+

From 593311ac8593bafc374978c3ab38a2bc8189e87e Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Thu, 1 Feb 2024 19:10:23 -0800
Subject: [PATCH 14/59] use images

---
 .github/workflows/quarto-publish.yml          | 59 +++++++------------
 .../{quarto.yaml => test-build.yaml}          |  3 -
 2 files changed, 22 insertions(+), 40 deletions(-)
 rename .github/workflows/{quarto.yaml => test-build.yaml} (87%)

diff --git a/.github/workflows/quarto-publish.yml b/.github/workflows/quarto-publish.yml
index 90cec110a..dbcd7caaf 100644
--- a/.github/workflows/quarto-publish.yml
+++ b/.github/workflows/quarto-publish.yml
@@ -1,44 +1,29 @@
-name: Render and deploy quarto files
 on:
+  workflow_dispatch:
   push:
-    branches:
-      - main  
+    branches: main
+
+name: Quarto Publish
 
 jobs:
-  quarto-render-and-deploy:
+  build-deploy:
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -l {0}
+    container: 
+      image: ghcr.io/boettiger-lab/nasa-tops:latest
+      options: --user root --security-opt seccomp=unconfined
+    permissions:
+      contents: write
     steps:
-    - uses: actions/checkout@v2
-    - uses: conda-incubator/setup-miniconda@v2
-      with:
-        python-version: 3.8
-        channels: conda-forge
-        miniforge-variant: Mambaforge
-        activate-environment: quarto-import
-        environment-file: _import/environment.yml
-            
-    - name: "Import external notebooks"
-      working-directory: ./_import
-      run: |
-        conda info
-        pytest
-        python quarto_import.py -f assets.json
-
-    - name: Set up Quarto
-      uses: quarto-dev/quarto-actions/setup@v2
-      with:
-        # To install LaTeX to build PDF book 
-        tinytex: true 
-        # uncomment below and fill to pin a version
-        # version: 0.9.600
+      - name: Quarto-inside-docker permissions
+        run: git config --system --add safe.directory '*'
+    
+      - name: Check out repository
+        uses: actions/checkout@v3
 
-    - name: Publish to GitHub Pages (and render)
-      uses: quarto-dev/quarto-actions/publish@v2
-      with:
-        target: gh-pages
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # this secret is always available for github actions
-      
+      - name: Render and Publish
+        if: github.repository == 'NASA-Openscapes/earthdata-cloud-cookbook'
+        uses: quarto-dev/quarto-actions/publish@v2
+        with:
+          target: gh-pages
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/quarto.yaml b/.github/workflows/test-build.yaml
similarity index 87%
rename from .github/workflows/quarto.yaml
rename to .github/workflows/test-build.yaml
index 1be6967ce..ffedcd8f5 100644
--- a/.github/workflows/quarto.yaml
+++ b/.github/workflows/test-build.yaml
@@ -20,9 +20,6 @@ jobs:
       - name: Check out repository
         uses: actions/checkout@v3
 
-#      - name: Set up Quarto
-#        uses: quarto-dev/quarto-actions/setup@v2
-
       - name: Render
         run: |
              rm -rf _freeze

From 505c0f4a567d5955150c412fa34d1b03a2d40e82 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Thu, 1 Feb 2024 19:13:32 -0800
Subject: [PATCH 15/59] minimal

---
 .devcontainer/conda_init.sh     |    5 -
 .devcontainer/devcontainer.json |   54 +-
 .devcontainer/renv.lock         | 1553 -------------------------------
 .devcontainer/setup.sh          |    6 -
 .devcontainer/welcome.sh        |   16 -
 5 files changed, 3 insertions(+), 1631 deletions(-)
 delete mode 100755 .devcontainer/conda_init.sh
 delete mode 100644 .devcontainer/renv.lock
 delete mode 100755 .devcontainer/setup.sh
 delete mode 100755 .devcontainer/welcome.sh

diff --git a/.devcontainer/conda_init.sh b/.devcontainer/conda_init.sh
deleted file mode 100755
index a4af87cc9..000000000
--- a/.devcontainer/conda_init.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/bash
-
-conda init &> /dev/null
-bash
-
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index de31a31bb..2621de76f 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,53 +1,5 @@
 {
-	  "image": "ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:latest",
+	  "image": "docker.io/cboettig/nasa",
 	  "runArgs": [ "--security-opt", "seccomp=unconfined" ],
-	  "name": "NASA OpenScapes 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 OpenScapes Environment"
+}
diff --git a/.devcontainer/renv.lock b/.devcontainer/renv.lock
deleted file mode 100644
index c72df7a06..000000000
--- a/.devcontainer/renv.lock
+++ /dev/null
@@ -1,1553 +0,0 @@
-{
-  "R": {
-    "Version": "4.2.3",
-    "Repositories": [
-      {
-        "Name": "CRAN",
-        "URL": "https://packagemanager.posit.co/cran/2023-04-20"
-      }
-    ]
-  },
-  "Packages": {
-    "BH": {
-      "Package": "BH",
-      "Version": "1.81.0-1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "68122010f01c4dcfbe58ce7112f2433d"
-    },
-    "DBI": {
-      "Package": "DBI",
-      "Version": "1.1.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "methods"
-      ],
-      "Hash": "b2866e62bab9378c3cc9476a1954226b"
-    },
-    "KernSmooth": {
-      "Package": "KernSmooth",
-      "Version": "2.23-20",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "stats"
-      ],
-      "Hash": "8dcfa99b14c296bc9f1fd64d52fd3ce7"
-    },
-    "MASS": {
-      "Package": "MASS",
-      "Version": "7.3-58.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "e02d1a0f6122fd3e634b25b433704344"
-    },
-    "Matrix": {
-      "Package": "Matrix",
-      "Version": "1.5-3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "graphics",
-        "grid",
-        "lattice",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "4006dffe49958d2dd591c17e61e60591"
-    },
-    "R6": {
-      "Package": "R6",
-      "Version": "2.5.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "470851b6d5d0ac559e9d01bb352b4021"
-    },
-    "RColorBrewer": {
-      "Package": "RColorBrewer",
-      "Version": "1.1-3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "45f0398006e83a5b10b72a90663d8d8c"
-    },
-    "Rcpp": {
-      "Package": "Rcpp",
-      "Version": "1.0.11",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "methods",
-        "utils"
-      ],
-      "Hash": "ae6cbbe1492f4de79c45fce06f967ce8"
-    },
-    "XML": {
-      "Package": "XML",
-      "Version": "3.99-0.14",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "methods",
-        "utils"
-      ],
-      "Hash": "e5c8af79df616c135b21eaeb1dc6bc5c"
-    },
-    "abind": {
-      "Package": "abind",
-      "Version": "1.4-5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "methods",
-        "utils"
-      ],
-      "Hash": "4f57884290cc75ab22f4af9e9d4ca862"
-    },
-    "askpass": {
-      "Package": "askpass",
-      "Version": "1.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "sys"
-      ],
-      "Hash": "e8a22846fff485f0be3770c2da758713"
-    },
-    "base64enc": {
-      "Package": "base64enc",
-      "Version": "0.1-3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "543776ae6848fde2f48ff3816d0628bc"
-    },
-    "bit": {
-      "Package": "bit",
-      "Version": "4.0.5",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "d242abec29412ce988848d0294b208fd"
-    },
-    "bit64": {
-      "Package": "bit64",
-      "Version": "4.0.5",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "bit",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "9fe98599ca456d6552421db0d6772d8f"
-    },
-    "bslib": {
-      "Package": "bslib",
-      "Version": "0.4.2",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "base64enc",
-        "cachem",
-        "grDevices",
-        "htmltools",
-        "jquerylib",
-        "jsonlite",
-        "memoise",
-        "mime",
-        "rlang",
-        "sass"
-      ],
-      "Hash": "a7fbf03946ad741129dc81098722fca1"
-    },
-    "cachem": {
-      "Package": "cachem",
-      "Version": "1.0.7",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "fastmap",
-        "rlang"
-      ],
-      "Hash": "cda74447c42f529de601fe4d4050daef"
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-      "Requirements": [
-        "R",
-        "stats",
-        "utils"
-      ],
-      "Hash": "e0ef355c12942cf7a6b91a6cfaea8b3e"
-    },
-    "purrr": {
-      "Package": "purrr",
-      "Version": "1.0.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "cli",
-        "lifecycle",
-        "magrittr",
-        "rlang",
-        "vctrs"
-      ],
-      "Hash": "d71c815267c640f17ddbf7f16144b4bb"
-    },
-    "rapidjsonr": {
-      "Package": "rapidjsonr",
-      "Version": "1.2.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "88b9f48c93d17cdb811b54079a6a414f"
-    },
-    "rappdirs": {
-      "Package": "rappdirs",
-      "Version": "0.3.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "5e3c5dc0b071b21fa128676560dbe94d"
-    },
-    "raster": {
-      "Package": "raster",
-      "Version": "3.6-23",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "Rcpp",
-        "methods",
-        "sp",
-        "terra"
-      ],
-      "Hash": "337d6d70f7d6bf78df236a5a53f09db0"
-    },
-    "readr": {
-      "Package": "readr",
-      "Version": "2.1.4",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "R6",
-        "cli",
-        "clipr",
-        "cpp11",
-        "crayon",
-        "hms",
-        "lifecycle",
-        "methods",
-        "rlang",
-        "tibble",
-        "tzdb",
-        "utils",
-        "vroom"
-      ],
-      "Hash": "b5047343b3825f37ad9d3b5d89aa1078"
-    },
-    "renv": {
-      "Package": "renv",
-      "Version": "0.17.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "RemoteType": "standard",
-      "RemotePkgRef": "renv",
-      "RemoteRef": "renv",
-      "RemoteRepos": "https://packagemanager.posit.co/cran/__linux__/jammy/2023-04-20",
-      "RemotePkgPlatform": "x86_64-pc-linux-gnu-ubuntu-22.04",
-      "RemoteSha": "0.17.3",
-      "Requirements": [
-        "utils"
-      ],
-      "Hash": "4543b8cd233ae25c6aba8548be9e747e"
-    },
-    "rlang": {
-      "Package": "rlang",
-      "Version": "1.1.0",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "utils"
-      ],
-      "Hash": "dc079ccd156cde8647360f473c1fa718"
-    },
-    "rmarkdown": {
-      "Package": "rmarkdown",
-      "Version": "2.21",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "bslib",
-        "evaluate",
-        "fontawesome",
-        "htmltools",
-        "jquerylib",
-        "jsonlite",
-        "knitr",
-        "methods",
-        "stringr",
-        "tinytex",
-        "tools",
-        "utils",
-        "xfun",
-        "yaml"
-      ],
-      "Hash": "493df4ae51e2e984952ea4d5c75786a3"
-    },
-    "rstac": {
-      "Package": "rstac",
-      "Version": "0.9.2-2",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "crayon",
-        "httr",
-        "jsonlite",
-        "lifecycle",
-        "magrittr",
-        "utils"
-      ],
-      "Hash": "3593eb433ef8af73d2559ca646f777c4"
-    },
-    "s2": {
-      "Package": "s2",
-      "Version": "1.1.4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "Rcpp",
-        "wk"
-      ],
-      "Hash": "f1cbe03bb3346f8e817518ffa20f9f5a"
-    },
-    "sass": {
-      "Package": "sass",
-      "Version": "0.4.5",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R6",
-        "fs",
-        "htmltools",
-        "rappdirs",
-        "rlang"
-      ],
-      "Hash": "2bb4371a4c80115518261866eab6ab11"
-    },
-    "scales": {
-      "Package": "scales",
-      "Version": "1.2.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "R6",
-        "RColorBrewer",
-        "farver",
-        "labeling",
-        "lifecycle",
-        "munsell",
-        "rlang",
-        "viridisLite"
-      ],
-      "Hash": "906cb23d2f1c5680b8ce439b44c6fa63"
-    },
-    "sf": {
-      "Package": "sf",
-      "Version": "1.0-14",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "DBI",
-        "R",
-        "Rcpp",
-        "classInt",
-        "grDevices",
-        "graphics",
-        "grid",
-        "magrittr",
-        "methods",
-        "s2",
-        "stats",
-        "tools",
-        "units",
-        "utils"
-      ],
-      "Hash": "e2111252a76984ca50bf8d6314348681"
-    },
-    "sfheaders": {
-      "Package": "sfheaders",
-      "Version": "0.4.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "Rcpp",
-        "geometries"
-      ],
-      "Hash": "0b0a55852e87b8f8478efb505eba2ebe"
-    },
-    "sp": {
-      "Package": "sp",
-      "Version": "2.0-0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics",
-        "grid",
-        "lattice",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "2551981e6f85d59c81652bf654d6c3ca"
-    },
-    "spData": {
-      "Package": "spData",
-      "Version": "2.2.2",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "sp"
-      ],
-      "Hash": "3ea10242e71aeba42d28cd183fb00feb"
-    },
-    "stars": {
-      "Package": "stars",
-      "Version": "0.6-4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "abind",
-        "classInt",
-        "methods",
-        "parallel",
-        "rlang",
-        "sf",
-        "units"
-      ],
-      "Hash": "8b4284bf9fddfb481d516877a2045023"
-    },
-    "stringi": {
-      "Package": "stringi",
-      "Version": "1.7.12",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "stats",
-        "tools",
-        "utils"
-      ],
-      "Hash": "ca8bd84263c77310739d2cf64d84d7c9"
-    },
-    "stringr": {
-      "Package": "stringr",
-      "Version": "1.5.0",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "cli",
-        "glue",
-        "lifecycle",
-        "magrittr",
-        "rlang",
-        "stringi",
-        "vctrs"
-      ],
-      "Hash": "671a4d384ae9d32fc47a14e98bfa3dc8"
-    },
-    "sys": {
-      "Package": "sys",
-      "Version": "3.4.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Hash": "34c16f1ef796057bfa06d3f4ff818a5d"
-    },
-    "terra": {
-      "Package": "terra",
-      "Version": "1.7-46",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "Rcpp",
-        "methods"
-      ],
-      "Hash": "d15182a8a20ffc5880e721bfa1bf4ce9"
-    },
-    "tibble": {
-      "Package": "tibble",
-      "Version": "3.2.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "fansi",
-        "lifecycle",
-        "magrittr",
-        "methods",
-        "pillar",
-        "pkgconfig",
-        "rlang",
-        "utils",
-        "vctrs"
-      ],
-      "Hash": "a84e2cc86d07289b3b6f5069df7a004c"
-    },
-    "tidyselect": {
-      "Package": "tidyselect",
-      "Version": "1.2.0",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "cli",
-        "glue",
-        "lifecycle",
-        "rlang",
-        "vctrs",
-        "withr"
-      ],
-      "Hash": "79540e5fcd9e0435af547d885f184fd5"
-    },
-    "tinytex": {
-      "Package": "tinytex",
-      "Version": "0.45",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "xfun"
-      ],
-      "Hash": "e4e357f28c2edff493936b6cb30c3d65"
-    },
-    "tmap": {
-      "Package": "tmap",
-      "Version": "3.3-4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "RColorBrewer",
-        "abind",
-        "classInt",
-        "grid",
-        "htmltools",
-        "htmlwidgets",
-        "leafem",
-        "leaflet",
-        "leafsync",
-        "methods",
-        "rlang",
-        "sf",
-        "stars",
-        "stats",
-        "tmaptools",
-        "units",
-        "utils",
-        "viridisLite",
-        "widgetframe"
-      ],
-      "Hash": "c65363bc002492caf754352499ce2386"
-    },
-    "tmaptools": {
-      "Package": "tmaptools",
-      "Version": "3.1-1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "RColorBrewer",
-        "XML",
-        "dichromat",
-        "grid",
-        "lwgeom",
-        "magrittr",
-        "methods",
-        "sf",
-        "stars",
-        "stats",
-        "units",
-        "viridisLite"
-      ],
-      "Hash": "dfcb77371df343b663d6668d2d63ac35"
-    },
-    "tzdb": {
-      "Package": "tzdb",
-      "Version": "0.3.0",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "cpp11"
-      ],
-      "Hash": "b2e1cbce7c903eaf23ec05c58e59fb5e"
-    },
-    "units": {
-      "Package": "units",
-      "Version": "0.8-4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "Rcpp"
-      ],
-      "Hash": "e0fbcea25008a7540c83c2c294135de0"
-    },
-    "utf8": {
-      "Package": "utf8",
-      "Version": "1.2.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "1fe17157424bb09c48a8b3b550c753bc"
-    },
-    "vctrs": {
-      "Package": "vctrs",
-      "Version": "0.6.2",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "cli",
-        "glue",
-        "lifecycle",
-        "rlang"
-      ],
-      "Hash": "a745bda7aff4734c17294bb41d4e4607"
-    },
-    "viridis": {
-      "Package": "viridis",
-      "Version": "0.6.4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "ggplot2",
-        "gridExtra",
-        "viridisLite"
-      ],
-      "Hash": "80cd127bc8c9d3d9f0904ead9a9102f1"
-    },
-    "viridisLite": {
-      "Package": "viridisLite",
-      "Version": "0.4.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "62f4b5da3e08d8e5bcba6cac15603f70"
-    },
-    "vroom": {
-      "Package": "vroom",
-      "Version": "1.6.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "bit64",
-        "cli",
-        "cpp11",
-        "crayon",
-        "glue",
-        "hms",
-        "lifecycle",
-        "methods",
-        "progress",
-        "rlang",
-        "stats",
-        "tibble",
-        "tidyselect",
-        "tzdb",
-        "vctrs",
-        "withr"
-      ],
-      "Hash": "7015a74373b83ffaef64023f4a0f5033"
-    },
-    "widgetframe": {
-      "Package": "widgetframe",
-      "Version": "0.3.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "htmltools",
-        "htmlwidgets",
-        "magrittr",
-        "purrr",
-        "tools",
-        "utils"
-      ],
-      "Hash": "0ee89e6cb58182d39b30a5b506e04808"
-    },
-    "withr": {
-      "Package": "withr",
-      "Version": "2.5.0",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics",
-        "stats"
-      ],
-      "Hash": "c0e49a9760983e81e55cdd9be92e7182"
-    },
-    "wk": {
-      "Package": "wk",
-      "Version": "0.8.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "aaf7e20556e3125a09d53453814ad339"
-    },
-    "xfun": {
-      "Package": "xfun",
-      "Version": "0.38",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "stats",
-        "tools"
-      ],
-      "Hash": "1ed71215d45e85562d3b1b29a068ccec"
-    },
-    "yaml": {
-      "Package": "yaml",
-      "Version": "2.3.7",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Hash": "0d0056cc5383fbc240ccd0cb584bf436"
-    }
-  }
-}
diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh
deleted file mode 100755
index b89dcf16d..000000000
--- a/.devcontainer/setup.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-
-sudo cp /etc/rstudio/disable_auth_rserver.conf /etc/rstudio/rserver.conf
-sudo sudo bash -c 'echo "USER=rstudio" >>/etc/environment'
-sudo /init &> /dev/null &
-
diff --git a/.devcontainer/welcome.sh b/.devcontainer/welcome.sh
deleted file mode 100755
index 89aab9b8c..000000000
--- a/.devcontainer/welcome.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-mkdir -p ~/.local/share/rstudio/projects_settings
-export RPROJ"=$(ls ${CODESPACE_VSCODE_FOLDER}/*.Rproj)"
-echo ${RPROJ} > ~/.local/share/rstudio/projects_settings/last-project-path
-
-
-# Construct the message
-message="## [Open in RStudio](https://$CODESPACE_NAME-8787.app.github.dev)
-"
-# Echo the message to the terminal
-echo "
-👋 Welcome to Codespaces! You are on our custom image. 
-   - It includes runtimes and tools for Python & R using Jupyter, Quarto, or RStudio 
-
-🌐 Open the RStudio editor here: https://$CODESPACE_NAME-8787.app.github.dev
-   - (This may take a few seconds to load, retry if necessary)
-"

From 76feab110e66a21f3c122f21e1920e5ebaeeb309 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Thu, 1 Feb 2024 19:17:01 -0800
Subject: [PATCH 16/59] deps

---
 .devcontainer/install.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.devcontainer/install.R b/.devcontainer/install.R
index 85481126a..a80731cee 100755
--- a/.devcontainer/install.R
+++ b/.devcontainer/install.R
@@ -4,7 +4,7 @@
 # We could use renv.lock approach here instead, but will force re-creation of environment from scratch
 # Does not provide a good way to ensure that sf/terra/gdalcubes are installed from source while other packages can be binary
 install.packages("pak")
-install.packages(c("rstac", "spData", "earthdatalogin", "quarto"))
+pak::pkg_install(c("rstac", "spData", "earthdatalogin", "quarto", "aws.s3"))
 pak::pkg_install('github::r-tmap/tmap')
 
 #pak::pkg_install("httpgd")

From fdeacf52fb1e87bbb632609f00e97d7f331a4b73 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Fri, 2 Feb 2024 12:58:12 -0800
Subject: [PATCH 17/59] permissions

---
 .devcontainer/Dockerfile | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index 569fbdb9b..d57715101 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -1,11 +1,10 @@
 ## devcontainer-focused Rocker
-FROM docker.io/rocker/binder:4.3
-
-USER root
+FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
 
 ## latest version of geospatial libs
 RUN /rocker_scripts/experimental/install_dev_osgeo.sh
 RUN apt-get update -qq && apt-get -y install vim
+RUN /rocker_scripts/install_jupyter.sh
 
 # conda
 ENV CONDA_ENV=/opt/miniforge3
@@ -19,6 +18,10 @@ RUN chown ${NB_USER}:staff -R ${CONDA_ENV}
 RUN chown ${NB_USER}:staff -R ${VIRTUAL_ENV}
 RUN chown ${NB_USER}:staff -R ${R_HOME}/site-library
 
+# some teaching preferences
+RUN git config --system pull.rebase false && \
+    git config --system credential.helper 'cache --timeout=36000'
+
 
 
 ## codeserver
@@ -50,8 +53,4 @@ RUN ${MY_ENV}/bin/python -m pip install ipykernel && \
     ${MY_ENV}/bin/python -m ipykernel install --prefix /opt/venv --name=openscapes
 
 
-# some teaching preferences
-RUN git config --system pull.rebase false && \
-    git config --system credential.helper 'cache --timeout=36000'
-
 

From 51acaf2bc22752f38879e3761d0f88b68ada8379 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Sat, 3 Feb 2024 13:01:39 -0800
Subject: [PATCH 18/59] :broom:

---
 .devcontainer/Dockerfile | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index d57715101..b785c1b1c 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -3,18 +3,22 @@ FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
 
 ## latest version of geospatial libs
 RUN /rocker_scripts/experimental/install_dev_osgeo.sh
-RUN apt-get update -qq && apt-get -y install vim
-RUN /rocker_scripts/install_jupyter.sh
+RUN apt-get update -qq && apt-get -y install vim texlive-science
 
-# conda
+# standard python/jupyter setup
+ENV NB_USER=rstudio
+ENV VIRTUAL_ENV=/opt/venv
+ENV PATH=${VIRTUAL_ENV}/bin:${PATH}
+RUN wget https://github.com/rocker-org/rocker-versioned2/raw/master/scripts/install_jupyter.sh && bash -e install_jupyter.sh && rm install_jupyter.sh
+
+# Set up conda
 ENV CONDA_ENV=/opt/miniforge3
 ENV PATH=${PATH}:$CONDA_ENV/bin
 RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" && \
     bash Miniforge3-$(uname)-$(uname -m).sh -b -p ${CONDA_ENV} 
-
 RUN chown ${NB_USER}:staff -R ${CONDA_ENV}
 
-# podman doesn not understand group permissions
+# podman doesn't not understand group permissions
 RUN chown ${NB_USER}:staff -R ${VIRTUAL_ENV}
 RUN chown ${NB_USER}:staff -R ${R_HOME}/site-library
 
@@ -23,32 +27,28 @@ RUN git config --system pull.rebase false && \
     git config --system credential.helper 'cache --timeout=36000'
 
 
-
 ## codeserver
 RUN curl -fsSL https://code-server.dev/install.sh | sh
 
+
+## Openscapes-specific configs
 USER rstudio
 WORKDIR /home/rstudio
 RUN usermod -s /bin/bash rstudio
 
+# install into the default environment
 COPY requirements.txt requirements.txt
-ENV PATH=$PATH:/home/rstudio/.local/bin
-
 RUN python -m pip install -r requirements.txt && rm requirements.txt
 COPY install.R install.R
 RUN Rscript install.R && rm install.R
 
-# equivalent path to -n openscapes
+# Create a conda-based env and install into it without using conda init/conda activate
+# (this yaml file doesn't include everything from pangeo, consider a different one...)
 ENV MY_ENV=${CONDA_ENV}/envs/openscapes
 RUN wget https://github.com/NASA-Openscapes/corn/raw/main/ci/environment.yml && \
     conda env create -p ${MY_ENV} -f environment.yml
 
-# NOTES: 
-# conda (base) just means $CONDA_ENV/bin/
-# conda (openscapes) means $MY_ENV, identically, $CONDA_ENV/envs/openscapes/bin/
-# Rather than activate it or alter path, we just get it set up as an optional kernel
-# We could easily make either the default by putting either bin path at the start of PATH 
-
+# This won't be the default enviornment but we register it
 RUN ${MY_ENV}/bin/python -m pip install ipykernel && \
     ${MY_ENV}/bin/python -m ipykernel install --prefix /opt/venv --name=openscapes
 

From 1b6fdc710010d7fcfae663a93cbec78ecb978640 Mon Sep 17 00:00:00 2001
From: Carl Boettiger <cboettig@gmail.com>
Date: Sat, 3 Feb 2024 13:59:19 -0800
Subject: [PATCH 19/59] Update test-build.yaml

---
 .github/workflows/test-build.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test-build.yaml b/.github/workflows/test-build.yaml
index ffedcd8f5..7747cd9ab 100644
--- a/.github/workflows/test-build.yaml
+++ b/.github/workflows/test-build.yaml
@@ -9,7 +9,7 @@ jobs:
   build-deploy:
     runs-on: ubuntu-latest
     container: 
-      image: ghcr.io/boettiger-lab/nasa-tops:latest
+      image: ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:latest
       options: --user root --security-opt seccomp=unconfined
     permissions:
       contents: write

From 9fb213bbd91e159d8c1150b21c8a070da2844ca8 Mon Sep 17 00:00:00 2001
From: Carl Boettiger <cboettig@gmail.com>
Date: Sat, 3 Feb 2024 13:59:48 -0800
Subject: [PATCH 20/59] Update devcontainer.json

---
 .devcontainer/devcontainer.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 2621de76f..bfd91d5d4 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,5 +1,5 @@
 {
-	  "image": "docker.io/cboettig/nasa",
+	  "image": "ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:latest",
 	  "runArgs": [ "--security-opt", "seccomp=unconfined" ],
 	  "name": "NASA OpenScapes Environment"
 }

From 93c4a16420ca4c524340084e8dc5d168c81c16ad Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Sat, 3 Feb 2024 14:13:47 -0800
Subject: [PATCH 21/59] smaller build

---
 .devcontainer/Dockerfile       |   4 +-
 .devcontainer/requirements.txt | 187 +--------------------------------
 2 files changed, 4 insertions(+), 187 deletions(-)

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index b785c1b1c..2fdb13a53 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -2,8 +2,8 @@
 FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
 
 ## latest version of geospatial libs
-RUN /rocker_scripts/experimental/install_dev_osgeo.sh
-RUN apt-get update -qq && apt-get -y install vim texlive-science
+# RUN /rocker_scripts/experimental/install_dev_osgeo.sh
+RUN apt-get update -qq && apt-get -y install vim texlive-base
 
 # standard python/jupyter setup
 ENV NB_USER=rstudio
diff --git a/.devcontainer/requirements.txt b/.devcontainer/requirements.txt
index ab9cefdb9..640ab367f 100644
--- a/.devcontainer/requirements.txt
+++ b/.devcontainer/requirements.txt
@@ -1,74 +1,3 @@
-affine==2.4.0
-aiobotocore==2.9.0
-aiohttp==3.9.1
-aioitertools==0.11.0
-aiosignal==1.3.1
-annotated-types==0.6.0
-anyio==4.0.0
-argon2-cffi==23.1.0
-argon2-cffi-bindings==21.2.0
-arrow==1.2.3
-asciitree==0.3.3
-asttokens==2.4.0
-async-lru==2.0.4
-async-timeout==4.0.3
-attrs==23.1.0
-Babel==2.12.1
-backcall==0.2.0
-beautifulsoup4==4.12.2
-bleach==6.0.0
-bokeh==3.3.2
-botocore==1.33.13
-Bottleneck==1.3.7
-bounded-pool-executor==0.0.3
-cachetools==5.3.2
-certifi==2023.7.22
-cf-xarray==0.8.6
-cffi==1.15.1
-cftime==1.6.3
-charset-normalizer==3.2.0
-click==8.1.7
-click-plugins==1.1.1
-cligj==0.7.2
-cloudpickle==2.2.1
-comm==0.1.4
-contourpy==1.1.1
-cycler==0.11.0
-dask==2023.11.0
-debugpy==1.8.0
-decorator==5.1.1
-defusedxml==0.7.1
-distributed==2023.11.0
-earthaccess==0.8.2
-exceptiongroup==1.1.3
-executing==1.2.0
-fasteners==0.19
-fastjsonschema==2.18.0
-Fiona==1.9.4.post1
-flox==0.8.5
-fonttools==4.42.1
-fqdn==1.5.1
-frozenlist==1.4.1
-fsspec==2023.12.2
-geopandas==0.14.0
-geopolars==0.1.0a4
-Glances==3.4.0.3
-h5netcdf==1.3.0
-h5py==3.10.0
-idna==3.4
-importlib-metadata==6.8.0
-importlib-resources==6.1.1
-ipykernel==6.25.2
-ipython==8.15.0
-ipywidgets==8.1.1
-isoduration==20.11.0
-jedi==0.19.0
-Jinja2==3.1.2
-jmespath==1.0.1
-json5==0.9.14
-jsonpointer==2.4
-jsonschema==4.19.1
-jsonschema-specifications==2023.7.1
 jupyter==1.0.0
 jupyter-console==6.6.3
 jupyter-events==0.7.0
@@ -78,127 +7,15 @@ jupyter_core==5.3.2
 jupyter_server==2.7.3
 jupyter_server_terminals==0.4.4
 jupyter-vscode-proxy==0.5
-jupyterlab==4.0.9
 jupyterlab-pygments==0.2.2
 jupyterlab-widgets==3.0.9
 jupyterlab_server==2.25.0
-kiwisolver==1.4.5
-llvmlite==0.41.1
-locket==1.0.0
-lxml==4.9.4
-lz4==4.3.2
-MarkupSafe==2.1.3
-matplotlib==3.8.0
-matplotlib-inline==0.1.6
-mistune==3.0.1
-msgpack==1.0.7
-multidict==6.0.4
-multimethod==1.10
-nbclient==0.8.0
 nbconvert==7.8.0
 nbformat==5.9.2
-nc-time-axis==1.4.1
-nest-asyncio==1.5.8
-netCDF4==1.6.5
-notebook==7.0.6
-notebook_shim==0.2.3
-numba==0.58.1
-numbagg==0.6.8
-numcodecs==0.12.1
-numpy==1.26.0
-numpy-groupies==0.10.2
-odc-geo==0.4.1
 odc-stac==0.3.8
-overrides==7.4.0
-packaging==23.1
-pandas==2.1.0
-pandocfilters==1.5.0
-parso==0.8.3
-partd==1.4.1
-pexpect==4.8.0
-pickleshare==0.7.5
-Pillow==10.0.1
 planetary-computer==1.0.0
-platformdirs==3.10.0
-polars==0.19.15
-pooch==1.8.0
-pqdm==0.2.0
-prometheus-client==0.17.1
-prompt-toolkit==3.0.39
-psutil==5.9.5
-ptyprocess==0.7.0
-pure-eval==0.2.2
-pyarrow==14.0.1
-pyarrow-hotfix==0.6
-pycparser==2.21
-pydantic==2.5.3
-pydantic_core==2.14.6
-Pygments==2.16.1
-pyparsing==3.1.1
-pyproj==3.6.1
-pystac==1.8.4
+polars
+pyarrow
 pystac-client==0.7.5
-python-cmr==0.9.0
-python-dateutil==2.8.2
-python-dotenv==1.0.0
-python-json-logger==2.0.7
-pytz==2023.3.post1
-PyYAML==6.0.1
-pyzmq==25.1.1
-qtconsole==5.5.1
-QtPy==2.4.1
-radian==0.6.7
-rasterio==1.3.8
-rasterstats==0.19.0
-rchitect==0.4.2
-referencing==0.30.2
-requests==2.31.0
-rfc3339-validator==0.1.4
-rfc3986-validator==0.1.1
-rioxarray==0.15.0
-rpds-py==0.10.3
-s3fs==2023.12.2
-scipy==1.11.3
-seaborn==0.13.0
-Send2Trash==1.8.2
-shapely==2.0.1
-simplejson==3.19.2
-six==1.16.0
-sniffio==1.3.0
-snuggs==1.4.7
-sortedcontainers==2.4.0
-soupsieve==2.5
-sparse==0.14.0
-stack-data==0.6.2
-stackstac==0.5.0
-tblib==3.0.0
-terminado==0.17.1
-timebudget==0.7.1
-tinycss2==1.2.1
-tinynetrc==1.3.1
-tomli==2.0.1
-toolz==0.12.0
-tornado==6.3.3
-tqdm==4.66.1
-traitlets==5.10.1
-types-python-dateutil==2.8.19.14
-typing_extensions==4.8.0
-tzdata==2023.3
-ujson==5.8.0
-uri-template==1.3.0
-urllib3==2.0.5
-wcwidth==0.2.6
-webcolors==1.13
-webencodings==0.5.1
-websocket-client==1.6.3
-widgetsnbextension==4.0.9
-wrapt==1.16.0
-xarray==2023.8.0
-xesmf==0.8.2
-xyzservices==2023.10.1
-yarl==1.9.4
-zarr==2.16.1
-zict==3.0.0
-zipp==3.17.0
 gh-scoped-creds
 

From f79aac0aed36c8baa3f1a7088710d05d5f0969bc Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Sat, 3 Feb 2024 15:46:11 -0800
Subject: [PATCH 22/59] use images

---
 .devcontainer/Dockerfile       | 16 +++++++++-------
 .devcontainer/requirements.txt |  7 +++++++
 2 files changed, 16 insertions(+), 7 deletions(-)

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index 2fdb13a53..48cbf4ac2 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -1,32 +1,34 @@
 ## devcontainer-focused Rocker
 FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
 
+#RUN /rocker_scripts/install_geospatial.sh
 ## latest version of geospatial libs
-# RUN /rocker_scripts/experimental/install_dev_osgeo.sh
-RUN apt-get update -qq && apt-get -y install vim texlive-base
+RUN /rocker_scripts/experimental/install_dev_osgeo.sh
+RUN apt-get update -qq && apt-get -y install vim texlive
 
 # standard python/jupyter setup
 ENV NB_USER=rstudio
 ENV VIRTUAL_ENV=/opt/venv
 ENV PATH=${VIRTUAL_ENV}/bin:${PATH}
-RUN wget https://github.com/rocker-org/rocker-versioned2/raw/master/scripts/install_jupyter.sh && bash -e install_jupyter.sh && rm install_jupyter.sh
+RUN wget https://github.com/rocker-org/rocker-versioned2/raw/master/scripts/install_jupyter.sh && \
+  bash -e install_jupyter.sh && \
+  rm install_jupyter.sh && \
+  chown ${NB_USER}:staff -R ${VIRTUAL_ENV}
 
 # Set up conda
 ENV CONDA_ENV=/opt/miniforge3
 ENV PATH=${PATH}:$CONDA_ENV/bin
 RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" && \
-    bash Miniforge3-$(uname)-$(uname -m).sh -b -p ${CONDA_ENV} 
-RUN chown ${NB_USER}:staff -R ${CONDA_ENV}
+    bash Miniforge3-$(uname)-$(uname -m).sh -b -p ${CONDA_ENV} && \
+    chown ${NB_USER}:staff -R ${CONDA_ENV}
 
 # podman doesn't not understand group permissions
-RUN chown ${NB_USER}:staff -R ${VIRTUAL_ENV}
 RUN chown ${NB_USER}:staff -R ${R_HOME}/site-library
 
 # some teaching preferences
 RUN git config --system pull.rebase false && \
     git config --system credential.helper 'cache --timeout=36000'
 
-
 ## codeserver
 RUN curl -fsSL https://code-server.dev/install.sh | sh
 
diff --git a/.devcontainer/requirements.txt b/.devcontainer/requirements.txt
index 640ab367f..7a2a4b6b1 100644
--- a/.devcontainer/requirements.txt
+++ b/.devcontainer/requirements.txt
@@ -18,4 +18,11 @@ polars
 pyarrow
 pystac-client==0.7.5
 gh-scoped-creds
+scikit-image
+hvplot
+geoviews
+earthaccess
+pyresample
+contextily
+pygeoweaver
 

From 950e96ae8150d44893e63c415a2b4efe542daabb Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Sat, 3 Feb 2024 20:38:27 -0800
Subject: [PATCH 23/59] conda docker

---
 .devcontainer/Dockerfile                      |  1 -
 .devcontainer/conda.Dockerfile                | 47 ++++++++++
 .devcontainer/devcontainer.json               |  2 +-
 .devcontainer/environment.yml                 | 87 +++++++++++++++++++
 .devcontainer/install.R                       | 11 +--
 .devcontainer/jupyter-environment.yml         | 21 +++++
 ...requirements.txt => nasa-requirements.txt} |  5 +-
 .devcontainer/venv.Dockerfile                 | 36 ++++++++
 .github/workflows/docker-image.yml            |  2 +-
 9 files changed, 203 insertions(+), 9 deletions(-)
 create mode 100644 .devcontainer/conda.Dockerfile
 create mode 100644 .devcontainer/environment.yml
 create mode 100644 .devcontainer/jupyter-environment.yml
 rename .devcontainer/{requirements.txt => nasa-requirements.txt} (89%)
 create mode 100644 .devcontainer/venv.Dockerfile

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index 48cbf4ac2..e3b7df4f3 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -1,7 +1,6 @@
 ## devcontainer-focused Rocker
 FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
 
-#RUN /rocker_scripts/install_geospatial.sh
 ## latest version of geospatial libs
 RUN /rocker_scripts/experimental/install_dev_osgeo.sh
 RUN apt-get update -qq && apt-get -y install vim texlive
diff --git a/.devcontainer/conda.Dockerfile b/.devcontainer/conda.Dockerfile
new file mode 100644
index 000000000..0ab2cf93b
--- /dev/null
+++ b/.devcontainer/conda.Dockerfile
@@ -0,0 +1,47 @@
+## devcontainer-focused Rocker
+FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
+
+## latest version of geospatial libs
+RUN /rocker_scripts/experimental/install_dev_osgeo.sh
+RUN apt-get update -qq && apt-get -y install vim
+
+# podman doesn't not understand group permissions
+RUN chown rstudio:staff -R ${R_HOME}/site-library
+
+# some teaching preferences
+RUN git config --system pull.rebase false && \
+    git config --system credential.helper 'cache --timeout=36000'
+
+## codeserver
+RUN curl -fsSL https://code-server.dev/install.sh | sh
+
+# Set up conda
+ENV NB_USER=rstudio
+ENV CONDA_ENV=/opt/miniforge3
+ENV PATH=${CONDA_ENV}/bin:${PATH}
+RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" && \
+    bash Miniforge3-$(uname)-$(uname -m).sh -b -p ${CONDA_ENV} && \
+    chown ${NB_USER}:staff -R ${CONDA_ENV}
+
+
+# Initialize conda by default for all users:
+RUN conda init --system
+
+## Openscapes-specific configs
+USER ${NB_USER} 
+WORKDIR /home/${NB_USER}
+RUN usermod -s /bin/bash ${NB_USER} 
+
+# install into the default environment
+COPY install.R install.R
+RUN Rscript install.R && rm install.R
+
+# consider installing jupyter-like stuff into base env instead?
+# Create a conda-based env and install into it without using conda init/conda activate
+# (this yaml file doesn't include everything from pangeo, consider a different one...)
+ENV MY_ENV=${CONDA_ENV}/envs/openscapes
+COPY environment.yml environment.yml
+RUN conda env create -p ${MY_ENV} -f environment.yml
+
+ENV PATH=${MY_ENV}/bin:${PATH}
+
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 2621de76f..dfa558902 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,5 +1,5 @@
 {
-	  "image": "docker.io/cboettig/nasa",
+	  "image": "ghcr.io/eeholmes/earthdata-cloud-cookbook",
 	  "runArgs": [ "--security-opt", "seccomp=unconfined" ],
 	  "name": "NASA OpenScapes Environment"
 }
diff --git a/.devcontainer/environment.yml b/.devcontainer/environment.yml
new file mode 100644
index 000000000..e17a0a114
--- /dev/null
+++ b/.devcontainer/environment.yml
@@ -0,0 +1,87 @@
+name: openscapes
+channels:
+  - conda-forge
+dependencies:
+  - python=3.10
+  - dask
+  - dask-gateway
+  - graphviz
+  - distributed
+  - rioxarray
+  - xarray>=2022.12
+  - h5netcdf
+  - netcdf4>=1.6.4
+  - h5py
+  - gdal~=3.8
+  - geoviews
+  - holoviews=1.16.2
+  - matplotlib-base
+  - seaborn
+  - intake
+  - hvplot
+  - datashader
+  - pyproj
+  - bqplot
+  - geopandas
+  - zarr
+  - cartopy
+  - pynco
+  - rasterio
+  - shapely
+  - pyresample
+  - icepyx
+  - joblib
+  - pystac-client
+  - pydap
+  - lxml
+  - ipyleaflet
+  # when jlab 4 gets released we can upgrade dask-labextension
+  # - dask-labextension
+  # - dask-labextension==6.2.0
+  - dask-labextension
+  - jupyter-server-proxy
+  - jupyter-vscode-proxy
+  - jupyter-rsession-proxy
+  - ipywidgets
+  - jupyter-book
+  - jupyterlab>4
+  - jupyterlab-myst
+  - jupyterhub-singleuser
+  - jupyterlab-geojson
+  - jupyterlab-favorites
+  - jupyterlab-git
+  - jupyter-resource-usage
+  - jupyterlab-h5web
+  - hdf5plugin
+  - ipympl
+  - conda-lock
+  - pooch
+  - earthaccess>=0.8.2
+  - sliderule>=3.6.0
+  # QGIS
+  - qgis~=3.28
+  - pyopencl
+  - ocl-icd-system
+  - websockify>=0.10
+  # /QGIS 
+  - h5coro
+  - git >=2.39
+  - itslive
+  - rasterstats
+  - kerchunk
+  - rechunker
+  - pqdm
+  - spectral
+  - scikit-image
+  - coiled
+  - s3fs
+  - nbgitpuller
+  - awscliv2
+  - jupyter-server-proxy
+  - jupyter-vscode-proxy
+  # https://github.com/jupyterlab/jupyter-collaboration/issues/202
+  # - jupyter-collaboration
+  - code-server >=3.2
+  - pip
+platforms:
+  - linux-64
diff --git a/.devcontainer/install.R b/.devcontainer/install.R
index a80731cee..f4e85dc93 100755
--- a/.devcontainer/install.R
+++ b/.devcontainer/install.R
@@ -3,11 +3,12 @@
 
 # We could use renv.lock approach here instead, but will force re-creation of environment from scratch
 # Does not provide a good way to ensure that sf/terra/gdalcubes are installed from source while other packages can be binary
-install.packages("pak")
-pak::pkg_install(c("rstac", "spData", "earthdatalogin", "quarto", "aws.s3"))
-pak::pkg_install('github::r-tmap/tmap')
+# Likewise, pak insists on installing old gdal from apt instead of respecting system library source builds
+# install.packages("pak")
+install.packages(c("rstac", "spData", "earthdatalogin", "quarto", "aws.s3", "tmap"))
+remotes::install_github('r-tmap/tmap')
 
 #pak::pkg_install("httpgd")
-pak::pkg_install(c("IRkernel", "languageserver"))
-IRkernel::installspec()
+#pak::pkg_install(c("IRkernel", "languageserver"))
+#IRkernel::installspec()
 
diff --git a/.devcontainer/jupyter-environment.yml b/.devcontainer/jupyter-environment.yml
new file mode 100644
index 000000000..82f71375b
--- /dev/null
+++ b/.devcontainer/jupyter-environment.yml
@@ -0,0 +1,21 @@
+name: openscapes
+channels:
+  - conda-forge
+dependencies:
+  - python=3.10
+  - dask-labextension
+  - jupyter-server-proxy
+  - jupyter-vscode-proxy
+  - jupyter-rsession-proxy
+  - ipywidgets
+  - jupyter-book
+  - jupyterlab>4
+  - jupyterlab-myst
+  - jupyterhub-singleuser
+  - jupyterlab-geojson
+  - jupyterlab-favorites
+  - jupyterlab-git
+  - jupyter-resource-usage
+  - jupyterlab-h5web
+  - code-server >=3.2
+  - pip
diff --git a/.devcontainer/requirements.txt b/.devcontainer/nasa-requirements.txt
similarity index 89%
rename from .devcontainer/requirements.txt
rename to .devcontainer/nasa-requirements.txt
index 7a2a4b6b1..c8dc3a7c5 100644
--- a/.devcontainer/requirements.txt
+++ b/.devcontainer/nasa-requirements.txt
@@ -1,4 +1,7 @@
-jupyter==1.0.0
+jupyterhub
+jupyterlab
+notebook
+jupyter-rsession-proxy
 jupyter-console==6.6.3
 jupyter-events==0.7.0
 jupyter-lsp==2.2.0
diff --git a/.devcontainer/venv.Dockerfile b/.devcontainer/venv.Dockerfile
new file mode 100644
index 000000000..a91a50b14
--- /dev/null
+++ b/.devcontainer/venv.Dockerfile
@@ -0,0 +1,36 @@
+## devcontainer-focused Rocker
+FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
+
+## latest version of geospatial libs
+RUN /rocker_scripts/experimental/install_dev_osgeo.sh
+RUN apt-get update -qq && apt-get -y install vim
+
+# standard python/jupyter setup
+ENV NB_USER=rstudio
+ENV VIRTUAL_ENV=/opt/venv
+ENV PATH=${VIRTUAL_ENV}/bin:${PATH}
+RUN /rocker_scripts/install_python.sh && \
+  chown ${NB_USER}:staff -R ${VIRTUAL_ENV}
+
+# podman doesn't not understand group permissions
+RUN chown ${NB_USER}:staff -R ${R_HOME}/site-library
+
+# some teaching preferences
+RUN git config --system pull.rebase false && \
+    git config --system credential.helper 'cache --timeout=36000'
+
+## codeserver
+RUN curl -fsSL https://code-server.dev/install.sh | sh
+
+## Openscapes-specific configs
+USER rstudio
+WORKDIR /home/rstudio
+RUN usermod -s /bin/bash rstudio
+
+# install into the default environment
+COPY nasa-requirements.txt requirements.txt
+RUN python -m pip install -r requirements.txt && rm requirements.txt
+COPY install.R install.R
+RUN Rscript install.R && rm install.R
+
+
diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml
index 3fa257c41..64ed1c7c3 100644
--- a/.github/workflows/docker-image.yml
+++ b/.github/workflows/docker-image.yml
@@ -18,7 +18,7 @@ jobs:
           password: ${{secrets.GITHUB_TOKEN}}
       - name: Build the Docker image
         if: github.repository == 'eeholmes/earthdata-cloud-cookbook'
-        run: docker build .devcontainer --tag ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:latest
+        run: docker build .devcontainer -f .devcontainer/conda.Dockerfile  --tag ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:latest
       - name: Publish
         if: github.repository == 'eeholmes/earthdata-cloud-cookbook'
         run: docker push ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:latest

From 487fa62255e031ac0ea0b52fd997b5fdb94fdda6 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Sat, 3 Feb 2024 20:51:33 -0800
Subject: [PATCH 24/59] run monthly using this docker image

---
 .github/workflows/test-build.yaml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test-build.yaml b/.github/workflows/test-build.yaml
index 7747cd9ab..0dc65ed9e 100644
--- a/.github/workflows/test-build.yaml
+++ b/.github/workflows/test-build.yaml
@@ -2,6 +2,8 @@ on:
   workflow_dispatch:
   push:
     branches: main
+  schedule:
+        - cron: "0 0 1 * *" # monthly
 
 name: Quarto Test Build
 
@@ -22,5 +24,4 @@ jobs:
 
       - name: Render
         run: |
-             rm -rf _freeze
-             quarto render
+             quarto render --no-cache

From 766bdfa3eb6187c4528365bd5586581abbd5a98f Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Sat, 3 Feb 2024 22:00:40 -0800
Subject: [PATCH 25/59] build both

---
 .github/workflows/docker-image.yml | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml
index 64ed1c7c3..3f9e161f1 100644
--- a/.github/workflows/docker-image.yml
+++ b/.github/workflows/docker-image.yml
@@ -18,7 +18,12 @@ jobs:
           password: ${{secrets.GITHUB_TOKEN}}
       - name: Build the Docker image
         if: github.repository == 'eeholmes/earthdata-cloud-cookbook'
-        run: docker build .devcontainer -f .devcontainer/conda.Dockerfile  --tag ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:latest
+        run: |
+          docker build .devcontainer -f .devcontainer/conda.Dockerfile  --tag ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:latest
+          docker build .devcontainer -f .devcontainer/venv.Dockerfile  --tag ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:venv
       - name: Publish
         if: github.repository == 'eeholmes/earthdata-cloud-cookbook'
-        run: docker push ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:latest
+        run: |
+          docker push ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:latest
+          docker push ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:venv
+

From 58302e52708a1ebbcbab7b38c9cfc303f76b1af1 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Sat, 3 Feb 2024 22:01:06 -0800
Subject: [PATCH 26/59] venv is smaller

---
 .devcontainer/devcontainer.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index bfd91d5d4..43f3b554e 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,5 +1,5 @@
 {
-	  "image": "ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:latest",
+	  "image": "ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:venv",
 	  "runArgs": [ "--security-opt", "seccomp=unconfined" ],
 	  "name": "NASA OpenScapes Environment"
 }

From f618b7c5d41bfa1b4f856a7fbffc18a12a7f52fc Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Sat, 3 Feb 2024 22:22:31 -0800
Subject: [PATCH 27/59] set PATH in Renviron too

---
 .devcontainer/conda.Dockerfile | 20 +++++++++-----------
 1 file changed, 9 insertions(+), 11 deletions(-)

diff --git a/.devcontainer/conda.Dockerfile b/.devcontainer/conda.Dockerfile
index 0ab2cf93b..4af531664 100644
--- a/.devcontainer/conda.Dockerfile
+++ b/.devcontainer/conda.Dockerfile
@@ -1,7 +1,7 @@
-## devcontainer-focused Rocker
+# devcontainer-focused Rocker
 FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
 
-## latest version of geospatial libs
+# latest version of geospatial libs
 RUN /rocker_scripts/experimental/install_dev_osgeo.sh
 RUN apt-get update -qq && apt-get -y install vim
 
@@ -12,7 +12,7 @@ RUN chown rstudio: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
 
 # Set up conda
@@ -23,11 +23,15 @@ RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/downloa
     bash Miniforge3-$(uname)-$(uname -m).sh -b -p ${CONDA_ENV} && \
     chown ${NB_USER}:staff -R ${CONDA_ENV}
 
-
 # Initialize conda by default for all users:
 RUN conda init --system
 
-## Openscapes-specific configs
+# Set up a primary conda environment distinct from (base)
+ENV MY_ENV=${CONDA_ENV}/envs/openscapes
+ENV PATH=${MY_ENV}/bin:${PATH}
+RUN echo "PATH=${PATH}" >>"${R_HOME}/etc/Renviron.site"
+
+# Standard user setup here
 USER ${NB_USER} 
 WORKDIR /home/${NB_USER}
 RUN usermod -s /bin/bash ${NB_USER} 
@@ -36,12 +40,6 @@ RUN usermod -s /bin/bash ${NB_USER}
 COPY install.R install.R
 RUN Rscript install.R && rm install.R
 
-# consider installing jupyter-like stuff into base env instead?
-# Create a conda-based env and install into it without using conda init/conda activate
-# (this yaml file doesn't include everything from pangeo, consider a different one...)
-ENV MY_ENV=${CONDA_ENV}/envs/openscapes
 COPY environment.yml environment.yml
 RUN conda env create -p ${MY_ENV} -f environment.yml
 
-ENV PATH=${MY_ENV}/bin:${PATH}
-

From 5404f04ff692e0c2750d336c0fda2dd0c0fa2cda Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Sat, 3 Feb 2024 22:29:41 -0800
Subject: [PATCH 28/59] explore conda init behavior

---
 .devcontainer/conda.Dockerfile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.devcontainer/conda.Dockerfile b/.devcontainer/conda.Dockerfile
index 4af531664..e4aa5ea9c 100644
--- a/.devcontainer/conda.Dockerfile
+++ b/.devcontainer/conda.Dockerfile
@@ -23,14 +23,14 @@ RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/downloa
     bash Miniforge3-$(uname)-$(uname -m).sh -b -p ${CONDA_ENV} && \
     chown ${NB_USER}:staff -R ${CONDA_ENV}
 
-# Initialize conda by default for all users:
-RUN conda init --system
-
 # Set up a primary conda environment distinct from (base)
 ENV MY_ENV=${CONDA_ENV}/envs/openscapes
 ENV PATH=${MY_ENV}/bin:${PATH}
 RUN echo "PATH=${PATH}" >>"${R_HOME}/etc/Renviron.site"
 
+# Initialize conda by default for all users:
+RUN conda init --system
+
 # Standard user setup here
 USER ${NB_USER} 
 WORKDIR /home/${NB_USER}

From 7d022c192df39bb770688dbcfe269ababd96b2cc Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Sat, 3 Feb 2024 23:07:22 -0800
Subject: [PATCH 29/59] :broom:

---
 .devcontainer/conda.Dockerfile | 5 ++++-
 .devcontainer/venv.Dockerfile  | 3 +--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/.devcontainer/conda.Dockerfile b/.devcontainer/conda.Dockerfile
index e4aa5ea9c..2218c4236 100644
--- a/.devcontainer/conda.Dockerfile
+++ b/.devcontainer/conda.Dockerfile
@@ -21,7 +21,8 @@ ENV CONDA_ENV=/opt/miniforge3
 ENV PATH=${CONDA_ENV}/bin:${PATH}
 RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" && \
     bash Miniforge3-$(uname)-$(uname -m).sh -b -p ${CONDA_ENV} && \
-    chown ${NB_USER}:staff -R ${CONDA_ENV}
+    chown ${NB_USER}:staff -R ${CONDA_ENV} && \
+    rm Miniforge3*.sh *.deb
 
 # Set up a primary conda environment distinct from (base)
 ENV MY_ENV=${CONDA_ENV}/envs/openscapes
@@ -43,3 +44,5 @@ RUN Rscript install.R && rm install.R
 COPY environment.yml environment.yml
 RUN conda env create -p ${MY_ENV} -f environment.yml
 
+RUN rm -rf .cache && conda clean --all
+
diff --git a/.devcontainer/venv.Dockerfile b/.devcontainer/venv.Dockerfile
index a91a50b14..7bf6a108f 100644
--- a/.devcontainer/venv.Dockerfile
+++ b/.devcontainer/venv.Dockerfile
@@ -29,8 +29,7 @@ RUN usermod -s /bin/bash rstudio
 
 # install into the default environment
 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
 
-

From 5121c63926bcb5b92fe306afaf535c2948870c2e Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Sat, 3 Feb 2024 23:29:41 -0800
Subject: [PATCH 30/59] :broom:

---
 .devcontainer/Dockerfile       | 4 ++--
 .devcontainer/conda.Dockerfile | 8 +++-----
 .devcontainer/install.R        | 2 +-
 .devcontainer/venv.Dockerfile  | 7 ++++---
 4 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index e3b7df4f3..9efb06a4f 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -29,7 +29,7 @@ RUN git config --system pull.rebase false && \
     git config --system credential.helper 'cache --timeout=36000'
 
 ## codeserver
-RUN curl -fsSL https://code-server.dev/install.sh | sh
+RUN curl -fsSL https://code-server.dev/install.sh | sh && rm -rf .cache
 
 
 ## Openscapes-specific configs
@@ -38,7 +38,7 @@ WORKDIR /home/rstudio
 RUN usermod -s /bin/bash rstudio
 
 # install into the default environment
-COPY requirements.txt requirements.txt
+COPY nasa-requirements.txt requirements.txt
 RUN python -m pip install -r requirements.txt && rm requirements.txt
 COPY install.R install.R
 RUN Rscript install.R && rm install.R
diff --git a/.devcontainer/conda.Dockerfile b/.devcontainer/conda.Dockerfile
index 2218c4236..4463c563e 100644
--- a/.devcontainer/conda.Dockerfile
+++ b/.devcontainer/conda.Dockerfile
@@ -2,11 +2,11 @@
 FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
 
 # latest version of geospatial libs
-RUN /rocker_scripts/experimental/install_dev_osgeo.sh
+RUN /rocker_scripts/experimental/install_dev_osgeo.sh && rm -rf /build_*
 RUN apt-get update -qq && apt-get -y install vim
 
 # podman doesn't not understand group permissions
-RUN chown rstudio:staff -R ${R_HOME}/site-library
+# RUN chown rstudio:staff -R ${R_HOME}/site-library
 
 # some teaching preferences
 RUN git config --system pull.rebase false && \
@@ -42,7 +42,5 @@ COPY install.R install.R
 RUN Rscript install.R && rm install.R
 
 COPY environment.yml environment.yml
-RUN conda env create -p ${MY_ENV} -f environment.yml
-
-RUN rm -rf .cache && conda clean --all
+RUN conda env create -p ${MY_ENV} -f environment.yml && conda clean --all
 
diff --git a/.devcontainer/install.R b/.devcontainer/install.R
index f4e85dc93..2c7a2835f 100755
--- a/.devcontainer/install.R
+++ b/.devcontainer/install.R
@@ -6,7 +6,7 @@
 # Likewise, pak insists on installing old gdal from apt instead of respecting system library source builds
 # install.packages("pak")
 install.packages(c("rstac", "spData", "earthdatalogin", "quarto", "aws.s3", "tmap"))
-remotes::install_github('r-tmap/tmap')
+remotes::install_github('r-tmap/tmap', upgrade=FALSE)
 
 #pak::pkg_install("httpgd")
 #pak::pkg_install(c("IRkernel", "languageserver"))
diff --git a/.devcontainer/venv.Dockerfile b/.devcontainer/venv.Dockerfile
index 7bf6a108f..858f7111a 100644
--- a/.devcontainer/venv.Dockerfile
+++ b/.devcontainer/venv.Dockerfile
@@ -2,7 +2,7 @@
 FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
 
 ## latest version of geospatial libs
-RUN /rocker_scripts/experimental/install_dev_osgeo.sh
+RUN /rocker_scripts/experimental/install_dev_osgeo.sh && rm -rf build_*
 RUN apt-get update -qq && apt-get -y install vim
 
 # standard python/jupyter setup
@@ -13,14 +13,15 @@ RUN /rocker_scripts/install_python.sh && \
   chown ${NB_USER}:staff -R ${VIRTUAL_ENV}
 
 # podman doesn't not understand group permissions
-RUN chown ${NB_USER}:staff -R ${R_HOME}/site-library
+# RUN chown ${NB_USER}:staff -R ${R_HOME}/site-library
+RUN chown ${NB_USER}:staff ${R_HOME}/site-library
 
 # some teaching preferences
 RUN git config --system pull.rebase false && \
     git config --system credential.helper 'cache --timeout=36000'
 
 ## codeserver
-RUN curl -fsSL https://code-server.dev/install.sh | sh
+RUN curl -fsSL https://code-server.dev/install.sh | sh && rm -rf .cache
 
 ## Openscapes-specific configs
 USER rstudio

From f0a3cd1d05cb4db29b86d94a6719c5da6d316ab5 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Sat, 3 Feb 2024 23:40:50 -0800
Subject: [PATCH 31/59] permissions

---
 .devcontainer/conda.Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.devcontainer/conda.Dockerfile b/.devcontainer/conda.Dockerfile
index 4463c563e..5847a74d2 100644
--- a/.devcontainer/conda.Dockerfile
+++ b/.devcontainer/conda.Dockerfile
@@ -5,8 +5,8 @@ FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
 RUN /rocker_scripts/experimental/install_dev_osgeo.sh && rm -rf /build_*
 RUN apt-get update -qq && apt-get -y install vim
 
-# podman doesn't not understand group permissions
-# RUN chown rstudio:staff -R ${R_HOME}/site-library
+# podman doesn't understand group permissions
+RUN chown rstudio:staff ${R_HOME}/site-library
 
 # some teaching preferences
 RUN git config --system pull.rebase false && \

From 4b34a1313e49c9d08665ca2a7ef0017b591c17a5 Mon Sep 17 00:00:00 2001
From: Carl Boettiger <cboettig@gmail.com>
Date: Sat, 3 Feb 2024 23:48:19 -0800
Subject: [PATCH 32/59] Update devcontainer.json

---
 .devcontainer/devcontainer.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 43f3b554e..6dd5904c8 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,5 +1,5 @@
 {
-	  "image": "ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:venv",
+	  "image": "docker.io/cboettig/nasa:venv",
 	  "runArgs": [ "--security-opt", "seccomp=unconfined" ],
 	  "name": "NASA OpenScapes Environment"
 }

From 868f75ba67076a2b64fba0ec5070ee0c32070de2 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Sun, 4 Feb 2024 00:01:33 -0800
Subject: [PATCH 33/59] single conda env

---
 .devcontainer/conda.Dockerfile | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/.devcontainer/conda.Dockerfile b/.devcontainer/conda.Dockerfile
index 5847a74d2..332413349 100644
--- a/.devcontainer/conda.Dockerfile
+++ b/.devcontainer/conda.Dockerfile
@@ -24,9 +24,6 @@ RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/downloa
     chown ${NB_USER}:staff -R ${CONDA_ENV} && \
     rm Miniforge3*.sh *.deb
 
-# Set up a primary conda environment distinct from (base)
-ENV MY_ENV=${CONDA_ENV}/envs/openscapes
-ENV PATH=${MY_ENV}/bin:${PATH}
 RUN echo "PATH=${PATH}" >>"${R_HOME}/etc/Renviron.site"
 
 # Initialize conda by default for all users:
@@ -42,5 +39,5 @@ COPY install.R install.R
 RUN Rscript install.R && rm install.R
 
 COPY environment.yml environment.yml
-RUN conda env create -p ${MY_ENV} -f environment.yml && conda clean --all
+RUN conda env create -p ${CONDA_ENV} -f environment.yml && conda clean --all
 

From e944da613240a1b2d0022b0f9df10df454714600 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Sun, 4 Feb 2024 00:08:40 -0800
Subject: [PATCH 34/59] single conda env?

---
 .devcontainer/conda.Dockerfile | 2 +-
 .devcontainer/environment.yml  | 1 +
 .devcontainer/install.R        | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.devcontainer/conda.Dockerfile b/.devcontainer/conda.Dockerfile
index 332413349..d436df1cd 100644
--- a/.devcontainer/conda.Dockerfile
+++ b/.devcontainer/conda.Dockerfile
@@ -39,5 +39,5 @@ COPY install.R install.R
 RUN Rscript install.R && rm install.R
 
 COPY environment.yml environment.yml
-RUN conda env create -p ${CONDA_ENV} -f environment.yml && conda clean --all
+RUN conda env update -f environment.yml && conda clean --all
 
diff --git a/.devcontainer/environment.yml b/.devcontainer/environment.yml
index e17a0a114..05e2e4dfc 100644
--- a/.devcontainer/environment.yml
+++ b/.devcontainer/environment.yml
@@ -32,6 +32,7 @@ dependencies:
   - icepyx
   - joblib
   - pystac-client
+  - odc-stac
   - pydap
   - lxml
   - ipyleaflet
diff --git a/.devcontainer/install.R b/.devcontainer/install.R
index 2c7a2835f..285c58dc2 100755
--- a/.devcontainer/install.R
+++ b/.devcontainer/install.R
@@ -5,7 +5,7 @@
 # Does not provide a good way to ensure that sf/terra/gdalcubes are installed from source while other packages can be binary
 # Likewise, pak insists on installing old gdal from apt instead of respecting system library source builds
 # install.packages("pak")
-install.packages(c("rstac", "spData", "earthdatalogin", "quarto", "aws.s3", "tmap"))
+install.packages(c("rstac", "spData", "earthdatalogin", "quarto", "aws.s3", "tmap", "reticulate"))
 remotes::install_github('r-tmap/tmap', upgrade=FALSE)
 
 #pak::pkg_install("httpgd")

From 6852bd0ec2099a5c906f9d4c525fe58740ec4f48 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Sun, 4 Feb 2024 00:11:29 -0800
Subject: [PATCH 35/59] wip

---
 .devcontainer/conda2.Dockerfile | 46 +++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 .devcontainer/conda2.Dockerfile

diff --git a/.devcontainer/conda2.Dockerfile b/.devcontainer/conda2.Dockerfile
new file mode 100644
index 000000000..d65dbf788
--- /dev/null
+++ b/.devcontainer/conda2.Dockerfile
@@ -0,0 +1,46 @@
+# devcontainer-focused Rocker
+FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
+
+# latest version of geospatial libs
+RUN /rocker_scripts/experimental/install_dev_osgeo.sh && rm -rf /build_*
+RUN apt-get update -qq && apt-get -y install vim
+
+# podman doesn't understand group permissions
+RUN chown rstudio:staff ${R_HOME}/site-library
+
+# some teaching preferences
+RUN git config --system pull.rebase false && \
+    git config --system credential.helper 'cache --timeout=36000'
+
+# codeserver
+RUN curl -fsSL https://code-server.dev/install.sh | sh
+
+# Set up conda
+ENV NB_USER=rstudio
+ENV CONDA_ENV=/opt/miniforge3
+ENV PATH=${CONDA_ENV}/bin:${PATH}
+RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" && \
+    bash Miniforge3-$(uname)-$(uname -m).sh -b -p ${CONDA_ENV} && \
+    chown ${NB_USER}:staff -R ${CONDA_ENV} && \
+    rm Miniforge3*.sh *.deb
+
+# Set up a primary conda environment distinct from (base)
+ENV MY_ENV=${CONDA_ENV}/envs/openscapes
+ENV PATH=${MY_ENV}/bin:${PATH}
+RUN echo "PATH=${PATH}" >>"${R_HOME}/etc/Renviron.site"
+
+# Initialize conda by default for all users:
+# RUN conda init --system # will cause terminal to start in base 
+
+# Standard user setup here
+USER ${NB_USER} 
+WORKDIR /home/${NB_USER}
+RUN usermod -s /bin/bash ${NB_USER} 
+
+# install into the default environment
+COPY install.R install.R
+RUN Rscript install.R && rm install.R
+
+COPY environment.yml environment.yml
+RUN conda env create -p ${MY_ENV} -f environment.yml && conda clean --all
+

From 53c84e093b21563cd399ffe1d94253c9cbe12152 Mon Sep 17 00:00:00 2001
From: Carl Boettiger <cboettig@gmail.com>
Date: Sun, 4 Feb 2024 10:56:21 -0800
Subject: [PATCH 36/59] conda tag

---
 .github/workflows/docker-image.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml
index 3f9e161f1..59ae6e9b7 100644
--- a/.github/workflows/docker-image.yml
+++ b/.github/workflows/docker-image.yml
@@ -19,11 +19,11 @@ jobs:
       - name: Build the Docker image
         if: github.repository == 'eeholmes/earthdata-cloud-cookbook'
         run: |
-          docker build .devcontainer -f .devcontainer/conda.Dockerfile  --tag ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:latest
+          docker build .devcontainer -f .devcontainer/conda.Dockerfile  --tag ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:conda
           docker build .devcontainer -f .devcontainer/venv.Dockerfile  --tag ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:venv
       - name: Publish
         if: github.repository == 'eeholmes/earthdata-cloud-cookbook'
         run: |
-          docker push ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:latest
+          docker push ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:conda
           docker push ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:venv
 

From 9dc1cc309e6c9dad7c5bf9887041ca882d6aaa0a Mon Sep 17 00:00:00 2001
From: Carl Boettiger <cboettig@gmail.com>
Date: Sun, 4 Feb 2024 10:57:12 -0800
Subject: [PATCH 37/59] Update devcontainer.json

use the venv container because it's smaller
---
 .devcontainer/devcontainer.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 6dd5904c8..43f3b554e 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,5 +1,5 @@
 {
-	  "image": "docker.io/cboettig/nasa:venv",
+	  "image": "ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:venv",
 	  "runArgs": [ "--security-opt", "seccomp=unconfined" ],
 	  "name": "NASA OpenScapes Environment"
 }

From 47b34d668389a1620a7d0fa216f4510cdc9bd816 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Sun, 4 Feb 2024 11:19:05 -0800
Subject: [PATCH 38/59] vscode / codespaces stuff

---
 .devcontainer/devcontainer.json | 45 ++++++++++++++++++++++++++++++---
 .devcontainer/setup.sh          |  6 +++++
 .devcontainer/welcome.sh        | 16 ++++++++++++
 3 files changed, 64 insertions(+), 3 deletions(-)
 create mode 100755 .devcontainer/setup.sh
 create mode 100755 .devcontainer/welcome.sh

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 6dd5904c8..c76206d67 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,5 +1,44 @@
 {
-	  "image": "docker.io/cboettig/nasa:venv",
+	  "image": "ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:venv",
+    // container run args for gdal netcdf vsi access
 	  "runArgs": [ "--security-opt", "seccomp=unconfined" ],
-	  "name": "NASA OpenScapes Environment"
-}
+	  "name": "NASA TOPS Environment",
+	  "waitFor": "onCreateCommand",
+	  "features": {
+		"ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {}
+	  },
+	  "customizations": {
+		"codespaces": {
+			"openFiles": ["README.md"]
+		  },
+		  "vscode": {
+		  "settings": {
+			"r.rterm.linux": "/usr/local/bin/radian",
+			"r.bracketedPaste": true,
+			"r.plot.useHttpgd": true,
+			"[r]": {
+			  "editor.wordSeparators": "`~!@#%$^&*()-=+[{]}\\|;:'\",<>/?"
+			}
+		  },
+		  "extensions": [
+			"reditorsupport.r",
+			"rdebugger.r-debugger",
+			"ms-toolsai.jupyter",
+			"ms-python.python"			
+			]
+		}
+	  },
+	  // Forward the RStudio ports
+	  "forwardPorts": [8787],
+	  "portsAttributes": {
+		"8787": {
+			"label": "Rstudio",
+			"requireLocalPort": true,
+			"onAutoForward": "ignore"
+		}
+	  },
+	  // Use 'postCreateCommand' to run commands after the container is created.
+	  "postCreateCommand": "bash .devcontainer/setup.sh",
+	  "postAttachCommand": "sudo rstudio-server start &> /dev/null && bash .devcontainer/welcome.sh",
+	  "remoteUser": "rstudio"
+	}
diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh
new file mode 100755
index 000000000..b89dcf16d
--- /dev/null
+++ b/.devcontainer/setup.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+
+sudo cp /etc/rstudio/disable_auth_rserver.conf /etc/rstudio/rserver.conf
+sudo sudo bash -c 'echo "USER=rstudio" >>/etc/environment'
+sudo /init &> /dev/null &
+
diff --git a/.devcontainer/welcome.sh b/.devcontainer/welcome.sh
new file mode 100755
index 000000000..89aab9b8c
--- /dev/null
+++ b/.devcontainer/welcome.sh
@@ -0,0 +1,16 @@
+mkdir -p ~/.local/share/rstudio/projects_settings
+export RPROJ"=$(ls ${CODESPACE_VSCODE_FOLDER}/*.Rproj)"
+echo ${RPROJ} > ~/.local/share/rstudio/projects_settings/last-project-path
+
+
+# Construct the message
+message="## [Open in RStudio](https://$CODESPACE_NAME-8787.app.github.dev)
+"
+# Echo the message to the terminal
+echo "
+👋 Welcome to Codespaces! You are on our custom image. 
+   - It includes runtimes and tools for Python & R using Jupyter, Quarto, or RStudio 
+
+🌐 Open the RStudio editor here: https://$CODESPACE_NAME-8787.app.github.dev
+   - (This may take a few seconds to load, retry if necessary)
+"

From 7db4f933becc89402da7ea5b544c9ec90cda0e1c Mon Sep 17 00:00:00 2001
From: Carl Boettiger <cboettig@gmail.com>
Date: Sun, 4 Feb 2024 11:38:08 -0800
Subject: [PATCH 39/59] Update docker-image.yml

---
 .github/workflows/docker-image.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml
index 59ae6e9b7..b5029936c 100644
--- a/.github/workflows/docker-image.yml
+++ b/.github/workflows/docker-image.yml
@@ -2,7 +2,7 @@ name: Docker Image CI
 on:
   workflow_dispatch: null
   push:
-    paths: ['.devcontainer/*']
+    paths: ['.devcontainer/*.Dockerfile', '.devcontainer/*requirements.txt', '.devcontainer/environment.yml']
 jobs:
   build:
     runs-on: ubuntu-latest

From e2128e195d033b1d8e2c7a0540aeac2d23565673 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Sun, 4 Feb 2024 12:16:04 -0800
Subject: [PATCH 40/59] wip

---
 .devcontainer/nasa-requirements.txt | 46 ++++++++++++++++++-----------
 1 file changed, 28 insertions(+), 18 deletions(-)

diff --git a/.devcontainer/nasa-requirements.txt b/.devcontainer/nasa-requirements.txt
index c8dc3a7c5..0bbe7a5b6 100644
--- a/.devcontainer/nasa-requirements.txt
+++ b/.devcontainer/nasa-requirements.txt
@@ -1,31 +1,41 @@
 jupyterhub
 jupyterlab
 notebook
+jupyterlab-quarto
 jupyter-rsession-proxy
-jupyter-console==6.6.3
-jupyter-events==0.7.0
-jupyter-lsp==2.2.0
-jupyter_client==8.3.1
-jupyter_core==5.3.2
-jupyter_server==2.7.3
-jupyter_server_terminals==0.4.4
-jupyter-vscode-proxy==0.5
-jupyterlab-pygments==0.2.2
-jupyterlab-widgets==3.0.9
-jupyterlab_server==2.25.0
-nbconvert==7.8.0
-nbformat==5.9.2
-odc-stac==0.3.8
-planetary-computer==1.0.0
+jupyter-vscode-proxy
+jupyter-console
+jupyter-events
+jupyter-lsp
+jupyter_client
+jupyter_core
+jupyter_server
+jupyter_server_terminals
+jupyterlab-pygments
+jupyterlab-widgets
+jupyterlab_server
+gh-scoped-creds
+nbconvert
+nbformat
+odc-stac
+planetary-computer
 polars
 pyarrow
-pystac-client==0.7.5
-gh-scoped-creds
+pystac-client
 scikit-image
 hvplot
 geoviews
 earthaccess
 pyresample
 contextily
-pygeoweaver
+rioxarray
+geopandas
+rasterstats
+dask
+distributed
+h5netcdf
+h5py
+netCDF4
+zarr
+lxml
 

From f8e1640053d064534e5d1e0f41b62ffe487f209a Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Fri, 16 Feb 2024 16:54:01 -0500
Subject: [PATCH 41/59] Update Dockerfile

---
 .devcontainer/Dockerfile | 22 +++++++++++++---------
 1 file changed, 13 insertions(+), 9 deletions(-)

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index 9efb06a4f..003559173 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -22,36 +22,40 @@ RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/downloa
     chown ${NB_USER}:staff -R ${CONDA_ENV}
 
 # podman doesn't not understand group permissions
-RUN chown ${NB_USER}:staff -R ${R_HOME}/site-library
+# RUN chown ${NB_USER}:staff -R ${R_HOME}/site-library
 
-# some teaching preferences
+# some teaching preferences; might replace with gh-creds
 RUN git config --system pull.rebase false && \
     git config --system credential.helper 'cache --timeout=36000'
 
-## codeserver
+## codeserver; Add VSCode button
 RUN curl -fsSL https://code-server.dev/install.sh | sh && rm -rf .cache
 
+## Install the R packages into site library
+COPY install.R install.R
+RUN Rscript install.R && rm install.R
 
 ## Openscapes-specific configs
 USER rstudio
 WORKDIR /home/rstudio
+# make bash the user default
 RUN usermod -s /bin/bash rstudio
 
-# install into the default environment
+# install into the default venv environment
 COPY nasa-requirements.txt requirements.txt
 RUN python -m pip install -r requirements.txt && rm requirements.txt
-COPY install.R install.R
-RUN Rscript install.R && rm install.R
 
 # Create a conda-based env and install into it without using conda init/conda activate
 # (this yaml file doesn't include everything from pangeo, consider a different one...)
-ENV MY_ENV=${CONDA_ENV}/envs/openscapes
+# pangeo uses the name 'notebook'
+ENV ENV_NAME=notebook
+ENV MY_ENV=${CONDA_ENV}/envs/${ENV_NAME}
 RUN wget https://github.com/NASA-Openscapes/corn/raw/main/ci/environment.yml && \
     conda env create -p ${MY_ENV} -f environment.yml
 
-# This won't be the default enviornment but we register it
+# This won't be the default environment but we register it
 RUN ${MY_ENV}/bin/python -m pip install ipykernel && \
-    ${MY_ENV}/bin/python -m ipykernel install --prefix /opt/venv --name=openscapes
+    ${MY_ENV}/bin/python -m ipykernel install --prefix /opt/venv --name=${ENV_NAME}
 
 
 

From 1df1a41cdd7b222af0866176750ec9c7e825ef77 Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Fri, 16 Feb 2024 16:56:34 -0500
Subject: [PATCH 42/59] Update Dockerfile

---
 .devcontainer/Dockerfile | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index 9efb06a4f..082628fb2 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -3,6 +3,9 @@ FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
 
 ## latest version of geospatial libs
 RUN /rocker_scripts/experimental/install_dev_osgeo.sh
+
+## install vim for convenience
+## texlive installed for install_jupyter.sh because it tries to install some basic tex libraries
 RUN apt-get update -qq && apt-get -y install vim texlive
 
 # standard python/jupyter setup

From 4156d62f4dc7736214cd90dd5ba472e8da366e19 Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Fri, 16 Feb 2024 17:11:52 -0500
Subject: [PATCH 43/59] Update conda.Dockerfile

---
 .devcontainer/conda.Dockerfile | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/.devcontainer/conda.Dockerfile b/.devcontainer/conda.Dockerfile
index d436df1cd..66ba9697d 100644
--- a/.devcontainer/conda.Dockerfile
+++ b/.devcontainer/conda.Dockerfile
@@ -3,17 +3,15 @@ FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
 
 # latest version of geospatial libs
 RUN /rocker_scripts/experimental/install_dev_osgeo.sh && rm -rf /build_*
+# install vim for convenience
 RUN apt-get update -qq && apt-get -y install vim
 
-# podman doesn't understand group permissions
-RUN chown rstudio:staff ${R_HOME}/site-library
-
 # some teaching preferences
 RUN git config --system pull.rebase false && \
     git config --system credential.helper 'cache --timeout=36000'
 
-# codeserver
-RUN curl -fsSL https://code-server.dev/install.sh | sh
+# codeserver; Adds the VSCode button
+RUN curl -fsSL https://code-server.dev/install.sh | sh && rm -rf .cache
 
 # Set up conda
 ENV NB_USER=rstudio
@@ -22,22 +20,24 @@ ENV PATH=${CONDA_ENV}/bin:${PATH}
 RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" && \
     bash Miniforge3-$(uname)-$(uname -m).sh -b -p ${CONDA_ENV} && \
     chown ${NB_USER}:staff -R ${CONDA_ENV} && \
-    rm Miniforge3*.sh *.deb
+    rm -f Miniforge3*.sh *.deb
 
+# Tell RStudio how to find Python
 RUN echo "PATH=${PATH}" >>"${R_HOME}/etc/Renviron.site"
 
+# install R packages into the site library
+COPY install.R install.R
+RUN Rscript install.R && rm install.R
+
 # Initialize conda by default for all users:
 RUN conda init --system
 
 # Standard user setup here
 USER ${NB_USER} 
 WORKDIR /home/${NB_USER}
+# make bash default shell
 RUN usermod -s /bin/bash ${NB_USER} 
 
-# install into the default environment
-COPY install.R install.R
-RUN Rscript install.R && rm install.R
-
 COPY environment.yml environment.yml
 RUN conda env update -f environment.yml && conda clean --all
 

From 31ea9855e9c7d2eeaad9b6ce54721f938187adb5 Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Fri, 16 Feb 2024 17:28:50 -0500
Subject: [PATCH 44/59] Update welcome.sh

---
 .devcontainer/welcome.sh | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.devcontainer/welcome.sh b/.devcontainer/welcome.sh
index 89aab9b8c..e749423a1 100755
--- a/.devcontainer/welcome.sh
+++ b/.devcontainer/welcome.sh
@@ -1,8 +1,9 @@
+# Need to add this so that RStudio knows the project it is in
 mkdir -p ~/.local/share/rstudio/projects_settings
+
 export RPROJ"=$(ls ${CODESPACE_VSCODE_FOLDER}/*.Rproj)"
 echo ${RPROJ} > ~/.local/share/rstudio/projects_settings/last-project-path
 
-
 # Construct the message
 message="## [Open in RStudio](https://$CODESPACE_NAME-8787.app.github.dev)
 "
@@ -13,4 +14,8 @@ echo "
 
 🌐 Open the RStudio editor here: https://$CODESPACE_NAME-8787.app.github.dev
    - (This may take a few seconds to load, retry if necessary)
+
+🌐 Open the JupyterLab editor here: https://$CODESPACE_NAME.app.github.dev?editor=jupyter
+   - (This may take a few seconds to load, retry if necessary)
+
 "

From 92b35e9b899b394813940ff66ab102dbdc522d37 Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Fri, 16 Feb 2024 17:30:04 -0500
Subject: [PATCH 45/59] Update venv.Dockerfile

---
 .devcontainer/venv.Dockerfile | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.devcontainer/venv.Dockerfile b/.devcontainer/venv.Dockerfile
index 858f7111a..5440644e8 100644
--- a/.devcontainer/venv.Dockerfile
+++ b/.devcontainer/venv.Dockerfile
@@ -1,6 +1,9 @@
 ## devcontainer-focused Rocker
 FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
 
+## Set the default shell
+ENV SHELL=/bin/bash
+
 ## latest version of geospatial libs
 RUN /rocker_scripts/experimental/install_dev_osgeo.sh && rm -rf build_*
 RUN apt-get update -qq && apt-get -y install vim

From 1e0dc8bc6ca8ce7ce53332f8aad40f66b96a805c Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Fri, 16 Feb 2024 17:30:40 -0500
Subject: [PATCH 46/59] Update conda.Dockerfile

---
 .devcontainer/conda.Dockerfile | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.devcontainer/conda.Dockerfile b/.devcontainer/conda.Dockerfile
index d436df1cd..528a96f10 100644
--- a/.devcontainer/conda.Dockerfile
+++ b/.devcontainer/conda.Dockerfile
@@ -1,6 +1,9 @@
 # devcontainer-focused Rocker
 FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
 
+## Set the default shell
+ENV SHELL=/bin/bash
+
 # latest version of geospatial libs
 RUN /rocker_scripts/experimental/install_dev_osgeo.sh && rm -rf /build_*
 RUN apt-get update -qq && apt-get -y install vim

From 920b6f0e9ecb157470a242ce6d427778379abed5 Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Fri, 16 Feb 2024 17:35:44 -0500
Subject: [PATCH 47/59] Update venv.Dockerfile

---
 .devcontainer/venv.Dockerfile | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/.devcontainer/venv.Dockerfile b/.devcontainer/venv.Dockerfile
index 5440644e8..a16dd2171 100644
--- a/.devcontainer/venv.Dockerfile
+++ b/.devcontainer/venv.Dockerfile
@@ -6,6 +6,8 @@ ENV SHELL=/bin/bash
 
 ## latest version of geospatial libs
 RUN /rocker_scripts/experimental/install_dev_osgeo.sh && rm -rf build_*
+
+## install vim
 RUN apt-get update -qq && apt-get -y install vim
 
 # standard python/jupyter setup
@@ -15,10 +17,6 @@ ENV PATH=${VIRTUAL_ENV}/bin:${PATH}
 RUN /rocker_scripts/install_python.sh && \
   chown ${NB_USER}:staff -R ${VIRTUAL_ENV}
 
-# podman doesn't not understand group permissions
-# RUN chown ${NB_USER}:staff -R ${R_HOME}/site-library
-RUN chown ${NB_USER}:staff ${R_HOME}/site-library
-
 # some teaching preferences
 RUN git config --system pull.rebase false && \
     git config --system credential.helper 'cache --timeout=36000'
@@ -26,14 +24,16 @@ RUN git config --system pull.rebase false && \
 ## codeserver
 RUN curl -fsSL https://code-server.dev/install.sh | sh && rm -rf .cache
 
+## Install R packages into the site library
+COPY install.R install.R
+RUN Rscript install.R && rm install.R
+
 ## Openscapes-specific configs
 USER rstudio
 WORKDIR /home/rstudio
 RUN usermod -s /bin/bash rstudio
 
-# install into the default environment
+# install into the default venv environment
 COPY nasa-requirements.txt 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
 

From f84a70b217729b3c2766a347f4162ff06c6867fb Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Fri, 16 Feb 2024 17:41:23 -0500
Subject: [PATCH 48/59] Update venv.Dockerfile

---
 .devcontainer/venv.Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.devcontainer/venv.Dockerfile b/.devcontainer/venv.Dockerfile
index a16dd2171..9ec7310e7 100644
--- a/.devcontainer/venv.Dockerfile
+++ b/.devcontainer/venv.Dockerfile
@@ -11,6 +11,7 @@ RUN /rocker_scripts/experimental/install_dev_osgeo.sh && rm -rf build_*
 RUN apt-get update -qq && apt-get -y install vim
 
 # standard python/jupyter setup
+# install python that is with the ubuntu install
 ENV NB_USER=rstudio
 ENV VIRTUAL_ENV=/opt/venv
 ENV PATH=${VIRTUAL_ENV}/bin:${PATH}

From d4a4618ee891e97e441e6905076eab2a3a384ce3 Mon Sep 17 00:00:00 2001
From: Carl Boettiger <cboettig@gmail.com>
Date: Fri, 16 Feb 2024 15:29:43 -0800
Subject: [PATCH 49/59] Update docker-image.yml

---
 .github/workflows/docker-image.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml
index b5029936c..112ef4ae2 100644
--- a/.github/workflows/docker-image.yml
+++ b/.github/workflows/docker-image.yml
@@ -3,6 +3,7 @@ on:
   workflow_dispatch: null
   push:
     paths: ['.devcontainer/*.Dockerfile', '.devcontainer/*requirements.txt', '.devcontainer/environment.yml']
+    branches: main
 jobs:
   build:
     runs-on: ubuntu-latest

From b57deacb22350f57c32b0147f26ade16aa100413 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Fri, 16 Feb 2024 16:11:07 -0800
Subject: [PATCH 50/59] fix conda PATH

---
 .devcontainer/conda.Dockerfile | 17 ++++++++++++++---
 .devcontainer/install.R        |  6 +++---
 2 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/.devcontainer/conda.Dockerfile b/.devcontainer/conda.Dockerfile
index 17c2ff553..94c4b5c84 100644
--- a/.devcontainer/conda.Dockerfile
+++ b/.devcontainer/conda.Dockerfile
@@ -4,9 +4,10 @@ FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.3
 ## Set the default shell
 ENV SHELL=/bin/bash
 
-# latest version of geospatial libs
-RUN /rocker_scripts/experimental/install_dev_osgeo.sh && rm -rf /build_*
+# latest version of geospatial libs -- big! 
+# RUN /rocker_scripts/experimental/install_dev_osgeo.sh && rm -rf /build_*
 # install vim for convenience
+
 RUN apt-get update -qq && apt-get -y install vim
 
 # some teaching preferences
@@ -16,8 +17,14 @@ RUN git config --system pull.rebase false && \
 # codeserver; Adds the VSCode button
 RUN curl -fsSL https://code-server.dev/install.sh | sh && rm -rf .cache
 
+# Rename the rstudio user as jovyan
+RUN usermod -l jovyan rstudio && \
+    usermod -d /home/jovyan -m jovyan && \
+    groupmod -n jovyan rstudio
+
+
 # Set up conda
-ENV NB_USER=rstudio
+ENV NB_USER=jovyan
 ENV CONDA_ENV=/opt/miniforge3
 ENV PATH=${CONDA_ENV}/bin:${PATH}
 RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" && \
@@ -41,6 +48,10 @@ WORKDIR /home/${NB_USER}
 # make bash default shell
 RUN usermod -s /bin/bash ${NB_USER} 
 
+
+ENV NOTEBOOK_ENV=${CONDA_ENV}/envs/openscapes
+ENV PATH=${NOTEBOOK_ENV}/bin:${PATH}
+
 COPY environment.yml environment.yml
 RUN conda env update -f environment.yml && conda clean --all
 
diff --git a/.devcontainer/install.R b/.devcontainer/install.R
index 285c58dc2..5bf6b8c13 100755
--- a/.devcontainer/install.R
+++ b/.devcontainer/install.R
@@ -4,9 +4,9 @@
 # We could use renv.lock approach here instead, but will force re-creation of environment from scratch
 # Does not provide a good way to ensure that sf/terra/gdalcubes are installed from source while other packages can be binary
 # Likewise, pak insists on installing old gdal from apt instead of respecting system library source builds
-# install.packages("pak")
-install.packages(c("rstac", "spData", "earthdatalogin", "quarto", "aws.s3", "tmap", "reticulate"))
-remotes::install_github('r-tmap/tmap', upgrade=FALSE)
+install.packages("pak")
+pak::pkg_install(c("rstac", "spData", "earthdatalogin", "quarto", "aws.s3", "tmap", "reticulate"))
+pak::pkg_install('r-tmap/tmap')
 
 #pak::pkg_install("httpgd")
 #pak::pkg_install(c("IRkernel", "languageserver"))

From a795f505d1d99b42556eaa319734944f416b96b3 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Fri, 16 Feb 2024 16:46:43 -0800
Subject: [PATCH 51/59] set path for rstudio too

---
 .devcontainer/conda.Dockerfile | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/.devcontainer/conda.Dockerfile b/.devcontainer/conda.Dockerfile
index 94c4b5c84..f9614d457 100644
--- a/.devcontainer/conda.Dockerfile
+++ b/.devcontainer/conda.Dockerfile
@@ -32,6 +32,9 @@ RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/downloa
     chown ${NB_USER}:staff -R ${CONDA_ENV} && \
     rm -f Miniforge3*.sh *.deb
 
+ENV NOTEBOOK_ENV=${CONDA_ENV}/envs/openscapes
+ENV PATH=${NOTEBOOK_ENV}/bin:${PATH}
+
 # Tell RStudio how to find Python
 RUN echo "PATH=${PATH}" >>"${R_HOME}/etc/Renviron.site"
 
@@ -39,7 +42,6 @@ RUN echo "PATH=${PATH}" >>"${R_HOME}/etc/Renviron.site"
 COPY install.R install.R
 RUN Rscript install.R && rm install.R
 
-# Initialize conda by default for all users:
 RUN conda init --system
 
 # Standard user setup here
@@ -48,10 +50,6 @@ WORKDIR /home/${NB_USER}
 # make bash default shell
 RUN usermod -s /bin/bash ${NB_USER} 
 
-
-ENV NOTEBOOK_ENV=${CONDA_ENV}/envs/openscapes
-ENV PATH=${NOTEBOOK_ENV}/bin:${PATH}
-
 COPY environment.yml environment.yml
 RUN conda env update -f environment.yml && conda clean --all
 

From 7ebd2c93f32de4f9e72a1049bdc14bd87db668cf Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Fri, 16 Feb 2024 16:59:58 -0800
Subject: [PATCH 52/59] follow pangeo for conda decorators

---
 .devcontainer/conda.Dockerfile | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/.devcontainer/conda.Dockerfile b/.devcontainer/conda.Dockerfile
index f9614d457..7a6a5b466 100644
--- a/.devcontainer/conda.Dockerfile
+++ b/.devcontainer/conda.Dockerfile
@@ -25,15 +25,20 @@ RUN usermod -l jovyan rstudio && \
 
 # Set up conda
 ENV NB_USER=jovyan
-ENV CONDA_ENV=/opt/miniforge3
-ENV PATH=${CONDA_ENV}/bin:${PATH}
+ENV CONDA_DIR=/opt/miniforge3
+ENV CONDA_ENV=openscapes
+ENV NB_PYTHON_PREFIX=${CONDA_DIR}/envs/${CONDA_ENV} 
+ENV PATH=${NB_PYTHON_PREFIX}/bin:/${CONDA_DIR}/bin:${PATH}
+
+# install conda
 RUN curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" && \
-    bash Miniforge3-$(uname)-$(uname -m).sh -b -p ${CONDA_ENV} && \
-    chown ${NB_USER}:staff -R ${CONDA_ENV} && \
+    bash Miniforge3-$(uname)-$(uname -m).sh -b -p ${CONDA_DIR} && \
+    chown ${NB_USER}:staff -R ${CONDA_DIR} && \
     rm -f Miniforge3*.sh *.deb
 
-ENV NOTEBOOK_ENV=${CONDA_ENV}/envs/openscapes
-ENV PATH=${NOTEBOOK_ENV}/bin:${PATH}
+# conda decorators
+RUN conda init --system
+RUN echo ". ${CONDA_DIR}/etc/profile.d/conda.sh ; conda activate ${CONDA_ENV}" > /etc/profile.d/init_conda.sh
 
 # Tell RStudio how to find Python
 RUN echo "PATH=${PATH}" >>"${R_HOME}/etc/Renviron.site"
@@ -42,8 +47,6 @@ RUN echo "PATH=${PATH}" >>"${R_HOME}/etc/Renviron.site"
 COPY install.R install.R
 RUN Rscript install.R && rm install.R
 
-RUN conda init --system
-
 # Standard user setup here
 USER ${NB_USER} 
 WORKDIR /home/${NB_USER}

From 79d84b79656afdb447c8cf2a361ea5f0f10db660 Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Fri, 16 Feb 2024 22:43:20 -0500
Subject: [PATCH 53/59] Create docker-build-conda.yml

---
 .github/workflows/docker-build-conda.yml | 30 ++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 .github/workflows/docker-build-conda.yml

diff --git a/.github/workflows/docker-build-conda.yml b/.github/workflows/docker-build-conda.yml
new file mode 100644
index 000000000..d2835361b
--- /dev/null
+++ b/.github/workflows/docker-build-conda.yml
@@ -0,0 +1,30 @@
+name: Docker Image CI conda
+on:
+  workflow_dispatch: null
+  push:
+    paths:
+      - '.devcontainer/conda.Dockerfile'
+      - '.devcontainer/environment.yml'
+      - '.github/workflows/docker-build-conda.yml'
+    branches: main
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions: write-all
+    steps:
+      - uses: actions/checkout@v3
+      - name: Login to GitHub Container Registry
+        if: github.repository == 'eeholmes/earthdata-cloud-cookbook'
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{github.actor}}
+          password: ${{secrets.GITHUB_TOKEN}}
+      - name: Build the Docker image
+        if: github.repository == 'eeholmes/earthdata-cloud-cookbook'
+        run: |
+          docker build .devcontainer -f .devcontainer/conda.Dockerfile  --tag ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook-conda:latest
+      - name: Publish
+        if: github.repository == 'eeholmes/earthdata-cloud-cookbook'
+        run: |
+          docker push ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook-conda:latest

From f3bdb058cdc91b9dd2cbd70d3c25170dd40bf1e1 Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Fri, 16 Feb 2024 22:43:40 -0500
Subject: [PATCH 54/59] Rename docker-build-conda.yml to docker-image-conda.yml

---
 .../workflows/{docker-build-conda.yml => docker-image-conda.yml}  | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename .github/workflows/{docker-build-conda.yml => docker-image-conda.yml} (100%)

diff --git a/.github/workflows/docker-build-conda.yml b/.github/workflows/docker-image-conda.yml
similarity index 100%
rename from .github/workflows/docker-build-conda.yml
rename to .github/workflows/docker-image-conda.yml

From 36d16b5b48c007ead7d1e89abee8eef7b4559b97 Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Fri, 16 Feb 2024 22:44:13 -0500
Subject: [PATCH 55/59] Rename docker-image.yml to docker-image-venv.yml

---
 .github/workflows/{docker-image.yml => docker-image-venv.yml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename .github/workflows/{docker-image.yml => docker-image-venv.yml} (100%)

diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image-venv.yml
similarity index 100%
rename from .github/workflows/docker-image.yml
rename to .github/workflows/docker-image-venv.yml

From e85e6c1b5ec668a535f6cb8983a7f37dfd989297 Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Fri, 16 Feb 2024 22:46:52 -0500
Subject: [PATCH 56/59] Update docker-image-venv.yml

---
 .github/workflows/docker-image-venv.yml | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/docker-image-venv.yml b/.github/workflows/docker-image-venv.yml
index 112ef4ae2..9fa4ceb2a 100644
--- a/.github/workflows/docker-image-venv.yml
+++ b/.github/workflows/docker-image-venv.yml
@@ -1,8 +1,11 @@
-name: Docker Image CI
+name: Docker Image CI venv
 on:
   workflow_dispatch: null
   push:
-    paths: ['.devcontainer/*.Dockerfile', '.devcontainer/*requirements.txt', '.devcontainer/environment.yml']
+    paths:
+      - '.devcontainer/venv.Dockerfile'
+      - '.devcontainer/nasa-requirements.txt'
+      - '.github/workflows/docker-image-venv.yml'
     branches: main
 jobs:
   build:
@@ -20,11 +23,9 @@ jobs:
       - name: Build the Docker image
         if: github.repository == 'eeholmes/earthdata-cloud-cookbook'
         run: |
-          docker build .devcontainer -f .devcontainer/conda.Dockerfile  --tag ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:conda
-          docker build .devcontainer -f .devcontainer/venv.Dockerfile  --tag ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:venv
+          docker build .devcontainer -f .devcontainer/venv.Dockerfile  --tag ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook-venv:latest
       - name: Publish
         if: github.repository == 'eeholmes/earthdata-cloud-cookbook'
         run: |
-          docker push ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:conda
-          docker push ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook:venv
+          docker push ghcr.io/eeholmes/earthdata-cloud-cookbook/cookbook-venv:latest
 

From 324a8ad1a8cb55eb7b06ea743e9b7c0a5d8b5cd2 Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Thu, 14 Mar 2024 11:33:31 -0700
Subject: [PATCH 57/59] Update conda.Dockerfile

---
 .devcontainer/conda.Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.devcontainer/conda.Dockerfile b/.devcontainer/conda.Dockerfile
index 7a6a5b466..9e03c16cb 100644
--- a/.devcontainer/conda.Dockerfile
+++ b/.devcontainer/conda.Dockerfile
@@ -55,4 +55,5 @@ RUN usermod -s /bin/bash ${NB_USER}
 
 COPY environment.yml environment.yml
 RUN conda env update -f environment.yml && conda clean --all
+RUN rm environment.yml
 

From 3baf4332cd0970ebc46e3fa4f589820fb1f727da Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Thu, 14 Mar 2024 11:34:41 -0700
Subject: [PATCH 58/59] Update conda2.Dockerfile

---
 .devcontainer/conda2.Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.devcontainer/conda2.Dockerfile b/.devcontainer/conda2.Dockerfile
index d65dbf788..d4306bfe1 100644
--- a/.devcontainer/conda2.Dockerfile
+++ b/.devcontainer/conda2.Dockerfile
@@ -40,6 +40,7 @@ RUN usermod -s /bin/bash ${NB_USER}
 # install into the default environment
 COPY install.R install.R
 RUN Rscript install.R && rm install.R
+RUN rm install.R
 
 COPY environment.yml environment.yml
 RUN conda env create -p ${MY_ENV} -f environment.yml && conda clean --all

From 5dff0e4bd48184937ad9a40c8826a4d8e606444e Mon Sep 17 00:00:00 2001
From: Eli Holmes - NOAA <eli.holmes@noaa.gov>
Date: Thu, 14 Mar 2024 11:35:44 -0700
Subject: [PATCH 59/59] Update venv.Dockerfile

---
 .devcontainer/venv.Dockerfile | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.devcontainer/venv.Dockerfile b/.devcontainer/venv.Dockerfile
index 9ec7310e7..85f6ac30a 100644
--- a/.devcontainer/venv.Dockerfile
+++ b/.devcontainer/venv.Dockerfile
@@ -28,6 +28,7 @@ RUN curl -fsSL https://code-server.dev/install.sh | sh && rm -rf .cache
 ## Install R packages into the site library
 COPY install.R install.R
 RUN Rscript install.R && rm install.R
+RUN rm install.R
 
 ## Openscapes-specific configs
 USER rstudio
@@ -37,4 +38,5 @@ RUN usermod -s /bin/bash rstudio
 # install into the default venv environment
 COPY nasa-requirements.txt requirements.txt
 RUN python -m pip install --no-cache-dir -r requirements.txt && rm requirements.txt
+RUN rm requirements.txt