From 301eb1c00cc8c0b6c280e12b6714ebc0e3c1b046 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Fri, 20 Sep 2024 15:29:57 -0700
Subject: [PATCH 01/11] wip

---
 jupyterhub/public-config.yaml | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/jupyterhub/public-config.yaml b/jupyterhub/public-config.yaml
index 72de6ab..64f7b89 100644
--- a/jupyterhub/public-config.yaml
+++ b/jupyterhub/public-config.yaml
@@ -28,6 +28,15 @@ singleuser:
       - name: shm-volume
         emptyDir:
           medium: Memory
+  extraFiles:
+    jupyter_server_config.json:
+        mountPath: /usr/local/etc/jupyter/jupyter_server_config.json
+        data:
+          # Allow JupyterLab to show the 'View -> Show Hidden Files' option
+          # in the menu. Defaults are not changed.
+          # https://github.com/jupyterlab/jupyterlab/issues/11304#issuecomment-945466766
+          ContentsManager:
+            allow_hidden: true
   profileList:
     - display_name: "CPU"
       slug: rocker
@@ -52,8 +61,13 @@ singleuser:
               kubespawner_override:
                 mem_guarantee: 59861460992
                 mem_limit: 59861460992
+            special:
+              display_name: Special-use (up to 120 GB RAM)
+              kubespawner_override:
+                mem_guarantee: 59861460992
+                mem_limit: 122861460992
       kubespawner_override:
-        image: zcr.thelio.carlboettiger.info/boettiger-lab/k8s:latest
+        image: "ghcr.io/boettiger-lab/k8s:latest"
         default_url: /lab # change to /rstudio to go straight to RStudio
         working_dir: /home/rstudio
     - display_name: "GPU"
@@ -62,7 +76,7 @@ singleuser:
       profile_options:
         resource_allocation: *profile_options_resource_allocation 
       kubespawner_override:
-        image: zcr.thelio.carlboettiger.info/boettiger-lab/k8s-gpu:latest 
+        image: "ghcr.io/boettiger-lab/k8s-gpu:latest"
         default_url: /lab # change to /rstudio to go straight to RStudio
         working_dir: /home/rstudio
     - display_name: "Pangeo"
@@ -85,6 +99,7 @@ singleuser:
               image: "{value}"
           choices: {}
 hub:
+  allowNamedServers: true
   config:
     # Shared settings. we don't need nvidia to be default
     KubeSpawner:

From 4d7a12a7374b0841078689b311aa9b0ea4c5fe9a Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Fri, 20 Sep 2024 17:09:43 -0700
Subject: [PATCH 02/11] pytorch

---
 .github/workflows/pytorch-image.yml | 34 +++++++++++++++++++++++++++++
 images/Dockerfile.pytorch           |  4 ++++
 images/jupyter-ai.yml               |  7 ++++++
 3 files changed, 45 insertions(+)
 create mode 100644 .github/workflows/pytorch-image.yml
 create mode 100644 images/Dockerfile.pytorch
 create mode 100644 images/jupyter-ai.yml

diff --git a/.github/workflows/pytorch-image.yml b/.github/workflows/pytorch-image.yml
new file mode 100644
index 0000000..1b670da
--- /dev/null
+++ b/.github/workflows/pytorch-image.yml
@@ -0,0 +1,34 @@
+name: Docker GPU Image
+on:
+  workflow_dispatch: null
+  push:
+    paths: ['images/*']
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions: write-all
+    steps:
+    # For biggish images, github actions runs out of disk space.
+    # So we cleanup some unwanted things in the disk image, and reclaim that space for our docker use
+    # https://github.com/actions/virtual-environments/issues/2606#issuecomment-772683150
+    # and https://github.com/easimon/maximize-build-space/blob/b4d02c14493a9653fe7af06cc89ca5298071c66e/action.yml#L104
+    # This gives us a total of about 52G of free space, which should be enough for now
+      - name: cleanup disk space
+        run: |
+          sudo rm -rf /usr/local/lib/android /usr/share/dotnet /opt/ghc
+          df -h
+      - uses: actions/checkout@v3
+      - name: Login to GitHub Container Registry
+        if: github.repository == 'boettiger-lab/k8s'
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{github.actor}}
+          password: ${{secrets.GITHUB_TOKEN}}
+      - name: Build the Docker image
+        if: github.repository == 'boettiger-lab/k8s'
+        run: docker build images/ -f images/Dockerfile.pytorch --tag ghcr.io/boettiger-lab/pytorch:latest
+      - name: Publish
+        if: github.repository == 'boettiger-lab/k8s'
+        run: docker push ghcr.io/boettiger-lab/pytorch:latest
+
diff --git a/images/Dockerfile.pytorch b/images/Dockerfile.pytorch
new file mode 100644
index 0000000..5ffe3ec
--- /dev/null
+++ b/images/Dockerfile.pytorch
@@ -0,0 +1,4 @@
+FROM quay.io/jupyter/pytorch-notebook:cuda12-2024-04-22
+COPY jupyter-ai.yml environment.yml
+RUN conda env update --file environment.yml
+
diff --git a/images/jupyter-ai.yml b/images/jupyter-ai.yml
new file mode 100644
index 0000000..8c98215
--- /dev/null
+++ b/images/jupyter-ai.yml
@@ -0,0 +1,7 @@
+name: base 
+channels:
+  - conda-forge
+dependencies:
+  - jupyterlab-myst
+  - jupyter-ai
+

From 565b4eb9144aa38dbf8d65536f174ad205b35eb5 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Fri, 20 Sep 2024 19:54:28 -0700
Subject: [PATCH 03/11] more stuff

---
 images/Dockerfile.pytorch | 8 ++++++++
 images/jupyter-ai.yml     | 3 +++
 2 files changed, 11 insertions(+)

diff --git a/images/Dockerfile.pytorch b/images/Dockerfile.pytorch
index 5ffe3ec..bc2f3b3 100644
--- a/images/Dockerfile.pytorch
+++ b/images/Dockerfile.pytorch
@@ -2,3 +2,11 @@ FROM quay.io/jupyter/pytorch-notebook:cuda12-2024-04-22
 COPY jupyter-ai.yml environment.yml
 RUN conda env update --file environment.yml
 
+USER root
+RUN curl -L https://ollama.com/download/ollama-linux-amd64 -o /usr/local/bin/ollama && chmod +x /usr/local/bin/ollama
+RUN curl -fsSL https://code-server.dev/install.sh | sh && rm -rf .cache
+RUN git config --system pull.rebase false && \
+    git config --system credential.helper 'cache --timeout=30000' && \
+    echo '"\e[5~": history-search-backward' >> /etc/inputrc && \
+    echo '"\e[6~": history-search-forward' >> /etc/inputrc
+
diff --git a/images/jupyter-ai.yml b/images/jupyter-ai.yml
index 8c98215..1a6f808 100644
--- a/images/jupyter-ai.yml
+++ b/images/jupyter-ai.yml
@@ -4,4 +4,7 @@ channels:
 dependencies:
   - jupyterlab-myst
   - jupyter-ai
+  - jupyter-tensorboard-proxy 
+  - jupyter-resource-usage
+  - jupyter-vscode-proxy
 

From c69bf2ae0b8fd67387fc1e4d0de884713ceeed71 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Fri, 20 Sep 2024 20:27:45 -0700
Subject: [PATCH 04/11] update

---
 images/jupyter-ai.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/images/jupyter-ai.yml b/images/jupyter-ai.yml
index 1a6f808..3a7aca9 100644
--- a/images/jupyter-ai.yml
+++ b/images/jupyter-ai.yml
@@ -4,7 +4,8 @@ channels:
 dependencies:
   - jupyterlab-myst
   - jupyter-ai
-  - jupyter-tensorboard-proxy 
   - jupyter-resource-usage
   - jupyter-vscode-proxy
+  - pip:
+    - jupyter-tensorboard-proxy
 

From 71a39ff1f98d703aa9da7dba25d8439a7dfcdbdd Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Fri, 20 Sep 2024 20:32:57 -0700
Subject: [PATCH 05/11] rename action

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

diff --git a/.github/workflows/pytorch-image.yml b/.github/workflows/pytorch-image.yml
index 1b670da..a7912c3 100644
--- a/.github/workflows/pytorch-image.yml
+++ b/.github/workflows/pytorch-image.yml
@@ -1,4 +1,4 @@
-name: Docker GPU Image
+name: PyTorch-notebook Image
 on:
   workflow_dispatch: null
   push:

From 21852a00c472bbd4a39eecd32db58df42e038f7e Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Fri, 20 Sep 2024 21:10:32 -0700
Subject: [PATCH 06/11] here we go!

---
 images/Dockerfile.pytorch | 6 ++++--
 images/jupyter-ai.yml     | 1 +
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/images/Dockerfile.pytorch b/images/Dockerfile.pytorch
index bc2f3b3..3b241a5 100644
--- a/images/Dockerfile.pytorch
+++ b/images/Dockerfile.pytorch
@@ -1,6 +1,8 @@
-FROM quay.io/jupyter/pytorch-notebook:cuda12-2024-04-22
+FROM quay.io/jupyter/pytorch-notebook:cuda12-ubuntu-24.04
 COPY jupyter-ai.yml environment.yml
-RUN conda env update --file environment.yml
+
+RUN conda update -n base -c conda-forge conda && \
+    conda env update --file environment.yml
 
 USER root
 RUN curl -L https://ollama.com/download/ollama-linux-amd64 -o /usr/local/bin/ollama && chmod +x /usr/local/bin/ollama
diff --git a/images/jupyter-ai.yml b/images/jupyter-ai.yml
index 3a7aca9..2cc1106 100644
--- a/images/jupyter-ai.yml
+++ b/images/jupyter-ai.yml
@@ -6,6 +6,7 @@ dependencies:
   - jupyter-ai
   - jupyter-resource-usage
   - jupyter-vscode-proxy
+  - pip
   - pip:
     - jupyter-tensorboard-proxy
 

From fc8c5ab249d1984c574274c8ae999a2544cb3c2c Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Fri, 20 Sep 2024 21:15:02 -0700
Subject: [PATCH 07/11] names

---
 .github/workflows/jupyter-image.yml |   2 +-
 github-actions/.gitignore           |   2 +
 github-actions/arc_values.yaml      | 132 ----------------------------
 jupyterhub/cirrus.sh                |   4 +-
 4 files changed, 5 insertions(+), 135 deletions(-)
 create mode 100644 github-actions/.gitignore
 delete mode 100644 github-actions/arc_values.yaml

diff --git a/.github/workflows/jupyter-image.yml b/.github/workflows/jupyter-image.yml
index c2d1280..7f54b8c 100644
--- a/.github/workflows/jupyter-image.yml
+++ b/.github/workflows/jupyter-image.yml
@@ -1,4 +1,4 @@
-name: Docker Image CI
+name: Jupyter Image
 on:
   workflow_dispatch: null
   push:
diff --git a/github-actions/.gitignore b/github-actions/.gitignore
new file mode 100644
index 0000000..487fe52
--- /dev/null
+++ b/github-actions/.gitignore
@@ -0,0 +1,2 @@
+helm-secrets.sh
+
diff --git a/github-actions/arc_values.yaml b/github-actions/arc_values.yaml
deleted file mode 100644
index 8e74317..0000000
--- a/github-actions/arc_values.yaml
+++ /dev/null
@@ -1,132 +0,0 @@
-# Default values for gha-runner-scale-set-controller.
-# This is a YAML-formatted file.
-# Declare variables to be passed into your templates.
-labels: {}
-
-# leaderElection will be enabled when replicaCount>1,
-# So, only one replica will in charge of reconciliation at a given time
-# leaderElectionId will be set to {{ define gha-runner-scale-set-controller.fullname }}.
-replicaCount: 1
-
-image:
-  repository: "ghcr.io/actions/gha-runner-scale-set-controller"
-  pullPolicy: IfNotPresent
-  # Overrides the image tag whose default is the chart appVersion.
-  tag: ""
-
-imagePullSecrets: []
-nameOverride: ""
-fullnameOverride: ""
-
-env:
-## Define environment variables for the controller pod
-#  - name: "ENV_VAR_NAME_1"
-#    value: "ENV_VAR_VALUE_1"
-#  - name: "ENV_VAR_NAME_2"
-#    valueFrom:
-#      secretKeyRef:
-#        key: ENV_VAR_NAME_2
-#        name: secret-name
-#        optional: true
-
-serviceAccount:
-  # Specifies whether a service account should be created for running the controller pod
-  create: true
-  # Annotations to add to the service account
-  annotations: {}
-  # The name of the service account to use.
-  # If not set and create is true, a name is generated using the fullname template
-  # You can not use the default service account for this.
-  name: ""
-
-podAnnotations: {}
-
-podLabels: {}
-
-podSecurityContext: {}
-# fsGroup: 2000
-
-securityContext: {}
-# capabilities:
-#   drop:
-#   - ALL
-# readOnlyRootFilesystem: true
-# runAsNonRoot: true
-# runAsUser: 1000
-
-resources: {}
-## We usually recommend not to specify default resources and to leave this as a conscious
-## choice for the user. This also increases chances charts run on environments with little
-## resources, such as Minikube. If you do want to specify resources, uncomment the following
-## lines, adjust them as necessary, and remove the curly braces after 'resources:'.
-# limits:
-#   cpu: 100m
-#   memory: 128Mi
-# requests:
-#   cpu: 100m
-#   memory: 128Mi
-
-nodeSelector: {}
-
-tolerations: []
-
-affinity: {}
-
-topologySpreadConstraints: []
-
-# Mount volumes in the container.
-volumes: []
-volumeMounts: []
-
-# Leverage a PriorityClass to ensure your pods survive resource shortages
-# ref: https://kubernetes.io/docs/concepts/configuration/pod-priority-preemption/
-# PriorityClass: system-cluster-critical
-priorityClassName: ""
-
-## If `metrics:` object is not provided, or commented out, the following flags
-## will be applied the controller-manager and listener pods with empty values:
-## `--metrics-addr`, `--listener-metrics-addr`, `--listener-metrics-endpoint`.
-## This will disable metrics.
-##
-## To enable metrics, uncomment the following lines.
-# metrics:
-#   controllerManagerAddr: ":8080"
-#   listenerAddr: ":8080"
-#   listenerEndpoint: "/metrics"
-
-flags:
-  ## Log level can be set here with one of the following values: "debug", "info", "warn", "error".
-  ## Defaults to "debug".
-  logLevel: "debug"
-  ## Log format can be set with one of the following values: "text", "json"
-  ## Defaults to "text"
-  logFormat: "text"
-
-  ## Restricts the controller to only watch resources in the desired namespace.
-  ## Defaults to watch all namespaces when unset.
-  # watchSingleNamespace: ""
-
-  ## Defines how the controller should handle upgrades while having running jobs.
-  ##
-  ## The strategies available are:
-  ## - "immediate": (default) The controller will immediately apply the change causing the
-  ##   recreation of the listener and ephemeral runner set. This can lead to an
-  ##   overprovisioning of runners, if there are pending / running jobs. This should not
-  ##   be a problem at a small scale, but it could lead to a significant increase of
-  ##   resources if you have a lot of jobs running concurrently.
-  ##
-  ## - "eventual": The controller will remove the listener and ephemeral runner set
-  ##   immediately, but will not recreate them (to apply changes) until all
-  ##   pending / running jobs have completed.
-  ##   This can lead to a longer time to apply the change but it will ensure
-  ##   that you don't have any overprovisioning of runners.
-  updateStrategy: "immediate"
-
-  ## Defines a list of prefixes that should not be propagated to internal resources.
-  ## This is useful when you have labels that are used for internal purposes and should not be propagated to internal resources.
-  ## See https://github.com/actions/actions-runner-controller/issues/3533 for more information.
-  ##
-  ## By default, all labels are propagated to internal resources
-  ## Labels that match prefix specified in the list are excluded from propagation.
-  # excludeLabelPropagationPrefixes:
-  #   - "argocd.argoproj.io/instance"
diff --git a/jupyterhub/cirrus.sh b/jupyterhub/cirrus.sh
index 3f75561..9e7d8a1 100755
--- a/jupyterhub/cirrus.sh
+++ b/jupyterhub/cirrus.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
-helm repo add jupyterhub https://hub.jupyter.org/helm-chart/
-helm repo update
+#helm repo add jupyterhub https://hub.jupyter.org/helm-chart/
+#helm repo update
 
 ## use your name for install name and namespace name
 helm upgrade --cleanup-on-fail \

From c597fb1463f4bfe46582e5b5c3417052e2b34a90 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Fri, 20 Sep 2024 21:15:42 -0700
Subject: [PATCH 08/11] conda+venv

---
 images/Dockerfile.dual | 57 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 images/Dockerfile.dual

diff --git a/images/Dockerfile.dual b/images/Dockerfile.dual
new file mode 100644
index 0000000..e3b7df4
--- /dev/null
+++ b/images/Dockerfile.dual
@@ -0,0 +1,57 @@
+## 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 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 && \
+  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} && \
+    chown ${NB_USER}:staff -R ${CONDA_ENV}
+
+# podman doesn't not understand group permissions
+RUN chown ${NB_USER}:staff -R ${R_HOME}/site-library
+
+# some teaching preferences
+RUN git config --system pull.rebase false && \
+    git config --system credential.helper 'cache --timeout=36000'
+
+## codeserver
+RUN curl -fsSL https://code-server.dev/install.sh | sh
+
+
+## Openscapes-specific configs
+USER rstudio
+WORKDIR /home/rstudio
+RUN usermod -s /bin/bash rstudio
+
+# install into the default environment
+COPY requirements.txt requirements.txt
+RUN python -m pip install -r requirements.txt && rm requirements.txt
+COPY install.R install.R
+RUN Rscript install.R && rm install.R
+
+# Create a conda-based env and install into it without using conda init/conda activate
+# (this yaml file doesn't include everything from pangeo, consider a different one...)
+ENV MY_ENV=${CONDA_ENV}/envs/openscapes
+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
+RUN ${MY_ENV}/bin/python -m pip install ipykernel && \
+    ${MY_ENV}/bin/python -m ipykernel install --prefix /opt/venv --name=openscapes
+
+
+

From e11b66bed9ffaaab558819a1ce59ebc0008b26af Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Fri, 20 Sep 2024 21:34:11 -0700
Subject: [PATCH 09/11] new ollama distribution mechanism

---
 images/Dockerfile.pytorch | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/images/Dockerfile.pytorch b/images/Dockerfile.pytorch
index 3b241a5..7435ac6 100644
--- a/images/Dockerfile.pytorch
+++ b/images/Dockerfile.pytorch
@@ -5,7 +5,8 @@ RUN conda update -n base -c conda-forge conda && \
     conda env update --file environment.yml
 
 USER root
-RUN curl -L https://ollama.com/download/ollama-linux-amd64 -o /usr/local/bin/ollama && chmod +x /usr/local/bin/ollama
+RUN curl -L https://ollama.com/download/ollama-linux-amd64.tgz -o ollama-linux-amd64.tgz && tar -C /usr -xzf ollama-linux-amd64.tgz
+
 RUN curl -fsSL https://code-server.dev/install.sh | sh && rm -rf .cache
 RUN git config --system pull.rebase false && \
     git config --system credential.helper 'cache --timeout=30000' && \

From 6d6b323bab532aae2cf836bc0fb287e0c4d07ace Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Wed, 25 Sep 2024 16:01:51 -0700
Subject: [PATCH 10/11] revised ollama

---
 images/Dockerfile.gpu | 3 +--
 images/jupyter-ai.yml | 1 +
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/images/Dockerfile.gpu b/images/Dockerfile.gpu
index c1a42b3..b5eb254 100644
--- a/images/Dockerfile.gpu
+++ b/images/Dockerfile.gpu
@@ -19,8 +19,7 @@ RUN curl -fsSL https://code-server.dev/install.sh | sh && rm -rf .cache
 #RUN wget https://github.com/coder/code-server/releases/download/v4.89.1/code-server_4.89.1_amd64.deb && dpkg -i code-server*.deb && rm code-server*.deb
 
 # ollama
-# RUN curl -fsSL https://ollama.com/install.sh | sh
-RUN curl -L https://ollama.com/download/ollama-linux-amd64 -o /usr/local/bin/ollama && chmod +x /usr/local/bin/ollama
+RUN curl -L https://ollama.com/download/ollama-linux-amd64.tgz -o ollama-linux-amd64.tgz && tar -C /usr -xzf ollama-linux-amd64.tgz
 
 
 # some preferences
diff --git a/images/jupyter-ai.yml b/images/jupyter-ai.yml
index 2cc1106..2e476dc 100644
--- a/images/jupyter-ai.yml
+++ b/images/jupyter-ai.yml
@@ -6,6 +6,7 @@ dependencies:
   - jupyter-ai
   - jupyter-resource-usage
   - jupyter-vscode-proxy
+  - pypdf
   - pip
   - pip:
     - jupyter-tensorboard-proxy

From 16a77fb1b94f3562ed6870cb1a469fbf9783d4d2 Mon Sep 17 00:00:00 2001
From: Carl <cboettig@gmail.com>
Date: Thu, 26 Sep 2024 08:42:26 -0700
Subject: [PATCH 11/11] new gpu image

---
 images/Dockerfile.gpu  | 54 +++++++++++++++---------------------------
 images/jupyter-ai.yml  |  2 ++
 images/rl-env.yml      | 20 ++++++++++++++++
 images/spatial-env.yml | 38 +++++++++++++++++++++++++++++
 4 files changed, 79 insertions(+), 35 deletions(-)
 create mode 100644 images/rl-env.yml
 create mode 100644 images/spatial-env.yml

diff --git a/images/Dockerfile.gpu b/images/Dockerfile.gpu
index b5eb254..2623353 100644
--- a/images/Dockerfile.gpu
+++ b/images/Dockerfile.gpu
@@ -1,51 +1,35 @@
-FROM docker.io/rocker/ml
+FROM quay.io/jupyter/pytorch-notebook:cuda12-ubuntu-24.04
 
-ENV NB_USER rstudio
-ENV VIRTUAL_ENV /opt/venv
-ENV PATH ${VIRTUAL_ENV}/bin:$PATH
+COPY jupyter-ai.yml environment.yml
+RUN conda update -n base -c conda-forge conda && \
+    conda env update --file environment.yml
 
-RUN /rocker_scripts/install_jupyter.sh
-RUN python3 -m pip install numpy
-RUN chown -R ${NB_USER}:staff ${VIRTUAL_ENV} && chmod -R g+rw ${VIRTUAL_ENV}
+USER root
+RUN curl -L https://ollama.com/download/ollama-linux-amd64.tgz -o ollama-linux-amd64.tgz && tar -C /usr -xzf ollama-linux-amd64.tgz
 
-RUN /rocker_scripts/experimental/install_dev_osgeo.sh
-RUN chown -R ${NB_USER}:staff ${VIRTUAL_ENV} && chmod -R g+rw ${VIRTUAL_ENV}
+RUN curl -fsSL https://code-server.dev/install.sh | sh && rm -rf .cache
+RUN git config --system pull.rebase false && \
+    echo '"\e[5~": history-search-backward' >> /etc/inputrc && \
+    echo '"\e[6~": history-search-forward' >> /etc/inputrc
+
+#git config --system credential.helper 'cache --timeout=30000' && \
 
-COPY apt.txt apt.txt
-RUN apt-get update -qq && xargs sudo apt-get -y install < apt.txt
+RUN apt-get update -qq && apt-get -y install vim git-lfs
 
 # install codeserver
 RUN curl -fsSL https://code-server.dev/install.sh | sh && rm -rf .cache
-#RUN wget https://github.com/coder/code-server/releases/download/v4.89.1/code-server_4.89.1_amd64.deb && dpkg -i code-server*.deb && rm code-server*.deb
 
 # ollama
 RUN curl -L https://ollama.com/download/ollama-linux-amd64.tgz -o ollama-linux-amd64.tgz && tar -C /usr -xzf ollama-linux-amd64.tgz
 
-
-# some preferences
-RUN git config --system pull.rebase false && \
-    git config --system credential.helper 'cache --timeout=30000' && \
-    echo '"\e[5~": history-search-backward' >> /etc/inputrc && \
-    echo '"\e[6~": history-search-forward' >> /etc/inputrc
-
 USER ${NB_USER}
-WORKDIR /home/${NB_USER}
-
-RUN usermod -s /bin/bash ${NB_USER}
-COPY spatial-requirements.txt /tmp/spatial-requirements.txt
-RUN python3 -m pip install --no-cache-dir -r /tmp/spatial-requirements.txt
-COPY rl-requirements.txt /tmp/rl-requirements.txt
-RUN python3 -m pip install --no-cache-dir -r /tmp/rl-requirements.txt
-COPY jupyter-requirements.txt /tmp/jupyter-requirements.txt
-RUN python3 -m pip install --no-cache-dir -r /tmp/jupyter-requirements.txt
-
-## Register the environment with ipykernel, mostly for vscode to find it
-RUN python3 -m ipykernel install --user --name=venv
+COPY spatial-env.yml spatial-env.yml
+RUN conda update -n base -c conda-forge conda && \
+    conda env update --file spatial-env.yml
 
+COPY rl-env.yml rl-env.yml
+RUN conda update -n base -c conda-forge conda && \
+    conda env update --file rl-env.yml
 
-#USER root 
-#COPY install.R /tmp/install.R
-#RUN Rscript /tmp/install.R && rm /tmp/install.R && chown -R ${NB_USER}:staff ${R_HOME}/site-library 
-#USER ${NB_USER}
 
 
diff --git a/images/jupyter-ai.yml b/images/jupyter-ai.yml
index 2e476dc..da4f940 100644
--- a/images/jupyter-ai.yml
+++ b/images/jupyter-ai.yml
@@ -2,12 +2,14 @@ name: base
 channels:
   - conda-forge
 dependencies:
+  - ibis-duckdb
   - jupyterlab-myst
   - jupyter-ai
   - jupyter-resource-usage
   - jupyter-vscode-proxy
   - pypdf
   - pip
+  - seaborn
   - pip:
     - jupyter-tensorboard-proxy
 
diff --git a/images/rl-env.yml b/images/rl-env.yml
new file mode 100644
index 0000000..52a9be6
--- /dev/null
+++ b/images/rl-env.yml
@@ -0,0 +1,20 @@
+name: base 
+channels:
+  - conda-forge
+dependencies:
+  - darts
+  - gymnasium
+  - gputil
+  - huggingface_hub
+  - nox
+  - nvitop
+  - plotnine
+  - PyYaml
+  - pytest
+  - stable-baselines3
+  - sb3-contrib
+  - scikit-optimize
+  - pip:
+    - ray[rllib,tune]
+    - huggingface_sb3
+
diff --git a/images/spatial-env.yml b/images/spatial-env.yml
new file mode 100644
index 0000000..d104af8
--- /dev/null
+++ b/images/spatial-env.yml
@@ -0,0 +1,38 @@
+name: base 
+channels:
+  - conda-forge
+dependencies:
+  - awscliv2
+  - distributed
+  - earthaccess
+  - fiona
+  - fsspec
+  - geopandas
+  - geocube
+  - leafmap[maplibregl]
+  - localtileserver
+  - mapclassify
+  - maplibre
+  - minio
+  - netCDF4
+  - odc-geo
+  - odc-stac
+  - planetary-computer
+  - pmtiles
+  - polars
+  - pyarrow
+  - pydeck
+  - pyogrio
+  - pystac
+  - pystac-client
+  - rasterio
+  - rasterstats
+  - requests
+  - rio-cogeo
+  - rioxarray
+  - stackstac
+  - streamlit
+  - tqdm
+  - xarray
+  - zarr
+