From 83c583ac32a323b8a3de4cb26d7b05f04033cb6d Mon Sep 17 00:00:00 2001
From: Elsa Culler <eculler@gmail.com>
Date: Mon, 10 Apr 2023 12:09:14 -0600
Subject: [PATCH 01/77] Updating to Python 3.11

---
 environment.yml | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/environment.yml b/environment.yml
index 32402e0..9ba9af7 100644
--- a/environment.yml
+++ b/environment.yml
@@ -4,8 +4,9 @@ channels:
   - defaults
 
 dependencies:
-  - python=3.8
+  - python=3.11
   - pip
+  
   # Core scientific python
   - numpy
   - pyqt
@@ -34,6 +35,7 @@ dependencies:
   - tweepy
   - xarray
   - rioxarray>=0.3.0
+  - xarray-spatial
   - scipy
   - netcdf4
   - nc-time-axis
@@ -45,7 +47,6 @@ dependencies:
 
   # Jupyter Environment
   - papermill
-  - autopep8
   - jupyterlab
   - notebook
   - ipython
@@ -53,6 +54,12 @@ dependencies:
   - nbclean
   - nbresuse
   
+  # QA
+  - flake8
+  - black
+  - autopep8
+  - pydocstyle
+  - nbqa
+  
   # Autograding
-  - matplotcheck>=0.1.3
   - nbgrader

From f569c7367a9186155bb5ada110f229093882df4d Mon Sep 17 00:00:00 2001
From: Elsa Culler <eculler@gmail.com>
Date: Tue, 11 Apr 2023 14:05:37 -0600
Subject: [PATCH 02/77] Update build-test-envt.yml to run only manually

---
 .github/workflows/build-test-envt.yml | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/.github/workflows/build-test-envt.yml b/.github/workflows/build-test-envt.yml
index 961ac5c..975c15e 100644
--- a/.github/workflows/build-test-envt.yml
+++ b/.github/workflows/build-test-envt.yml
@@ -4,13 +4,7 @@
 
 name: Test EA Python Envt Mac, Linux, Windows
 
-on:
-  push:
-    branches:
-      - '*'
-  pull_request:
-    branches:
-      - '*'
+on: workflow_dispatch
 
 jobs:
   runtests:

From de0f41951b3af7b4a270d9572de59842bd422b8e Mon Sep 17 00:00:00 2001
From: Elsa Culler <eculler@gmail.com>
Date: Tue, 11 Apr 2023 14:06:12 -0600
Subject: [PATCH 03/77] Update build-push-image.yml to run only manually

---
 .github/workflows/build-push-image.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/build-push-image.yml b/.github/workflows/build-push-image.yml
index af3f644..1648b91 100644
--- a/.github/workflows/build-push-image.yml
+++ b/.github/workflows/build-push-image.yml
@@ -2,9 +2,7 @@
 # main  branch only
 name: Push to Docker Hub from Main Branch
 
-on:
-  push:
-    branches: main
+on: workflow_dispatch
 
 jobs:
   build-push-image:

From cb510c00761acad7de2f35a26a8d223e3315be66 Mon Sep 17 00:00:00 2001
From: Elsa Culler <eculler@gmail.com>
Date: Tue, 11 Apr 2023 14:08:09 -0600
Subject: [PATCH 04/77] Delete build-image.yml

---
 .github/workflows/build-image.yml | 33 -------------------------------
 1 file changed, 33 deletions(-)
 delete mode 100644 .github/workflows/build-image.yml

diff --git a/.github/workflows/build-image.yml b/.github/workflows/build-image.yml
deleted file mode 100644
index f414b9b..0000000
--- a/.github/workflows/build-image.yml
+++ /dev/null
@@ -1,33 +0,0 @@
-# This build will only build the image on any branch (besides main) where there is a push
-name: Build Docker Image
-
-on:
-  push:
-    branches:
-      - '*'
-      - '!main'
-
-jobs:
-  build-image:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v2
-
-      - name: Login to DockerHub
-        uses: docker/login-action@v1
-        with:
-          username: ${{ secrets.DOCKER_HUB_USERNAME }}
-          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
-
-      - name: Build Image
-        id: docker_build
-        uses: docker/build-push-action@v2
-        with:
-          context: ./
-          file: ./Dockerfile
-          push: false
-          tags: earthlab/r-python-eds-lessons-env:latest
-
-      - name: Image digest
-        run: echo ${{ steps.docker_build.outputs.digest }}

From b43ebd3d5f4470928abd53cb3b455a409eea8bf3 Mon Sep 17 00:00:00 2001
From: Elsa Culler <eculler@gmail.com>
Date: Tue, 11 Apr 2023 14:10:31 -0600
Subject: [PATCH 05/77] Create build-for-docker.yml

---
 .github/workflows/build-for-docker.yml | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 .github/workflows/build-for-docker.yml

diff --git a/.github/workflows/build-for-docker.yml b/.github/workflows/build-for-docker.yml
new file mode 100644
index 0000000..2b8cebb
--- /dev/null
+++ b/.github/workflows/build-for-docker.yml
@@ -0,0 +1,25 @@
+name: Test environment for Docker
+
+on: workflow_dispatch
+
+jobs:
+  runtests:
+    name: "Set up environment"
+    runs-on: "ubuntu-latest"
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniconda-version: 'latest'
+          channels: conda-forge
+          channel-priority: true
+          auto-update-conda: false
+          auto-activate-base: false
+          environment-file: environment.yml
+          activate-environment: earth-analytics-python
+      - run: conda list
+      - run: python -c "import earthpy"
+      - run: python -c "import rasterio"

From 73e9c7464cdd8e929269427cc6a4d1d6f52526ee Mon Sep 17 00:00:00 2001
From: Elsa Culler <eculler@gmail.com>
Date: Tue, 11 Apr 2023 14:27:26 -0600
Subject: [PATCH 06/77] New token for dockerhub

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

diff --git a/.github/workflows/build-push-image.yml b/.github/workflows/build-push-image.yml
index 1648b91..3dd09fb 100644
--- a/.github/workflows/build-push-image.yml
+++ b/.github/workflows/build-push-image.yml
@@ -24,7 +24,7 @@ jobs:
           context: ./
           file: ./Dockerfile
           push: true
-          tags: earthlab/r-python-eds-lessons-env:latest
+          tags: earthlab/earth-analytics-python-env:latest
 
       - name: Image digest
         run: echo ${{ steps.docker_build.outputs.digest }}

From de22a9127ef6d5e51ab9700c08b4a7f8f530a04b Mon Sep 17 00:00:00 2001
From: Elsa Culler <eculler@gmail.com>
Date: Wed, 12 Apr 2023 14:13:49 -0600
Subject: [PATCH 07/77] Adding ML libraries, back to 3.10

---
 environment.yml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 9ba9af7..09a35f6 100644
--- a/environment.yml
+++ b/environment.yml
@@ -2,9 +2,10 @@ name: earth-analytics-python
 channels:
   - conda-forge
   - defaults
+  - pytorch
 
 dependencies:
-  - python=3.11
+  - python=3.10
   - pip
   
   # Core scientific python
@@ -13,6 +14,11 @@ dependencies:
   - tqdm
   - kiwisolver
   
+  # ML
+  - scikit-learn
+  - pytorch
+  - torchvision
+  
   # Plotting
   - matplotlib
   - plotly

From 46adcd0fa9f0f0178b075f12ef8dec150c4c612f Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 12 Apr 2023 14:18:27 -0600
Subject: [PATCH 08/77] Dockerfile improvements from Tyson

---
 Dockerfile | 35 ++++++++++++++++++++++++-----------
 1 file changed, 24 insertions(+), 11 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index ffe8187..5c18063 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,16 +1,29 @@
-FROM jupyter/minimal-notebook
+FROM harbor.cyverse.org/vice/jupyter/datascience:latest
 
-MAINTAINER Leah Wasser <leah.wasser@colorado.edu>
+USER jovyan
 
-COPY environment.yml environment.yml
+RUN conda update conda 
+RUN conda config --remove channels conda-forge
+RUN conda config --add channels conda-forge
+RUN conda config --set channel_priority strict
 
-RUN conda env update --name base --file environment.yml \
-  && conda info --envs \
-  && conda list \
-  && rm environment.yml
+COPY environment.yml /home/jovyan/ 
+RUN mamba env create -f /home/jovyan/environment.yml
+# using ~/.bash_profile instead of ~/.bashrc for non-interactive tty (-it) containers
+RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> /home/jovyan/.bash_profile && \
+    echo "conda deactivate" >> /home/jovyan/.bash_profile && \
+    echo "conda activate earth-analytics-python" >> /home/jovyan/.bash_profile
+RUN . /opt/conda/etc/profile.d/conda.sh && conda activate Earthlab && python -m ipykernel install --user --name earth-analytics-python     
+RUN source /home/jovyan/.bash_profile
 
-ENV PROJ_LIB $CONDA_DIR/share/proj
+# Install JupyterLab widget extensions
+RUN sudo chown -R 1000:100 /opt/conda/share
+RUN jupyter labextension install \
+    ipyvolume \
+    itkwidgets \    
+    jupyterlab_iframe \ 
+    jupyter-leaflet \
+    jupyter-threejs \
+ && npm cache clean --force
 
-# Test imports
-RUN python -c "import rasterio"
-RUN python -c "import earthpy"
+RUN jupyter lab build

From f05fb83b27b9df531f97d515a69b1f8296771c9b Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 12 Apr 2023 14:21:07 -0600
Subject: [PATCH 09/77] Update build-push-image.yml

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

diff --git a/.github/workflows/build-push-image.yml b/.github/workflows/build-push-image.yml
index 1648b91..3dd09fb 100644
--- a/.github/workflows/build-push-image.yml
+++ b/.github/workflows/build-push-image.yml
@@ -24,7 +24,7 @@ jobs:
           context: ./
           file: ./Dockerfile
           push: true
-          tags: earthlab/r-python-eds-lessons-env:latest
+          tags: earthlab/earth-analytics-python-env:latest
 
       - name: Image digest
         run: echo ${{ steps.docker_build.outputs.digest }}

From 36314b763f4aae71fe88253e38b59a301a3f7409 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 12 Apr 2023 16:04:25 -0600
Subject: [PATCH 10/77] replacing environment name

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

diff --git a/Dockerfile b/Dockerfile
index 5c18063..a4b1b87 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -13,7 +13,7 @@ RUN mamba env create -f /home/jovyan/environment.yml
 RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> /home/jovyan/.bash_profile && \
     echo "conda deactivate" >> /home/jovyan/.bash_profile && \
     echo "conda activate earth-analytics-python" >> /home/jovyan/.bash_profile
-RUN . /opt/conda/etc/profile.d/conda.sh && conda activate Earthlab && python -m ipykernel install --user --name earth-analytics-python     
+RUN . /opt/conda/etc/profile.d/conda.sh && conda activate earth-analytics-python && python -m ipykernel install --user --name earth-analytics-python     
 RUN source /home/jovyan/.bash_profile
 
 # Install JupyterLab widget extensions

From a335ce18fa41caa23c62857b71864985ed12a0b8 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Thu, 13 Apr 2023 12:41:33 -0600
Subject: [PATCH 11/77] Roll back base image

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

diff --git a/Dockerfile b/Dockerfile
index a4b1b87..5a17d60 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM harbor.cyverse.org/vice/jupyter/datascience:latest
+FROM jupyter/minimal-notebook
 
 USER jovyan
 

From 196e418b06c3b8f45d3927d677d6c83c0fcaa560 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Thu, 13 Apr 2023 12:57:00 -0600
Subject: [PATCH 12/77] Removing breaking permissions link

---
 Dockerfile | 1 -
 1 file changed, 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 5a17d60..a9275a4 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -17,7 +17,6 @@ RUN . /opt/conda/etc/profile.d/conda.sh && conda activate earth-analytics-python
 RUN source /home/jovyan/.bash_profile
 
 # Install JupyterLab widget extensions
-RUN sudo chown -R 1000:100 /opt/conda/share
 RUN jupyter labextension install \
     ipyvolume \
     itkwidgets \    

From f99c6772081ce604e3241c7168e2a3159a5f4f27 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Thu, 13 Apr 2023 12:57:26 -0600
Subject: [PATCH 13/77] Update build-push-image.yml

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

diff --git a/.github/workflows/build-push-image.yml b/.github/workflows/build-push-image.yml
index 3dd09fb..5b98344 100644
--- a/.github/workflows/build-push-image.yml
+++ b/.github/workflows/build-push-image.yml
@@ -1,6 +1,6 @@
 # This build will build and push the image to docker hub upon a commit to the
 # main  branch only
-name: Push to Docker Hub from Main Branch
+name: Push to Docker Hub
 
 on: workflow_dispatch
 

From 46ca895f97d0b4f0ae6a291b789a31108722d2aa Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Thu, 13 Apr 2023 12:59:48 -0600
Subject: [PATCH 14/77] tag with branch

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

diff --git a/.github/workflows/build-push-image.yml b/.github/workflows/build-push-image.yml
index 5b98344..b20f425 100644
--- a/.github/workflows/build-push-image.yml
+++ b/.github/workflows/build-push-image.yml
@@ -24,7 +24,7 @@ jobs:
           context: ./
           file: ./Dockerfile
           push: true
-          tags: earthlab/earth-analytics-python-env:latest
+          tags: earthlab/earth-analytics-python-env:${GITHUB_REF##*/}
 
       - name: Image digest
         run: echo ${{ steps.docker_build.outputs.digest }}

From e03267fb9cac2cee87420e7a20cd36a2934ee074 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Thu, 13 Apr 2023 13:31:45 -0600
Subject: [PATCH 15/77] miniconda base image

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

diff --git a/Dockerfile b/Dockerfile
index a9275a4..5b70249 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM jupyter/minimal-notebook
+FROM continuumio/miniconda3
 
 USER jovyan
 

From fc589719848ee6ea59989a8b65db29ad3ff1db8c Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Thu, 13 Apr 2023 13:32:37 -0600
Subject: [PATCH 16/77] Comment out new libraries

---
 environment.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/environment.yml b/environment.yml
index 09a35f6..ae2f90f 100644
--- a/environment.yml
+++ b/environment.yml
@@ -16,8 +16,8 @@ dependencies:
   
   # ML
   - scikit-learn
-  - pytorch
-  - torchvision
+  # - pytorch
+  # - torchvision
   
   # Plotting
   - matplotlib
@@ -41,7 +41,8 @@ dependencies:
   - tweepy
   - xarray
   - rioxarray>=0.3.0
-  - xarray-spatial
+  # - xarray-spatial
+  # - h5py
   - scipy
   - netcdf4
   - nc-time-axis

From 9e71ef1cba1cfa6789f9bc4ed51761688aa8096c Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Thu, 13 Apr 2023 13:35:22 -0600
Subject: [PATCH 17/77] Adding jovyan user

---
 Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Dockerfile b/Dockerfile
index 5b70249..aa3e98e 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,5 +1,6 @@
 FROM continuumio/miniconda3
 
+RUN useradd -ms /bin/bash jovyan
 USER jovyan
 
 RUN conda update conda 

From 47073cb49efd8a2e7229cb467c7e46e331d084af Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Thu, 13 Apr 2023 13:41:02 -0600
Subject: [PATCH 18/77] Switch back to jupyter base image

---
 Dockerfile | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index aa3e98e..a9275a4 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,6 +1,5 @@
-FROM continuumio/miniconda3
+FROM jupyter/minimal-notebook
 
-RUN useradd -ms /bin/bash jovyan
 USER jovyan
 
 RUN conda update conda 

From 10c464d9b173729b67c30d173642be72170c657f Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 19 Apr 2023 10:47:06 -0600
Subject: [PATCH 19/77] Add nbgrader install

---
 Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Dockerfile b/Dockerfile
index a9275a4..e1079a2 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -23,6 +23,7 @@ RUN jupyter labextension install \
     jupyterlab_iframe \ 
     jupyter-leaflet \
     jupyter-threejs \
+    nbgrader \
  && npm cache clean --force
 
 RUN jupyter lab build

From c9a360b724673c26de795fd5fe6eee3f46592c59 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 19 Apr 2023 11:35:08 -0600
Subject: [PATCH 20/77] remove nbgrader

---
 Dockerfile | 1 -
 1 file changed, 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index e1079a2..a9275a4 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -23,7 +23,6 @@ RUN jupyter labextension install \
     jupyterlab_iframe \ 
     jupyter-leaflet \
     jupyter-threejs \
-    nbgrader \
  && npm cache clean --force
 
 RUN jupyter lab build

From 3e150c699587a6b52e18c85f34bdedf7dce5aad9 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 19 Apr 2023 12:20:47 -0600
Subject: [PATCH 21/77] install as base environment on docker

---
 Dockerfile | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index a9275a4..d4900a9 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -8,12 +8,12 @@ RUN conda config --add channels conda-forge
 RUN conda config --set channel_priority strict
 
 COPY environment.yml /home/jovyan/ 
-RUN mamba env create -f /home/jovyan/environment.yml
+RUN mamba env create -n base -f /home/jovyan/environment.yml
 # using ~/.bash_profile instead of ~/.bashrc for non-interactive tty (-it) containers
 RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> /home/jovyan/.bash_profile && \
     echo "conda deactivate" >> /home/jovyan/.bash_profile && \
-    echo "conda activate earth-analytics-python" >> /home/jovyan/.bash_profile
-RUN . /opt/conda/etc/profile.d/conda.sh && conda activate earth-analytics-python && python -m ipykernel install --user --name earth-analytics-python     
+    echo "conda activate base" >> /home/jovyan/.bash_profile
+RUN . /opt/conda/etc/profile.d/conda.sh && conda activate base && python -m ipykernel install --user --name base     
 RUN source /home/jovyan/.bash_profile
 
 # Install JupyterLab widget extensions
@@ -23,6 +23,7 @@ RUN jupyter labextension install \
     jupyterlab_iframe \ 
     jupyter-leaflet \
     jupyter-threejs \
+    nbgrader \
  && npm cache clean --force
 
 RUN jupyter lab build

From 3364d7432e840b73d8af53b2b2e670952a69e8f1 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 19 Apr 2023 12:42:16 -0600
Subject: [PATCH 22/77] update not create base environment

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

diff --git a/Dockerfile b/Dockerfile
index d4900a9..78115c6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -8,7 +8,7 @@ RUN conda config --add channels conda-forge
 RUN conda config --set channel_priority strict
 
 COPY environment.yml /home/jovyan/ 
-RUN mamba env create -n base -f /home/jovyan/environment.yml
+RUN mamba env update -n base -f /home/jovyan/environment.yml
 # using ~/.bash_profile instead of ~/.bashrc for non-interactive tty (-it) containers
 RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> /home/jovyan/.bash_profile && \
     echo "conda deactivate" >> /home/jovyan/.bash_profile && \

From e676ec754610b2ab351a9b745c1337f3e6d3fab8 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 19 Apr 2023 14:18:24 -0600
Subject: [PATCH 23/77] revert

---
 Dockerfile | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 78115c6..a9275a4 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -8,12 +8,12 @@ RUN conda config --add channels conda-forge
 RUN conda config --set channel_priority strict
 
 COPY environment.yml /home/jovyan/ 
-RUN mamba env update -n base -f /home/jovyan/environment.yml
+RUN mamba env create -f /home/jovyan/environment.yml
 # using ~/.bash_profile instead of ~/.bashrc for non-interactive tty (-it) containers
 RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> /home/jovyan/.bash_profile && \
     echo "conda deactivate" >> /home/jovyan/.bash_profile && \
-    echo "conda activate base" >> /home/jovyan/.bash_profile
-RUN . /opt/conda/etc/profile.d/conda.sh && conda activate base && python -m ipykernel install --user --name base     
+    echo "conda activate earth-analytics-python" >> /home/jovyan/.bash_profile
+RUN . /opt/conda/etc/profile.d/conda.sh && conda activate earth-analytics-python && python -m ipykernel install --user --name earth-analytics-python     
 RUN source /home/jovyan/.bash_profile
 
 # Install JupyterLab widget extensions
@@ -23,7 +23,6 @@ RUN jupyter labextension install \
     jupyterlab_iframe \ 
     jupyter-leaflet \
     jupyter-threejs \
-    nbgrader \
  && npm cache clean --force
 
 RUN jupyter lab build

From e7d761aebd6d30b368727565a9455daaf332d0b3 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 19 Apr 2023 15:15:38 -0600
Subject: [PATCH 24/77] Redo changes

---
 Dockerfile | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index a9275a4..78115c6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -8,12 +8,12 @@ RUN conda config --add channels conda-forge
 RUN conda config --set channel_priority strict
 
 COPY environment.yml /home/jovyan/ 
-RUN mamba env create -f /home/jovyan/environment.yml
+RUN mamba env update -n base -f /home/jovyan/environment.yml
 # using ~/.bash_profile instead of ~/.bashrc for non-interactive tty (-it) containers
 RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> /home/jovyan/.bash_profile && \
     echo "conda deactivate" >> /home/jovyan/.bash_profile && \
-    echo "conda activate earth-analytics-python" >> /home/jovyan/.bash_profile
-RUN . /opt/conda/etc/profile.d/conda.sh && conda activate earth-analytics-python && python -m ipykernel install --user --name earth-analytics-python     
+    echo "conda activate base" >> /home/jovyan/.bash_profile
+RUN . /opt/conda/etc/profile.d/conda.sh && conda activate base && python -m ipykernel install --user --name base     
 RUN source /home/jovyan/.bash_profile
 
 # Install JupyterLab widget extensions
@@ -23,6 +23,7 @@ RUN jupyter labextension install \
     jupyterlab_iframe \ 
     jupyter-leaflet \
     jupyter-threejs \
+    nbgrader \
  && npm cache clean --force
 
 RUN jupyter lab build

From cbc9146d61a8221f990b69c38157fc73df268bc9 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Mon, 24 Apr 2023 17:52:07 -0600
Subject: [PATCH 25/77] add h5py

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index ae2f90f..3dbc081 100644
--- a/environment.yml
+++ b/environment.yml
@@ -42,7 +42,7 @@ dependencies:
   - xarray
   - rioxarray>=0.3.0
   # - xarray-spatial
-  # - h5py
+  - h5py
   - scipy
   - netcdf4
   - nc-time-axis

From 77e7303af83dcc6452d7639e8745f7d983063d73 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Sun, 30 Apr 2023 13:35:50 -0600
Subject: [PATCH 26/77] Added flake8-import-order

---
 environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/environment.yml b/environment.yml
index 3dbc081..fadf2d0 100644
--- a/environment.yml
+++ b/environment.yml
@@ -63,6 +63,7 @@ dependencies:
   
   # QA
   - flake8
+  - flake8-import-order
   - black
   - autopep8
   - pydocstyle

From 7e8372750b05c22872ef24b1dfc984218967e958 Mon Sep 17 00:00:00 2001
From: nkorinek <nathan.korinek@colorado.edu>
Date: Fri, 23 Jun 2023 12:17:15 -0600
Subject: [PATCH 27/77] duplicating docker build for both docker environments

---
 .github/workflows/build-push-image.yml | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/.github/workflows/build-push-image.yml b/.github/workflows/build-push-image.yml
index 5b98344..ae8c397 100644
--- a/.github/workflows/build-push-image.yml
+++ b/.github/workflows/build-push-image.yml
@@ -17,6 +17,18 @@ jobs:
           username: ${{ secrets.DOCKER_HUB_USERNAME }}
           password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
 
+      - name: Build and push image
+        id: website_docker_build
+        uses: docker/build-push-action@v2
+        with:
+          context: ./
+          file: ./Dockerfile
+          push: true
+          tags: earthlab/r-python-eds-lessons-env:latest
+      
+      - name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}
+
       - name: Build and push image
         id: docker_build
         uses: docker/build-push-action@v2

From 36cd6b14627b9f589aa379f8e3917a6678e306f3 Mon Sep 17 00:00:00 2001
From: nkorinek <nathan.korinek@colorado.edu>
Date: Tue, 27 Jun 2023 14:44:24 -0600
Subject: [PATCH 28/77] Updated Dockerfile to run

---
 Dockerfile | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 78115c6..672ee22 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM jupyter/minimal-notebook
+FROM jupyter/minimal-notebook:python-3.10
 
 USER jovyan
 
@@ -6,6 +6,7 @@ RUN conda update conda
 RUN conda config --remove channels conda-forge
 RUN conda config --add channels conda-forge
 RUN conda config --set channel_priority strict
+RUN conda install mamba -c conda-forge
 
 COPY environment.yml /home/jovyan/ 
 RUN mamba env update -n base -f /home/jovyan/environment.yml
@@ -26,4 +27,4 @@ RUN jupyter labextension install \
     nbgrader \
  && npm cache clean --force
 
-RUN jupyter lab build
+RUN jupyter lab build
\ No newline at end of file

From 2532a51fe3b7a35a914ab825d2fdd95f733f9e84 Mon Sep 17 00:00:00 2001
From: nkorinek <nathan.korinek@colorado.edu>
Date: Tue, 27 Jun 2023 15:27:23 -0600
Subject: [PATCH 29/77] Changing ubuntu version due to possible bug with GitHub
 actions

---
 .github/workflows/build-for-docker.yml | 2 +-
 .github/workflows/build-test-envt.yml  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-for-docker.yml b/.github/workflows/build-for-docker.yml
index 2b8cebb..f73251b 100644
--- a/.github/workflows/build-for-docker.yml
+++ b/.github/workflows/build-for-docker.yml
@@ -5,7 +5,7 @@ on: workflow_dispatch
 jobs:
   runtests:
     name: "Set up environment"
-    runs-on: "ubuntu-latest"
+    runs-on: "ubuntu-22.04"
     defaults:
       run:
         shell: bash -l {0}
diff --git a/.github/workflows/build-test-envt.yml b/.github/workflows/build-test-envt.yml
index 975c15e..4356514 100644
--- a/.github/workflows/build-test-envt.yml
+++ b/.github/workflows/build-test-envt.yml
@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        os: ["ubuntu-22.04", "macos-latest", "windows-latest"]
     defaults:
       run:
         shell: bash -l {0}

From 10086ac21b0fe430f579f7d5fd10c0e1b641dcb2 Mon Sep 17 00:00:00 2001
From: nkorinek <nathan.korinek@colorado.edu>
Date: Tue, 27 Jun 2023 15:39:21 -0600
Subject: [PATCH 30/77] downgrading ubuntu build for github actions

---
 .github/workflows/build-for-docker.yml | 2 +-
 .github/workflows/build-test-envt.yml  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-for-docker.yml b/.github/workflows/build-for-docker.yml
index f73251b..bad69b9 100644
--- a/.github/workflows/build-for-docker.yml
+++ b/.github/workflows/build-for-docker.yml
@@ -5,7 +5,7 @@ on: workflow_dispatch
 jobs:
   runtests:
     name: "Set up environment"
-    runs-on: "ubuntu-22.04"
+    runs-on: "ubuntu-20.04"
     defaults:
       run:
         shell: bash -l {0}
diff --git a/.github/workflows/build-test-envt.yml b/.github/workflows/build-test-envt.yml
index 4356514..fbffc62 100644
--- a/.github/workflows/build-test-envt.yml
+++ b/.github/workflows/build-test-envt.yml
@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-22.04", "macos-latest", "windows-latest"]
+        os: ["ubuntu-20.04", "macos-latest", "windows-latest"]
     defaults:
       run:
         shell: bash -l {0}

From 90ff496bfa7568db4ad3c62efaf82c7252e4252e Mon Sep 17 00:00:00 2001
From: nkorinek <nathan.korinek@colorado.edu>
Date: Mon, 21 Aug 2023 15:45:01 -0600
Subject: [PATCH 31/77] added packages to build jupyter books and improve
 plotting

---
 environment.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/environment.yml b/environment.yml
index fadf2d0..5ab59c0 100644
--- a/environment.yml
+++ b/environment.yml
@@ -23,6 +23,7 @@ dependencies:
   - matplotlib
   - plotly
   - seaborn
+  - hvplot
 
   # Spatial packages
   - pysal
@@ -60,6 +61,11 @@ dependencies:
   - jupyter_contrib_nbextensions
   - nbclean
   - nbresuse
+
+  # Textbook Format
+  - jupyter-book
+  - sphinx-exercise
+  - ghp-import
   
   # QA
   - flake8

From a81b0da10687b8a33cac8b16b5653c767469b0d1 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 20 Sep 2023 11:05:34 -0600
Subject: [PATCH 32/77] Update environment.yml

---
 environment.yml | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/environment.yml b/environment.yml
index 5ab59c0..8b4202c 100644
--- a/environment.yml
+++ b/environment.yml
@@ -2,7 +2,6 @@ name: earth-analytics-python
 channels:
   - conda-forge
   - defaults
-  - pytorch
 
 dependencies:
   - python=3.10
@@ -16,14 +15,13 @@ dependencies:
   
   # ML
   - scikit-learn
-  # - pytorch
-  # - torchvision
   
   # Plotting
   - matplotlib
   - plotly
   - seaborn
   - hvplot
+  - geoviews
 
   # Spatial packages
   - pysal
@@ -33,7 +31,6 @@ dependencies:
   - cartopy
   - descartes
   - contextily
-  - earthpy
   - folium
   - geojson
   - mapboxgl
@@ -42,7 +39,6 @@ dependencies:
   - tweepy
   - xarray
   - rioxarray>=0.3.0
-  # - xarray-spatial
   - h5py
   - scipy
   - netcdf4
@@ -58,7 +54,6 @@ dependencies:
   - jupyterlab
   - notebook
   - ipython
-  - jupyter_contrib_nbextensions
   - nbclean
   - nbresuse
 

From 803d1de434ba0f6d5f8c04f45c5cbf4d281b362b Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 20 Sep 2023 11:07:23 -0600
Subject: [PATCH 33/77] Update Dockerfile

---
 Dockerfile | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 672ee22..741070d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -17,6 +17,9 @@ RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> /home/jovyan/.bash_profile &&
 RUN . /opt/conda/etc/profile.d/conda.sh && conda activate base && python -m ipykernel install --user --name base     
 RUN source /home/jovyan/.bash_profile
 
+# Install dev version of Earthpy
+RUN pip install git+https://github.com/earthlab/earthpy@apppears
+
 # Install JupyterLab widget extensions
 RUN jupyter labextension install \
     ipyvolume \
@@ -27,4 +30,4 @@ RUN jupyter labextension install \
     nbgrader \
  && npm cache clean --force
 
-RUN jupyter lab build
\ No newline at end of file
+RUN jupyter lab build

From 4540ef209c218002fc4a743b5ec1535531a74354 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 20 Sep 2023 11:09:07 -0600
Subject: [PATCH 34/77] Update build-push-image.yml

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

diff --git a/.github/workflows/build-push-image.yml b/.github/workflows/build-push-image.yml
index ae8c397..d5f37a6 100644
--- a/.github/workflows/build-push-image.yml
+++ b/.github/workflows/build-push-image.yml
@@ -36,7 +36,7 @@ jobs:
           context: ./
           file: ./Dockerfile
           push: true
-          tags: earthlab/earth-analytics-python-env:latest
+          tags: earthlab/earth-analytics-dev-env:latest
 
       - name: Image digest
         run: echo ${{ steps.docker_build.outputs.digest }}

From dec5306ab97ef18a98fa480347d6d7e6d6d912f1 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 20 Sep 2023 11:22:01 -0600
Subject: [PATCH 35/77] Update Dockerfile

---
 Dockerfile | 12 ------------
 1 file changed, 12 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 741070d..5477a7b 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -19,15 +19,3 @@ RUN source /home/jovyan/.bash_profile
 
 # Install dev version of Earthpy
 RUN pip install git+https://github.com/earthlab/earthpy@apppears
-
-# Install JupyterLab widget extensions
-RUN jupyter labextension install \
-    ipyvolume \
-    itkwidgets \    
-    jupyterlab_iframe \ 
-    jupyter-leaflet \
-    jupyter-threejs \
-    nbgrader \
- && npm cache clean --force
-
-RUN jupyter lab build

From 690d37f83b890f15db4975039d17db4ce4eff571 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 20 Sep 2023 13:12:12 -0600
Subject: [PATCH 36/77] Update Dockerfile

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

diff --git a/Dockerfile b/Dockerfile
index 5477a7b..2db8344 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -19,3 +19,6 @@ RUN source /home/jovyan/.bash_profile
 
 # Install dev version of Earthpy
 RUN pip install git+https://github.com/earthlab/earthpy@apppears
+
+# Install gnome keyring
+RUN apt-get install -y gnome-keyring

From 4981dfbc39b026fdb5baa3eaba04818e439ca8f1 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 20 Sep 2023 13:22:15 -0600
Subject: [PATCH 37/77] Update Dockerfile

---
 Dockerfile | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Dockerfile b/Dockerfile
index 2db8344..3e5f2ea 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -21,4 +21,6 @@ RUN source /home/jovyan/.bash_profile
 RUN pip install git+https://github.com/earthlab/earthpy@apppears
 
 # Install gnome keyring
+USER root
 RUN apt-get install -y gnome-keyring
+USER jovyan

From deb0ecf3e1b5d02c210a8bf395725c3a13f7866a Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 20 Sep 2023 13:31:20 -0600
Subject: [PATCH 38/77] Update Dockerfile

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

diff --git a/Dockerfile b/Dockerfile
index 3e5f2ea..19589b5 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -22,5 +22,5 @@ RUN pip install git+https://github.com/earthlab/earthpy@apppears
 
 # Install gnome keyring
 USER root
-RUN apt-get install -y gnome-keyring
+RUN apt-get install -y libgnome-keyring
 USER jovyan

From 418db36de26522fdc282d5e0be97e2d341963fbb Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 20 Sep 2023 13:40:03 -0600
Subject: [PATCH 39/77] Update Dockerfile

---
 Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 19589b5..bfcdfb3 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -22,5 +22,6 @@ RUN pip install git+https://github.com/earthlab/earthpy@apppears
 
 # Install gnome keyring
 USER root
-RUN apt-get install -y libgnome-keyring
+RUN apt-get install -y libdbus-glib-1-dev
+RUN pip install secretstorage dbus-python
 USER jovyan

From fdc54ef546cf174acfa5129fa46710884daec024 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 20 Sep 2023 13:50:52 -0600
Subject: [PATCH 40/77] REvert

---
 Dockerfile | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index bfcdfb3..5477a7b 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -19,9 +19,3 @@ RUN source /home/jovyan/.bash_profile
 
 # Install dev version of Earthpy
 RUN pip install git+https://github.com/earthlab/earthpy@apppears
-
-# Install gnome keyring
-USER root
-RUN apt-get install -y libdbus-glib-1-dev
-RUN pip install secretstorage dbus-python
-USER jovyan

From bf9063eb5b5396bef383786415cb805185429398 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Thu, 28 Sep 2023 12:50:45 -0600
Subject: [PATCH 41/77] Update environment.yml

---
 environment.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 8b4202c..ce96fda 100644
--- a/environment.yml
+++ b/environment.yml
@@ -21,7 +21,9 @@ dependencies:
   - plotly
   - seaborn
   - hvplot
-  - geoviews
+  - geoviews>=1.10
+  - selenium
+  - phantomjs
 
   # Spatial packages
   - pysal

From dd57e6efa803a8385cb46692e67ee36693dbe1f2 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Thu, 28 Sep 2023 12:54:59 -0600
Subject: [PATCH 42/77] Update build-push-image.yml

---
 .github/workflows/build-push-image.yml | 12 ------------
 1 file changed, 12 deletions(-)

diff --git a/.github/workflows/build-push-image.yml b/.github/workflows/build-push-image.yml
index d5f37a6..af1700a 100644
--- a/.github/workflows/build-push-image.yml
+++ b/.github/workflows/build-push-image.yml
@@ -17,18 +17,6 @@ jobs:
           username: ${{ secrets.DOCKER_HUB_USERNAME }}
           password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
 
-      - name: Build and push image
-        id: website_docker_build
-        uses: docker/build-push-action@v2
-        with:
-          context: ./
-          file: ./Dockerfile
-          push: true
-          tags: earthlab/r-python-eds-lessons-env:latest
-      
-      - name: Image digest
-        run: echo ${{ steps.docker_build.outputs.digest }}
-
       - name: Build and push image
         id: docker_build
         uses: docker/build-push-action@v2

From d8e7ed24fbb262ffc30e3ca53d4d0de279264cfa Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Fri, 6 Oct 2023 12:39:10 -0500
Subject: [PATCH 43/77] Update environment.yml

---
 environment.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/environment.yml b/environment.yml
index ce96fda..1484382 100644
--- a/environment.yml
+++ b/environment.yml
@@ -24,6 +24,7 @@ dependencies:
   - geoviews>=1.10
   - selenium
   - phantomjs
+  - jupyter_bokeh
 
   # Spatial packages
   - pysal
@@ -46,6 +47,7 @@ dependencies:
   - netcdf4
   - nc-time-axis
   - regionmask
+  - pyogrio
 
   # Natural language processing
   - nltk

From aa6cf88ee2cdeb864f5b7142e0b3749c2aa4a424 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Mon, 27 Nov 2023 10:18:18 -0600
Subject: [PATCH 44/77] Update environment.yml

---
 environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/environment.yml b/environment.yml
index 1484382..8ce4da2 100644
--- a/environment.yml
+++ b/environment.yml
@@ -42,6 +42,7 @@ dependencies:
   - tweepy
   - xarray
   - rioxarray>=0.3.0
+  - xarray-spatial
   - h5py
   - scipy
   - netcdf4

From e391d6b27d1828578ed71a819ce4831914554c8d Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Mon, 27 Nov 2023 10:32:46 -0600
Subject: [PATCH 45/77] Update Dockerfile

---
 Dockerfile | 1 -
 1 file changed, 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 5477a7b..d630023 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -6,7 +6,6 @@ RUN conda update conda
 RUN conda config --remove channels conda-forge
 RUN conda config --add channels conda-forge
 RUN conda config --set channel_priority strict
-RUN conda install mamba -c conda-forge
 
 COPY environment.yml /home/jovyan/ 
 RUN mamba env update -n base -f /home/jovyan/environment.yml

From 184509bbea0dbcaf192c4221f92e69c6b79882a1 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Tue, 28 Nov 2023 14:11:35 -0600
Subject: [PATCH 46/77] Update Dockerfile

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

diff --git a/Dockerfile b/Dockerfile
index d630023..d1afab8 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -8,7 +8,7 @@ RUN conda config --add channels conda-forge
 RUN conda config --set channel_priority strict
 
 COPY environment.yml /home/jovyan/ 
-RUN mamba env update -n base -f /home/jovyan/environment.yml
+RUN conda env update -n base -f /home/jovyan/environment.yml
 # using ~/.bash_profile instead of ~/.bashrc for non-interactive tty (-it) containers
 RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> /home/jovyan/.bash_profile && \
     echo "conda deactivate" >> /home/jovyan/.bash_profile && \

From ce31cf0e5a8e58813f433bcd366894c2dbb2b938 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 10 Jan 2024 11:15:56 -0700
Subject: [PATCH 47/77] Update environment.yml

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 8ce4da2..3138bad 100644
--- a/environment.yml
+++ b/environment.yml
@@ -4,7 +4,7 @@ channels:
   - defaults
 
 dependencies:
-  - python=3.10
+  - python=3.11
   - pip
   
   # Core scientific python

From d85d8902f036a8846cf50a4a88e0b5a39d9690a6 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 10 Jan 2024 11:29:27 -0700
Subject: [PATCH 48/77] Update Dockerfile

---
 Dockerfile | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/Dockerfile b/Dockerfile
index d1afab8..ff2ff13 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -2,6 +2,10 @@ FROM jupyter/minimal-notebook:python-3.10
 
 USER jovyan
 
+RUN apt-get update && \
+    apt install -y \
+    libfmt-dev
+
 RUN conda update conda 
 RUN conda config --remove channels conda-forge
 RUN conda config --add channels conda-forge

From 4034d7d045eacb7e9343271ca59847cd1e8fc01b Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 10 Jan 2024 11:35:08 -0700
Subject: [PATCH 49/77] fix users for libfmt install

---
 Dockerfile | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index ff2ff13..aa9444b 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,23 +1,28 @@
 FROM jupyter/minimal-notebook:python-3.10
 
-USER jovyan
-
+# Installing package for libmamba
+USER root
 RUN apt-get update && \
     apt install -y \
     libfmt-dev
+USER jovyan
 
+# Set up conda
 RUN conda update conda 
 RUN conda config --remove channels conda-forge
 RUN conda config --add channels conda-forge
 RUN conda config --set channel_priority strict
 
+# Create environment
 COPY environment.yml /home/jovyan/ 
 RUN conda env update -n base -f /home/jovyan/environment.yml
-# using ~/.bash_profile instead of ~/.bashrc for non-interactive tty (-it) containers
+
+# Activating environment
 RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> /home/jovyan/.bash_profile && \
     echo "conda deactivate" >> /home/jovyan/.bash_profile && \
     echo "conda activate base" >> /home/jovyan/.bash_profile
-RUN . /opt/conda/etc/profile.d/conda.sh && conda activate base && python -m ipykernel install --user --name base     
+RUN . /opt/conda/etc/profile.d/conda.sh && conda activate base && python -m ipykernel install --user --name base
+# using ~/.bash_profile instead of ~/.bashrc for non-interactive tty (-it) containers
 RUN source /home/jovyan/.bash_profile
 
 # Install dev version of Earthpy

From dfd5d0ab7a3c72b380e92bb526f22a6e3eb335c6 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 10 Jan 2024 11:39:56 -0700
Subject: [PATCH 50/77] Update build-push-image.yml

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

diff --git a/.github/workflows/build-push-image.yml b/.github/workflows/build-push-image.yml
index af1700a..6514ec5 100644
--- a/.github/workflows/build-push-image.yml
+++ b/.github/workflows/build-push-image.yml
@@ -19,7 +19,7 @@ jobs:
 
       - name: Build and push image
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5.1.0
         with:
           context: ./
           file: ./Dockerfile

From a7f6305eb094fe4abeb607616d205e43290343cd Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 10 Jan 2024 12:10:01 -0700
Subject: [PATCH 51/77] add scikit-fuzzy

---
 environment.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 3138bad..f66c5e4 100644
--- a/environment.yml
+++ b/environment.yml
@@ -13,8 +13,9 @@ dependencies:
   - tqdm
   - kiwisolver
   
-  # ML
+  # ML and modeling
   - scikit-learn
+  - scikit-fuzzy
   
   # Plotting
   - matplotlib

From 2cd44106e7889ad23cc3fe5db571929570edae21 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Fri, 12 Jan 2024 15:08:58 -0700
Subject: [PATCH 52/77] Adding pystac-client needed for data searching and
 access

---
 environment.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/environment.yml b/environment.yml
index f66c5e4..1aec1a8 100644
--- a/environment.yml
+++ b/environment.yml
@@ -16,6 +16,10 @@ dependencies:
   # ML and modeling
   - scikit-learn
   - scikit-fuzzy
+
+  # Data access
+  - earthpy
+  - pystac-client
   
   # Plotting
   - matplotlib

From ea8084f44e813d09d78530ee1c7629c1def957bc Mon Sep 17 00:00:00 2001
From: earthlab <erve3705@colorado.edu>
Date: Thu, 18 Jan 2024 10:43:00 -0700
Subject: [PATCH 53/77] Chaning channel order and installing libmft-dev

---
 Dockerfile      | 7 ++++---
 environment.yml | 2 +-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index aa9444b..d9690d8 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,9 +1,9 @@
-FROM jupyter/minimal-notebook:python-3.10
+FROM jupyter/minimal-notebook:python-3.11
 
 # Installing package for libmamba
 USER root
 RUN apt-get update && \
-    apt install -y \
+    apt-get install -y \
     libfmt-dev
 USER jovyan
 
@@ -11,7 +11,8 @@ USER jovyan
 RUN conda update conda 
 RUN conda config --remove channels conda-forge
 RUN conda config --add channels conda-forge
-RUN conda config --set channel_priority strict
+#RUN conda config --set channel_priority strict
+#RUN conda config --set solver classic
 
 # Create environment
 COPY environment.yml /home/jovyan/ 
diff --git a/environment.yml b/environment.yml
index 1aec1a8..da5da64 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,7 +1,7 @@
 name: earth-analytics-python
 channels:
-  - conda-forge
   - defaults
+  - conda-forge
 
 dependencies:
   - python=3.11

From 84c69434e1130a9728f97d1c9df9ec3a3bd5f438 Mon Sep 17 00:00:00 2001
From: Erick Verleye <35341779+Ckster@users.noreply.github.com>
Date: Thu, 18 Jan 2024 11:01:03 -0700
Subject: [PATCH 54/77] Update build-push-image.yml

---
 .github/workflows/build-push-image.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/build-push-image.yml b/.github/workflows/build-push-image.yml
index 6514ec5..84e3f6b 100644
--- a/.github/workflows/build-push-image.yml
+++ b/.github/workflows/build-push-image.yml
@@ -10,6 +10,8 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v2
+        with:
+          ref: upgrade-to-3.9
 
       - name: Login to DockerHub
         uses: docker/login-action@v1

From 8bcb38f1f207c2b73e31cc0af051d7925e5d02dd Mon Sep 17 00:00:00 2001
From: Erick Verleye <35341779+Ckster@users.noreply.github.com>
Date: Thu, 18 Jan 2024 14:36:28 -0700
Subject: [PATCH 55/77] Update build-test-envt.yml

---
 .github/workflows/build-test-envt.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/build-test-envt.yml b/.github/workflows/build-test-envt.yml
index fbffc62..c16a50a 100644
--- a/.github/workflows/build-test-envt.yml
+++ b/.github/workflows/build-test-envt.yml
@@ -19,6 +19,8 @@ jobs:
         shell: bash -l {0}
     steps:
       - uses: actions/checkout@v2
+        with:
+            ref: upgrade-to-3.9
       - uses: conda-incubator/setup-miniconda@v2
         with:
           miniconda-version: 'latest'

From 989149f545090db7580f4488b4a4ace0cff40a4c Mon Sep 17 00:00:00 2001
From: Erick Verleye <35341779+Ckster@users.noreply.github.com>
Date: Tue, 26 Mar 2024 11:32:37 -0600
Subject: [PATCH 56/77] Update environment.yml

Adding libtiff to environment.yml for macOS build
---
 environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/environment.yml b/environment.yml
index da5da64..b55e533 100644
--- a/environment.yml
+++ b/environment.yml
@@ -32,6 +32,7 @@ dependencies:
   - jupyter_bokeh
 
   # Spatial packages
+  - libtiff
   - pysal
   - pyproj>=3.0
   - rasterstats

From f6719f62cdd14e3e839c030db0847effa3c1b6e9 Mon Sep 17 00:00:00 2001
From: earthlab <erve3705@colorado.edu>
Date: Tue, 23 Apr 2024 13:15:44 -0600
Subject: [PATCH 57/77] Adding libtiff5 for geopandas

---
 Dockerfile | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index d9690d8..efe33dc 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -4,7 +4,9 @@ FROM jupyter/minimal-notebook:python-3.11
 USER root
 RUN apt-get update && \
     apt-get install -y \
-    libfmt-dev
+    libfmt-dev \ 
+    libtiff5
+
 USER jovyan
 
 # Set up conda

From b1575704081003b200bb5fc28326990a21ed2dad Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Fri, 21 Jun 2024 12:58:11 -0600
Subject: [PATCH 58/77] Update environment.yml

---
 environment.yml | 81 +++++++++++++++++++++----------------------------
 1 file changed, 34 insertions(+), 47 deletions(-)

diff --git a/environment.yml b/environment.yml
index b55e533..ebe1059 100644
--- a/environment.yml
+++ b/environment.yml
@@ -9,9 +9,34 @@ dependencies:
   
   # Core scientific python
   - numpy
-  - pyqt
+  - pandas
+  - scipy
+
+  # Geospatial libraries
+  # Coordinates and CRSs
+  - pyproj>=3.0
+  - geopy
+  - cartopy
+  # Vector data
+  - geopandas
+  - geojson
+  - pyogrio
+  # Raster data
+  - xarray
+  - h5py
+  - netcdf4
+  - rioxarray>=0.3.0
+  - xarray-spatial
+  - regionmask
+  
+  # Interactive computing
+  - ipython
+  - jupyterlab
+  - notebook
   - tqdm
-  - kiwisolver
+  - nbresuse
+  - papermill
+  - nbclean
   
   # ML and modeling
   - scikit-learn
@@ -19,59 +44,24 @@ dependencies:
 
   # Data access
   - earthpy
+  - earthaccess
   - pystac-client
   
   # Plotting
+  # Matplotlib
   - matplotlib
-  - plotly
+  - nc-time-axis
+  - descartes
+  - contextily
   - seaborn
+  # Holoviews
   - hvplot
   - geoviews>=1.10
   - selenium
   - phantomjs
   - jupyter_bokeh
-
-  # Spatial packages
-  - libtiff
-  - pysal
-  - pyproj>=3.0
-  - rasterstats
-  - geopy
-  - cartopy
-  - descartes
-  - contextily
+  # Folium
   - folium
-  - geojson
-  - mapboxgl
-  - hydrofunctions
-  - geocoder
-  - tweepy
-  - xarray
-  - rioxarray>=0.3.0
-  - xarray-spatial
-  - h5py
-  - scipy
-  - netcdf4
-  - nc-time-axis
-  - regionmask
-  - pyogrio
-
-  # Natural language processing
-  - nltk
-  - textblob
-
-  # Jupyter Environment
-  - papermill
-  - jupyterlab
-  - notebook
-  - ipython
-  - nbclean
-  - nbresuse
-
-  # Textbook Format
-  - jupyter-book
-  - sphinx-exercise
-  - ghp-import
   
   # QA
   - flake8
@@ -80,6 +70,3 @@ dependencies:
   - autopep8
   - pydocstyle
   - nbqa
-  
-  # Autograding
-  - nbgrader

From 2b9890918495228c157b70ae921d13ca2c6f2607 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Fri, 21 Jun 2024 13:00:38 -0600
Subject: [PATCH 59/77] Update build-test-envt.yml

---
 .github/workflows/build-test-envt.yml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/.github/workflows/build-test-envt.yml b/.github/workflows/build-test-envt.yml
index 975c15e..8842ce6 100644
--- a/.github/workflows/build-test-envt.yml
+++ b/.github/workflows/build-test-envt.yml
@@ -1,7 +1,3 @@
-# This workflow  runs tests for earthpy
-# Because we want a conda environment -  and that builds  slower,
-# we divided up  tests from linting and docs  to make  for simpler  install envts
-
 name: Test EA Python Envt Mac, Linux, Windows
 
 on: workflow_dispatch
@@ -19,7 +15,7 @@ jobs:
         shell: bash -l {0}
     steps:
       - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3.0.4
         with:
           miniconda-version: 'latest'
           channels: conda-forge

From 875326a6edb907d090cc93616757e78b61153abb Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Fri, 21 Jun 2024 13:01:34 -0600
Subject: [PATCH 60/77] Update build-test-envt.yml

---
 .github/workflows/build-test-envt.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-test-envt.yml b/.github/workflows/build-test-envt.yml
index c16a50a..8807081 100644
--- a/.github/workflows/build-test-envt.yml
+++ b/.github/workflows/build-test-envt.yml
@@ -18,10 +18,10 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4.1.7
         with:
             ref: upgrade-to-3.9
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3.0.4
         with:
           miniconda-version: 'latest'
           channels: conda-forge

From 85c7654e949d4fcc448828d531d1db61b992b472 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Fri, 21 Jun 2024 13:06:58 -0600
Subject: [PATCH 61/77] Update environment.yml

---
 environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/environment.yml b/environment.yml
index ebe1059..a6b5ae9 100644
--- a/environment.yml
+++ b/environment.yml
@@ -23,6 +23,7 @@ dependencies:
   - pyogrio
   # Raster data
   - xarray
+  - libtiff
   - h5py
   - netcdf4
   - rioxarray>=0.3.0

From d6a8fadcb8a6e481fa755b153563d9da1beb3c6f Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Fri, 21 Jun 2024 13:15:08 -0600
Subject: [PATCH 62/77] Update environment.yml

---
 environment.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index a6b5ae9..ebe1059 100644
--- a/environment.yml
+++ b/environment.yml
@@ -23,7 +23,6 @@ dependencies:
   - pyogrio
   # Raster data
   - xarray
-  - libtiff
   - h5py
   - netcdf4
   - rioxarray>=0.3.0

From cb3d64ae550a212e838323c82d5caf4bba91299f Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Fri, 21 Jun 2024 13:24:17 -0600
Subject: [PATCH 63/77] Update build-test-envt.yml

---
 .github/workflows/build-test-envt.yml | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/build-test-envt.yml b/.github/workflows/build-test-envt.yml
index 8807081..f5ebf41 100644
--- a/.github/workflows/build-test-envt.yml
+++ b/.github/workflows/build-test-envt.yml
@@ -1,7 +1,3 @@
-# This workflow  runs tests for earthpy
-# Because we want a conda environment -  and that builds  slower,
-# we divided up  tests from linting and docs  to make  for simpler  install envts
-
 name: Test EA Python Envt Mac, Linux, Windows
 
 on: workflow_dispatch
@@ -16,20 +12,16 @@ jobs:
         os: ["ubuntu-20.04", "macos-latest", "windows-latest"]
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash -el {0}
     steps:
       - uses: actions/checkout@v4.1.7
         with:
             ref: upgrade-to-3.9
       - uses: conda-incubator/setup-miniconda@v3.0.4
         with:
-          miniconda-version: 'latest'
-          channels: conda-forge
-          channel-priority: true
-          auto-update-conda: false
           auto-activate-base: false
           environment-file: environment.yml
           activate-environment: earth-analytics-python
       - run: conda list
       - run: python -c "import earthpy"
-      - run: python -c "import rasterio"
+      - run: python -c "import rioxarray"

From 6765c27aa945039e593056f56a6a936a897f256a Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Fri, 21 Jun 2024 13:36:57 -0600
Subject: [PATCH 64/77] Update build-test-envt.yml

---
 .github/workflows/build-test-envt.yml | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-test-envt.yml b/.github/workflows/build-test-envt.yml
index f5ebf41..ed6d5ec 100644
--- a/.github/workflows/build-test-envt.yml
+++ b/.github/workflows/build-test-envt.yml
@@ -9,14 +9,18 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-20.04", "macos-latest", "windows-latest"]
+        os: 
+          - "ubuntu-20.04"
+          - "macos-latest-large"
+          - "macos-latest-xlarge"
+          - "windows-latest"
     defaults:
       run:
         shell: bash -el {0}
     steps:
       - uses: actions/checkout@v4.1.7
         with:
-            ref: upgrade-to-3.9
+            ref: ${{ github.head_ref || github.ref_name }}
       - uses: conda-incubator/setup-miniconda@v3.0.4
         with:
           auto-activate-base: false
@@ -24,4 +28,5 @@ jobs:
           activate-environment: earth-analytics-python
       - run: conda list
       - run: python -c "import earthpy"
+      - run: python -c "import geopandas"
       - run: python -c "import rioxarray"

From c7c4823597321523637dae3a49c1eaf45db2d485 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Fri, 21 Jun 2024 13:45:40 -0600
Subject: [PATCH 65/77] Update build-test-envt.yml

---
 .github/workflows/build-test-envt.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build-test-envt.yml b/.github/workflows/build-test-envt.yml
index ed6d5ec..e14957c 100644
--- a/.github/workflows/build-test-envt.yml
+++ b/.github/workflows/build-test-envt.yml
@@ -10,9 +10,9 @@ jobs:
       fail-fast: false
       matrix:
         os: 
-          - "ubuntu-20.04"
-          - "macos-latest-large"
-          - "macos-latest-xlarge"
+          - "ubuntu-latest"
+          - "macos-13"
+          - "macos-latest"
           - "windows-latest"
     defaults:
       run:

From 6295b69d2e291fff842d69740cff2fd0aede73ef Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Fri, 21 Jun 2024 13:48:21 -0600
Subject: [PATCH 66/77] Update environment.yml

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index ebe1059..87d2688 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,7 +1,7 @@
 name: earth-analytics-python
 channels:
-  - defaults
   - conda-forge
+  - defaults
 
 dependencies:
   - python=3.11

From b2b0a28cac1569b23aef3760342235a1ffd3cb6e Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Tue, 1 Oct 2024 13:37:15 -0600
Subject: [PATCH 67/77] Update build-push-image.yml

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

diff --git a/.github/workflows/build-push-image.yml b/.github/workflows/build-push-image.yml
index 84e3f6b..ba4024b 100644
--- a/.github/workflows/build-push-image.yml
+++ b/.github/workflows/build-push-image.yml
@@ -26,7 +26,7 @@ jobs:
           context: ./
           file: ./Dockerfile
           push: true
-          tags: earthlab/earth-analytics-dev-env:latest
+          tags: earthlab/earth-analytics-python-env:latest
 
       - name: Image digest
         run: echo ${{ steps.docker_build.outputs.digest }}

From faf5bf3a83b0bbb54e8e2ac9d43fdce875028d53 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 2 Oct 2024 14:39:15 -0600
Subject: [PATCH 68/77] Update build-push-image.yml

---
 .github/workflows/build-push-image.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/build-push-image.yml b/.github/workflows/build-push-image.yml
index ba4024b..56d44ac 100644
--- a/.github/workflows/build-push-image.yml
+++ b/.github/workflows/build-push-image.yml
@@ -10,8 +10,6 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v2
-        with:
-          ref: upgrade-to-3.9
 
       - name: Login to DockerHub
         uses: docker/login-action@v1

From bb47d9d658bd4f563b8798efc2d3b8558d460e3a Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Wed, 2 Oct 2024 17:35:23 -0600
Subject: [PATCH 69/77] Update Dockerfile

---
 Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index efe33dc..01e415d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -18,7 +18,8 @@ RUN conda config --add channels conda-forge
 
 # Create environment
 COPY environment.yml /home/jovyan/ 
-RUN conda env update -n base -f /home/jovyan/environment.yml
+RUN conda install -n base -c conda-forge mamba
+RUN mamba env update -n base -f /home/jovyan/environment.yml
 
 # Activating environment
 RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> /home/jovyan/.bash_profile && \

From a644c844eca1b87c0f00b2fb93e0081205dfaeb8 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Mon, 19 May 2025 13:25:36 -0600
Subject: [PATCH 70/77] Update environment.yml

---
 environment.yml | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 87d2688..82a481c 100644
--- a/environment.yml
+++ b/environment.yml
@@ -4,13 +4,14 @@ channels:
   - defaults
 
 dependencies:
-  - python=3.11
+  - python=3.12
   - pip
   
   # Core scientific python
   - numpy
   - pandas
   - scipy
+  - dask
 
   # Geospatial libraries
   # Coordinates and CRSs
@@ -46,6 +47,9 @@ dependencies:
   - earthpy
   - earthaccess
   - pystac-client
+  - adlfs
+  - dataretrieval
+  - osmnx
   
   # Plotting
   # Matplotlib
@@ -55,6 +59,8 @@ dependencies:
   - contextily
   - seaborn
   # Holoviews
+  # --- Avoid compatibility issues with bokeh and new holoviews
+  - holoviews<=1.19
   - hvplot
   - geoviews>=1.10
   - selenium
@@ -70,3 +76,6 @@ dependencies:
   - autopep8
   - pydocstyle
   - nbqa
+
+  - pip:
+    - pygbif

From 366e59ea8a36287cbb90bd02a8eee3dd39bbfb7b Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Mon, 19 May 2025 16:06:52 -0600
Subject: [PATCH 71/77] Update Dockerfile

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

diff --git a/Dockerfile b/Dockerfile
index 01e415d..530052c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -30,4 +30,4 @@ RUN . /opt/conda/etc/profile.d/conda.sh && conda activate base && python -m ipyk
 RUN source /home/jovyan/.bash_profile
 
 # Install dev version of Earthpy
-RUN pip install git+https://github.com/earthlab/earthpy@apppears
+RUN pip install git+https://github.com/earthlab/earthpy@main

From f61ecbc9c6d4df8eeb638cd4eef24c5743a3452b Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Mon, 19 May 2025 16:47:36 -0600
Subject: [PATCH 72/77] Update Dockerfile

---
 Dockerfile | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 530052c..93824a6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -13,13 +13,10 @@ USER jovyan
 RUN conda update conda 
 RUN conda config --remove channels conda-forge
 RUN conda config --add channels conda-forge
-#RUN conda config --set channel_priority strict
-#RUN conda config --set solver classic
 
 # Create environment
 COPY environment.yml /home/jovyan/ 
-RUN conda install -n base -c conda-forge mamba
-RUN mamba env update -n base -f /home/jovyan/environment.yml
+RUN conda env update -n base -f /home/jovyan/environment.yml
 
 # Activating environment
 RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> /home/jovyan/.bash_profile && \

From 8f8c8d05d30e707cf259c534a73d8b9b4cc8bfab Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Mon, 19 May 2025 17:51:00 -0600
Subject: [PATCH 73/77] Update Dockerfile to 3.12

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

diff --git a/Dockerfile b/Dockerfile
index 93824a6..7f2e45c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM jupyter/minimal-notebook:python-3.11
+FROM jupyter/minimal-notebook:python-3.12
 
 # Installing package for libmamba
 USER root

From f57459433b8f6f0d2d60c3c0f5dc4dec80df9132 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Mon, 19 May 2025 18:01:06 -0600
Subject: [PATCH 74/77] Use miniconda instead of jupyter base image

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

diff --git a/Dockerfile b/Dockerfile
index 7f2e45c..543b80a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM jupyter/minimal-notebook:python-3.12
+FROM continuumio/miniconda3:25.1.1-2
 
 # Installing package for libmamba
 USER root

From a9c6cb6e3f28ffc039d2fcf1e98b139862db28a5 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Tue, 20 May 2025 07:34:11 -0600
Subject: [PATCH 75/77] Update environment.yml

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 82a481c..d495389 100644
--- a/environment.yml
+++ b/environment.yml
@@ -4,7 +4,7 @@ channels:
   - defaults
 
 dependencies:
-  - python=3.12
+  - python=3.11
   - pip
   
   # Core scientific python

From c99fb91cfc58ebb643e621f673a9ab644ab05bb8 Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Tue, 20 May 2025 07:35:57 -0600
Subject: [PATCH 76/77] Reverting to 3.11 -- base images are not compatible

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

diff --git a/Dockerfile b/Dockerfile
index 543b80a..93824a6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM continuumio/miniconda3:25.1.1-2
+FROM jupyter/minimal-notebook:python-3.11
 
 # Installing package for libmamba
 USER root

From b53f77b2cf87bdf9fb764f8aff9a6f0b20969e1b Mon Sep 17 00:00:00 2001
From: Elsa Culler <elsa.culler@colorado.edu>
Date: Tue, 20 May 2025 07:52:56 -0600
Subject: [PATCH 77/77] Update Dockerfile

---
 Dockerfile | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 93824a6..530052c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -13,10 +13,13 @@ USER jovyan
 RUN conda update conda 
 RUN conda config --remove channels conda-forge
 RUN conda config --add channels conda-forge
+#RUN conda config --set channel_priority strict
+#RUN conda config --set solver classic
 
 # Create environment
 COPY environment.yml /home/jovyan/ 
-RUN conda env update -n base -f /home/jovyan/environment.yml
+RUN conda install -n base -c conda-forge mamba
+RUN mamba env update -n base -f /home/jovyan/environment.yml
 
 # Activating environment
 RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> /home/jovyan/.bash_profile && \