images

images/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}
+

images/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

images/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")
-install.packages(c("rstac", "spData", "earthdatalogin", "quarto"))
-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()
 

images/nasa-openscapes.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
@@ -40,22 +39,18 @@ 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/
 # 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
+    ${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'
 
 

images/nasa-requirements.txt

@@ -0,0 +1,31 @@
+jupyterhub
+jupyterlab
+notebook
+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
+polars
+pyarrow
+pystac-client==0.7.5
+gh-scoped-creds
+scikit-image
+hvplot
+geoviews
+earthaccess
+pyresample
+contextily
+pygeoweaver
+

images/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 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
+
+