From 131a74a4618a2ecde4fd6a0b7ff289f782b4f07b Mon Sep 17 00:00:00 2001
From: Mike Gottlieb <gottlieb@unavco.org>
Date: Thu, 16 May 2024 08:16:02 -0700
Subject: [PATCH] add hub image

---
 strain-hub/Dockerfile      | 68 ++++++++++++++++++++++++++++++++++++++
 strain-hub/build_docker.sh |  2 ++
 strain-hub/environment.yml | 21 ++++++++++++
 3 files changed, 91 insertions(+)
 create mode 100644 strain-hub/Dockerfile
 create mode 100755 strain-hub/build_docker.sh
 create mode 100644 strain-hub/environment.yml

diff --git a/strain-hub/Dockerfile b/strain-hub/Dockerfile
new file mode 100644
index 0000000..7ab5d54
--- /dev/null
+++ b/strain-hub/Dockerfile
@@ -0,0 +1,68 @@
+FROM ghcr.io/earthscope/strain-processing-notebooks
+
+#from https://github.com/2i2c-org/coessing-image/blob/main/Dockerfile
+USER root
+#ENV DEBIAN_FRONTEND=noninteractive
+#ENV PATH ${NB_PYTHON_PREFIX}/bin:$PATH
+
+#https://github.com/pangeo-data/pangeo-docker-images/blob/master/base-image/Dockerfile
+# Setup environment to match variables set by repo2docker as much as possible
+# The name of the conda environment into which the requested packages are installed
+ENV CONDA_ENV=notebook \
+    # Tell apt-get to not block installs by asking for interactive human input
+    DEBIAN_FRONTEND=noninteractive \
+    # Set username, uid and gid (same as uid) of non-root user the container will be run as
+    NB_USER=jovyan \
+    NB_UID=1000 \
+    # Use /bin/bash as shell, not the default /bin/sh (arrow keys, etc don't work then)
+    SHELL=/bin/bash \
+    # Setup locale to be UTF-8, avoiding gnarly hard to debug encoding errors
+    LANG=C.UTF-8  \
+    LC_ALL=C.UTF-8 \
+    # Install conda in the same place repo2docker does
+    #CONDA_DIR=/srv/conda
+    # Change to where docker stacks does https://github.com/EarthScope/strain-processing-notebooks/blob/aba9f9b5d2a199e75462c239ebf57a96dd33ffbf/docker-stacks-foundation/Dockerfile#L44C5-L44C25
+    CONDA_DIR=/opt/conda
+# All env vars that reference other env vars need to be in their own ENV block
+# Path to the python environment where the jupyter notebook packages are installed
+ENV NB_PYTHON_PREFIX=${CONDA_DIR}/envs/${CONDA_ENV} \
+    # Home directory of our non-root user
+    HOME=/home/${NB_USER}
+
+# Add both our notebook env as well as default conda installation to $PATH
+# Thus, when we start a `python` process (for kernels, or notebooks, etc),
+# it loads the python in the notebook conda environment, as that comes
+# first here.
+ENV PATH=${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${PATH}
+
+# Ask dask to read config from ${CONDA_DIR}/etc rather than
+# the default of /etc, since the non-root jovyan user can write
+# to ${CONDA_DIR}/etc but not to /etc
+ENV DASK_ROOT_CONFIG=${CONDA_DIR}/etc
+
+# Run conda activate each time a bash shell starts, so users don't have to manually type conda activate
+# Note this is only read by shell, but not by the jupyter notebook - that relies
+# on us starting the correct `python` process, which we do by adding the notebook conda environment's
+# bin to PATH earlier ($NB_PYTHON_PREFIX/bin)
+RUN echo ". ${CONDA_DIR}/etc/profile.d/conda.sh ; conda activate ${CONDA_ENV}" > /etc/profile.d/init_conda.sh
+
+# Needed for apt-key to work
+RUN apt-get update -qq --yes > /dev/null && \
+    apt-get install --yes -qq gnupg2 > /dev/null
+
+USER ${NB_USER}
+
+COPY environment.yml /tmp/
+
+RUN mamba env update --name ${CONDA_ENV} -f /tmp/environment.yml
+
+# Remove nb_conda_kernels from the env for now
+RUN mamba remove -n ${CONDA_ENV} nb_conda_kernels
+
+#COPY install-jupyter-extensions.bash /tmp/install-jupyter-extensions.bash
+#RUN /tmp/install-jupyter-extensions.bash
+
+# Set bash as shell in terminado.
+#ADD jupyter_notebook_config.py  ${NB_PYTHON_PREFIX}/etc/jupyter/
+# Disable history.
+#ADD ipython_config.py ${NB_PYTHON_PREFIX}/etc/ipython/
\ No newline at end of file
diff --git a/strain-hub/build_docker.sh b/strain-hub/build_docker.sh
new file mode 100755
index 0000000..e2ffc1d
--- /dev/null
+++ b/strain-hub/build_docker.sh
@@ -0,0 +1,2 @@
+docker build --rm -f Dockerfile -t ghcr.io/earthscope/strain-hub .
+docker push ghcr.io/earthscope/strain-hub
\ No newline at end of file
diff --git a/strain-hub/environment.yml b/strain-hub/environment.yml
new file mode 100644
index 0000000..c30dd1e
--- /dev/null
+++ b/strain-hub/environment.yml
@@ -0,0 +1,21 @@
+# This is the standard conda configuration file. Use this file to list
+# the conda packages that you need installed in your environment.
+channels:
+  - conda-forge
+
+dependencies:
+  - jupyter_contrib_nbextensions==0.5.1
+  # Required until https://github.com/jupyterhub/repo2docker/pull/1196 is merged
+  - jupyterhub-singleuser>=3.0,<4.0
+  # Set default python version to 3.10 - repo2docker sets it to 3.7 instead by default,
+  # which can limit us to older package versions
+  - python=3.10
+  # extensions fail with notebook>7? https://stackoverflow.com/questions/76893872/modulenotfounderror-no-module-named-notebook-base-when-installing-nbextension
+  - notebook==6.4.12
+  # Everyone wants to use nbgitpuller for everything, so let's do that
+  - nbgitpuller=1.1.*
+  # Add other packages here
+  - nb_conda_kernels
+  - pip
+  - pip: 
+    - 'earthscopestraintools[mseed,tiledb]'
\ No newline at end of file