Add missed file, removed FIXME

Author: leshikus

.github/dockerfiles/env/entrypoint.sh

@@ -0,0 +1,63 @@
+#!/bin/bash
+
+set -e
+set -vx
+
+conda_prefix=$HOME/.conda
+jupyterlab_env="base"
+kernel_env="python-3.9"
+
+# Fix the owner and permissions for /home/jovyan
+# TODO: check if passwordless sudo is enabled
+sudo chown jovyan:jovyan /home/jovyan
+sudo chmod 00700 /home/jovyan
+
+cd ~
+
+if [[ ! -d $conda_prefix ]]; then
+  echo "$conda_prefix does not exists, copying from /template"
+  tar x -Ipixz -f /template/conda.tar.xz
+fi
+
+if [[ ! -f ~/.profile ]]; then
+  echo "No .profile in $HOME, creating one"
+  echo "source $conda_prefix/etc/profile.d/conda.sh" >> ~/.profile
+  echo "conda activate python-3.9" >> ~/.profile
+fi
+
+if [[ ! -f ~/.jupyter/jupyter_config.json ]]; then
+  echo "no .jupyter/jupyter_config.json in $HOME, creating one"
+  mkdir -p ~/.jupyter
+  # Use kernel display_name, filter out a kernel from jupyterlab environment
+  cat <<EOF > ~/.jupyter/jupyter_config.json
+{
+  "CondaKernelSpecManager": {
+    "conda_only": true,
+    "name_format": "{display_name}"
+  }
+}
+EOF
+
+  # Use environment name for display_name
+  kernel_json=$conda_prefix/envs/$kernel_env/share/jupyter/kernels/python3/kernel.json
+  jq ".display_name = \"$kernel_env\"" $kernel_json > /tmp/kernel.json
+  mv /tmp/kernel.json $kernel_json
+  unset kernel_json
+fi
+
+source $conda_prefix/etc/profile.d/conda.sh
+conda activate $jupyterlab_env
+
+unset conda_prefix
+unset jupyterlab_env
+unset kernel_env
+
+# Remove default kernel
+jupyter kernelspec remove -y python3 || true
+
+# Remove lost+found
+rm -rf lost+found
+
+find ~/.conda -name '*singleuser'
+
+exec jupyterhub-singleuser