Merge pull request #82 from andrewdelman/cloud_compatibility

Cloud compatibility

Author: andrewdelman

Cloud_Setup/install_conda_mamba.sh

@@ -25,7 +25,7 @@ fi
 echo -e "${red_start}Starting Miniforge3 installation${nocolor_start}"
 
 # download Miniforge 
-if [ -f ~/Miniforge3.sh ]; then
+if [ ! -f ~/Miniforge3.sh ]; then
    wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh" -O ~/Miniforge3.sh
 else
    echo "Miniforge already downloaded!"
@@ -34,16 +34,23 @@ fi
 # install Miniforge 
 # default directory is ~/miniforge3
 
+if [ -d ~/miniforge3 ]; then
+    echo "~/miniforge3 directory already exists"
+    echo "deleting and re-installing Miniforge"
+    rm -r ~/miniforge3
+fi
 sh ~/Miniforge3.sh -b
 
 # add conda and mamba to .bashrc or equivalent
 ~/miniforge3/bin/conda init
 ~/miniforge3/bin/mamba init
+source ~/.bashrc
 
 echo -e "${red_start}Completed Miniforge3 installation${nocolor_start}"
-echo -e "${red_start}Restart your shell${nocolor_start}"
+# echo -e "${red_start}Restart your shell${nocolor_start}"
 
-mamba update -n base -c conda-forge conda
+mamba update -n base -c conda-forge conda -y
 
 # this one is a bit of a mystery, but required
 echo "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:~/miniforge3/lib" >> ~/.bashrc
+source ~/.bashrc

Cloud_Setup/install_packages.sh

@@ -21,7 +21,7 @@ red_start='\033[0;31m'
 blue_start='\033[0;34m'
 nocolor_start='\033[0m'
 
-# # set paths to environment and package directories
+mamba init
 
 # create jupyter environment
 mamba create --name jupyter python=3.11 -y

Cloud_Setup/install_packages_bigmem.sh

@@ -14,7 +14,9 @@ red_start='\033[0;31m'
 blue_start='\033[0;34m'
 nocolor_start='\033[0m'
 
-# # set paths to environment and package directories
+
+conda init
+
 # create conda environment called 'jupyter'
 env_name='jupyter'
 
@@ -47,7 +49,6 @@ mamba install -n ${env_name} xarray[complete] jupyterlab dask_labextension s3fs
 mamba install -n ${env_name} pyresample -y
 
 # install remaining packages using pip
-# (mamba installs tend to get killed on t2.micro)
 pip install ecco_v4_py --no-cache-dir
 
 echo -e "${red_start}Completed Python package installations${nocolor_start}"

Cloud_Setup/jupyter_lab_start.sh

@@ -7,10 +7,12 @@ red_start='\033[0;31m'
 blue_start='\033[0;34m'
 nocolor_start='\033[0m'
 
-source ~/conda/bin/activate
+
+conda init
+source ~/miniforge3/bin/activate
 conda activate jupyter
 
-echo "Staring Jupyter lab session!"
+echo "Starting Jupyter lab session!"
 echo ""
 
 read -p 'Which port do you want to use [default 9889]: ' user_port
@@ -24,7 +26,7 @@ echo "Enter password to access Jupyter lab from browser,"
 echo "or leave blank to not require a password."
 
 PW="$(python3 -c 'from jupyter_server.auth import passwd; import getpass; print(passwd(getpass.getpass(), algorithm="sha256"))')"
-jlab_start="jupyter Space lab Space --no-browser Space --autoreload Space --port=\"${user_port}\" Space --ip='127.0.0.1' Space --NotebookApp.token='' Space --NotebookApp.password=\"$PW\" Space --notebook-dir=\"~/ECCO-v4-Python-Tutorial\""
+jlab_start="jupyter Space lab Space --no-browser Space --autoreload Space --port=\"${user_port}\" Space --ip='127.0.0.1' Space --IdentityProvider.token='' Space --PasswordIdentityProvider.hashed_password=\"$PW\" Space --notebook-dir=\"~/ECCO-v4-Python-Tutorial\""
 
 # Start new tmux session
 tmux new -d -s jupyterlab