Merge branch 'master' of github.com:AtMoDat/atmodat_data_checker

ancillary/README.md

@@ -1,3 +1,13 @@
 Ancillary files contained in this folder:
 
-install_adc.sh: shell script to automate the installation of the atmodat data checker (adc) and the installation of Jupyter Lab with an adc kernel
+install_adc.sh: shell script to automate the installation of the atmodat data checker (adc).
+The script allows you to define the name of the conda environment in which the checker is installed.
+Besides the atmodat data checker, the scripts also installs CDOs, NCOs and Jupyter Lab (with a adc kernel).
+
+To use the script, please make sure the install_adc.sh is executable (chmod +x install_adc.sh).
+Then run the script either like
+./install_adc.sh
+--> installation of atmodat checker in conda environment named 'atmodat'
+./install_adc.sh myenvname 
+--> installation of atmodat checker in conda environment named 'myenvname'
+

ancillary/install_adc.sh

@@ -1,31 +1,34 @@
 #!/bin/bash
 
-git clone https://github.com/AtMoDat/atmodat_data_checker.git
-cd atmodat_data_checker || exit
-
-
 if [ $# -gt 0 ] ; then
    new_env=$1
+   git clone https://github.com/AtMoDat/atmodat_data_checker.git $new_env
+   cd $new_env || exit
    sed -i.bak "s/atmodat/${new_env}/" environment.yml
+else
+   git clone https://github.com/AtMoDat/atmodat_data_checker.git
+   cd atmodat_data_checker || exit
 fi
 
 env_name=$(sed -n 2p environment.yml |cut -d: -f2|tr -d ' ')
-echo "Installing atmodat checker in environment" "{$env_name}"
+echo "Installing atmodat checker in environment" "$env_name"
 
 conda env create         # environment name is retrieved from environment.yml
 
-# shellcheck disable=SC1090
 source ~/anaconda3/bin/activate "$env_name"      #-- equivalent to conda activate ${env_name} in terminal
-#source ~/anaconda3/etc/profile.d/conda.sh
-
+mamba install --yes --file mamba_requirements.txt
 pip install -U -e .
 git submodule init
-git submodule update
+git submodule update --remote --recursive
 
 
 #=== install jupyterlab and create ipykernel with name of the environment
-
+#=== also install cdo and nco
 mamba install --yes -c conda-forge jupyterlab
-python -m ipykernel install --user --name "{$env_name}"kernel
+mamba install --yes -c conda-forge cdo nco
 
+python -m ipykernel install --user --name "$env_name"kernel
 
+echo "finished installing $env_name
+      you can now activate the atmodat checker environment with
+      conda activate $env_name"