Merge branch 'improvements' into 'master'

Improve everything

See merge request !1

activate.sh

 #!/bin/bash
-RELATIVE_PATH=`dirname ${BASH_SOURCE}`
-ABSOLUTE_PATH=`realpath ${RELATIVE_PATH}`
 
-[[ $0 != $BASH_SOURCE ]] && echo "The activation script must be sourced, otherwise the virtual environment will not work." || ( echo "Vars script must be sourced." && exit 1) ;
+# See https://stackoverflow.com/a/28336473
+SOURCE_PATH="${BASH_SOURCE[0]:-${(%):-%x}}"
 
-source ${ABSOLUTE_PATH}/config.sh
-source ${ABSOLUTE_PATH}/modules.sh
-
-export PYTHONPATH=`echo ${ENV_DIR}/lib/python*/site-packages`:${PYTHONPATH}
-
-source ${ENV_DIR}/bin/activate
+RELATIVE_PATH="$(dirname "$SOURCE_PATH")"
+ABSOLUTE_PATH="$(realpath "${RELATIVE_PATH}")"
 
+[[ "$0" != "${SOURCE_PATH}" ]] && echo "The activation script must be sourced, otherwise the virtual environment will not work." || ( echo "Vars script must be sourced." && exit 1) ;
 
+source "${ABSOLUTE_PATH}"/config.sh
+source "${ABSOLUTE_PATH}"/modules.sh
 
+export PYTHONPATH="$(echo "${ENV_DIR}"/lib/python*/site-packages):${PYTHONPATH}"
 
+source "${ENV_DIR}"/bin/activate

config.sh

+SOURCE_PATH="${BASH_SOURCE[0]:-${(%):-%x}}"
+
 ## Check if this script is sourced
-[[ $0 != $BASH_SOURCE ]] && echo "Setting vars" || ( echo "Vars script must be sourced." && exit 1) ;
+[[ "$0" != "${SOURCE_PATH}" ]] && echo "Setting vars" || ( echo "Vars script must be sourced." && exit 1) ;
 ## Determine location of this file
-RELATIVE_PATH=`dirname ${BASH_SOURCE}`
-ABSOLUTE_PATH=`realpath ${RELATIVE_PATH}`
+RELATIVE_PATH="$(dirname "$SOURCE_PATH")"
+ABSOLUTE_PATH="$(realpath "${RELATIVE_PATH}")"
 ####################################
 
 ### User Configuration
-export ENV_NAME=`basename $ABSOLUTE_PATH`             # Default Name of the venv is the directory that contains this file
-export ENV_DIR=${ABSOLUTE_PATH}/venv         # Default location of this VENV is "./venv"
-
+export ENV_NAME="$(basename "$ABSOLUTE_PATH")"             # Default Name of the venv is the directory that contains this file
+export ENV_DIR="${ABSOLUTE_PATH}"/venv         # Default location of this VENV is "./venv"

create_kernel.sh

 #!/bin/bash
 
-RELATIVE_PATH=`dirname ${BASH_SOURCE}`
-ABSOLUTE_PATH=`realpath ${RELATIVE_PATH}`
-source ${ABSOLUTE_PATH}/config.sh
+SOURCE_PATH="${BASH_SOURCE[0]:-${(%):-%x}}"
 
-KERNELFILE=${ENV_DIR}/kernel.sh
+RELATIVE_PATH="$(dirname "$SOURCE_PATH")"
+ABSOLUTE_PATH="$(realpath "${RELATIVE_PATH}")"
+source "${ABSOLUTE_PATH}"/config.sh
 
-echo the name is $ENV_NAME
+KERNELFILE="${ENV_DIR}"/kernel.sh
 
-echo "Setting up the kernel script in the following dir: " ${KERNELFILE}
+echo the name is "$ENV_NAME"
+
+echo "Setting up the kernel script in the following dir: " "${KERNELFILE}"
 
 echo '#!/bin/bash
 
-source '"${ABSOLUTE_PATH}"'/activate.sh
+source "'"${ABSOLUTE_PATH}"'"/activate.sh
 
-exec python -m ipykernel $@' > ${KERNELFILE}
+exec python -m ipykernel "$@"' > "${KERNELFILE}"
 
-chmod a+x ${KERNELFILE}
+chmod a+x "${KERNELFILE}"
 
-mkdir -p ~/.local/share/jupyter/kernels/${ENV_NAME}
+mkdir -p ~/.local/share/jupyter/kernels/"${ENV_NAME}"
 echo '{
  "argv": [
   "'"${KERNELFILE}"'",
   "-f",
   "{connection_file}"
  ],
- "display_name": "'${ENV_NAME}'",
+ "display_name": "'"${ENV_NAME}"'",
  "language": "python"
-}' > ~/.local/share/jupyter/kernels/${ENV_NAME}/kernel.json
+}' > ~/.local/share/jupyter/kernels/"${ENV_NAME}"/kernel.json

modules.sh

-ml GCC/9.3.0  ParaStationMPI/5.4.7-1  Python/3.8.5
+module purge
+module load GCC/10.3.0  ParaStationMPI/5.4.10-1  Python/3.8.5

readme.md

@@ -10,12 +10,12 @@ curated and optimized, including compilers, MPI version etc. Extra Python packag
 with pip into user space. This, however, does not create a reproducible environment that can be used
 by other users as well.
 
-Conceptuall, with Virtual Environments, it is easily possible to create project-based virtual environments.
-These scripts streamline the creation und usage of such environments and make it easy for a users to share a setup
+Conceptually, with Virtual Environments, it is easily possible to create project-based virtual environments.
+These scripts streamline the creation and usage of such environments and make it easy for a users to share a setup
 and to put it under version control with the main code.
 
 Furthermore, in typical compute setup of scientific projects, one or more packages possibly are in active
-developement. In the context of these setups, it is intended to include them as submodules and add integrate
+development. In the context of these setups, it is intended to include them as submodules and add integrate
 them into the workflow. This can e.g. mean that a compilation step is added in the setup step and
 setting appropriate environment variables is included in the activation step.
 
@@ -32,16 +32,16 @@ packages to this file to reproducibly add them to the venv.
 
 The script `setup.sh` creates the venv according to the config given in `config.sh`. Please **edit** this
 file to add a setup step for submodules (e.g. compilation of libraries). If only plain venvs are used, this file
-can remain unchanged.
+can remain unchanged. Note that the script *must* be ran at least once after the above configurations to actually create the environment.
 
 The script `activate.sh` sets the environment variables such that the venv can be used. Please **edit** this file
-to add environment variables for submodules. Note that it the script must be *sourced* to take effect. Example:
+to add environment variables for submodules. Note that the script must be *sourced* to take effect. Example:
 ```bash
 source <path_to_venv>/activate.sh
 ```
 
 The script `create_kernel.sh` will create a kernel json file in the user's home directory that can be found
-by jupyter and a helper script in the virtual environment folder.
+by Jupyter and a helper script in the virtual environment folder.
 
 
 
@@ -50,4 +50,5 @@ by jupyter and a helper script in the virtual environment folder.
 2. Edit `modules.sh` to change the modules loaded prior to the creation of the venv.
 3. Edit `requirements.txt` to change the packages to be installed during setup.
 4. Edit `setup.sh` and `activate.sh` to add extra steps for custom modules.
-5. Create a kernel with `create_kernel.sh`
+5. Create the environment with `bash setup.sh`.
+6. Create a kernel with `bash create_kernel.sh`.

setup.sh

 #!/bin/bash
-RELATIVE_PATH=`dirname ${BASH_SOURCE}`
-ABSOLUTE_PATH=`realpath ${RELATIVE_PATH}`
 
-source ${ABSOLUTE_PATH}/config.sh
-source ${ABSOLUTE_PATH}/modules.sh
+SOURCE_PATH="${BASH_SOURCE[0]:-${(%):-%x}}"
 
-python -m venv --prompt $ENV_NAME --system-site-packages ${ENV_DIR}
+RELATIVE_PATH="$(dirname "$SOURCE_PATH")"
+ABSOLUTE_PATH="$(realpath "${RELATIVE_PATH}")"
 
-source ${ABSOLUTE_PATH}/activate.sh
-
-pip install -r ${ABSOLUTE_PATH}/requirements.txt
+source "${ABSOLUTE_PATH}"/config.sh
+source "${ABSOLUTE_PATH}"/modules.sh
 
+python -m venv --prompt "$ENV_NAME" --system-site-packages "${ENV_DIR}"
 
+source "${ABSOLUTE_PATH}"/activate.sh
 
+python -m pip install -r "${ABSOLUTE_PATH}"/requirements.txt