Updated the installation of ARC use the Makefile (#98)

devtools/install_all.sh

@@ -1,5 +1,9 @@
+#!/bin/bash
 CONDA_BASE=$(conda info --base)
-source $CONDA_BASE/etc/profile.d/conda.sh
+
+# shellcheck source=/dev/null
+source "$CONDA_BASE/etc/profile.d/conda.sh"
+
 ###Check if Mamba is installed####
 #Check if mamba/conda is installed
 if [ -x "$(command -v mamba)" ]; then
@@ -17,26 +21,29 @@ pushd .
 cd ..
 
 if [ -d "./RMG-database" ]; then
-    cd RMG-database
+    cd RMG-database || exit
     git pull https://github.com/ReactionMechanismGenerator/RMG-database
     cd ..
 else
     git clone https://github.com/ReactionMechanismGenerator/RMG-database
 fi;
 
 if [ -d "./RMG-Py" ]; then
-    cd RMG-Py
+    cd RMG-Py || exit
     git pull https://github.com/ReactionMechanismGenerator/RMG-Py
 else
     git clone https://github.com/ReactionMechanismGenerator/RMG-Py
-    cd RMG-Py
+    cd RMG-Py || exit
 fi;
 
 
 echo "export PYTHONPATH=$PYTHONPATH:$(pwd)" >> ~/.bashrc
 echo "export PATH=$PATH:$(pwd)" >> ~/.bashrc 
-export PYTHONPATH=$PYTHONPATH:$(pwd)
-export PATH=$PATH:$(pwd)
+PYTHONPATH=$PYTHONPATH:$(pwd)
+export PYTHONPATH
+PATH=$PATH:$(pwd)
+export PATH
+# shellcheck source=~/.bashrc
 source ~/.bashrc
 
 #Creating rmg_env environment (or updating if it already exists)
@@ -50,10 +57,10 @@ fi;
 #Prior to activation of the environment, the LD_LIBRARY_PATH needs to be set as an environmnet variable when rmg_env is activated.
 #This exporting and unsetting will solve the RMS installation during the Julia compile and also when the environment is deactivated
 #the original LD_LIBRARY_PATH is set.
-echo "export OLD_LD_LIBRARY_PATH=${LD_LIBRARY_PATH}" >> $CONDA_BASE/envs/rmg_env/etc/conda/activate.d/env_vars.sh
-echo "export LD_LIBRARY_PATH=$CONDA_BASE/envs/rmg_env/lib:$LD_LIBRARY_PATH" >> $CONDA_BASE/envs/rmg_env/etc/conda/activate.d/env_vars.sh
-echo "export LD_LIBRARY_PATH=${OLD_LD_LIBRARY_PATH}" >> $CONDA_BASE/envs/rmg_env/etc/conda/deactivate.d/env_vars.sh
-echo "unset OLD_LD_LIBRARY_PATH" >> $CONDA_BASE/envs/rmg_env/etc/conda/deactivate.d/env_vars.sh
+echo "export OLD_LD_LIBRARY_PATH=${LD_LIBRARY_PATH}" >> "$CONDA_BASE/envs/rmg_env/etc/conda/activate.d/env_vars.sh"
+echo "export LD_LIBRARY_PATH=$CONDA_BASE/envs/rmg_env/lib:$LD_LIBRARY_PATH" >> "$CONDA_BASE/envs/rmg_env/etc/conda/activate.d/env_vars.sh"
+echo "export LD_LIBRARY_PATH=${OLD_LD_LIBRARY_PATH}" >> "$CONDA_BASE/envs/rmg_env/etc/conda/deactivate.d/env_vars.sh"
+echo "unset OLD_LD_LIBRARY_PATH" >> "$CONDA_BASE/envs/rmg_env/etc/conda/deactivate.d/env_vars.sh"
 
 
 #Active rmg_env environment
@@ -74,10 +81,6 @@ conda activate rmg_env
 python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
 julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main"));using ReactionMechanismSimulator'
 
-
-
-
-
 conda activate t3_env
 # check that Python and Julia are being accessed from the t3_env
 echo checking which python...
@@ -87,32 +90,27 @@ which julia
 echo linking python-jl to python...
 ln -sfn $(which python-jl) $(which python)
 
-
-
 cd ..
 if [ -d "./ARC" ]; then
-    cd ARC
+    cd ARC || exit
     git pull https://github.com/ReactionMechanismGenerator/ARC
 else
     git clone https://github.com/ReactionMechanismGenerator/ARC
-    cd ARC
+    cd ARC || exit
 fi;
 
-export PYTHONPATH=$PYTHONPATH:$(pwd)
+PYTHONPATH=$PYTHONPATH:$(pwd)
+export PYTHONPATH
 echo "export PYTHONPATH=$PYTHONPATH:$(pwd)" >> ~/.bashrc
 if { conda env list | grep 'arc_env'; } >/dev/null 2>&1; then
     $COMMAND_PKG env update -n arc_env -f environment.yml
 else
     $COMMAND_PKG env create -f environment.yml
 fi;
+
 conda activate arc_env
-#make install-all
-###Temp### To be used until ARC repo install is properly updated
-$COMMAND_PKG create -n xtb_env python=3.7 -y
-conda activate xtb_env
-$COMMAND_PKG install -c conda-forge xtb -y
-$COMMAND_PKG install -c anaconda pyyaml -y
-##########
+make install-all
+
 
 conda deactivate