Linting

.github/workflows/documentation.yml

@@ -26,4 +26,3 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
         run: julia docs/make.jl
-

.github/workflows/install_and_test.yml

@@ -8,7 +8,7 @@ on:
     branches: [main]
   push:
       branches: [main]
-  
+
 jobs:
   install:
     runs-on: ubuntu-latest
@@ -19,7 +19,7 @@ jobs:
       # Setup system
       - name: NetCDF
         run: |
-          sudo apt update 
+          sudo apt update
           sudo apt-get install libnetcdff-dev netcdf-bin gfortran gcc
 
       # Setup AGNI
@@ -34,16 +34,16 @@ jobs:
         with:
           repository: 'nichollsh/SOCRATES'
           path: 'socrates'
-        
+
       - name: Build SOCRATES
         run: |
           export LD_LIBRARY_PATH=""
           cd socrates
           ./configure
-          ./build_code 
-          source set_rad_env 
+          ./build_code
+          source set_rad_env
           cd ..
-        
+
       - name: Build AGNI
         run: |
           source socrates/set_rad_env
@@ -55,5 +55,5 @@ jobs:
           source socrates/set_rad_env
           export LD_LIBRARY_PATH=""
           ./test/runtests.jl
-          
-    
+
+

agni.jl

@@ -3,21 +3,21 @@
 # Don't show plot windows
 ENV["GKSwstype"] = "100"
 
-# Check RAD_DIR 
+# Check RAD_DIR
 if !("RAD_DIR" in keys(ENV))
     error("Cannot find SOCRATES! Have you set RAD_DIR?")
-end 
+end
 
 # Activate environment
 import Pkg
 Pkg.activate(dirname(abspath(@__FILE__)))
 
 # Include AGNI
 include("src/AGNI.jl")
-import .AGNI 
+import .AGNI
 
 # Run
 if AGNI.main()
     exit(0)
-end 
+end
 exit(1)

deps/build.jl

@@ -13,11 +13,11 @@ include(wrap)
 
 # Build libSOCRATES
 println("Build libSOCRATES")
-cd(joinpath(RAD_DIR,"julia/lib/")) do 
+cd(joinpath(RAD_DIR,"julia/lib/")) do
     run(`make`)
-end 
+end
 
-# Download basic data 
+# Download basic data
 println("Get data")
 get_data = joinpath(ROOT_DIR,"get_data.sh")
 run(`bash $get_data basic`)

get_data.sh

@@ -3,20 +3,20 @@
 # All files can be found on OSF at https://osf.io/8dumn/
 
 # Exit script if any of the commands fail
-set -e 
+set -e
 
-# Check that curl is installed 
+# Check that curl is installed
 if ! [ -x "$(command -v curl)" ]; then
   echo 'ERROR: curl is not installed.' >&2
   exit 1
 fi
 
-# Root and resources folders 
+# Root and resources folders
 root=$(dirname $(realpath $0))
 res="$root/res/"
 
-# Make basic data folders 
-mkdir -p $res 
+# Make basic data folders
+mkdir -p $res
 mkdir -p "$res/spectral_files"
 mkdir -p "$res/stellar_spectra"
 
@@ -32,7 +32,7 @@ Call structure:
     ./get_data [TARGET]
 
 Where [TARGET] can be any of the following:
-    basic 
+    basic
         $help_basic
     highres
         $help_highres
@@ -42,21 +42,21 @@ Where [TARGET] can be any of the following:
         $help_stellar
 "
 
-# Generic OSF downloader function 
+# Generic OSF downloader function
 function osf {
     # $1 = OSF identifier
-    # $2 = target folder 
+    # $2 = target folder
     # $3 = target filename
 
     # target file path
     tgt="$2/$3"
-    
+
     # exists?
     if [[ -f "$tgt" ]]; then
         echo "    $1 > file already exists"
         return 0
     fi
-    
+
     # get data
     echo "    $1 > $tgt"
     mkdir -p $2
@@ -65,12 +65,12 @@ function osf {
     return 0
 }
 
-# Handle request for downloading a group of data 
+# Handle request for downloading a group of data
 function handle_request {
     case $1 in
         "basic")
             echo $help_basic
-            
+
             osf qmp4e $res/spectral_files/Oak/318/ Oak.sf
             osf 5fxr7 $res/spectral_files/Oak/318/ Oak.sf_k
 
@@ -104,7 +104,7 @@ function handle_request {
             ;;
 
         "stellar")
-            echo $help_stellar 
+            echo $help_stellar
             osf mabp2 $res/stellar_spectra trappist-1.txt
             osf rk7mj $res/stellar_spectra eps-eri.txt
             osf agsrq $res/stellar_spectra hd97658.txt

get_fastchem.sh

@@ -10,7 +10,7 @@ git clone https://github.com/NewStrangeWorlds/FastChem.git "$fcpath"
 # Compile FastChem
 cd "$fcpath"
 mkdir build
-cd build 
+cd build
 
 cmake ".."
 make

get_socrates.sh

@@ -3,9 +3,9 @@
 
 # Check SSH access to GitHub
 ssh -T git@github.com
-if [ $? -eq 1 ]; then 
+if [ $? -eq 1 ]; then
     use_ssh=true
-else 
+else
     use_ssh=false
 fi
 
@@ -16,7 +16,7 @@ if [ "$use_ssh" = true ]; then
     git clone git@github.com:nichollsh/SOCRATES.git "$socpath"
 else
     git clone https://github.com/nichollsh/SOCRATES.git "$socpath"
-fi 
+fi
 
 # Compile SOCRATES
 cd "$socpath"