diff --git a/.github/workflows/pretty.yml b/.github/workflows/pretty.yml
index f2c1fd761..68ea46ea8 100644
--- a/.github/workflows/pretty.yml
+++ b/.github/workflows/pretty.yml
@@ -15,5 +15,5 @@ jobs:
     steps:
     - uses: actions/checkout@v3
 
-    - name: Count
+    - name: Format diff
       run: ./mfc.sh format diff
diff --git a/src/common/include/inline_conversions.fpp b/src/common/include/inline_conversions.fpp
index ec02ccfe8..9811290a8 100644
--- a/src/common/include/inline_conversions.fpp
+++ b/src/common/include/inline_conversions.fpp
@@ -20,7 +20,7 @@
             c = (1d0/(rho*(adv(1)/blkmod1 + adv(2)/blkmod2)))
         elseif (model_eqns == 3) then
             c = 0d0
-!$acc loop seq
+            !$acc loop seq
             do q = 1, num_fluids
                 c = c + adv(q)*(1d0/gammas(q) + 1d0)* &
                     (pres + pi_infs(q)/(gammas(q) + 1d0))
diff --git a/src/common/include/macros.fpp b/src/common/include/macros.fpp
index 2f2d2fcf6..b33eb1f17 100644
--- a/src/common/include/macros.fpp
+++ b/src/common/include/macros.fpp
@@ -22,7 +22,7 @@
 #:def DEALLOCATE(*args)
     @:LOG({'@:DEALLOCATE(${re.sub(' +', ' ', ', '.join(args))}$)'})
     deallocate (${', '.join(args)}$)
-    !$acc exit data delete(${', '.join(args)}$)
+!$acc exit data delete(${', '.join(args)}$)
 #:enddef DEALLOCATE
 
 #define t_vec3   real(kind(0d0)), dimension(1:3)
diff --git a/toolchain/bootstrap/format.sh b/toolchain/bootstrap/format.sh
index e4853a40c..ccafd4fc9 100644
--- a/toolchain/bootstrap/format.sh
+++ b/toolchain/bootstrap/format.sh
@@ -19,7 +19,10 @@ if [ "$1" == "diff" ]; then
 fi
 
 # Indent acc directives
-for filename in src/*/*.f*; do
+srcfiles=( src/*/*.f* )
+includefiles=( src/*/include/*.f* )
+files=( "${srcfiles[@]}" "${includefiles[@]}" )
+for filename in ${files[@]}; do
     python3 toolchain/indenter.py "$filename"
 done
 
diff --git a/toolchain/indenter.py b/toolchain/indenter.py
old mode 100755
new mode 100644
index 0779111e4..a535ccc2e
--- a/toolchain/indenter.py
+++ b/toolchain/indenter.py
@@ -5,13 +5,14 @@
 def main():
     num_args = len(sys.argv)
     if num_args != 2:
-       AssertionError('Invalid number of arguments, found ', num_args)
+        raise Exception('Invalid number of arguments, found ', num_args)
 
     infile = str(sys.argv[1])
     outfile = infile+".new"
     adjust_indentation(infile, outfile)
     os.replace(outfile,infile)
 
+# pylint: disable=too-many-branches
 def adjust_indentation(input_file, output_file):
     startingchar='!$acc'
     startingloop1='!$acc parallel loop'
@@ -22,8 +23,10 @@ def adjust_indentation(input_file, output_file):
         lines = file_in.readlines()
 
         # this makes sure !$acc lines that have line continuations get indented at proper level
-        for kk in range(10):
+        # pylint: disable=too-many-nested-blocks
+        for _ in range(10):
             # loop through file
+            # pylint: disable=consider-using-enumerate
             for i in range(len(lines)):
                 if lines[i].lstrip().startswith(startingchar) and i + 1 < len(lines):
                     j = i + 1
@@ -50,7 +53,7 @@ def adjust_indentation(input_file, output_file):
                         while k >= 0:
                             # if line above is not empty
                             if lines[k].strip() != '':
-                                # if line 2 above ends with line continuation, indent at that level 
+                                # if line 2 above ends with line continuation, indent at that level
                                 if lines[k-1].strip().endswith('&'):
                                     indent = len(lines[k-1]) - len(lines[k-1].lstrip())
                                 # else indent at level of line above