diff --git a/marzipan/TODO.md b/marzipan/TODO.md
index 57d8813..9de1703 100644
--- a/marzipan/TODO.md
+++ b/marzipan/TODO.md
@@ -15,9 +15,9 @@
 
 * `pretty_output` Bash function
   * ~~pretty_output_line~~
+  * ~~click function intervention weirdness~~
+  * ~~why is everything red in the pretty output? (see line 96 in __init__.py)~~
   * awk RESULT flush in marzipan()
-  * click function intervention weirdness
-  * why is everything red in the pretty output? (see line 96 in __init__.py)
 * move the whole metaverif function to Python
 * move the whole analyze function to Python
   * find the files
diff --git a/marzipan/src/__init__.py b/marzipan/src/__init__.py
index c317c4a..227333c 100644
--- a/marzipan/src/__init__.py
+++ b/marzipan/src/__init__.py
@@ -53,11 +53,6 @@ def awk_prep(cpp_prep, awk_prep):
         file.write("\nprocess main")
 
 
-#@click.command()
-#@click.argument("prefix", required=True)
-#@click.argument("mark", required=True)
-#@click.argument("color", required=True)
-#@click.argument("text", default='')
 def pretty_output_line(prefix, mark, color, text):
     prefix = f"[grey42]{prefix}[/grey42]"
     content = f"[{color}]{mark} {text}[/{color}]"
@@ -93,7 +88,11 @@ def pretty_output(file_path):
 
     for outp in pkgs.sys.stdin:
         tz = pkgs.time.time()
-        if outp == expected[ctr]:
+
+        # Output from ProVerif contains a trailing newline, which we do not have in the expected output. Remove it for meaningful matching.
+        outp_clean = outp.rstrip()
+
+        if outp_clean == expected[ctr]:
             pretty_output_line(f"{int(tz - ta)}s ", "✔", "green", descs[ctr])
         else:
             res = 1
@@ -154,6 +153,5 @@ main.add_command(clean)
 main.add_command(run_proverif)
 main.add_command(cpp)
 main.add_command(awk_prep)
-#main.add_command(pretty_output_line)
 main.add_command(pretty_output)
 main.add_command(clean_warnings)
diff --git a/marzipan/src/analyze.sh b/marzipan/src/analyze.sh
old mode 100755
new mode 100644
index 1825ef1..4840e5a
--- a/marzipan/src/analyze.sh
+++ b/marzipan/src/analyze.sh
@@ -24,10 +24,6 @@ color_clear=''
 checkmark="✔"
 cross="❌"
 
-pretty_output_line() {
-  exc rosenpass-marzipan pretty-output-line "${@}"
-}
-
 pretty_output() {
   exc rosenpass-marzipan pretty-output "${@}"
 }