Exite non-zero on failed validation.

validation/validate-mmcif-file.py

@@ -695,6 +695,12 @@ def _main():
         print(f"Writing results of CifCheck to '{opts.out_file}'")
     cifcheck.make_json_output()
 
+    if cifcheck.got_issues():
+        # If CifCheck found issues with the mmCIF file, exit with code 2. Exit
+        # code 1 is reserved for general issues running the command, like "file
+        # not found".
+        sys.exit(2)
+
 
 if __name__ == "__main__":
     _main()