Update example with new code and new ref bindump

test/ALLTESTS.sh

@@ -2,6 +2,7 @@
 
 export TMP=/tmp/MNXtools_test/$USER/tests/$$ # scratch dir
 mkdir -p $TMP
+export MNX_DEFAULT_CACHE=../cache/ChemSpace.bindump
 
 for PERL in perl;
 do

test/README.md

@@ -8,9 +8,8 @@ Principles:
 
 * Tests are stored in `*.test` files.
 * Every test consists in a single UNIX command, that must start with `TEST=<test-name>`
-* A test is succesful if the exit code is zero.
+* A test is successful if the exit code is zero.
 
 In addition to `TEST`, a couple of environment variables are used to write the tests.
 These are documented and initialised in `./ALLTESTS.sh` and used in the `*.test` files.
 
-

test/convert.test

@@ -1,6 +1,5 @@
 TEST=CONVERT
-$PERL ../bin/convert_mnet.pl $MNET/unmapped $TMP \
+$PERL ../bin/convert_mnet.pl -V ${MNX_CACHE:=$MNX_DEFAULT_CACHE} $MNET/unmapped $TMP \
 && $PERL ./mnet_diff.pl $MNET/mapped $TMP \
 && diff $MNET/mapped/convert_log.yaml $TMP/convert_log.yaml
 
-

test/run_test.pl

@@ -33,20 +33,20 @@
     next if /^\s*$/;
     if( /^TEST=(.+)/ ){
         $rank++;
-		$test_id = $1;
-		$tb->die( "Duplicated test: $test_id" ) if exists $test_info{$test_id};
-		$test_info{$test_id} = {
-			rank   => $rank,
-			cmd    => '',
-		}
-	}
+        $test_id = $1;
+        $tb->die( "Duplicated test: $test_id" ) if exists $test_info{$test_id};
+        $test_info{$test_id} = {
+            rank   => $rank,
+            cmd    => '',
+        }
+    }
     else{
         $tb->die( "Not test defined yet: $_" ) unless $test_id;
         while( /\$(\w+)/g ){
             $tb->die( "Environment variable '$1' not set in line: $_" ) unless exists $ENV{$1};
         }
         $test_info{$test_id}{cmd} .= $_;
-	}
+    }
 }
 
 foreach my $test_id ( sort { $test_info{$a}{rank} <=> $test_info{$b}{rank} } keys %test_info ){

test/tab_diff.pl

@@ -15,7 +15,7 @@
 options: -h          this help
 
          -t <real>   tolerance (absolute value) for real number
-					 comparison (1e-6 by default)
+                     comparison (1e-6 by default)
          -z          Zombie mode: do not die on error!
 
 In addition the environment variable
@@ -47,22 +47,22 @@
 my $L = @$tsv_1;
 $tb->die( "The two input files have a different number of lines!" ) unless $L == @$tsv_2;
 foreach my $i ( 0 .. @format -1 ){
-	if( $format[$i] eq 's' ){ # string comparison
-		foreach( 0 .. $L - 1 ){
+    if( $format[$i] eq 's' ){ # string comparison
+        foreach( 0 .. $L - 1 ){
             $tsv_1->[$_][$i] =~ s/_(B|LR|RL)$//;
             $tsv_2->[$_][$i] =~ s/_(B|LR|RL)$//;
-			unless( $tsv_1->[$_][$i] eq $tsv_2->[$_][$i] ){
-				msg(
+            unless( $tsv_1->[$_][$i] eq $tsv_2->[$_][$i] ){
+                msg(
                     "Strings differ: $tsv_1->[$_][$i] vs $tsv_2->[$_][$i] at line "
                     . ( $_ + 1 )
                     . ', col '
                     . ($i + 1 )
                 );
-			}
-		}
-	}
-	elsif( $format[$i] eq 'i' ){ # integer comparison
-		foreach( 0 .. $L - 1 ){
+            }
+        }
+    }
+    elsif( $format[$i] eq 'i' ){ # integer comparison
+        foreach( 0 .. $L - 1 ){
             unless( $tsv_1->[$_][$i] == $tsv_2->[$_][$i] ){
                 msg(
                     "Numbers not equal: $tsv_1->[$_][$i] vs $tsv_2->[$_][$i] at line "
@@ -72,9 +72,9 @@
                 );
             }
         }
-	}
-	elsif( $format[$i] eq 'r' ){ # real comparison (with some tolerance)
-		foreach my $j ( 0 .. $L - 1 ){
+    }
+    elsif( $format[$i] eq 'r' ){ # real comparison (with some tolerance)
+        foreach my $j ( 0 .. $L - 1 ){
             if( abs( $tsv_1->[$j][$i] - $tsv_2->[$j][$i] ) > $opt{t} ) {
                 msg(
                     "Numbers differ too much: $tsv_1->[$j][$i] vs $tsv_2->[$j][$i] at line "
@@ -84,13 +84,13 @@
                 );
             }
         }
-	}
-	elsif( $format[$i] eq '.' ){ # skip that column
+    }
+    elsif( $format[$i] eq '.' ){ # skip that column
 
-	}
-	else{
-		$tb->die( "Unsupported column format: $format[$i]" );
-	}
+    }
+    else{
+        $tb->die( "Unsupported column format: $format[$i]" );
+    }
 }
 
 sub msg{