print "Regenerating $doxy_target/python3 ...\n\n";
my $doxy_bin = `which doxygen`;
chomp $doxy_bin;
die "Cannot run doxygen binary, please make sure it is installed and is in the path.\n" unless(-r $doxy_bin);
my $doxypypy = `which doxypypy`;
chomp $doxypypy;
die "Cannot find the Doxygen Python filter 'doxypypy' in the current PATH.\n" unless -e $doxypypy;
my @cmds = (
"rm -rf $doxy_target/python3",
"mkdir -p $doxy_target/python3",
"doxygen -g -",
"echo 'PROJECT_NAME = ensembl-hive-python3'",
"echo 'PROJECT_NUMBER = $code_ver'",
"echo 'OUTPUT_DIRECTORY = $doxy_target'",
"echo 'STRIP_FROM_PATH = $ehrd/wrappers/python3'",
"echo 'INPUT = $ehrd/wrappers/python3'",
"echo 'HTML_OUTPUT = python3'",
"echo 'FILE_PATTERNS = *.py README.md'",
"echo 'FILTER_PATTERNS = *.py=$ehrd/scripts/dev/doxypypy_filter.sh'",
"echo 'EXTRACT_PRIVATE = YES'",
"echo 'EXTRACT_STATIC = YES'",
"echo 'CLASS_DIAGRAMS = YES'",
"echo 'CALL_GRAPH = YES'",
"echo 'CALLER_GRAPH = YES'",
"echo 'COLLABORATION_GRAPH = NO'",
@shared_params,
);
my $full_cmd = '('.join(' ; ', @cmds).") | doxygen -";
print "Running the following command:\n\t$full_cmd\n\n";
system( $full_cmd );
}