print "Regenerating $ehrd/wrappers/python3/doxygen ...\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 $doxy_filter = `which doxypy`;
chomp $doxy_filter;
die "Cannot find the Doxygen Python filter 'doxypy' in the current PATH.\n" unless -e $doxy_filter;
my @cmds = (
"rm -rf $ehrd/wrappers/python3/doxygen",
"doxygen -g -",
"echo 'PROJECT_NAME = ensembl-hive-python3'",
"echo 'PROJECT_NUMBER = $code_ver'",
"echo 'OUTPUT_DIRECTORY = $ehrd/wrappers/python3'",
"echo 'STRIP_FROM_PATH = $ehrd/wrappers/python3'",
"echo 'INPUT = $ehrd/wrappers/python3'",
"echo 'INPUT_FILTER = $doxy_filter'",
"echo 'HTML_OUTPUT = doxygen'",
"echo 'EXTRACT_ALL = YES'",
"echo 'EXTRACT_PRIVATE = YES'",
"echo 'EXTRACT_STATIC = YES'",
"echo 'FILE_PATTERNS = *.py README.md'",
"echo 'USE_MDFILE_AS_MAINPAGE = README.md'",
"echo 'ENABLE_PREPROCESSING = NO'",
"echo 'RECURSIVE = YES'",
"echo 'EXAMPLE_PATTERNS = *'",
"echo 'HTML_TIMESTAMP = NO'",
"echo 'HTML_DYNAMIC_SECTIONS = YES'",
"echo 'GENERATE_TREEVIEW = YES'",
"echo 'GENERATE_LATEX = NO'",
"echo 'CLASS_DIAGRAMS = YES'",
"echo 'HAVE_DOT = YES'",
"echo 'CALL_GRAPH = YES'",
"echo 'CALLER_GRAPH = YES'",
"echo 'COLLABORATION_GRAPH = NO'",
"echo 'SOURCE_BROWSER = YES'",
);
my $full_cmd = '('.join(' ; ', @cmds).") | doxygen -";
print "Running the following command:\n\t$full_cmd\n\n";
system( $full_cmd );
}