8c4162c3666a2b238b2b60c3f94bb8102c4ef6cf,pysb/kappa.py,,set_kappa_path,#Any#,35

Before Change

    global _kappa_path
    _kappa_path = dir
    // Check locations of both KaSim and KaSa
    for kappa_prog in ["KaSim", "KaSa"]:
        kappa_prog_path = os.path.join(dir, kappa_prog)
        // Make sure file exists and is not a directory
        if not os.access(kappa_prog_path, os.F_OK) or \
           not os.path.isfile(kappa_prog_path):
            raise Exception("Could not find %s in %s." %
                            (kappa_prog, os.path.abspath(dir)))
        // Make sure file has executable permissions
        elif not os.access(kappa_prog_path, os.X_OK):
            raise Exception("%s in %s does not have executable permissions." %
                            (kappa_prog, os.path.abspath(dir)))


def _get_bng_path():
    
    Return the path to BioNetGen"s BNG2.pl.

After Change

    kasa_path = _check_dist_dir("KaSa", dir)

    // Check that KaSim executable exists and is not a directory
    if kasim_path is None:
        raise Exception("Could not find KaSim in %s." % os.path.abspath(dir))
    else:
        _kasim_path = kasim_path

    // Check KaSa, but only raise a warning if it"s not found because it"s
    // not installed by default with the KaSim distribution.
    if kasa_path is None:
        warnings.warn("Could not find KaSa in %s; install KaSa for static "
                      "analysis features." % os.path.abspath(dir))
    else:

Instances