How to use the forcebalance.parser.parse_inputs function in forcebalance

def runTest(self):
        """Check liquid target with existing simulation data"""
        if not sys.version_info <= (2,7):
            self.skipTest("Existing pickle file only works with Python 3")
        
        self.logger.debug("\nSetting input file to 'single.in'\n")
        input_file='single.in'

        ## The general options and target options that come from parsing the input file
        self.logger.debug("Parsing inputs...\n")
        options, tgt_opts = parse_inputs(input_file)
        self.logger.debug("options:\n%s\n\ntgt_opts:\n%s\n\n" % (str(options), str(tgt_opts)))

        forcefield  = FF(options)
        objective   = Objective(options, tgt_opts, forcefield)
        ## The optimizer component of the project
        self.logger.debug("Creating optimizer: ")
        optimizer   = Optimizer(options, objective, forcefield)
        self.assertEqual(Optimizer, type(optimizer), msg="\nExpected forcebalance optimizer object")
        self.logger.debug(str(optimizer) + "\n")

        ## Actually run the optimizer.
        self.logger.debug("Done setting up! Running optimizer...\n")
        result = optimizer.Run()
        self.logger.debug("\nOptimizer finished. Final results:\n")
        self.logger.debug(str(result) + '\n')

def setUp(self):
        super(ForceBalanceTestCase,self).setUp()
        os.chdir('studies/001_water_tutorial')
        self.input_file='very_simple.in'
        targets = tarfile.open('targets.tar.bz2','r')
        targets.extractall()
        targets.close()

        self.options, self.tgt_opts = forcebalance.parser.parse_inputs(self.input_file)

        self.options.update({'writechk':'checkfile.tmp'})

        self.forcefield  = forcebalance.forcefield.FF(self.options)
        self.objective   = forcebalance.objective.Objective(self.options, self.tgt_opts, self.forcefield)
        try: self.optimizer   = forcebalance.optimizer.Optimizer(self.options, self.objective, self.forcefield)
        except: self.fail("\nCouldn't create optimizer")

def test_parse_inputs_yields_consistent_results(self):
        """Check parse_inputs() gives consistent results"""
        output1 = forcebalance.parser.parse_inputs('test/files/very_simple.in')
        output2 = forcebalance.parser.parse_inputs('test/files/very_simple.in')
        self.assertEqual(output1,output2)

        os.chdir('test/files')

        output3 = forcebalance.parser.parse_inputs('very_simple.in')
        output4 = forcebalance.parser.parse_inputs('very_simple.in')
        self.assertEqual(output3,output4)

        # directory change should lead to different result in output['root']
        self.assertNotEqual(output1,output3)

        # different parameters from the same file should yield different results
        shutil.copyfile('0.energy_force.in', 'test.in')
        output5 = forcebalance.parser.parse_inputs('test.in')
        shutil.copyfile('1.netforce_torque.in','test.in')
        output6 = forcebalance.parser.parse_inputs('test.in')
        self.assertNotEqual(output5,output6)
        os.remove('test.in')

self.assertEqual(output1,output2)

        os.chdir('test/files')

        output3 = forcebalance.parser.parse_inputs('very_simple.in')
        output4 = forcebalance.parser.parse_inputs('very_simple.in')
        self.assertEqual(output3,output4)

        # directory change should lead to different result in output['root']
        self.assertNotEqual(output1,output3)

        # different parameters from the same file should yield different results
        shutil.copyfile('0.energy_force.in', 'test.in')
        output5 = forcebalance.parser.parse_inputs('test.in')
        shutil.copyfile('1.netforce_torque.in','test.in')
        output6 = forcebalance.parser.parse_inputs('test.in')
        self.assertNotEqual(output5,output6)
        os.remove('test.in')

def main():
    """ Print out all of the options available to ForceBalance. """
    options = None
    tgt_opts = [None]
    if len(sys.argv) == 2:
        options, tgt_opts = parser.parse_inputs(sys.argv[1])
    out = []
    out.append("# ForceBalance input file generated by MakeInputFile.py")
    out.append("# The octothorpe '#' is a comment symbol")
    out.append("# There are two sections, the main options ($options) and the target options ($target)")
    out.append("# A ForceBalance calculation will have one $options section and as one $target section per optimization target")
    out.append("# The most important options are listed at the top; options are also roughly grouped by their application")
    out.append("# Note: If the specified value is 'None' then the option will truly be set to None - not the string 'None'")
    out.append("# Note: Section option types are more complicated and may require you to read the documentation")
    out.append("# Note: Boolean option types require no value, the key being present implies 'True'")
    out.append("# Note: List option types are specified using spaces as the delimiter - i.e. forcefield ff1.itp ff2.itp ; delete empty brackets before use [] ")
    out.append("")
    out += parser.printsection("$options",options,parser.gen_opts_types)
    for tgt_opt in tgt_opts:
        out.append("\n")
        out += parser.printsection("$target",tgt_opt,parser.tgt_opts_types)
    for line in out:

def recover(self):
        ## Determine the save file name.
        base, ext = os.path.splitext(self.input_file)
        if not base.endswith(".sav"):
            savfnm = base+".sav"
        else:
            savfnm = base+ext
        ## Parse the save file for mvals, if exist.
        if os.path.exists(savfnm):
            soptions, stgt_opts = parse_inputs(savfnm)
            if soptions['read_mvals'] and np.max(np.abs(self.mvals0)) != 0.0:
                warn_press_key("Save file read_mvals will overwrite input file.\nInput file: %s\nSave file : %s\n" % (soptions['read_mvals'], self.mvals0))
            self.mvals0 = np.array(soptions['read_mvals'])
            self.read_mvals = np.array(soptions['read_mvals'])

        maxrd = max([T.maxrd() for T in self.Objective.Targets])
        if maxrd < 0: return
        ## This will be invoked if we quit RIGHT at the start of an iteration (i.e. jobs were launched but none were finished)
        if len(set([T.maxrd() for T in self.Objective.Targets])) == 1 and any([((T.maxid() - T.maxrd()) > 0) for T in self.Objective.Targets]):
            maxrd += 1
        printcool("Continuing optimization from iteration %i\nThese targets will load data from disk:\n%s" % \
                      (maxrd, '\n'.join([T.name for T in self.Objective.Targets if T.maxrd() == maxrd])), color=4)
        ## If data exists in the temp-dir corresponding to the highest
        ## iteration number, read the data.
        for T in self.Objective.Targets:
            if T.maxrd() == maxrd:

""" Create instances of ForceBalance components and run the optimizer.

    The triumvirate, trifecta, or trinity of components are:
    - The force field
    - The objective function
    - The optimizer
    Cipher: "All I gotta do here is pull this plug... and there you have to watch Apoc die"
    Apoc: "TRINITY" *chunk*

    The force field is a class defined in forcefield.py.
    The objective function is a combination of target classes and a penalty function class.
    The optimizer is a class defined in this file.
    """
    try:
        ## The general options and target options that come from parsing the input file
        options, tgt_opts = parse_inputs(input_file)
        ## Set the continue_ option.
        if continue_: options['continue'] = True
        ## The force field component of the project
        forcefield  = FF(options)
        ## The objective function
        objective   = Objective(options, tgt_opts, forcefield)
        ## The optimizer component of the project
        optimizer   = Optimizer(options, objective, forcefield)
        ## Actually run the optimizer.
        optimizer.Run()
    except:
        import traceback
        traceback.print_exc()
        if debug:
            import pdb
            pdb.post_mortem()