Instruction:
Can you generate the documentation for the following Python 3 function
def det_dataset(eb, passband, dataid, comp, time):

    """
    Since RV datasets can have values related to each component in phoebe2, but are component specific in phoebe1
    , it is important to determine which dataset to add parameters to. This function will do that.
    eb - bundle
    rvpt - relevant phoebe 1 parameters

    """
    rvs = eb.get_dataset(kind='rv').datasets
    #first check to see if there are currently in RV datasets
    if dataid == 'Undefined':
        dataid = None
#    if len(rvs) == 0:
    #if there isn't we add one the easy part

    try:
        eb._check_label(dataid)

        rv_dataset = eb.add_dataset('rv', dataset=dataid, times=[])

    except ValueError:

        logger.warning("The name picked for the radial velocity curve is forbidden. Applying default name instead")
        rv_dataset = eb.add_dataset('rv', times=[])

#     else:
#     #now we have to determine if we add to an existing dataset or make a new one
#         rvs = eb.get_dataset(kind='rv').datasets
#         found = False
#         #set the component of the companion
#
#         if comp == 'primary':
#             comp_o = 'primary'
#         else:
#             comp_o = 'secondary'
#         for x in rvs:
#             test_dataset = eb.get_dataset(x, check_visible=False)
#
#
#             if len(test_dataset.get_value(qualifier='rvs', component=comp_o, check_visible=False)) == 0:                #so at least it has an empty spot now check against filter and length
# #               removing reference to time_o. If there are no rvs there should be no times
# #                time_o = test_dataset.get_value('times', component=comp_o)
#                 passband_o = test_dataset.get_value('passband')
#
# #                if np.all(time_o == time) and (passband == passband_o):
#                 if (passband == passband_o):
#                     rv_dataset = test_dataset
#                     found = True
#
#         if not found:
#             try:
#                 eb._check_label(dataid)
#
#                 rv_dataset = eb.add_dataset('rv', dataset=dataid, times=[])
#
#             except ValueError:
#
#                 logger.warning("The name picked for the lightcurve is forbidden. Applying default name instead")
#                 rv_dataset = eb.add_dataset('rv', times=[])

    return rv_dataset

Response: This function will remove the dataset from the RV and passband from the RV and passband of the RV.


Instruction:
Make a summary of the following Python 3 code
def N_to_Ntriangles(N):

    theta = np.array([np.pi/2*(k-0.5)/N for k in range(1, N+1)])
    phi = np.array([[np.pi*(l-0.5)/Mk for l in range(1, Mk+1)] for Mk in np.array(1 + 1.3*N*np.sin(theta), dtype=int)])
    Ntri = 2*np.array([len(p) for p in phi]).sum()

    return Ntri

Response:
Converts a WD style grid size N to the number of triangles on the
    surface.


Instruction:
Given the following Python 3 function, write the documentation
def pot_for_component(pot, q, component=1, reverse=False):
    # currently only used by legacy wrapper: consider moving/removing
    if component==1:
        return pot
    elif component==2:
        if reverse:
            return pot/q + 0.5*(q-1)/q
        else:
            return q*pot - 0.5 * (q-1)
    else:
        raise NotImplementedError

Response: returns the potential for a given component


Instruction:
Can you generate the documentation for the following Python 3 function
def roche_misaligned_critical_requiv(q, F, d, s, scale=1.0):
    volume_critical = libphoebe.roche_misaligned_critical_volume(q, F, d, s)
    logger.debug("libphoebe.roche_misaligned_critical_volume(q={}, F={}, d={}, s={}) => {}".format(q, F, d, s, volume_critical))

    requiv_critical = scale * (volume_critical * 3./4 * 1./np.pi)**(1./3)
    # logger.debug("roche.roche_misaligned_critical_requiv = {}".format(requiv_critical))

    return requiv_critical

Response: calculate the misaligned critical requiv


Instruction:
How would you code a function in Python 3 to
transform polar radius to surface potential

Response:
def rpole_to_pot_aligned(rpole, sma, q, F, d, component=1):
    """
    Transforms polar radius to surface potential
    """
    q = q_for_component(q, component=component)
    rpole_ = np.array([0, 0, rpole/sma])
    logger.debug("libphoebe.roche_Omega(q={}, F={}, d={}, rpole={})".format(q, F, d, rpole_))
    pot = libphoebe.roche_Omega(q, F, d, rpole_)
    return pot_for_component(pot, component, reverse=True)


Instruction:
Can you tell what is the following Python 3 function doing
def pot_to_rpole_aligned(pot, sma, q, F, d, component=1):
    q = q_for_component(q, component=component)
    Phi = pot_for_component(pot, q, component=component)
    logger.debug("libphobe.roche_pole(q={}, F={}, d={}, Omega={})".format(q, F, d, pot))
    return libphoebe.roche_pole(q, F, d, pot) * sma

Response: Transforms surface potential to polar radius


Instruction:
Here you have a function in Python 3, explain what it does
def BinaryRoche (r, D, q, F, Omega=0.0):
    return 1.0/sqrt(r[0]*r[0]+r[1]*r[1]+r[2]*r[2]) + q*(1.0/sqrt((r[0]-D)*(r[0]-D)+r[1]*r[1]+r[2]*r[2])-r[0]/D/D) + 0.5*F*F*(1+q)*(r[0]*r[0]+r[1]*r[1]) - Omega

Response: r Computes a value of the asynchronous eccentric Roche potential.


Instruction:
Can you generate the documentation for the following Python 3 function
def dBinaryRochedx (r, D, q, F):
    return -r[0]*(r[0]*r[0]+r[1]*r[1]+r[2]*r[2])**-1.5 -q*(r[0]-D)*((r[0]-D)*(r[0]-D)+r[1]*r[1]+r[2]*r[2])**-1.5 -q/D/D + F*F*(1+q)*r[0]

Response: Computes a derivative of the potential with respect to x.


Instruction:
Implement a function in Python 3 to
compute second derivative of the potential with respect to x.

Response:
def d2BinaryRochedx2(r, D, q, F):
    """
    Computes second derivative of the potential with respect to x.

    @param r:      relative radius vector (3 components)
    @param D:      instantaneous separation
    @param q:      mass ratio
    @param F:      synchronicity parameter
    """
    return (2*r[0]*r[0]-r[1]*r[1]-r[2]*r[2])/(r[0]*r[0]+r[1]*r[1]+r[2]*r[2])**2.5 +\
          q*(2*(r[0]-D)*(r[0]-D)-r[1]*r[1]-r[2]*r[2])/((r[0]-D)*(r[0]-D)+r[1]*r[1]+r[2]*r[2])**2.5 +\
          F*F*(1+q)


Instruction:
Can you implement a function in Python 3 that
computes a derivative of the potential with respect to y.

Response:
def dBinaryRochedy (r, D, q, F):
    """
    Computes a derivative of the potential with respect to y.

    @param r:      relative radius vector (3 components)
    @param D:      instantaneous separation
    @param q:      mass ratio
    @param F:      synchronicity parameter
    """
    return -r[1]*(r[0]*r[0]+r[1]*r[1]+r[2]*r[2])**-1.5 -q*r[1]*((r[0]-D)*(r[0]-D)+r[1]*r[1]+r[2]*r[2])**-1.5 + F*F*(1+q)*r[1]


Instruction:
Implement a function in Python 3 to
compute a derivative of the potential with respect to z.

Response:
def  dBinaryRochedz(r, D, q, F):
    """
    Computes a derivative of the potential with respect to z.

    @param r:      relative radius vector (3 components)
    @param D:      instantaneous separation
    @param q:      mass ratio
    @param F:      synchronicity parameter
    """
    return -r[2]*(r[0]*r[0]+r[1]*r[1]+r[2]*r[2])**-1.5 -q*r[2]*((r[0]-D)*(r[0]-D)+r[1]*r[1]+r[2]*r[2])**-1.5


Instruction:
Can you generate a brief explanation for the following Python 3 code
def dBinaryRochedr (r, D, q, F):

    r2 = (r*r).sum()
    r1 = np.sqrt(r2)

    return -1./r2 - q*(r1-r[0]/r1*D)/((r[0]-D)*(r[0]-D)+r[1]*r[1]+r[2]*r[2])**1.5 - q*r[0]/r1/D/D + F*F*(1+q)*(1-r[2]*r[2]/r2)*r1

Response: Computes a derivative of the potential with respect to r.


Instruction:
Here you have a function in Python 3, explain what it does
def settings(**kwargs):

    params = []

    params += [StringParameter(qualifier='phoebe_version', value=kwargs.get('phoebe_version', __version__), description='Version of PHOEBE - change with caution')]
    params += [BoolParameter(qualifier='log_history', value=kwargs.get('log_history', False), description='Whether to log history (undo/redo)')]
    params += [DictParameter(qualifier='dict_filter', value=kwargs.get('dict_filter', {}), description='Filters to use when using dictionary access')]
    params += [BoolParameter(qualifier='dict_set_all', value=kwargs.get('dict_set_all', False), description='Whether to set all values for dictionary access that returns more than 1 result')]

    # params += [ChoiceParameter(qualifier='plotting_backend', value=kwargs.get('plotting_backend', 'mpl'), choices=['mpl', 'mpld3', 'mpl2bokeh', 'bokeh'] if conf.devel else ['mpl'], description='Default backend to use for plotting')]

    # problem with try_sympy parameter: it can't be used during initialization... so this may need to be a phoebe-level setting
    # params += [BoolParameter(qualifier='try_sympy', value=kwargs.get('try_sympy', True), description='Whether to use sympy if installed for constraints')]

    # This could be complicated - because then we'll have to specifically watch to see when its enabled and then run all constraints - not sure if that is worth the time savings
    # params += [BoolParameter(qualifier='run_constraints', value=kwargs.get('run_constraints', True), description='Whether to run_constraints whenever a parameter changes (warning: turning off will disable constraints until enabled at which point all constraints will be run)')]

    return ParameterSet(params)

Response: Returns a new set of parameters that can be used to initialize a new resource bundle.


Instruction:
Implement a function in Python 3 to
intercept and send to the server if bundle is in client mode.

Response:
def send_if_client(fctn):
    """Intercept and send to the server if bundle is in client mode."""
    @functools.wraps(fctn)
    def _send_if_client(self, *args, **kwargs):
        fctn_map = {'set_quantity': 'set_value'}
        b = self._bundle
        if b is not None and b.is_client:
            # TODO: self._filter???
            # TODO: args???
            method = fctn_map.get(fctn.__name__, fctn.__name__)
            d = self._filter if hasattr(self, '_filter') \
                else {'twig': self.twig}
            d['bundleid'] = b._bundleid
            for k, v in kwargs.items():
                d[k] = v

            logger.info('emitting to {}({}) to server'.format(method, d))
            b._socketio.emit(method, d)

            if fctn.__name__ in ['run_compute', 'run_fitting']:
                # then we're expecting a quick response with an added jobparam
                # let's add that now
                self._bundle.client_update()
        else:
            return fctn(self, *args, **kwargs)
    return _send_if_client


Instruction:
Can you create a Python 3 function that
intercepts and check updates from server if bundle is in client mode.

Response:
def update_if_client(fctn):
    """Intercept and check updates from server if bundle is in client mode."""
    @functools.wraps(fctn)
    def _update_if_client(self, *args, **kwargs):
        b = self._bundle
        if b is None or not hasattr(b, 'is_client'):
            return fctn(self, *args, **kwargs)
        elif b.is_client and \
                (b._last_client_update is None or
                (datetime.now() - b._last_client_update).seconds > 1):

            b.client_update()
        return fctn(self, *args, **kwargs)
    return _update_if_client


Instruction:
How would you implement a function in Python 3 that
returns a unique string with length n.

Response:
def _uniqueid(n=30):
    """Return a unique string with length n.

    :parameter int N: number of character in the uniqueid
    :return: the uniqueid
    :rtype: str
    """
    return ''.join(random.SystemRandom().choice(
                   string.ascii_uppercase + string.ascii_lowercase)
                   for _ in range(n))


Instruction:
Write a Python 3 script for
loading a single parameter from a JSON dictionary.

Response:
def parameter_from_json(dictionary, bundle=None):
    """Load a single parameter from a JSON dictionary.

    :parameter dict dictionary: the dictionary containing the parameter
        information
    :parameter bundle: (optional)
    :return: instantiated :class:`Parameter` object
    """
    if isinstance(dictionary, str):
        dictionary = json.loads(dictionary, object_pairs_hook=parse_json)

    classname = dictionary.pop('Class')

    if classname not in _parameter_class_that_require_bundle:
        bundle = None

    # now let's do some dirty magic and get the actual classitself
    # from THIS module.  __name__ is a string to lookup this module
    # from the sys.modules dictionary
    cls = getattr(sys.modules[__name__], classname)

    return cls._from_json(bundle, **dictionary)


Instruction:
How would you explain what the following Python 3 function does
def get_meta(self, ignore=['uniqueid']):
        return OrderedDict([(k, getattr(self, k))
                            for k in _meta_fields_twig
                            if k not in ignore])

Response: Returns a dictionary of all meta - tags that are shared by ALL Parameters.


Instruction:
Can you create a Python 3 function that
sets the value of tags for all Parameters in this ParameterSet.

Response:
def set_meta(self, **kwargs):
        """Set the value of tags for all Parameters in this ParameterSet."""
        for param in self.to_list():
            for k, v in kwargs.items():
                # Here we'll set the attributes (_context, _qualifier, etc)
                if getattr(param, '_{}'.format(k)) is None:
                    setattr(param, '_{}'.format(k), v)


Instruction:
Explain what the following Python 3 code does
def tags(self):
        ret = {}
        for typ in _meta_fields_twig:
            if typ in ['uniqueid', 'plugin', 'feedback', 'fitting', 'history', 'twig', 'uniquetwig']:
                continue

            k = '{}s'.format(typ)
            ret[k] = getattr(self, k)

        return ret

Response:
Returns a dictionary that lists all available tags that can be used
        for further filtering


Instruction:
Implement a Python 3 function for
returning the common twig of all items in this ParameterSet.

Response:
def common_twig(self):
        """
        The twig that is common between all items in this ParameterSet.
        This twig gives a single string which can point back to this ParameterSet
        (but may include other entries as well)

        see also :meth:`uniquetwig`

        :return: twig (full) of this Parameter
        """
        return "@".join([getattr(self, k) for k in _meta_fields_twig if self.meta.get(k) is not None])


Instruction:
Can you generate the documentation for the following Python 3 function
def _set_meta(self):
        # we want to set meta-fields that are shared by ALL params in the PS
        for field in _meta_fields_twig:
            keys_for_this_field = set([getattr(p, field)
                                       for p in self.to_list()
                                       if getattr(p, field) is not None])
            if len(keys_for_this_field)==1:
                setattr(self, '_'+field, list(keys_for_this_field)[0])
            else:
                setattr(self, '_'+field, None)

Response: Set the meta - fields of the ParameterSet as those that are shared by ALL parameters in the ParameterSet.


Instruction:
How would you implement a function in Python 3 that
gets the least unique twig for the parameter given by twig that will return a single result for THIS PS

Response:
def _uniquetwig(self, twig, force_levels=['qualifier']):
        """
        get the least unique twig for the parameter given by twig that
        will return this single result for THIS PS

        :parameter str twig: a twig that will return a single Parameter from
                THIS PS
        :parameter list force_levels: (optional) a list of "levels"
            (eg. context) that should be included whether or not they are
            necessary
        :return: the unique twig
        :rtype: str
        """
        for_this_param = self.filter(twig, check_visible=False)

        metawargs = {}

        # NOTE: self.contexts is INCREDIBLY expensive
        # if len(self.contexts) and 'context' not in force_levels:
        if 'context' not in force_levels:
            # then let's force context to be included
            force_levels.append('context')

        for k in force_levels:
            metawargs[k] = getattr(for_this_param, k)

        prev_count = len(self)
        # just to fake in case no metawargs are passed at all
        ps_for_this_search = []
        for k in _meta_fields_twig:
            metawargs[k] = getattr(for_this_param, k)
            if getattr(for_this_param, k) is None:
                continue

            ps_for_this_search = self.filter(check_visible=False, **metawargs)

            if len(ps_for_this_search) < prev_count and k not in force_levels:
                prev_count = len(ps_for_this_search)
            elif k not in force_levels:
                # this didn't help us
                metawargs[k] = None

        if len(ps_for_this_search) != 1:
            # TODO: after fixing regex in twig (t0type vs t0)
            # change this to raise Error instead of return
            return twig

        # now we go in the other direction and try to remove each to make sure
        # the count goes up
        for k in _meta_fields_twig:
            if metawargs[k] is None or k in force_levels:
                continue

            ps_for_this_search = self.filter(check_visible=False,
                                             **{ki: metawargs[k]
                                                for ki in _meta_fields_twig
                                                if ki != k})

            if len(ps_for_this_search) == 1:
                # then we didn't need to use this tag
                metawargs[k] = None

        # and lastly, we make sure that the tag corresponding to the context
        # is present
        context = for_this_param.context
        if hasattr(for_this_param, context):
            metawargs[context] = getattr(for_this_param, context)

        return "@".join([metawargs[k]
                         for k in _meta_fields_twig
                         if metawargs[k] is not None])


Instruction:
Create a Python 3 function to
attach a list of parameters or ParameterSet to this ParameterSet.

Response:
def _attach_params(self, params, **kwargs):
        """Attach a list of parameters (or ParameterSet) to this ParameterSet.

        :parameter list params: list of parameters, or ParameterSet
        :parameter **kwargs: attributes to set for each parameter (ie tags)
        """
        lst = params.to_list() if isinstance(params, ParameterSet) else params
        for param in lst:
            param._bundle = self

            for k, v in kwargs.items():
                # Here we'll set the attributes (_context, _qualifier, etc)
                if getattr(param, '_{}'.format(k)) is None:
                    setattr(param, '_{}'.format(k), v)
            self._params.append(param)

        self._check_copy_for()

        return


Instruction:
Write a Python 3 script for
checking the value of copy_for and make appropriate copies.

Response:
def _check_copy_for(self):
        """Check the value of copy_for and make appropriate copies."""
        if not self._bundle:
            return

        # read the following at your own risk - I just wrote it and it still
        # confuses me and baffles me that it works
        for param in self.to_list():
            if param.copy_for:
                # copy_for tells us how to filter and what set of attributes
                # needs a copy of this parameter
                #
                # copy_for = {'kind': ['star', 'disk', 'custombody'], 'component': '*'}
                # means that this should exist for each component (since that has a wildcard) which
                # has a kind in [star, disk, custombody]
                #
                # copy_for = {'kind': ['rv_dep'], 'component': '*', 'dataset': '*'}
                # means that this should exist for each component/dataset pair with the
                # rv_dep kind

                attrs = [k for k,v in param.copy_for.items() if '*' in v]
                # attrs is a list of the attributes for which we need a copy of
                # this parameter for any pair

                ps = self._bundle.filter(check_visible=False, check_default=False, force_ps=True, **param.copy_for)
                metawargs = {k:v for k,v in ps.meta.items() if v is not None and k in attrs}
                for k,v in param.meta.items():
                    if k not in ['twig', 'uniquetwig'] and k not in attrs:
                        metawargs[k] = v
                # metawargs is a list of the shared tags that will be used to filter for
                # existing parameters so that we know whether they already exist or
                # still need to be created

                # logger.debug("_check_copy_for {}: attrs={}".format(param.twig, attrs))
                for attrvalues in itertools.product(*(getattr(ps, '{}s'.format(attr)) for attr in attrs)):
                    # logger.debug("_check_copy_for {}: attrvalues={}".format(param.twig, attrvalues))
                    # for each attrs[i] (ie component), attrvalues[i] (star01)
                    # we need to look for this parameter, and if it does not exist
                    # then create it by copying param

                    for attr, attrvalue in zip(attrs, attrvalues):
                        #if attrvalue=='_default' and not getattr(param, attr):
                        #    print "SKIPPING", attr, attrvalue
                        #    continue
                        metawargs[attr] = attrvalue

                    # logger.debug("_check_copy_for {}: metawargs={}".format(param.twig, metawargs))
                    if not len(self._bundle.filter(check_visible=False, **metawargs)):
                        # then we need to make a new copy
                        logger.debug("copying '{}' parameter for {}".format(param.qualifier, {attr: attrvalue for attr, attrvalue in zip(attrs, attrvalues)}))

                        newparam = param.copy()

                        for attr, attrvalue in zip(attrs, attrvalues):
                            setattr(newparam, '_{}'.format(attr), attrvalue)

                        newparam._copy_for = False
                        if newparam._visible_if and newparam._visible_if.lower() == 'false':
                            newparam._visible_if = None
                        newparam._bundle = self._bundle

                        self._params.append(newparam)

                    # Now we need to handle copying constraints.  This can't be
                    # in the previous if statement because the parameters can be
                    # copied before constraints are ever attached.
                    if hasattr(param, 'is_constraint') and param.is_constraint:

                        param_constraint = param.is_constraint

                        copied_param = self._bundle.get_parameter(check_visible=False, check_default=False, **metawargs)

                        if not copied_param.is_constraint:
                            constraint_kwargs = param_constraint.constraint_kwargs.copy()
                            for attr, attrvalue in zip(attrs, attrvalues):
                                if attr in constraint_kwargs.keys():
                                    constraint_kwargs[attr] = attrvalue

                            logger.debug("copying constraint '{}' parameter for {}".format(param_constraint.constraint_func, {attr: attrvalue for attr, attrvalue in zip(attrs, attrvalues)}))
                            self.add_constraint(func=param_constraint.constraint_func, **constraint_kwargs)

        return


Instruction:
Write a Python 3 script to
check to see if the label is allowed.

Response:
def _check_label(self, label):
        """Check to see if the label is allowed."""

        if not isinstance(label, str):
            label = str(label)

        if label.lower() in _forbidden_labels:
            raise ValueError("'{}' is forbidden to be used as a label"
                             .format(label))
        if not re.match("^[a-z,A-Z,0-9,_]*$", label):
            raise ValueError("label '{}' is forbidden - only alphabetic, numeric, and '_' characters are allowed in labels".format(label))
        if len(self.filter(twig=label, check_visible=False)):
            raise ValueError("label '{}' is already in use".format(label))
        if label[0] in ['_']:
            raise ValueError("first character of label is a forbidden character")


Instruction:
Can you tell what is the following Python 3 function doing
def open(cls, filename):
        filename = os.path.expanduser(filename)
        f = open(filename, 'r')
        if _can_ujson:
            # NOTE: this will not parse the unicode.  Bundle.open always calls
            # json instead of ujson for this reason.
            data = ujson.load(f)
        else:
            data = json.load(f, object_pairs_hook=parse_json)
        f.close()
        return cls(data)

Response: Open a ParameterSet from a JSON - formatted file.


Instruction:
Create a Python 3 function to
save the ParameterSet to a JSON - formatted ASCII file.

Response:
def save(self, filename, incl_uniqueid=False, compact=False):
        """
        Save the ParameterSet to a JSON-formatted ASCII file

        :parameter str filename: relative or fullpath to the file
        :parameter bool incl_uniqueid: whether to including uniqueids in the
            file (only needed if its necessary to maintain the uniqueids when
            reloading)
        :parameter bool compact: whether to use compact file-formatting (maybe
            be quicker to save/load, but not as easily readable)
        :return: filename
        :rtype: str
        """
        filename = os.path.expanduser(filename)
        f = open(filename, 'w')
        if compact:
            if _can_ujson:
                ujson.dump(self.to_json(incl_uniqueid=incl_uniqueid), f,
                           sort_keys=False, indent=0)
            else:
                logger.warning("for faster compact saving, install ujson")
                json.dump(self.to_json(incl_uniqueid=incl_uniqueid), f,
                          sort_keys=False, indent=0)
        else:
            json.dump(self.to_json(incl_uniqueid=incl_uniqueid), f,
                      sort_keys=True, indent=0, separators=(',', ': '))
        f.close()

        return filename


Instruction:
Create a Python 3 function for
opening the web interface of the bundle in client mode.

Response:
def ui(self, client='http://localhost:4200', **kwargs):
        """
        [NOT IMPLEMENTED]

        The bundle must be in client mode in order to open the web-interface.
        See :meth:`Bundle:as_client` to switch to client mode.

        :parameter str client: URL of the running client which must be connected
            to the same server as the bundle
        :return: URL of the parameterset of this bundle in the client (will also
            attempt to open webbrowser)
        :rtype: str
        """
        if self._bundle is None or not self._bundle.is_client:
            raise ValueError("bundle must be in client mode")

        if len(kwargs):
            return self.filter(**kwargs).ui(client=client)

        querystr = "&".join(["{}={}".format(k, v)
                             for k, v in self._filter.items()])
        # print self._filter
        url = "{}/{}?{}".format(client, self._bundle._bundleid, querystr)

        logger.info("opening {} in browser".format(url))
        webbrowser.open(url)
        return url


Instruction:
Write a Python 3 script to
convert the : class:`ParameterSet` to a list of class:`Parameter objects.

Response:
def to_list(self, **kwargs):
        """
        Convert the :class:`ParameterSet` to a list of :class:`Parameter`s

        :return: list of class:`Parameter` objects
        """
        if kwargs:
            return self.filter(**kwargs).to_list()
        return self._params


Instruction:
Write a Python 3 function that can
convert the : class:`ParameterSet` to a list of the dictionary representation

Response:
def to_list_of_dicts(self, **kwargs):
        """
        Convert the :class:`ParameterSet` to a list of the dictionary representation
        of each :class:`Parameter`

        :return: list of dicts
        """
        if kwargs:
            return self.filter(**kwargs).to_list_of_dicts()
        return [param.to_dict() for param in self._params]


Instruction:
Here you have a function in Python 3, explain what it does
def to_flat_dict(self, **kwargs):
        if kwargs:
            return self.filter(**kwargs).to_flat_dict()
        return {param.uniquetwig: param for param in self._params}

Response:
Convert the : class:`ParameterSet` to a flat dictionary with keys being
        uniquetwigs to access the parameter and values being the parameter objects themselves.


Instruction:
Write a Python 3 script to
convert the ParameterSet to a structured dictionary with keys at and the ParameterSet of the matching items.

Response:
def to_dict(self, field=None, **kwargs):
        """
        Convert the ParameterSet to a structured (nested) dictionary
        to allow traversing the structure from the bottom up

        :parameter str field: (optional) build the dictionary with keys at
            a given level/field.  Can be any of the keys in
            :func:`meta`.  If None, the keys will be the lowest
            level in which Parameters have different values.
        :return: dict of :class:`Parameter`s or :class:`ParameterSet`s
        """
        if kwargs:
            return self.filter(**kwargs).to_dict(field=field)

        if field is not None:
            keys_for_this_field = set([getattr(p, field)
                                       for p in self.to_list()
                                       if getattr(p, field) is not None])
            return {k: self.filter(check_visible=False, **{field: k}) for k in keys_for_this_field}

        # we want to find the first level (from the bottom) in which filtering
        # further would shorten the list (ie there are more than one unique
        # item for that field)

        # so let's go through the fields in reverse (context up to (but not
        # including) qualifier)
        for field in reversed(_meta_fields_twig[1:]):
            # then get the unique keys in this field among the params in this
            # PS
            keys_for_this_field = set([getattr(p, field)
                                       for p in self.to_list()
                                       if getattr(p, field) is not None])
            # and if there are more than one, then return a dictionary with
            # those keys and the ParameterSet of the matching items
            if len(keys_for_this_field) > 1:
                self._next_field = field
                return {k: self.filter(check_visible=False, **{field: k})
                        for k in keys_for_this_field}

        # if we've survived, then we're at the bottom and only have times or
        # qualifier left
        if self.context in ['hierarchy']:
            self._next_field = 'qualifier'
            return {param.qualifier: param for param in self._params}
        else:
            self._next_field = 'time'
            return {param.time: param for param in self._params}


Instruction:
Implement a function in Python 3 to
set the value of a Parameter in the ParameterSet.

Response:
def set(self, key, value, **kwargs):
        """
        Set the value of a Parameter in the ParameterSet.

        If :func:`get` would retrieve a Parameter, this will set the
        value of that parameter.

        Or you can provide 'value@...' or 'default_unit@...', etc
        to specify what attribute to set.

        :parameter str key: the twig (called key here to be analagous
            to a normal dict)
        :parameter value: value to set
        :parameter **kwargs: other filter parameters (must result in
            returning a single :class:`Parameter`)
        :return: the value of the :class:`Parameter` after setting the
            new value (including converting units if applicable)
        """
        twig = key

        method = None
        twigsplit = re.findall(r"[\w']+", twig)
        if twigsplit[0] == 'value':
            twig = '@'.join(twigsplit[1:])
            method = 'set_value'
        elif twigsplit[0] == 'quantity':
            twig = '@'.join(twigsplit[1:])
            method = 'set_quantity'
        elif twigsplit[0] in ['unit', 'default_unit']:
            twig = '@'.join(twigsplit[1:])
            method = 'set_default_unit'
        elif twigsplit[0] in ['timederiv']:
            twig = '@'.join(twigsplit[1:])
            method = 'set_timederiv'
        elif twigsplit[0] in ['description']:
            raise KeyError("cannot set {} of {}".format(twigsplit[0], '@'.join(twigsplit[1:])))

        if self._bundle is not None and self._bundle.get_setting('dict_set_all').get_value() and len(self.filter(twig=twig, **kwargs)) > 1:
            # then we need to loop through all the returned parameters and call set on them
            for param in self.filter(twig=twig, **kwargs).to_list():
                self.set('{}@{}'.format(method, param.twig) if method is not None else param.twig, value)
        else:

            if method is None:
                return self.set_value(twig=twig, value=value, **kwargs)
            else:
                param = self.get_parameter(twig=twig, **kwargs)

                return getattr(param, method)(value)


Instruction:
Can you generate the documentation for the following Python 3 function
def to_json(self, incl_uniqueid=False):
        lst = []
        for context in _contexts:
            lst += [v.to_json(incl_uniqueid=incl_uniqueid)
                    for v in self.filter(context=context,
                                         check_visible=False,
                                         check_default=False).to_list()]
        return lst

Response: Convert the ParameterSet to a json - compatible dictionary.


Instruction:
Can you generate a brief explanation for the following Python 3 code
def filter(self, twig=None, check_visible=True, check_default=True, **kwargs):
        kwargs['check_visible'] = check_visible
        kwargs['check_default'] = check_default
        kwargs['force_ps'] = True
        return self.filter_or_get(twig=twig, **kwargs)

Response:
Filter the ParameterSet based on the meta - tags of the Parameters
        and return another ParameterSet.


Instruction:
Here you have a function in Python 3, explain what it does
def get(self, twig=None, check_visible=True, check_default=True, **kwargs):
        kwargs['check_visible'] = check_visible
        kwargs['check_default'] = check_default
        # print "***", kwargs
        ps = self.filter(twig=twig, **kwargs)
        if not len(ps):
            # TODO: custom exception?
            raise ValueError("0 results found")
        elif len(ps) != 1:
            # TODO: custom exception?
            raise ValueError("{} results found: {}".format(len(ps), ps.twigs))
        else:
            # then only 1 item, so return the parameter
            return ps._params[0]

Response: This method returns a single parameter from this ParameterSet.


Instruction:
Can you generate the documentation for the following Python 3 function
def exclude(self, twig=None, check_visible=True, **kwargs):
        return self - self.filter(twig=twig,
                                  check_visible=check_visible,
                                  **kwargs)

Response: Exclude the results from this ParameterSet.


Instruction:
Can you tell what is the following Python 3 function doing
def get_or_create(self, qualifier, new_parameter, **kwargs):
        ps = self.filter_or_get(qualifier=qualifier, **kwargs)
        if isinstance(ps, Parameter):
            return ps, False
        elif len(ps):
            # TODO: custom exception?
            raise ValueError("more than 1 result was found")
        else:
            self._attach_params(ParameterSet([new_parameter]), **kwargs)

            logger.debug("creating and attaching new parameter: {}".format(new_parameter.qualifier))

            return self.filter_or_get(qualifier=qualifier, **kwargs), True

Response: Get a Parameter from the ParameterSet if it does not exist create it and return it.


Instruction:
Write a Python 3 function for
removing a Parameter from the ParameterSet

Response:
def _remove_parameter(self, param):
        """
        Remove a Parameter from the ParameterSet

        :parameter param: the :class:`Parameter` object to be removed
        :type param: :class:`Parameter`
        """
        # TODO: check to see if protected (required by a current constraint or
        # by a backend)
        self._params = [p for p in self._params if p != param]


Instruction:
How would you code a function in Python 3 to
remove a Parameter from the ParameterSet

Response:
def remove_parameter(self, twig=None, **kwargs):
        """
        Remove a :class:`Parameter` from the ParameterSet

        Note: removing Parameters from a ParameterSet will not remove
        them from any parent ParameterSets
        (including the :class:`phoebe.frontend.bundle.Bundle`)

        :parameter str twig: the twig to search for the parameter
        :parameter **kwargs: meta-tags to search
        :raises ValueError: if 0 or more than 1 results are found using the
                provided search criteria.
        """
        param = self.get(twig=twig, **kwargs)

        self._remove_parameter(param)


Instruction:
Make a summary of the following Python 3 code
def remove_parameters_all(self, twig=None, **kwargs):
        params = self.filter(twig=twig, check_visible=False, check_default=False, **kwargs)

        for param in params.to_list():
            self._remove_parameter(param)

Response: Remove all Parameters that match the search from the ParameterSet.


Instruction:
Given the following Python 3 function, write the documentation
def get_quantity(self, twig=None, unit=None,
                     default=None, t=None, **kwargs):
        """
        TODO: add documentation
        """
        # TODO: for time derivatives will need to use t instead of time (time
        # gets passed to twig filtering)

        if default is not None is not None:
            # then we need to do a filter first to see if parameter exists
            if not len(self.filter(twig=twig, **kwargs)):
                return default

        param = self.get_parameter(twig=twig, **kwargs)

        if param.qualifier in kwargs.keys():
            # then we have an "override" value that was passed, and we should
            # just return that.
            # Example b.get_value('teff', teff=6000) returns 6000
            return kwargs.get(param.qualifier)

        return param.get_quantity(unit=unit, t=t)

Response: get a value from the resource


Instruction:
Write a Python 3 script to
set the quantity of the current parameter.

Response:
def set_quantity(self, twig=None, value=None, **kwargs):
        """
        TODO: add documentation
        """
        # TODO: handle twig having parameter key (value@, default_unit@, adjust@, etc)
        # TODO: does this return anything (update the docstring)?
        return self.get_parameter(twig=twig, **kwargs).set_quantity(value=value, **kwargs)


Instruction:
Can you create a Python 3 function that
gets the value of a ParameterSet s object in this ParameterSet.

Response:
def get_value(self, twig=None, unit=None, default=None, t=None, **kwargs):
        """
        Get the value of a :class:`Parameter` in this ParameterSet

        :parameter str twig: the twig to search for the parameter
        :parameter unit: units for the returned result (if
            applicable).  If None or not provided, the value will
            be returned in that Parameter's default_unit (if
            applicable)
        :type unit: str or astropy.units.Unit
        :parameter default: what to return if the parameter cannot be found.
            If this is None (default) then an error will be raised instead.
            Note that the units of default will not be converted.
        :parameter time: time at which to compute the
            value (will only affect time-dependent parameters).  If provided
            as a float it is assumed that the units are the same as t0.
            NOTE: this is not fully supported yet, use with caution.
        :parameter **kwargs: meta-tags to search
        :return: value (type depeding on the type of the :class:`Parameter`)
        """
        # TODO: for time derivatives will need to use t instead of time (time
        # gets passed to twig filtering)

        if default is not None:
            # then we need to do a filter first to see if parameter exists
            if not len(self.filter(twig=twig, **kwargs)):
                return default

        param = self.get_parameter(twig=twig, **kwargs)

        # if hasattr(param, 'default_unit'):
        # This breaks for constraint parameters
        if isinstance(param, FloatParameter) or\
                isinstance(param,FloatArrayParameter):
            return param.get_value(unit=unit, t=t, **kwargs)

        return param.get_value(**kwargs)


Instruction:
Given the following Python 3 function, write the documentation
def set_value(self, twig=None, value=None, **kwargs):
        # TODO: handle twig having parameter key (value@, default_unit@, adjust@, etc)
        # TODO: does this return anything (update the docstring)?
        if twig is not None and value is None:
            # then try to support value as the first argument if no matches with twigs
            if not isinstance(twig, str):
                value = twig
                twig = None

            elif not len(self.filter(twig=twig, check_default=check_default, **kwargs)):
                value = twig
                twig = None

        if "index" in kwargs.keys():
            return self.get_parameter(twig=twig,
                                      **kwargs).set_index_value(value=value,
                                                                **kwargs)

        if "time" in kwargs.keys():
            if not len(self.filter(**kwargs)):
                # then let's try filtering without time and seeing if we get a
                # FloatArrayParameter so that we can use set_index_value instead
                time = kwargs.pop("time")

                param = self.get_parameter(twig=twig, **kwargs)
                if not isinstance(param, FloatArrayParameter):
                    raise TypeError

                # TODO: do we need to be more clever about time qualifier for
                # ETV datasets? TODO: is this robust enough... this won't search
                # for times outside the existing ParameterSet.  We could also
                # try param.get_parent_ps().get_parameter('time'), but this
                # won't work when outside the bundle (which is used within
                # backends.py to set fluxes, etc) print "***
                # get_parameter(qualifier='times', **kwargs)", {k:v for k,v in
                # kwargs.items() if k not in ['qualifier']}
                time_param = self.get_parameter(qualifier='times', **{k:v for k,v in kwargs.items() if k not in ['qualifier']})
                index = np.where(time_param.get_value()==time)[0]

                return param.set_index_value(value=value, index=index, **kwargs)

        return self.get_parameter(twig=twig,
                                  **kwargs).set_value(value=value,
                                                      **kwargs)

Response: Set the value of a Parameter in this ParameterSet.


Instruction:
Write a Python 3 script for
setting the value of all returned ParameterSet s in this ParameterSet.

Response:
def set_value_all(self, twig=None, value=None, check_default=False, **kwargs):
        """
        Set the value of all returned :class:`Parameter`s in this ParameterSet.

        Any :class:`Parameter` that would be included in the resulting ParameterSet
        from a :func:`filter` call with the same arguments will have
        their value set.

        Note: setting the value of a Parameter in a ParameterSet WILL
        change that Parameter across any parent ParameterSets (including
        the :class:`phoebe.frontend.bundle.Bundle`)

        :parameter str twig: the twig to search for the parameter
        :parameter value: the value to set.  Provide units, if necessary, by
                sending a Quantity object (ie 2.4*u.rad)
        :parameter bool check_default: whether to exclude any default values.
                Defaults to False (unlike all filtering).  Note that this
                acts on the current ParameterSet so any filtering done before
                this call will EXCLUDE defaults by default.
        :parameter **kwargs: meta-tags to search
        """
        if twig is not None and value is None:
            # then try to support value as the first argument if no matches with twigs
            if not isinstance(twig, str):
                value = twig
                twig = None

            elif not len(self.filter(twig=twig, check_default=check_default, **kwargs)):
                value = twig
                twig = None

        params = self.filter(twig=twig,
                             check_default=check_default,
                             **kwargs).to_list()

        if not kwargs.pop('ignore_none', False) and not len(params):
            raise ValueError("no parameters found")

        for param in params:
            if "index" in kwargs.keys():
                return self.get_parameter(twig=twig,
                                          **kwargs).set_index_value(value=value,
                                                                    **kwargs)
            param.set_value(value=value, **kwargs)


Instruction:
Implement a function in Python 3 to
get the default unit for this tag

Response:
def get_default_unit(self, twig=None, **kwargs):
        """
        TODO: add documentation
        """
        return self.get_parameter(twig=twig, **kwargs).get_default_unit()


Instruction:
Can you tell what is the following Python 3 function doing
def set_default_unit(self, twig=None, unit=None, **kwargs):
        if twig is not None and unit is None:
            # then try to support value as the first argument if no matches with twigs
            if isinstance(unit, u.Unit) or not isinstance(twig, str):
                unit = twig
                twig = None

            elif not len(self.filter(twig=twig, check_default=check_default, **kwargs)):
                unit = twig
                twig = None

        return self.get_parameter(twig=twig, **kwargs).set_default_unit(unit)

Response: Set the default unit of the current resource.


Instruction:
How would you explain what the following Python 3 function does
def set_default_unit_all(self, twig=None, unit=None, **kwargs):
        if twig is not None and unit is None:
            # then try to support value as the first argument if no matches with twigs
            if isinstance(unit, u.Unit) or not isinstance(twig, str):
                unit = twig
                twig = None

            elif not len(self.filter(twig=twig, check_default=check_default, **kwargs)):
                unit = twig
                twig = None

        for param in self.filter(twig=twig, **kwargs).to_list():
            param.set_default_unit(unit)

Response: Set default unit for all parameters in this resource.


Instruction:
Can you implement a function in Python 3 that
gets the description of the current object

Response:
def get_description(self, twig=None, **kwargs):
        """
        TODO: add documentation
        """
        return self.get_parameter(twig=twig, **kwargs).get_description()


Instruction:
Given the following Python 3 function, write the documentation
def plot(self, twig=None, **kwargs):
        if not _use_autofig:
            if os.getenv('PHOEBE_ENABLE_PLOTTING', 'TRUE').upper() != 'TRUE':
                raise ImportError("cannot plot because PHOEBE_ENABLE_PLOTTING environment variable is disasbled")
            else:
                raise ImportError("autofig not imported, cannot plot")

        # since we used the args trick above, all other options have to be in kwargs
        save = kwargs.pop('save', False)
        show = kwargs.pop('show', False)
        tight_layout = kwargs.pop('tight_layout', False)
        draw_sidebars = kwargs.pop('draw_sidebars', False)
        draw_title = kwargs.pop('draw_title', False)
        subplot_grid = kwargs.pop('subplot_grid', None)
        animate = kwargs.pop('animate', False)
        time = kwargs.get('time', None)  # don't pop since time may be used for filtering

        if twig is not None:
            kwargs['twig'] = twig

        plot_kwargss = self._unpack_plotting_kwargs(**kwargs)

        # this loop handles any of the automatically-generated
        # multiple plotting calls, passing each on to autofig
        for plot_kwargs in plot_kwargss:
            y = plot_kwargs.get('y', [])
            if (isinstance(y, u.Quantity) and isinstance(y.value, float)) or (hasattr(y, 'value') and isinstance(y.value, float)):
                pass
            elif not len(y):
                # a dataset without observational data, for example
                continue

            autofig_method = plot_kwargs.pop('autofig_method', 'plot')
            # we kept the qualifiers around so we could do some default-logic,
            # but it isn't necessary to pass them on to autofig.
            plot_kwargs = {k:v for k,v in plot_kwargs.items() if 'qualifier' not in k}
            logger.info("calling autofig.{}({})".format(autofig_method, ", ".join(["{}={}".format(k,v if not isinstance(v, np.ndarray) else "<data ({})>".format(v.shape)) for k,v in plot_kwargs.items()])))
            func = getattr(self.gcf(), autofig_method)

            func(**plot_kwargs)

        if save or show or animate:
            # NOTE: time, times, will all be included in kwargs
            try:
                return self._show_or_save(save, show, animate,
                                          draw_sidebars=draw_sidebars,
                                          draw_title=draw_title,
                                          tight_layout=tight_layout,
                                          subplot_grid=subplot_grid,
                                          **kwargs)
            except Exception as err:
                self.clf()
                raise err
        else:
            afig = self.gcf()
            fig = None

            return afig, fig

Response: This function will plot the data for the current time and time of the current time.


Instruction:
How would you explain what the following Python 3 function does
def _show_or_save(self, save, show, animate,
                      draw_sidebars=True,
                      draw_title=True,
                      tight_layout=False,
                      subplot_grid=None,
                      **kwargs):
        """
        Draw/animate and show and/or save a autofig plot
        """
        if animate and not show and not save:
            logger.warning("setting show to True since animate=True and save not provided")
            show = True

        if animate:
            # prefer times over time
            times = kwargs.get('times', kwargs.get('time', None))
            save_kwargs = kwargs.get('save_kwargs', {})

            if times is None:
                # then let's try to get all SYNTHETIC times
                # it would be nice to only do ENABLED, but then we have to worry about compute
                # it would also be nice to worry about models... but then you should filter first
                logger.info("no times were providing, so defaulting to animate over all dataset times")
                times = []
                for dataset in self.datasets:
                    ps = self.filter(dataset=dataset, context='model')
                    if len(ps.times):
                        # for the case of meshes/spectra
                        times += [float(t) for t in ps.times]
                    else:
                        for param in ps.filter(qualifier='times').to_list():
                            times += list(param.get_value())

                times = sorted(list(set(times)))

            logger.info("calling autofig.animate(i={}, draw_sidebars={}, draw_title={}, tight_layout={}, save={}, show={}, save_kwargs={})".format(times, draw_sidebars, draw_title, tight_layout, save, show, save_kwargs))

            mplanim = self.gcf().animate(i=times,
                                         draw_sidebars=draw_sidebars,
                                         draw_title=draw_title,
                                         tight_layout=tight_layout,
                                         subplot_grid=subplot_grid,
                                         save=save,
                                         show=show,
                                         save_kwargs=save_kwargs)

            afig = self.gcf()

            # clear the autofig figure
            self.clf()

            return afig, mplanim

        else:
            time = kwargs.get('time', None)

            if isinstance(time, str):
                time = self.get_value(time, context=['component', 'system'])

            logger.info("calling autofig.draw(i={}, draw_sidebars={}, draw_title={}, tight_layout={}, save={}, show={})".format(time, draw_sidebars, draw_title, tight_layout, save, show))
            fig = self.gcf().draw(i=time,
                                  draw_sidebars=draw_sidebars,
                                  draw_title=draw_title,
                                  tight_layout=tight_layout,
                                  subplot_grid=subplot_grid,
                                  save=save, show=show)
            # clear the figure so next call will start over and future shows will work
            afig = self.gcf()
            self.clf()

            return afig, fig

Response: Show or save a single object in the system.


Instruction:
Can you tell what is the following Python 3 function doing
def show(self, **kwargs):
        kwargs.setdefault('show', True)
        kwargs.setdefault('save', False)
        kwargs.setdefault('animate', False)
        return self._show_or_save(**kwargs)

Response: Draw and show the plot.


Instruction:
Write a Python 3 function that can
draw and save the plot.

Response:
def savefig(self, filename, **kwargs):
        """
        Draw and save the plot.

        :parameter str filename: filename to save to.  Be careful of extensions here...
                matplotlib accepts many different image formats while other
                backends will only export to html.
        """
        filename = os.path.expanduser(filename)
        kwargs.setdefault('show', False)
        kwargs.setdefault('save', filename)
        kwargs.setdefault('animate', False)
        return self._show_or_save(**kwargs)


Instruction:
Can you generate the documentation for the following Python 3 function
def copy(self):
        s = self.to_json()
        cpy = parameter_from_json(s)
        # TODO: may need to subclass for Parameters that require bundle by using this line instead:
        # cpy = parameter_from_json(s, bundle=self._bundle)
        cpy.set_uniqueid(_uniqueid())
        return cpy

Response:
Deepcopy the parameter (with a new uniqueid).  All other tags will remain
        the same... so some other tag should be changed before attaching back to
        a ParameterSet or Bundle.

        :return: the copied :class:`Parameter` object


Instruction:
Create a Python 3 function to
return a shorter abreviated string reprentation of the parameter

Response:
def to_string_short(self):
        """
        see also :meth:`to_string`

        :return: a shorter abreviated string reprentation of the parameter
        """
        if hasattr(self, 'constrained_by') and len(self.constrained_by) > 0:
            return "* {:>30}: {}".format(self.uniquetwig_trunc, self.get_quantity() if hasattr(self, 'quantity') else self.get_value())
        else:
            return "{:>32}: {}".format(self.uniquetwig_trunc, self.get_quantity() if hasattr(self, 'quantity') else self.get_value())


Instruction:
Can you generate a brief explanation for the following Python 3 code
def save(self, filename, incl_uniqueid=False):
        filename = os.path.expanduser(filename)
        f = open(filename, 'w')
        json.dump(self.to_json(incl_uniqueid=incl_uniqueid), f,
                   sort_keys=True, indent=0, separators=(',', ': '))
        f.close()

        return filename

Response: Save the Parameter to a JSON - formatted ASCII file.


Instruction:
How would you explain what the following Python 3 function does
def to_json(self, incl_uniqueid=False):
        def _parse(k, v):
            """
            """
            if k=='value':
                if isinstance(self._value, nparray.ndarray):
                    if self._value.unit is not None and hasattr(self, 'default_unit'):
                        v = self._value.to(self.default_unit).to_dict()
                    else:
                        v = self._value.to_dict()
                if isinstance(v, u.Quantity):
                    v = self.get_value() # force to be in default units
                if isinstance(v, np.ndarray):
                    v = v.tolist()
                return v
            elif k=='limits':
                return [vi.value if hasattr(vi, 'value') else vi for vi in v]
            elif v is None:
                return v
            elif isinstance(v, str):
                return v
            elif isinstance(v, dict):
                return v
            elif isinstance(v, float) or isinstance(v, int) or isinstance(v, list):
                return v
            elif _is_unit(v):
                return str(v.to_string())
            else:
                try:
                    return str(v)
                except:
                    raise NotImplementedError("could not parse {} of '{}' to json".format(k, self.uniquetwig))

        return {k: _parse(k, v) for k,v in self.to_dict().items() if (v is not None and k not in ['twig', 'uniquetwig', 'quantity'] and (k!='uniqueid' or incl_uniqueid or self.qualifier=='detached_job'))}

Response: Returns a JSON - ready dictionary holding all information for this parameter.


Instruction:
Given the following Python 3 function, write the documentation
def get_meta(self, ignore=['uniqueid']):
        return OrderedDict([(k, getattr(self, k)) for k in _meta_fields_all if k not in ignore])

Response: Returns the meta - tag properties for this Parameter


Instruction:
Make a summary of the following Python 3 code
def uniquetwig(self, ps=None):
        if ps is None:
            ps = self._bundle

        if ps is None:
            return self.twig
        return ps._uniquetwig(self.twig)

Response: Returns the uniquetwig for this parameter.


Instruction:
Here you have a function in Python 3, explain what it does
def twig(self):
        return "@".join([getattr(self, k) for k in _meta_fields_twig if getattr(self, k) is not None])

Response:
Returns a single string with the individual
        and the meta tags separated by '@' symbols.


Instruction:
Can you tell what is the following Python 3 function doing
def is_visible(self):
        def is_visible_single(visible_if):
            # visible_if syntax: [ignore,these]qualifier:value

            if visible_if.lower() == 'false':
                return False

            # otherwise we need to find the parameter we're referencing and check its value
            if visible_if[0]=='[':
                remove_metawargs, visible_if = visible_if[1:].split(']')
                remove_metawargs = remove_metawargs.split(',')
            else:
                remove_metawargs = []

            qualifier, value = visible_if.split(':')

            if 'hierarchy.' in qualifier:
                # TODO: set specific syntax (hierarchy.get_meshables:2)
                # then this needs to do some logic on the hierarchy
                hier = self._bundle.hierarchy
                if not len(hier.get_value()):
                    # then hierarchy hasn't been set yet, so we can't do any
                    # of these tests
                    return True

                method = qualifier.split('.')[1]

                if value in ['true', 'True']:
                    value = True
                elif value in ['false', 'False']:
                    value = False

                return getattr(hier, method)(self.component) == value

            else:

                # the parameter needs to have all the same meta data except qualifier
                # TODO: switch this to use self.get_parent_ps ?
                metawargs = {k:v for k,v in self.get_meta(ignore=['twig', 'uniquetwig', 'uniqueid']+remove_metawargs).items() if v is not None}
                metawargs['qualifier'] = qualifier
                # metawargs['twig'] = None
                # metawargs['uniquetwig'] = None
                # metawargs['uniqueid'] = None
                # if metawargs.get('component', None) == '_default':
                    # metawargs['component'] = None

                try:
                    # this call is quite expensive and bloats every get_parameter(check_visible=True)
                    param = self._bundle.get_parameter(check_visible=False, check_default=False, **metawargs)
                except ValueError:
                    # let's not let this hold us up - sometimes this can happen when copying
                    # parameters (from copy_for) in order that the visible_if parameter
                    # happens later
                    logger.debug("parameter not found when trying to determine if visible, {}".format(metawargs))
                    return True

                #~ print "***", qualifier, param.qualifier, param.get_value(), value

                if isinstance(param, BoolParameter):
                    if value in ['true', 'True']:
                        value = True
                    elif value in ['false', 'False']:
                        value = False

                if isinstance(value, str) and value[0] in ['!', '~']:
                    return param.get_value() != value[1:]
                elif value=='<notempty>':
                    return len(param.get_value()) > 0
                else:
                    return param.get_value() == value

        if self.visible_if is None:
            return True

        if not self._bundle:
            # then we may not be able to do the check, for now let's just return True
            return True

        return np.all([is_visible_single(visible_if_i) for visible_if_i in self.visible_if.split(',')])

Response: returns True if this parameter is currently visible


Instruction:
Explain what the following Python 3 code does
def get_parent_ps(self):
        if self._bundle is None:
            return None

        metawargs = {k:v for k,v in self.meta.items() if k not in ['qualifier', 'twig', 'uniquetwig']}

        return self._bundle.filter(**metawargs)

Response:
Return a : class:`ParameterSet` of all Parameters in the same
        meta - tags except qualifier twig and uniquetwig


Instruction:
Write a Python 3 function that can
expand the selection to account for wildcards

Response:
def expand_value(self, **kwargs):
        """
        expand the selection to account for wildcards
        """
        selection = []
        for v in self.get_value(**kwargs):
            for choice in self.choices:
                if v==choice and choice not in selection:
                    selection.append(choice)
                elif fnmatch(choice, v) and choice not in selection:
                    selection.append(choice)

        return selection


Instruction:
How would you code a function in Python 3 to
update the value to remove any that are not valid

Response:
def remove_not_valid_selections(self):
        """
        update the value to remove any that are (no longer) valid
        """
        value = [v for v in self.get_value() if self.valid_selection(v)]
        self.set_value(value)


Instruction:
How would you explain what the following Python 3 function does
def within_limits(self, value):

        return (self.limits[0] is None or value >= self.limits[0]) and (self.limits[1] is None or value <= self.limits[1])

Response: check whether a value falls within the set limits


Instruction:
Here you have a function in Python 3, explain what it does
def within_limits(self, value):

        if isinstance(value, int) or isinstance(value, float):
            value = value * self.default_unit

        return (self.limits[0] is None or value >= self.limits[0]) and (self.limits[1] is None or value <= self.limits[1])

Response: check whether a value falls within the set limits


Instruction:
Create a Python 3 function to
return the expression of the constraint that constrains this parameter

Response:
def is_constraint(self):
        """
        returns the expression of the constraint that constrains this parameter
        """
        if self._is_constraint is None:
            return None
        return self._bundle.get_parameter(context='constraint', uniqueid=self._is_constraint)


Instruction:
Explain what the following Python 3 code does
def constrained_by(self):
        if self._is_constraint is None:
            return []
        params = []
        for var in self.is_constraint._vars:
            param = var.get_parameter()
            if param.uniqueid != self.uniqueid:
                params.append(param)
        return params

Response: returns a list of parameters that constrain this parameter


Instruction:
Create a Python 3 function for
returning a list of the expressions in which this parameter constrains another

Response:
def in_constraints(self):
        """
        returns a list of the expressions in which this parameter constrains another
        """
        expressions = []
        for uniqueid in self._in_constraints:
            expressions.append(self._bundle.get_parameter(context='constraint', uniqueid=uniqueid))
        return expressions


Instruction:
Create a Python 3 function to
return a list of parameters that are constrained by this parameter

Response:
def constrains(self):
        """
        returns a list of parameters that are constrained by this parameter
        """
        params = []
        for constraint in self.in_constraints:
            for var in constraint._vars:
                param = var.get_parameter()
                if param.component == constraint.component and param.qualifier == constraint.qualifier:
                    if param not in params and param.uniqueid != self.uniqueid:
                        params.append(param)
        return params


Instruction:
Create a Python 3 function to
return a list of all parameters that are either constrained by or constrain this parameter

Response:
def related_to(self):
        """
        returns a list of all parameters that are either constrained by or constrain this parameter
        """
        params = []
        constraints = self.in_constraints
        if self.is_constraint is not None:
            constraints.append(self.is_constraint)

        for constraint in constraints:
            for var in constraint._vars:
                param = var.get_parameter()
                if param not in params and param.uniqueid != self.uniqueid:
                    params.append(param)

        return params


Instruction:
Here you have a function in Python 3, explain what it does
def to_string_short(self):
        opt = np.get_printoptions()
        np.set_printoptions(threshold=8, edgeitems=3, linewidth=opt['linewidth']-len(self.uniquetwig)-2)
        str_ = super(FloatArrayParameter, self).to_string_short()
        np.set_printoptions(**opt)
        return str_

Response: returns a shorter abreviated string reprentation of the parameter


Instruction:
Here you have a function in Python 3, explain what it does
def interp_value(self, **kwargs):
        # TODO: add support for units
        # TODO: add support for non-linear interpolation (probably would need to use scipy)?
        # TODO: add support for interpolating in phase_space

        if len(kwargs.keys()) > 1:
            raise KeyError("interp_value only takes a single qualifier-value pair")

        qualifier, qualifier_interp_value = kwargs.items()[0]

        if isinstance(qualifier_interp_value, str):
            # then assume its a twig and try to resolve
            # for example: time='t0_supconj'
            qualifier_interp_value = self._bundle.get_value(qualifier_interp_value, context=['system', 'component'])

        parent_ps = self.get_parent_ps()

        if qualifier not in parent_ps.qualifiers:
            # TODO: handle plural to singular (having to say
            # interp_value(times=5) is awkward)
            raise KeyError("'{}' not valid qualifier (must be one of {})".format(qualifier, parent_ps.qualifiers))

        qualifier_parameter = parent_ps.get(qualifier=qualifier)

        if not isinstance(qualifier_parameter, FloatArrayParameter):
            raise KeyError("'{}' does not point to a FloatArrayParameter".format(qualifier))

        return np.interp(qualifier_interp_value, qualifier_parameter.get_value(), self.get_value())

Response: Interpolate to find the value in THIS array given a value from the parameter set ANOTHER array.


Instruction:
How would you code a function in Python 3 to
set any property of the underlying nparray object

Response:
def set_property(self, **kwargs):
        """
        set any property of the underlying nparray object
        """
        if not isinstance(self._value, nparray.ndarray):
            raise ValueError("value is not a nparray object")

        for property, value in kwargs.items():
            setattr(self._value, property, value)


Instruction:
Given the following Python 3 function, write the documentation
def _parse_repr(self):

         repr_ = self.get_value()
         repr_str = '["{}"]'.format(repr_.replace(', ', '", "').replace('(', '", ["').replace(')', '"]')).replace(']"', '"]').replace('""', '"').replace(']"', ']')
         return json.loads(repr_str)

Response: parse the representation of the node


Instruction:
Write a Python 3 function for
giving a nested structure from _parse_repr and find the trace route to get to item

Response:
def _recurse_find_trace(self, structure, item, trace=[]):
        """
        given a nested structure from _parse_repr and find the trace route to get to item
        """

        try:
            i = structure.index(item)
        except ValueError:
            for j,substructure in enumerate(structure):
                if isinstance(substructure, list):
                    return self._recurse_find_trace(substructure, item, trace+[j])
        else:
            return trace+[i]


Instruction:
Given the following Python 3 function, write the documentation
def _get_by_trace(self, structure, trace):
        for i in trace:
            structure = structure[i]

        return structure

Response: retrieve an item from the nested structure given a trace


Instruction:
Create a Python 3 function for
getting the component of all stars in order primary -> secondary

Response:
def get_stars(self):
        """
        get 'component' of all stars in order primary -> secondary
        """
        l = re.findall(r"[\w']+", self.get_value())
        # now search for indices of star and take the next entry from this flat list
        return [l[i+1] for i,s in enumerate(l) if s=='star']


Instruction:
Here you have a function in Python 3, explain what it does
def get_orbits(self):
        #~ l = re.findall(r"[\w']+", self.get_value())
        # now search for indices of orbit and take the next entry from this flat list
        #~ return [l[i+1] for i,s in enumerate(l) if s=='orbit']
        orbits = []
        for star in self.get_stars():
            parent = self.get_parent_of(star)
            if parent not in orbits and parent!='component' and parent is not None:
                orbits.append(parent)
        return orbits

Response: get list of all orbits in order primary -> secondary


Instruction:
How would you explain what the following Python 3 function does
def get_children_of(self, component, kind=None):

        structure, trace, item = self._get_structure_and_trace(component)
        item_kind, item_label = item.split(':')

        if isinstance(kind, str):
            kind = [kind]

        if item_kind not in ['orbit']:
            # return None
            return []
        else:
            items = self._get_by_trace(structure, trace[:-1]+[trace[-1]+1])
            # we want to ignore suborbits
            #return [str(ch.split(':')[-1]) for ch in items if isinstance(ch, unicode)]
            return [str(ch.split(':')[-1]) for ch in items if isinstance(ch, unicode) and (kind is None or ch.split(':')[0] in kind)]

Response: get to component labels of the children of a given component


Instruction:
Make a summary of the following Python 3 code
def get_child_of(self, component, ind, kind=None):
        children = self.get_children_of(component, kind=kind)
        if children is None:
            return None
        else:
            return children[ind]

Response: get a child of a given component


Instruction:
Create a Python 3 function to
return whether a given component is the primary or secondary

Response:
def get_primary_or_secondary(self, component, return_ind=False):
        """
        return whether a given component is the 'primary' or 'secondary'
        component in its parent orbit
        """
        parent = self.get_parent_of(component)
        if parent is None:
            # then this is a single component, not in a binary
            return 'primary'

        children_of_parent = self.get_children_of(parent)

        ind = children_of_parent.index(component)

        if ind > 1:
            return None

        if return_ind:
            return ind + 1

        return ['primary', 'secondary'][ind]


Instruction:
Write a Python 3 function that can
return a list of components that are meshable

Response:
def get_meshables(self):
        """
        return a list of components that are meshable (generally stars, but handles
            the envelope for an contact_binary)
        """

        l = re.findall(r"[\w']+", self.get_value())
        # now search for indices of star and take the next entry from this flat list
        meshables = [l[i+1] for i,s in enumerate(l) if s in ['star', 'envelope']]

        # now we want to remove any star which has a sibling envelope
        has_sibling_envelope = []
        for item in meshables:
            if self.get_sibling_of(item, kind='envelope'):
                has_sibling_envelope.append(item)

        return [m for m in meshables if m not in has_sibling_envelope]


Instruction:
Create a Python 3 function to
return True if any component is part of a contact_binary

Response:
def is_contact_binary(self, component):
        """
        especially useful for constraints

        tells whether any component (star, envelope) is part of a contact_binary
        by checking its siblings for an envelope
        """
        if component not in self._is_contact_binary.keys():
            self._update_cache()

        return self._is_contact_binary.get(component)


Instruction:
Create a Python 3 function for
returning True if the component is a binary component.

Response:
def is_binary(self, component):
        """
        especially useful for constraints

        tells whether any component (star, envelope) is part of a binary
        by checking its parent
        """
        if component not in self._is_binary.keys():
            self._update_cache()

        return self._is_binary.get(component)


Instruction:
Can you generate the documentation for the following Python 3 function
def vars(self):
        # cache _var_params
        if self._var_params is None:
            self._var_params = ParameterSet([var.get_parameter() for var in self._vars])
        return self._var_params

Response: return all the variables in a PS


Instruction:
Can you create a Python 3 function that
gets a parameter from those that are variables

Response:
def get_parameter(self, twig=None, **kwargs):
        """
        get a parameter from those that are variables
        """
        kwargs['twig'] = twig
        kwargs['check_default'] = False
        kwargs['check_visible'] = False
        ps = self.vars.filter(**kwargs)
        if len(ps)==1:
            return ps.get(check_visible=False, check_default=False)
        elif len(ps) > 1:
            # TODO: is this safe?  Some constraints may have a parameter listed
            # twice, so we can do this then, but maybe should check to make sure
            # all items have the same uniqueid?  Maybe check len(ps.uniqueids)?
            return ps.to_list()[0]
        else:
            raise KeyError("no result found")


Instruction:
Write a Python 3 script to
flip the constraint to solve for any of the parameters in the expression

Response:
def flip_for(self, twig=None, expression=None, **kwargs):
        """
        flip the constraint to solve for for any of the parameters in the expression

        expression (optional if sympy available, required if not)
        """

        _orig_expression = self.get_value()

        # try to get the parameter from the bundle
        kwargs['twig'] = twig
        newly_constrained_var = self._get_var(**kwargs)
        newly_constrained_param = self.get_parameter(**kwargs)

        check_kwargs = {k:v for k,v in newly_constrained_param.meta.items() if k not in ['context', 'twig', 'uniquetwig']}
        check_kwargs['context'] = 'constraint'
        if len(self._bundle.filter(**check_kwargs)):
            raise ValueError("'{}' is already constrained".format(newly_constrained_param.twig))

        currently_constrained_var = self._get_var(qualifier=self.qualifier, component=self.component)
        currently_constrained_param = currently_constrained_var.get_parameter() # or self.constrained_parameter

        import constraint
        if self.constraint_func is not None and hasattr(constraint, self.constraint_func):
            # then let's see if the method is capable of resolving for use
            # try:
            if True:
                # TODO: this is not nearly general enough, each method takes different arguments
                # and getting solve_for as newly_constrained_param.qualifier

                lhs, rhs, constraint_kwargs = getattr(constraint, self.constraint_func)(self._bundle, solve_for=newly_constrained_param, **self.constraint_kwargs)
            # except NotImplementedError:
            #     pass
            # else:
                # TODO: this needs to be smarter and match to self._get_var().user_label instead of the current uniquetwig

                expression = rhs._value # safe expression
                #~ print "*** flip by recalling method success!", expression

        # print "***", lhs._value, rhs._value

        if expression is not None:
            expression = expression

        elif _use_sympy:

            eq_safe = "({}) - {}".format(self._value, currently_constrained_var.safe_label)

            #~ print "*** solving {} for {}".format(eq_safe, newly_constrained_var.safe_label)

            expression = sympy.solve(eq_safe, newly_constrained_var.safe_label)[0]

            #~ print "*** solution: {}".format(expression)

        else:
            # TODO: ability for built-in constraints to flip themselves
            # we could access self.kind and re-call that with a new solve_for option?
            raise ValueError("must either have sympy installed or provide a new expression")

        self._qualifier = newly_constrained_param.qualifier
        self._component = newly_constrained_param.component
        self._kind = newly_constrained_param.kind

        self._value = str(expression)
        # reset the default_unit so that set_default_unit doesn't complain
        # about incompatible units
        self._default_unit = None
        self.set_default_unit(newly_constrained_param.default_unit)

        self._update_bookkeeping()

        self._add_history(redo_func='flip_constraint', redo_kwargs={'expression': expression, 'uniqueid': newly_constrained_param.uniqueid}, undo_func='flip_constraint', undo_kwargs={'expression': _orig_expression, 'uniqueid': currently_constrained_param.uniqueid})


Instruction:
Can you tell what is the following Python 3 function doing
def get_status(self):
        if self._value == 'loaded':
            status = 'loaded'

        elif not _is_server and self._bundle is not None and self._server_status is not None:
            if not _can_requests:
                raise ImportError("requests module required for external jobs")

            if self._value in ['complete']:
                # then we have no need to bother checking again
                status = self._value
            else:
                url = self._server_status
                logger.info("checking job status on server from {}".format(url))
                # "{}/{}/parameters/{}".format(server, bundleid, self.uniqueid)
                r = requests.get(url, timeout=5)
                try:
                    rjson = r.json()
                except ValueError:
                    # TODO: better exception here - perhaps look for the status code from the response?
                    status = self._value
                else:
                    status = rjson['data']['attributes']['value']

        else:

            if self.status_method == 'exists':
                output_exists = os.path.isfile("_{}.out".format(self.uniqueid))
                if output_exists:
                    status = 'complete'
                else:
                    status = 'unknown'
            else:
                raise NotImplementedError

        # here we'll set the value to be the latest CHECKED status for the sake
        # of exporting to JSON and updating the status for clients.  get_value
        # will still call status so that it will return the CURRENT value.
        self._value = status
        return status

Response: Returns the status of the current job.


Instruction:
Implement a Python 3 function for
returning a new form with no data and files.

Response:
def get_unbound_form(self):
        """
        Overrides behavior of FormView.get_form_kwargs
        when method is POST or PUT
        """
        form_kwargs = self.get_form_kwargs()
        # @@@ remove fields that would cause the form to be bound
        # when instantiated
        bound_fields = ["data", "files"]
        for field in bound_fields:
            form_kwargs.pop(field, None)
        return self.get_form_class()(**form_kwargs)


Instruction:
Write a Python 3 script for
returning the JSON data returned when a valid form submission occurs.

Response:
def get_form_success_data(self, form):
        """
        Allows customization of the JSON data returned when a valid form submission occurs.
        """
        data = {
            "html": render_to_string(
                "pinax/teams/_invite_form.html",
                {
                    "invite_form": self.get_unbound_form(),
                    "team": self.team
                },
                request=self.request
            )
        }

        membership = self.membership
        if membership is not None:
            if membership.state == Membership.STATE_APPLIED:
                fragment_class = ".applicants"
            elif membership.state == Membership.STATE_INVITED:
                fragment_class = ".invitees"
            elif membership.state in (Membership.STATE_AUTO_JOINED, Membership.STATE_ACCEPTED):
                fragment_class = {
                    Membership.ROLE_OWNER: ".owners",
                    Membership.ROLE_MANAGER: ".managers",
                    Membership.ROLE_MEMBER: ".members"
                }[membership.role]
            data.update({
                "append-fragments": {
                    fragment_class: render_to_string(
                        "pinax/teams/_membership.html",
                        {
                            "membership": membership,
                            "team": self.team
                        },
                        request=self.request
                    )
                }
            })
        return data


Instruction:
Implement a function in Python 3 to
make sure to get a float make sure to get a float make sure to get a float make sure to get a float make sure to get a float

Response:
def _value(obj):
    """
    make sure to get a float
    """
    # TODO: this is ugly and makes everything ugly
    # can we handle this with a clean decorator or just requiring that only floats be passed??
    if hasattr(obj, 'value'):
        return obj.value
    elif isinstance(obj, np.ndarray):
        return np.array([o.value for o in obj])
    elif hasattr(obj, '__iter__'):
        return [_value(o) for o in obj]
    return obj


Instruction:
How would you explain what the following Python 3 function does
def _estimate_delta(ntriangles, area):
    return np.sqrt(4./np.sqrt(3) * float(area) / float(ntriangles))

Response: estimate the value for delta to send to marching based on the number of triangles requested and the surface area of the requested triangles


Instruction:
Explain what the following Python 3 code does
def from_bundle(cls, b, compute=None, datasets=[], **kwargs):

        hier = b.hierarchy

        if not len(hier.get_value()):
            raise NotImplementedError("Meshing requires a hierarchy to exist")

        # now pull general compute options
        if compute is not None:
            if isinstance(compute, str):
                compute_ps = b.get_compute(compute, check_visible=False)
            else:
                # then hopefully compute is the parameterset
                compute_ps = compute
            eclipse_method = compute_ps.get_value(qualifier='eclipse_method', **kwargs)
            horizon_method = compute_ps.get_value(qualifier='horizon_method', check_visible=False, **kwargs)
            dynamics_method = compute_ps.get_value(qualifier='dynamics_method', **kwargs)
            irrad_method = compute_ps.get_value(qualifier='irrad_method', **kwargs)
            boosting_method = compute_ps.get_value(qualifier='boosting_method', **kwargs)
            if conf.devel:
                mesh_init_phi = compute_ps.get_value(qualifier='mesh_init_phi', unit=u.rad, **kwargs)
            else:
                mesh_init_phi = 0.0
        else:
            eclipse_method = 'native'
            horizon_method = 'boolean'
            dynamics_method = 'keplerian'
            irrad_method = 'none'
            boosting_method = 'none'
            mesh_init_phi = 0.0

        # NOTE: here we use globals()[Classname] because getattr doesn't work in
        # the current module - now this doesn't really make sense since we only
        # support stars, but eventually the classname could be Disk, Spot, etc
        if 'dynamics_method' in kwargs.keys():
            # already set as default above
            _dump = kwargs.pop('dynamics_method')

        meshables = hier.get_meshables()
        def get_distortion_method(hier, compute_ps, component, **kwargs):
            if hier.get_kind_of(component) in ['envelope']:
                return 'roche'

            if compute_ps.get_value('mesh_method', component=component, **kwargs)=='wd':
                return 'roche'

            return compute_ps.get_value('distortion_method', component=component, **kwargs)

        bodies_dict = {comp: globals()[_get_classname(hier.get_kind_of(comp), get_distortion_method(hier, compute_ps, comp, **kwargs))].from_bundle(b, comp, compute, dynamics_method=dynamics_method, mesh_init_phi=mesh_init_phi, datasets=datasets, **kwargs) for comp in meshables}

        # envelopes need to know their relationships with the underlying stars
        parent_envelope_of = {}
        for meshable in meshables:
            if hier.get_kind_of(meshable) == 'envelope':
                for starref in hier.get_siblings_of(meshable):
                    parent_envelope_of[starref] = meshable

        return cls(bodies_dict, eclipse_method=eclipse_method,
                   horizon_method=horizon_method,
                   dynamics_method=dynamics_method,
                   irrad_method=irrad_method,
                   boosting_method=boosting_method,
                   parent_envelope_of=parent_envelope_of)

Response: Build a system from a bundle.


Instruction:
Explain what the following Python 3 code does
def get_body(self, component):
        if component in self._bodies.keys():
            return self._bodies[component]
        else:
            # then hopefully we're a child star of an contact_binary envelope
            parent_component = self._parent_envelope_of[component]
            return self._bodies[parent_component].get_half(component)

Response: get_body - Get the body of a given component


Instruction:
How would you explain what the following Python 3 function does
def update_positions(self, time, xs, ys, zs, vxs, vys, vzs,
                         ethetas, elongans, eincls,
                         ds=None, Fs=None, ignore_effects=False):
        """
        TODO: add documentation

        all arrays should be for the current time, but iterable over all bodies
        """
        self.xs = np.array(_value(xs))
        self.ys = np.array(_value(ys))
        self.zs = np.array(_value(zs))

        for starref,body in self.items():
            body.update_position(time, xs, ys, zs, vxs, vys, vzs,
                                 ethetas, elongans, eincls,
                                 ds=ds, Fs=Fs, ignore_effects=ignore_effects)

Response: Update the internal state of the internal state of the object.


Instruction:
Explain what the following Python 3 code does
def populate_observables(self, time, kinds, datasets, ignore_effects=False):

        if self.irrad_method is not 'none' and not ignore_effects:
            # TODO: only for kinds that require intensities (i.e. not orbit or
            # dynamical RVs, etc)
            self.handle_reflection()

        for kind, dataset in zip(kinds, datasets):
            for starref, body in self.items():
                body.populate_observable(time, kind, dataset)

Response: Populates the observable objects of all the objects in this object with the given time.


Instruction:
Can you implement a function in Python 3 that
detects the eclipses at the horizon and the eclipsed triangles and handle them if they are even possible.

Response:
def handle_eclipses(self, expose_horizon=False, **kwargs):
        """
        Detect the triangles at the horizon and the eclipsed triangles, handling
        any necessary subdivision.

        :parameter str eclipse_method: name of the algorithm to use to detect
            the horizon or eclipses (defaults to the value set by computeoptions)
        :parameter str subdiv_alg: name of the algorithm to use for subdivision
            (defaults to the value set by computeoptions)
        :parameter int subdiv_num: number of subdivision iterations (defaults
            the value set by computeoptions)
        """

        eclipse_method = kwargs.get('eclipse_method', self.eclipse_method)
        horizon_method = kwargs.get('horizon_method', self.horizon_method)

        # Let's first check to see if eclipses are even possible at these
        # positions.  If they are not, then we only have to do horizon
        #
        # To do that, we'll take the conservative max_r for each object
        # and their current positions, and see if the separations are larger
        # than sum of max_rs
        possible_eclipse = False
        if len(self.bodies) == 1:
            if self.bodies[0].__class__.__name__ == 'Envelope':
                possible_eclipse = True
            else:
                possible_eclipse = False
        else:
            logger.debug("system.handle_eclipses: determining if eclipses are possible from instantaneous_maxr")
            max_rs = [body.instantaneous_maxr for body in self.bodies]
            # logger.debug("system.handle_eclipses: max_rs={}".format(max_rs))
            for i in range(0, len(max_rs)-1):
                for j in range(i+1, len(max_rs)):
                    proj_sep_sq = sum([(c[i]-c[j])**2 for c in (self.xs,self.ys)])
                    max_sep_ecl = max_rs[i] + max_rs[j]

                    if proj_sep_sq < (1.05*max_sep_ecl)**2:
                        # then this pair has the potential for eclipsing triangles
                        possible_eclipse = True
                        break

        if not possible_eclipse and not expose_horizon and horizon_method=='boolean':
            eclipse_method = 'only_horizon'

        # meshes is an object which allows us to easily access and update columns
        # in the meshes *in memory*.  That is meshes.update_columns will propogate
        # back to the current mesh for each body.
        meshes = self.meshes

        # Reset all visibilities to be fully visible to start
        meshes.update_columns('visiblities', 1.0)

        ecl_func = getattr(eclipse, eclipse_method)

        if eclipse_method=='native':
            ecl_kwargs = {'horizon_method': horizon_method}
        else:
            ecl_kwargs = {}

        logger.debug("system.handle_eclipses: possible_eclipse={}, expose_horizon={}, calling {} with kwargs {}".format(possible_eclipse, expose_horizon, eclipse_method, ecl_kwargs))

        visibilities, weights, horizon = ecl_func(meshes,
                                                  self.xs, self.ys, self.zs,
                                                  expose_horizon=expose_horizon,
                                                  **ecl_kwargs)

        # NOTE: analytic horizons are called in backends.py since they don't
        # actually depend on the mesh at all.

        # visiblilities here is a dictionary with keys being the component
        # labels and values being the np arrays of visibilities.  We can pass
        # this dictionary directly and the columns will be applied respectively.
        meshes.update_columns('visibilities', visibilities)

        # weights is also a dictionary with keys being the component labels
        # and values and np array of weights.
        if weights is not None:
            meshes.update_columns('weights', weights)

        return horizon