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pep8 formatting and made compatible with networkx<2.0 #680

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115 changes: 68 additions & 47 deletions openmdao/core/group.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@
# regex to check for valid variable names.
namecheck_rgx = re.compile('[_a-zA-Z][_a-zA-Z0-9]*')


class Group(System):
"""A system that contains other systems.

Expand Down Expand Up @@ -188,12 +189,12 @@ def connect(self, source, targets, src_indices=None):
raise TypeError("src_indices must be an index array, did you mean"
" connect('{0}', {1})?".format(source, suggestion))

if isinstance(src_indices,np.ndarray):
if isinstance(src_indices, np.ndarray):
if not np.issubdtype(src_indices.dtype, np.integer):
raise TypeError("src_indices must contain integers, but connection in {0} "
"from {1} to {2} src_indices is {3}.".format(self.name, source, targets, src_indices.dtype.type))
elif isinstance(src_indices, Iterable):
types_in_src_idxs = set( type(idx) for idx in src_indices)
types_in_src_idxs = set(type(idx) for idx in src_indices)
for t in types_in_src_idxs:
if not np.issubdtype(t, np.integer):
raise TypeError("src_indices must contain integers, but connection in {0} "
Expand Down Expand Up @@ -229,7 +230,8 @@ def subsystems(self, local=False, recurse=False, typ=System, include_self=False)
if include_self and isinstance(self, typ):
yield self

subs = self._local_subsystems if local else itervalues(self._subsystems)
subs = self._local_subsystems if local else itervalues(
self._subsystems)

for sub in subs:
if isinstance(sub, typ):
Expand Down Expand Up @@ -273,10 +275,12 @@ def _init_sys_data(self, parent_path, probdata):
super(Group, self)._init_sys_data(parent_path, probdata)
self._sys_graph = None
self._gs_outputs = None
self.ln_solver.pathname = self.pathname + '.' + self.ln_solver.__class__.__name__
self.nl_solver.pathname = self.pathname + '.' + self.nl_solver.__class__.__name__
self.ln_solver.recorders.pathname = self.ln_solver.pathname+'.'+'recorders'
self.nl_solver.recorders.pathname = self.nl_solver.pathname+'.'+'recorders'
self.ln_solver.pathname = self.pathname + \
'.' + self.ln_solver.__class__.__name__
self.nl_solver.pathname = self.pathname + \
'.' + self.nl_solver.__class__.__name__
self.ln_solver.recorders.pathname = self.ln_solver.pathname + '.' + 'recorders'
self.nl_solver.recorders.pathname = self.nl_solver.pathname + '.' + 'recorders'

for sub in itervalues(self._subsystems):
sub._init_sys_data(self.pathname, probdata)
Expand Down Expand Up @@ -353,15 +357,15 @@ def _get_gs_outputs(self, mode, vois):
for voi in vois:
if voi in dumat:
outs[voi] = set([x for x in dumat[voi]._dat if
sub.dumat and x not in sub.dumat[voi]])
else: # rev
sub.dumat and x not in sub.dumat[voi]])
else: # rev
for sub in self._local_subsystems:
gs_outputs[sub.name] = outs = OrderedDict()
for voi in vois:
if voi in dumat:
outs[voi] = set([x for x in dumat[voi]._dat if
not sub.dumat or
(sub.dumat and x not in sub.dumat[voi])])
not sub.dumat or
(sub.dumat and x not in sub.dumat[voi])])
return self._gs_outputs

def _promoted_name(self, name, subsystem):
Expand Down Expand Up @@ -469,8 +473,10 @@ def _setup_vectors(self, param_owners, parent=None,

self._shared_dp_vec = np.zeros(max_psize)

# map promoted name in parent to corresponding promoted name in this view
self._relname_map = self._get_relname_map(parent._sysdata.to_prom_name)
# map promoted name in parent to corresponding promoted name in
# this view
self._relname_map = self._get_relname_map(
parent._sysdata.to_prom_name)
self._create_views(top_unknowns, parent, my_params, voi=None)

self._u_size_lists = self.unknowns._get_flattened_sizes()
Expand Down Expand Up @@ -505,7 +511,7 @@ def _setup_vectors(self, param_owners, parent=None,
# and cache a boolean flag telling us whether to run apply_linear for a
# given voi and a given child system.

self._do_apply = {} # dict of (child_pathname, voi) keyed to bool
self._do_apply = {} # dict of (child_pathname, voi) keyed to bool

for s in self.subsystems(recurse=True, include_self=True):
for voi, vec in iteritems(s.dpmat):
Expand Down Expand Up @@ -562,7 +568,7 @@ def _create_vecs(self, my_params, voi, impl):
alloc_complex=alloc_complex)

self.states = set(n for n, m in iteritems(self.unknowns)
if 'state' in m and m['state'])
if 'state' in m and m['state'])

# Create derivative VecWrappers
if voi is None or self._probdata.top_lin_gs:
Expand Down Expand Up @@ -637,7 +643,8 @@ def _get_fd_unknowns(self):
fd_unknowns = []
for name, meta in iteritems(self.unknowns):
# look up the subsystem containing the unknown
sub = self.find_subsystem(meta['pathname'].rsplit('.', 1)[0][len(mypath):])
sub = self.find_subsystem(
meta['pathname'].rsplit('.', 1)[0][len(mypath):])
if not isinstance(sub, IndepVarComp):
if not self.unknowns._dat[name].pbo:
fd_unknowns.append(name)
Expand Down Expand Up @@ -754,9 +761,11 @@ def children_solve_nonlinear(self, metadata):
if sub.is_active():
with sub._dircontext:
if isinstance(sub, Component):
sub._sys_solve_nonlinear(sub.params, sub.unknowns, sub.resids)
sub._sys_solve_nonlinear(
sub.params, sub.unknowns, sub.resids)
else:
sub.solve_nonlinear(sub.params, sub.unknowns, sub.resids, metadata)
sub.solve_nonlinear(
sub.params, sub.unknowns, sub.resids, metadata)

def _sys_apply_nonlinear(self, params, unknowns, resids, metadata=None):
"""
Expand Down Expand Up @@ -813,9 +822,11 @@ def apply_nonlinear(self, params, unknowns, resids, metadata=None):
self._transfer_data(sub.name)
if sub.is_active():
if isinstance(sub, Component):
sub._sys_apply_nonlinear(sub.params, sub.unknowns, sub.resids)
sub._sys_apply_nonlinear(
sub.params, sub.unknowns, sub.resids)
else:
sub.apply_nonlinear(sub.params, sub.unknowns, sub.resids, metadata)
sub.apply_nonlinear(
sub.params, sub.unknowns, sub.resids, metadata)

def linearize(self, params, unknowns, resids):
"""
Expand Down Expand Up @@ -868,11 +879,13 @@ def _sys_apply_linear(self, mode, do_apply, vois=(None,), gs_outputs=None,

if mode == 'fwd':
for voi in vois:
self._transfer_data(deriv=True, var_of_interest=voi) # Full Scatter
self._transfer_data(
deriv=True, var_of_interest=voi) # Full Scatter

if self.deriv_options['type'] is not 'user':
# parent class has the code to do the fd
super(Group, self)._sys_apply_linear(mode, do_apply, vois, gs_outputs)
super(Group, self)._sys_apply_linear(
mode, do_apply, vois, gs_outputs)

else:
for sub in self._local_subsystems:
Expand All @@ -882,7 +895,8 @@ def _sys_apply_linear(self, mode, do_apply, vois=(None,), gs_outputs=None,

if mode == 'rev':
for voi in vois:
self._transfer_data(mode='rev', deriv=True, var_of_interest=voi) # Full Scatter
self._transfer_data(mode='rev', deriv=True,
var_of_interest=voi) # Full Scatter

def solve_linear(self, dumat, drmat, vois, mode=None, solver=None, rel_inputs=None):
"""
Expand Down Expand Up @@ -1040,7 +1054,7 @@ def assemble_jacobian(self, mode='fwd', method='assemble', mult=None):
# is overridden.
if jac is None:
msg = "The 'assemble' jacobian_method is not supported when " + \
"'apply_linear' is used on a component (%s)." % sub.pathname
"'apply_linear' is used on a component (%s)." % sub.pathname
raise RuntimeError(msg)

sub_u = sub.unknowns
Expand Down Expand Up @@ -1080,10 +1094,12 @@ def assemble_jacobian(self, mode='fwd', method='assemble', mult=None):
else:
(o_start, o_end, i_start, i_end) = icache[key2]

if mode=='fwd':
partials[o_start:o_end, i_start:i_end] = jac[o_var, i_var]
if mode == 'fwd':
partials[o_start:o_end,
i_start:i_end] = jac[o_var, i_var]
else:
partials[i_start:i_end, o_start:o_end] = jac[o_var, i_var].T
partials[i_start:i_end,
o_start:o_end] = jac[o_var, i_var].T

return partials, icache

Expand Down Expand Up @@ -1115,7 +1131,8 @@ def set_order(self, new_order):

# Don't allow duplicates either.
if len(newset) < len(new_order):
dupes = [key for key, val in iteritems(Counter(new_order)) if val>1]
dupes = [key for key, val in iteritems(
Counter(new_order)) if val > 1]
msg = "Duplicate name(s) found in order list: %s" % dupes
raise ValueError(msg)

Expand All @@ -1127,7 +1144,7 @@ def set_order(self, new_order):

# reset locals
self._local_subsystems = [s for s in self._local_subsystems
if s.name in newset]
if s.name in newset]

self._order_set = True

Expand All @@ -1154,7 +1171,7 @@ def list_auto_order(self):
graph, broken_edges = self._break_cycles(self.list_order(),
self._get_sys_graph())
order = nx.topological_sort(graph)
sz = len(self.pathname)+1 if self.pathname else 0
sz = len(self.pathname) + 1 if self.pathname else 0
return [n[sz:] for n in order], broken_edges

def _get_sys_graph(self):
Expand All @@ -1166,15 +1183,16 @@ def _get_sys_graph(self):
path = self.pathname.split('.')
start = self.pathname + '.'
slen = len(start)
graph = sgraph.subgraph((n for n in sgraph if start == n[:slen]))
graph = sgraph.subgraph(
(n for n in sgraph if start == n[:slen]))
else:
path = []
graph = sgraph.subgraph(sgraph.nodes_iter())
graph = sgraph.subgraph(sgraph.nodes())

plen = len(path)+1
plen = len(path) + 1

renames = {}
for node in graph.nodes_iter():
for node in graph.nodes():
newnode = '.'.join(node.split('.')[:plen])
if newnode != node:
renames[node] = newnode
Expand Down Expand Up @@ -1242,7 +1260,7 @@ def dump(self, nest=0, out_stream=sys.stdout, verbose=False, dvecs=False,
pvec = getattr(self, pvecname)

template = "%s %s '%s'"
out_stream.write(template % (" "*nest, klass, self.name))
out_stream.write(template % (" " * nest, klass, self.name))

nl_solve = self.nl_solver.__class__.__name__
try:
Expand Down Expand Up @@ -1273,7 +1291,7 @@ def dump(self, nest=0, out_stream=sys.stdout, verbose=False, dvecs=False,
byobj_conns = dict(self._data_xfer[('', 'fwd', None)].byobj_conns)

# collect width info
lens = [len(u)+sum(map(len, v)) for u, v in
lens = [len(u) + sum(map(len, v)) for u, v in
chain(iteritems(vec_conns), iteritems(byobj_conns))]
if lens:
nwid = max(lens) + 9
Expand All @@ -1284,8 +1302,9 @@ def dump(self, nest=0, out_stream=sys.stdout, verbose=False, dvecs=False,
for v, acc in iteritems(uvec._dat):
if acc.pbo or acc.remote:
continue
out_stream.write(" "*(nest+8))
uslice = '{0}[{1[0]}:{1[1]}]'.format(ulabel, uvec._dat[v].slice)
out_stream.write(" " * (nest + 8))
uslice = '{0}[{1[0]}:{1[1]}]'.format(
ulabel, uvec._dat[v].slice)
pnames = [p for p, u in iteritems(vec_conns) if u == v]

if pnames:
Expand Down Expand Up @@ -1325,7 +1344,7 @@ def dump(self, nest=0, out_stream=sys.stdout, verbose=False, dvecs=False,

if not dvecs:
for dest, src in iteritems(byobj_conns):
out_stream.write(" "*(nest+8))
out_stream.write(" " * (nest + 8))
connstr = '%s -> %s:' % (src, dest)
template = "{0:<{nwid}} (by_obj) ({1})\n"
out_stream.write(template.format(connstr,
Expand Down Expand Up @@ -1424,7 +1443,8 @@ def _get_global_idxs(self, uname, pname, u_var_idxs,

ivar = u_var_idxs[uname]
if udist or pdist:
p_rank = self._owning_ranks[pname] if (rev and pacc.remote) else iproc
p_rank = self._owning_ranks[pname] if (
rev and pacc.remote) else iproc

if pdist and p_rank != iproc:
return self.params.make_idx_array(0, 0), self.params.make_idx_array(0, 0)
Expand Down Expand Up @@ -1644,13 +1664,13 @@ def _get_owning_ranks(self):
if MPI:
ranks = {}
local_vars = [k for k, acc in iteritems(self.unknowns._dat)
if not acc.remote]
if not acc.remote]
local_vars.extend(k for k, acc in iteritems(self.params._dat)
if not acc.remote)
if not acc.remote)
if trace: # pragma: no cover
debug("allgathering local varnames: locals = ", local_vars)
all_locals = self.comm.allgather(local_vars)
if trace: # pragma: no cover
if trace: # pragma: no cover
debug("allgather of local vars DONE")

# save all_locals for use later to determine if we can do a
Expand All @@ -1664,8 +1684,7 @@ def _get_owning_ranks(self):
else:
self._sysdata.all_locals = [n for n in chain(self.unknowns._dat,
self.params._dat)]
ranks = { n:0 for n in chain(self.unknowns._dat, self.params._dat) }

ranks = {n: 0 for n in chain(self.unknowns._dat, self.params._dat)}

return ranks

Expand All @@ -1686,7 +1705,8 @@ def _get_relname_map(self, parent_proms):
# unknowns is keyed on promoted name relative to the parent system
# unknowns_dict is keyed on absolute pathname

# use an ordered dict here so we can use this smaller dict to loop over in get_view
# use an ordered dict here so we can use this smaller dict to loop over
# in get_view
umap = OrderedDict()
for abspath, prom in iteritems(self._sysdata.to_prom_uname):
umap[parent_proms[abspath]] = prom
Expand Down Expand Up @@ -1727,7 +1747,8 @@ def _dump_dist_idxs(self, stream=sys.stdout, recurse=True): # pragma: no cover
"""

def _dump(g, stream=sys.stdout):
stream.write("\nDistributed u and p vecs for system '%s'\n\n" % g.pathname)
stream.write(
"\nDistributed u and p vecs for system '%s'\n\n" % g.pathname)
idx = 0
pdata = []
pnwid = 0
Expand Down
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