Error inside networkx

[wence-]

Steps to reproduce:

firedrake-install
. firedrake/bin/activate
git clone [email protected]:thetisproject/thetis
pip install -e thetis
pip install colorama
pip install scipy
cd thetis/test/swe2d
firedrake-clean
py.test test_steady_state_channel_mms.py -x -v -s
============================= test session starts ==============================
platform darwin -- Python 2.7.11, pytest-2.9.1, py-1.4.31, pluggy-0.3.1 -- /Users/lmitche1/Documents/work/src/fd-install/firedrake/bin/python2.7
cachedir: ../../.cache
benchmark: 3.0.0 (defaults: timer=time.time disable_gc=False min_rounds=5 min_time=5.00us max_time=1.00s calibration_precision=10 warmup=False warmup_iterations=100000)
rootdir: /Users/lmitche1/Documents/work/src/fd-install/thetis, inifile: 
plugins: benchmark-3.0.0, xdist-1.14
collecting 0 items--------------------------------------------------------------------------
Petsc Development GIT revision: v3.4.2-12173-g511e85b  GIT Date: 2016-04-07 00:39:56 -0500
       The PETSc Team
    [email protected]
 http://www.mcs.anl.gov/petsc/
See docs/changes/index.html for recent updates.
See docs/faq.html for problems.
See docs/manualpages/index.html for help. 
Libraries linked from /Users/lmitche1/Documents/work/src/fd-install/firedrake/lib/python2.7/site-packages/petsc/lib
--------------------------------------------------------------------------
collected 2 items 

test_steady_state_channel_mms.py::test_steady_state_channel_mms[mimetic] COFFEE finished in 0.00221896 seconds (flops: 0 -> 0)
COFFEE finished in 0.00326109 seconds (flops: 0 -> 0)
compute_form_data finished in 0.024508 seconds.
compile_integral finished in 0.0944471 seconds.
TSFC finished in 0.119004 seconds.
COFFEE finished in 0.0517299 seconds (flops: 4340 -> 1316)
COFFEE finished in 0.00372005 seconds (flops: 0 -> 0)
compute_form_data finished in 0.0209169 seconds.
compile_integral finished in 0.1691 seconds.
TSFC finished in 0.190075 seconds.
COFFEE finished in 0.0528538 seconds (flops: 1757 -> 749)
COFFEE finished in 0.00235796 seconds (flops: 0 -> 0)
COFFEE finished in 0.00304103 seconds (flops: 0 -> 0)
compute_form_data finished in 0.0181992 seconds.
compile_integral finished in 0.0292919 seconds.
TSFC finished in 0.047559 seconds.
COFFEE finished in 0.00383091 seconds (flops: 27 -> 27)
compute_form_data finished in 0.0216379 seconds.
compile_integral finished in 0.0289121 seconds.
TSFC finished in 0.0506079 seconds.
COFFEE finished in 0.0046041 seconds (flops: 27 -> 27)
compute_form_data finished in 0.019644 seconds.
compile_integral finished in 0.028259 seconds.
TSFC finished in 0.047955 seconds.
COFFEE finished in 0.0049181 seconds (flops: 27 -> 27)
compute_form_data finished in 0.022316 seconds.
compile_integral finished in 0.0296991 seconds.
TSFC finished in 0.052078 seconds.
COFFEE finished in 0.00385499 seconds (flops: 27 -> 27)
COFFEE finished in 0.00276399 seconds (flops: 0 -> 0)
COFFEE finished in 0.00211 seconds (flops: 0 -> 0)
dt = 10.0
compute_form_data finished in 0.872862 seconds.
compile_integral finished in 0.323892 seconds.
compile_integral finished in 0.125879 seconds.
compile_integral finished in 0.120333 seconds.
compile_integral finished in 0.112606 seconds.
compile_integral finished in 0.112715 seconds.
compile_integral finished in 0.303551 seconds.
TSFC finished in 1.97202 seconds.
COFFEE finished in 0.312116 seconds (flops: 21956 -> 10336)
COFFEE finished in 0.270186 seconds (flops: 18129 -> 7332)
COFFEE finished in 0.314766 seconds (flops: 18899 -> 12557)
COFFEE finished in 0.291351 seconds (flops: 6137 -> 4354)
COFFEE finished in 0.303944 seconds (flops: 6137 -> 4354)
FAILED

=================================== FAILURES ===================================
____________________ test_steady_state_channel_mms[mimetic] ____________________

options = {'no_exports': True}

    @pytest.mark.parametrize("options", [
        {"no_exports": True},  # default: mimetic
        {"no_exports": True, "mimetic": False, "continuous_pressure": True},
    ], ids=["mimetic", "pndp(n+1)"])
    def test_steady_state_channel_mms(options):
        lx = 5e3
        ly = 1e3

        order = 1
        # minimum resolution
        min_cells = 16
        n = 1  # number of timesteps
        dt = 10.
        g = physical_constants['g_grav'].dat.data[0]
        h0 = 10.  # depth at rest
        area = lx*ly

        k = 4.0*math.pi/lx
        q = h0*1.0  # flux (depth-integrated velocity)
        eta0 = 1.0  # free surface amplitude

        eta_expr = Expression("eta0*cos(k*x[0])", k=k, eta0=eta0)
        depth_expr = "H0+eta0*cos(k*x[0])"
        u_expr = Expression(("Q/({H})".format(H=depth_expr), 0.), k=k, Q=q, eta0=eta0, H0=h0)
        # source_expr = Expression("k*eta0*(pow(Q,2)/pow({H},3)-g)*sin(k*x[0])".format(H=depth_expr),
        #                          k=k, g=g, Q=q, eta0=eta0, H0=h0)
        source_expr = Expression(("k*eta0*(pow(Q,2)/pow({H},3)-g)*sin(k*x[0])".format(H=depth_expr), 0),
                                 k=k, g=g, Q=q, eta0=eta0, H0=h0)
        u_bcval = q/(h0+eta0)
        eta_bcval = eta0

        do_exports = not options['no_exports']
        if do_exports:
            diff_pvd = File('diff.pvd')
            udiff_pvd = File('udiff.pvd')
            source_pvd = File('source.pvd')

        eta_errs = []
        u_errs = []
        for i in range(5):
            mesh2d = RectangleMesh(min_cells*2**i, 1, lx, ly)

            # bathymetry
            p1_2d = FunctionSpace(mesh2d, 'CG', 1)
            bathymetry_2d = Function(p1_2d, name="bathymetry")
            bathymetry_2d.assign(h0)

            source_space = VectorFunctionSpace(mesh2d, 'DG', order+1)
            source_func = project(source_expr, source_space)

            # --- create solver ---
            solver_obj = solver2d.FlowSolver2d(mesh2d, bathymetry_2d, order=order)
            solver_obj.options.nonlin = True
            solver_obj.options.t_export = dt
            solver_obj.options.t_end = n*dt
            solver_obj.options.uv_source_2d = source_func
            solver_obj.options.timestepper_type = 'cranknicolson'
            solver_obj.options.timer_labels = []
            solver_obj.options.dt = dt
            solver_obj.options.update(options)

            # boundary conditions
            inflow_tag = 1
            outflow_tag = 2

            inflow_func = Function(p1_2d)
            inflow_func.interpolate(Expression(-u_bcval))
            inflow_bc = {'un': inflow_func}
            outflow_func = Function(p1_2d)
            outflow_func.interpolate(Expression(eta_bcval))
            outflow_bc = {'elev': outflow_func}
            solver_obj.bnd_functions['shallow_water'] = {inflow_tag: inflow_bc, outflow_tag: outflow_bc}
            # parameters['quadrature_degree']=5

>           solver_obj.create_equations()

test_steady_state_channel_mms.py:81: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
../../thetis/solver2d.py:143: in create_equations
    semi_implicit=self.options.use_linearized_semi_implicit_2d)
../../thetis/timeintegrator.py:503: in __init__
    self.update_solver()
../../thetis/timeintegrator.py:510: in update_solver
    options_prefix=self.name)
../../../firedrake/src/firedrake/firedrake/variational_solver.py:125: in __init__
    ctx = solving_utils._SNESContext(problem)
../../../firedrake/src/firedrake/firedrake/solving_utils.py:106: in __init__
    for problem in problems)
../../../firedrake/src/firedrake/firedrake/solving_utils.py:106: in <genexpr>
    for problem in problems)
../../../firedrake/src/firedrake/firedrake/assemble.py:66: in assemble
    inverse=inverse, nest=nest)
<decorator-gen-295>:2: in _assemble
    ???
../../../firedrake/src/firedrake/firedrake/utils.py:62: in wrapper
    return f(*args, **kwargs)
../../../firedrake/src/firedrake/firedrake/assemble.py:100: in _assemble
    inverse=inverse)
../../../firedrake/src/firedrake/firedrake/tsfc_interface.py:243: in compile_form
    number_map).kernels
../../../firedrake/src/PyOP2/pyop2/caching.py:203: in __new__
    obj = make_obj()
../../../firedrake/src/PyOP2/pyop2/caching.py:193: in make_obj
    obj.__init__(*args, **kwargs)
../../../firedrake/src/firedrake/firedrake/tsfc_interface.py:174: in __init__
    kernels.append(KernelInfo(kernel=Kernel(ast, ast.name, opts=opts),
../../../firedrake/src/PyOP2/pyop2/backends.py:118: in __call__
    return t(*args, **kwargs)
../../../firedrake/src/PyOP2/pyop2/caching.py:203: in __new__
    obj = make_obj()
../../../firedrake/src/PyOP2/pyop2/caching.py:193: in make_obj
    obj.__init__(*args, **kwargs)
../../../firedrake/src/PyOP2/pyop2/base.py:3848: in __init__
    self._code = self._ast_to_c(self._ast, self._opts)
../../../firedrake/src/PyOP2/pyop2/host.py:60: in _ast_to_c
    ast_handler.plan_cpu(self._opts)
../../../firedrake/src/COFFEE/coffee/plan.py:184: in plan_cpu
    _generate_cpu_code(self, kernel, **params)
../../../firedrake/src/COFFEE/coffee/plan.py:106: in _generate_cpu_code
    loop_opt.rewrite(rewrite)
../../../firedrake/src/COFFEE/coffee/optimizer.py:116: in rewrite
    ew.SGrewrite()
../../../firedrake/src/COFFEE/coffee/rewriter.py:454: in SGrewrite
    sgraph, mapper = sg_visitor.visit(self.stmt.rvalue)
../../../firedrake/src/COFFEE/coffee/visitor.py:106: in visit
    return meth(o, *args, **kwargs)
../../../firedrake/src/COFFEE/coffee/visitors/utilities.py:455: in visit_Sum
    ret = self.visit(op, ret=ret, syms=loc_syms[i], parent=o)
../../../firedrake/src/COFFEE/coffee/visitor.py:106: in visit
    return meth(o, *args, **kwargs)
../../../firedrake/src/COFFEE/coffee/visitors/utilities.py:439: in visit_Prod
    G.add_edges_from(loc_syms)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <networkx.classes.graph.Graph object at 0x1133d1bd0>
ebunch = [(('t1', ('facet[0]', 'ip', 'j'), ((1, 0), (1, 0), (1, 0))), ('t1', ('facet[1]', 'ip', 'k'), ((1, 0), (1, 0), (1, 0)))...]', 'ip', 'j'), ((1, 0), (1, 0), (1, 0))), ('t37', (), ()), ('t0', ('facet[1]', 'ip', 'k'), ((1, 0), (1, 0), (1, 0))))]
attr_dict = {}, attr = {}
e = (('t1', ('facet[0]', 'ip', 'j'), ((1, 0), (1, 0), (1, 0))), ('t37', (), ()), ('t1', ('facet[1]', 'ip', 'k'), ((1, 0), (1, 0), (1, 0))))
ne = 3, u = ('t1', ('facet[0]', 'ip', 'j'), ((1, 0), (1, 0), (1, 0)))
v = ('t37', (), ())
dd = ('t1', ('facet[1]', 'ip', 'k'), ((1, 0), (1, 0), (1, 0)))
datadict = {'t': '1'}

    def add_edges_from(self, ebunch, attr_dict=None, **attr):
        """Add all the edges in ebunch.

            Parameters
            ----------
            ebunch : container of edges
                Each edge given in the container will be added to the
                graph. The edges must be given as as 2-tuples (u,v) or
                3-tuples (u,v,d) where d is a dictionary containing edge
                data.
            attr_dict : dictionary, optional (default= no attributes)
                Dictionary of edge attributes.  Key/value pairs will
                update existing data associated with each edge.
            attr : keyword arguments, optional
                Edge data (or labels or objects) can be assigned using
                keyword arguments.


            See Also
            --------
            add_edge : add a single edge
            add_weighted_edges_from : convenient way to add weighted edges

            Notes
            -----
            Adding the same edge twice has no effect but any edge data
            will be updated when each duplicate edge is added.

            Edge attributes specified in edges take precedence
            over attributes specified generally.

            Examples
            --------
            >>> G = nx.Graph()   # or DiGraph, MultiGraph, MultiDiGraph, etc
            >>> G.add_edges_from([(0,1),(1,2)]) # using a list of edge tuples
            >>> e = zip(range(0,3),range(1,4))
            >>> G.add_edges_from(e) # Add the path graph 0-1-2-3

            Associate data to edges

            >>> G.add_edges_from([(1,2),(2,3)], weight=3)
            >>> G.add_edges_from([(3,4),(1,4)], label='WN2898')
            """
        # set up attribute dict
        if attr_dict is None:
            attr_dict = attr
        else:
            try:
                attr_dict.update(attr)
            except AttributeError:
                raise NetworkXError(
                    "The attr_dict argument must be a dictionary.")
        # process ebunch
        for e in ebunch:
            ne = len(e)
            if ne == 3:
                u, v, dd = e
            elif ne == 2:
                u, v = e
                dd = {}  # doesnt need edge_attr_dict_factory
            else:
                raise NetworkXError(
                    "Edge tuple %s must be a 2-tuple or 3-tuple." % (e,))
            if u not in self.node:
                self.adj[u] = self.adjlist_dict_factory()
                self.node[u] = {}
            if v not in self.node:
                self.adj[v] = self.adjlist_dict_factory()
                self.node[v] = {}
            datadict = self.adj[u].get(v, self.edge_attr_dict_factory())
            datadict.update(attr_dict)
>           datadict.update(dd)
E           ValueError: dictionary update sequence element #1 has length 3; 2 is required

../../../firedrake/lib/python2.7/site-packages/networkx/classes/graph.py:874: ValueError

[wence-]

This occurs both on my mac and on a linux box.