test:no-extras

Failed Started 4 years ago by
1Running with gitlab-runner 12.8.0 (1b659122)
2  on universal-tn3 a9da50a7
 3  Using Docker executor with image gitlab.kwant-project.org:5005/kwant/kwant ...  
  00:01
4Authenticating with credentials from job payload (GitLab Registry)
5Pulling docker image gitlab.kwant-project.org:5005/kwant/kwant ...
6Using docker image sha256:3b0a14e5028f34c59abed300d492408bf827d6fe5523e89ea589cab97af9f9c8 for gitlab.kwant-project.org:5005/kwant/kwant ...
 7  Authenticating with credentials from /root/.docker/config.json  
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8Running on runner-a9da50a7-project-1202-concurrent-1 via tnw-tn3.tudelft.net...
 9  Authenticating with credentials from /root/.docker/config.json  
  00:03
10Fetching changes...
11Reinitialized existing Git repository in /builds/quaeritis/kwant/.git/
12Checking out 888a0e6a as phi_matrix...
13Removing build.conf
14Removing build/
15Removing kwant/__pycache__/
16Removing kwant/_system.c
17Removing kwant/_system.cpython-37m-x86_64-linux-gnu.so
18Removing kwant/graph/core.c
19Removing kwant/graph/core.cpython-37m-x86_64-linux-gnu.so
20Removing kwant/graph/dijkstra.c
21Removing kwant/graph/dijkstra.cpython-37m-x86_64-linux-gnu.so
22Removing kwant/linalg/_mumps.c
23Removing kwant/linalg/_mumps.cpython-37m-x86_64-linux-gnu.so
24Removing kwant/linalg/lapack.c
25Removing kwant/linalg/lapack.cpython-37m-x86_64-linux-gnu.so
26Removing kwant/operator.c
27Removing kwant/operator.cpython-37m-x86_64-linux-gnu.so
28Skipping Git submodules setup
 29  Authenticating with credentials from /root/.docker/config.json  
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 30  Authenticating with credentials from /root/.docker/config.json  
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31Downloading artifacts for build:no-extras (157897)...
32Downloading artifacts from coordinator... ok        id=157897 responseStatus=200 OK token=8BDmxxFS
 33  Authenticating with credentials from job payload (GitLab Registry)  
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34$ source deactivate
35DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'.
36$ source activate kwant-stable-no-extras
37$ py.test -r w --flakes kwant --junitxml=tests.xml --durations=10
38============================= test session starts ==============================
39platform linux -- Python 3.7.8, pytest-6.1.2, py-1.9.0, pluggy-0.13.1
40rootdir: /builds/quaeritis/kwant, configfile: pytest.ini, testpaths: kwant
41plugins: cov-2.10.1, flakes-4.0.2, pep8-1.0.6
42ignoring kwant/continuum because the following dependencies are not installed: sympy
43collected 421 items
44kwant/__init__.py .                                                      [  0%]
45kwant/_colormaps.py .                                                    [  0%]
46kwant/_common.py .                                                       [  0%]
47kwant/_kwant_version.py .                                                [  0%]
48kwant/_plotter.py .                                                      [  1%]
49kwant/builder.py F                                                       [  1%]
50kwant/digest.py .                                                        [  1%]
51kwant/kpm.py .                                                           [  1%]
52kwant/lattice.py .                                                       [  2%]
53kwant/plotter.py .                                                       [  2%]
54kwant/qsymm.py .                                                         [  2%]
55kwant/rmt.py .                                                           [  2%]
56kwant/system.py .                                                        [  3%]
57kwant/version.py .                                                       [  3%]
58kwant/wraparound.py .                                                    [  3%]
59kwant/graph/__init__.py .                                                [  3%]
60kwant/graph/defs.py .                                                    [  4%]
61kwant/graph/tests/__init__.py .                                          [  4%]
62kwant/graph/tests/test_core.py .........                                 [  6%]
63kwant/graph/tests/test_scotch.py .                                       [  6%]
64kwant/linalg/__init__.py .                                               [  6%]
65kwant/linalg/cmumps.py .                                                 [  7%]
66kwant/linalg/decomp_ev.py .                                              [  7%]
67kwant/linalg/decomp_lu.py .                                              [  7%]
68kwant/linalg/decomp_schur.py .                                           [  7%]
69kwant/linalg/fortran_helpers.py .                                        [  8%]
70kwant/linalg/lll.py .                                                    [  8%]
71kwant/linalg/mumps.py .                                                  [  8%]
72kwant/linalg/tests/__init__.py .                                         [  8%]
73kwant/linalg/tests/_test_utils.py .                                      [  9%]
74kwant/linalg/tests/test_linalg.py ............                           [ 11%]
75kwant/linalg/tests/test_lll.py ...                                       [ 12%]
76kwant/linalg/tests/test_mumps.py .ssss                                   [ 13%]
77kwant/physics/__init__.py .                                              [ 14%]
78kwant/physics/dispersion.py .                                            [ 14%]
79kwant/physics/gauge.py .                                                 [ 14%]
80kwant/physics/leads.py .                                                 [ 14%]
81kwant/physics/noise.py .                                                 [ 14%]
82kwant/physics/symmetry.py .                                              [ 15%]
83kwant/physics/tests/__init__.py .                                        [ 15%]
84kwant/physics/tests/test_dispersion.py ........                          [ 17%]
85kwant/physics/tests/test_gauge.py ...................................... [ 26%]
86...............                                                          [ 29%]
87kwant/physics/tests/test_leads.py .........................              [ 35%]
88kwant/physics/tests/test_noise.py ...                                    [ 36%]
89kwant/physics/tests/test_symmetry.py ......                              [ 38%]
90kwant/solvers/__init__.py .                                              [ 38%]
91kwant/solvers/common.py .                                                [ 38%]
92kwant/solvers/default.py .                                               [ 38%]
93kwant/solvers/mumps.py .                                                 [ 38%]
94kwant/solvers/sparse.py .                                                [ 39%]
95kwant/solvers/tests/__init__.py .                                        [ 39%]
96kwant/solvers/tests/test_solvers.py .ssssss.ssssss.ssssss.ssssss.ssssss. [ 47%]
97ssssss.ssssss.ssssss.ssssss.ssssss.ssssss.ssssss.ssssss.ssssss.ssssss.ss [ 65%]
98ssss.                                                                    [ 66%]
99kwant/tests/__init__.py .                                                [ 66%]
100kwant/tests/test_builder.py .......................................F     [ 76%]
101kwant/tests/test_comprehensive.py ..                                     [ 76%]
102kwant/tests/test_kpm.py ...........................                      [ 82%]
103kwant/tests/test_lattice.py ....................                         [ 87%]
104kwant/tests/test_operator.py .................                           [ 91%]
105kwant/tests/test_plotter.py .s.sssss.ss..s                               [ 95%]
106kwant/tests/test_rmt.py ....                                             [ 95%]
107kwant/tests/test_system.py .....                                         [ 97%]
108kwant/tests/test_wraparound.py .........s..                              [100%]
109=================================== FAILURES ===================================
110________________________________ pyflakes-check ________________________________
111/builds/quaeritis/kwant/kwant/builder.py:1565: UndefinedName
112undefined name 'args'
113/builds/quaeritis/kwant/kwant/builder.py:1567: UndefinedName
114undefined name 'args'
115____________________________ test_add_peierls_phase ____________________________
116self = <kwant.builder.InfiniteSystem object at 0x7f63ec7dc690>, i = 1, j = 0
117params = {'phi': functools.partial(<function _finite_wrapper at 0x7f63efcbb050>, <kwant.builder.FiniteSystem object at 0x7f63ec...r.InfiniteSystem object at 0x7f63ec7dc850>, {(1, 6): (1+0j), (2, 7): (1+0j), (3, 8): (1+0j), (4, 9): (1+0j)}), 't': -1}
118args = <map object at 0x7f63ec7dced0>
119value = <function _add_peierls_phase.<locals>.const_hopping at 0x7f63ec2247a0>
120param_names = ('phi_lead0',)
121    def hamiltonian(self, i, j, *args, params=None):
122        if args and params:
123            raise TypeError("'args' and 'params' are mutually exclusive.")
124        if i == j:
125            value, param_names = self.onsites[i]
126            if param_names is not None:  # 'value' is callable
127                site = self.symmetry.to_fd(self.sites[i])
128                if params:
129                    # See body of _value_params_pair_cache().
130                    if isinstance(param_names, Exception):
131                        raise param_names
132                    args = map(params.__getitem__, param_names)
133                try:
134                    value = value(site, *args)
135                except Exception as exc:
136                    if isinstance(exc, KeyError) and params:
137                        missing = [p for p in param_names if p not in params]
138                        if missing:
139                            msg = ('System is missing required arguments: ',
140                                   ', '.join(map('"{}"'.format, missing)))
141                            raise TypeError(''.join(msg))
142                    _raise_user_error(exc, value)
143        else:
144            edge_id = self.graph.first_edge_id(i, j)
145            value, param_names = self.hoppings[edge_id]
146            conj = value is Other
147            if conj:
148                i, j = j, i
149                edge_id = self.graph.first_edge_id(i, j)
150                value, param_names = self.hoppings[edge_id]
151            if param_names is not None:  # 'value' is callable
152                sites = self.sites
153                site_i, site_j = self.symmetry.to_fd(sites[i], sites[j])
154                if params:
155                    # See body of _value_params_pair_cache().
156                    if isinstance(param_names, Exception):
157                        raise param_names
158                    args = map(params.__getitem__, param_names)
159                try:
160>                   value = value(site_i, site_j, *args)
161kwant/builder.py:1817: 
162_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
163a = Site(kwant.lattice.Monatomic([[1.0, 0.0], [0.0, 1.0]], [0.0, 0.0], '', 1), array([0, 1]))
164b = Site(kwant.lattice.Monatomic([[1.0, 0.0], [0.0, 1.0]], [0.0, 0.0], '', 1), array([0, 0]))
165phi = functools.partial(<function _infinite_wrapper at 0x7f63efcbb0e0>, <kwant.builder.InfiniteSystem object at 0x7f63ec7dc690>, {(1, 6): (1+0j), (2, 7): (1+0j), (3, 8): (1+0j), (4, 9): (1+0j)})
166    def const_hopping(a, b, phi):
167        if signs is not None:
168            return np.dot(hop(a, b, *args), phi_matrix(phi(a, b), signs))
169        else:
170>           return hop(a, b, *args) * phi(a, b)
171E           NameError: name 'args' is not defined
172kwant/builder.py:1567: NameError
173The above exception was the direct cause of the following exception:
174    def test_add_peierls_phase():
175    
176        lat = kwant.lattice.square(norbs=1)
177        syst = kwant.Builder()
178        syst[(lat(i, j) for i in range(5) for j in range(5))] = 4
179        syst[lat.neighbors()] = lambda a, b, t: -t
180    
181        lead = kwant.Builder(kwant.TranslationalSymmetry((-1, 0)))
182        lead[(lat(0, j) for j in range(5))] = 4
183        lead[lat.neighbors()] = -1
184    
185        # System without leads
186        syst_without_lead, phase_without_lead = builder.add_peierls_phase(syst)
187    
188        assert isinstance(syst_without_lead, builder.FiniteSystem)
189    
190        params_without_lead = phase_without_lead(1)
191    
192        assert all(p in params_without_lead for p in ('phi',))
193    
194        # System with leads
195        syst.attach_lead(lead)
196        syst.attach_lead(lead.reversed())
197    
198        syst, phase = builder.add_peierls_phase(syst)
199    
200        assert isinstance(syst, builder.FiniteSystem)
201    
202        params = phase(1, 0, 0)
203    
204        assert all(p in params for p in ('phi', 'phi_lead0', 'phi_lead1'))
205    
206>       kwant.smatrix(syst, energy=0.1, params=dict(t=-1, **params))
207kwant/tests/test_builder.py:1776: 
208_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
209kwant/_common.py:73: in inner
210    return f(*args, **kwargs)
211kwant/solvers/common.py:383: in smatrix
212    params=params)
213kwant/solvers/common.py:204: in _make_linear_sys
214    prop, stab = lead.modes(energy, args, params=params)
215kwant/_common.py:73: in inner
216    return f(*args, **kwargs)
217kwant/system.py:788: in modes
218    ham = self.cell_hamiltonian(args, params=params)
219kwant/_common.py:73: in inner
220    return f(*args, **kwargs)
221kwant/system.py:905: in cell_hamiltonian
222    sparse=sparse, params=params)
223kwant/_common.py:73: in inner
224    return f(*args, **kwargs)
225kwant/_system.pyx:340: in kwant._system.hamiltonian_submatrix
226    mat = func(ham, args, params, self.graph, diag, from_sites,
227kwant/_system.pyx:190: in kwant._system.make_dense
228    h = matrix(ham(ts, fs, *args, params=params), complex)
229kwant/builder.py:2798: in hamiltonian
230    return super().hamiltonian(i, j, *args, params=params)
231kwant/builder.py:1825: in hamiltonian
232    _raise_user_error(exc, value)
233_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
234exc = NameError("name 'args' is not defined")
235func = <function _add_peierls_phase.<locals>.const_hopping at 0x7f63ec2247a0>
236    def _raise_user_error(exc, func):
237        msg = ('Error occurred in user-supplied value function "{0}".\n'
238               'See the upper part of the above backtrace for more information.')
239>       raise UserCodeError(msg.format(func.__name__)) from exc
240E       kwant._common.UserCodeError: Error occurred in user-supplied value function "const_hopping".
241E       See the upper part of the above backtrace for more information.
242kwant/builder.py:1721: UserCodeError
243=============================== warnings summary ===============================
244kwant/solvers/default.py:18
245  /builds/quaeritis/kwant/kwant/solvers/default.py:18: RuntimeWarning: MUMPS is not available, SciPy built-in solver will be used as a fallback. Performance can be very poor in this case.
246    "Performance can be very poor in this case.", RuntimeWarning)
247kwant/_plotter.py:55
248  /builds/quaeritis/kwant/kwant/_plotter.py:55: RuntimeWarning: matplotlib is not available, if other engines are unavailable, only iterator-providing functions will work
249    RuntimeWarning)
250kwant/_plotter.py:72
251  /builds/quaeritis/kwant/kwant/_plotter.py:72: RuntimeWarning: plotly is not available, if other engines are unavailable, only iterator-providing functions will work
252    RuntimeWarning)
253-- Docs: https://docs.pytest.org/en/stable/warnings.html
254------------ generated xml file: /builds/quaeritis/kwant/tests.xml -------------
255============================= slowest 10 durations =============================
2566.33s call     kwant/physics/tests/test_leads.py::test_modes_symmetries
2573.73s call     kwant/tests/test_plotter.py::test_density_interpolation
2581.98s call     kwant/tests/test_plotter.py::test_current_interpolation
2591.66s call     kwant/physics/tests/test_gauge.py::test_minimal_cycle_basis[2-honeycomb-half-ring]
2601.62s call     kwant/tests/test_rmt.py::test_gaussian_distributions
2611.53s call     kwant/tests/test_comprehensive.py::test_qhe
2621.49s call     kwant/tests/test_kpm.py::test_check_convergence_decreasing_values
2631.21s call     kwant/physics/tests/test_leads.py::test_PHS_TRIM_degenerate_ordering
2641.15s call     kwant/physics/tests/test_leads.py::test_cons_blocks_sizes
2651.14s call     kwant/tests/test_kpm.py::test_convergence_custom_vector_factory
266=========== 2 failed, 309 passed, 110 skipped, 3 warnings in 46.58s ============
267/usr/local/envs/kwant-stable-no-extras/lib/python3.7/site-packages/pep8.py:110: FutureWarning: Possible nested set at position 1
268  EXTRANEOUS_WHITESPACE_REGEX = re.compile(r'[[({] | []}),;:]')
 269  Authenticating with credentials from /root/.docker/config.json  
  00:02
270Uploading artifacts...
271tests.xml: found 1 matching files                  
272Uploading artifacts to coordinator... ok            id=157902 responseStatus=201 Created token=VYvqV4dC
273ERROR: Job failed: exit code 1