test:stable

Failed Started 4 years ago by
1Running with gitlab-runner 12.9.0 (4c96e5ad)
2  on universal-tn4 d3cf9985
 3  Preparing the "docker" executor  
  00:00
4Using Docker executor with image gitlab.kwant-project.org:5005/kwant/kwant ...
5Authenticating with credentials from job payload (GitLab Registry)
6Pulling docker image gitlab.kwant-project.org:5005/kwant/kwant ...
7Using docker image sha256:3b0a14e5028f34c59abed300d492408bf827d6fe5523e89ea589cab97af9f9c8 for gitlab.kwant-project.org:5005/kwant/kwant ...
 8  Preparing environment  
  00:05
9Authenticating with credentials from /root/.docker/config.json
10Running on runner-d3cf9985-project-1202-concurrent-1 via tnw-tn4.tudelft.net...
 11  Getting source from Git repository  
  00:07
12Authenticating with credentials from /root/.docker/config.json
13Fetching changes...
14Reinitialized existing Git repository in /builds/quaeritis/kwant/.git/
15From https://gitlab.kwant-project.org/quaeritis/kwant
16 * [new ref]         refs/pipelines/49772 -> refs/pipelines/49772
17Checking out 888a0e6a as phi_matrix...
18Removing .pytest_cache/
19Removing __pycache__/
20Removing build.conf
21Removing build/
22Removing kwant/__pycache__/
23Removing kwant/_system.c
24Removing kwant/_system.cpython-37m-x86_64-linux-gnu.so
25Removing kwant/continuum/__pycache__/
26Removing kwant/continuum/tests/__pycache__/
27Removing kwant/graph/__pycache__/
28Removing kwant/graph/core.c
29Removing kwant/graph/core.cpython-37m-x86_64-linux-gnu.so
30Removing kwant/graph/dijkstra.c
31Removing kwant/graph/dijkstra.cpython-37m-x86_64-linux-gnu.so
32Removing kwant/graph/tests/__pycache__/
33Removing kwant/linalg/__pycache__/
34Removing kwant/linalg/_mumps.c
35Removing kwant/linalg/_mumps.cpython-37m-x86_64-linux-gnu.so
36Removing kwant/linalg/lapack.c
37Removing kwant/linalg/lapack.cpython-37m-x86_64-linux-gnu.so
38Removing kwant/linalg/tests/__pycache__/
39Removing kwant/operator.c
40Removing kwant/operator.cpython-37m-x86_64-linux-gnu.so
41Removing kwant/physics/__pycache__/
42Removing kwant/physics/tests/__pycache__/
43Removing kwant/solvers/__pycache__/
44Removing kwant/solvers/tests/__pycache__/
45Removing kwant/tests/__pycache__/
46Removing tests.xml
47Skipping Git submodules setup
 48  Restoring cache  
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49Authenticating with credentials from /root/.docker/config.json
 50  Downloading artifacts  
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51Authenticating with credentials from /root/.docker/config.json
52Downloading artifacts for build:stable (157896)...
53Downloading artifacts from coordinator... ok        id=157896 responseStatus=200 OK token=z7GhgKgj
 54  Running before_script and script  
  01:37
55Authenticating with credentials from job payload (GitLab Registry)
56$ source deactivate
57DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'.
58$ source activate kwant-stable
59$ py.test -r w --flakes kwant --junitxml=tests.xml --durations=10
60============================= test session starts ==============================
61platform linux -- Python 3.7.8, pytest-6.1.2, py-1.9.0, pluggy-0.13.1
62rootdir: /builds/quaeritis/kwant, configfile: pytest.ini, testpaths: kwant
63plugins: cov-2.10.1, flakes-4.0.2, pep8-1.0.6
64collected 550 items
65kwant/__init__.py .                                                      [  0%]
66kwant/_colormaps.py .                                                    [  0%]
67kwant/_common.py .                                                       [  0%]
68kwant/_kwant_version.py .                                                [  0%]
69kwant/_plotter.py .                                                      [  0%]
70kwant/builder.py F                                                       [  1%]
71kwant/digest.py .                                                        [  1%]
72kwant/kpm.py .                                                           [  1%]
73kwant/lattice.py .                                                       [  1%]
74kwant/plotter.py .                                                       [  1%]
75kwant/qsymm.py .                                                         [  2%]
76kwant/rmt.py .                                                           [  2%]
77kwant/system.py .                                                        [  2%]
78kwant/version.py .                                                       [  2%]
79kwant/wraparound.py .                                                    [  2%]
80kwant/continuum/__init__.py .                                            [  2%]
81kwant/continuum/_common.py .                                             [  3%]
82kwant/continuum/discretizer.py .                                         [  3%]
83kwant/continuum/landau_levels.py .                                       [  3%]
84kwant/continuum/tests/__init__.py .                                      [  3%]
85kwant/continuum/tests/test_common.py ................................... [ 10%]
86.....                                                                    [ 10%]
87kwant/continuum/tests/test_discretizer.py .............................. [ 16%]
88..............................                                           [ 21%]
89kwant/continuum/tests/test_landau_levels.py .......                      [ 23%]
90kwant/graph/__init__.py .                                                [ 23%]
91kwant/graph/defs.py .                                                    [ 23%]
92kwant/graph/tests/__init__.py .                                          [ 23%]
93kwant/graph/tests/test_core.py .........                                 [ 25%]
94kwant/graph/tests/test_scotch.py .                                       [ 25%]
95kwant/linalg/__init__.py .                                               [ 25%]
96kwant/linalg/cmumps.py .                                                 [ 25%]
97kwant/linalg/decomp_ev.py .                                              [ 26%]
98kwant/linalg/decomp_lu.py .                                              [ 26%]
99kwant/linalg/decomp_schur.py .                                           [ 26%]
100kwant/linalg/fortran_helpers.py .                                        [ 26%]
101kwant/linalg/lll.py .                                                    [ 26%]
102kwant/linalg/mumps.py .                                                  [ 26%]
103kwant/linalg/tests/__init__.py .                                         [ 27%]
104kwant/linalg/tests/_test_utils.py .                                      [ 27%]
105kwant/linalg/tests/test_linalg.py ............                           [ 29%]
106kwant/linalg/tests/test_lll.py ...                                       [ 30%]
107kwant/linalg/tests/test_mumps.py .....                                   [ 30%]
108kwant/physics/__init__.py .                                              [ 31%]
109kwant/physics/dispersion.py .                                            [ 31%]
110kwant/physics/gauge.py .                                                 [ 31%]
111kwant/physics/leads.py .                                                 [ 31%]
112kwant/physics/noise.py .                                                 [ 31%]
113kwant/physics/symmetry.py .                                              [ 32%]
114kwant/physics/tests/__init__.py .                                        [ 32%]
115kwant/physics/tests/test_dispersion.py ........                          [ 33%]
116kwant/physics/tests/test_gauge.py ...................................... [ 40%]
117...............                                                          [ 43%]
118kwant/physics/tests/test_leads.py .........................              [ 47%]
119kwant/physics/tests/test_noise.py ...                                    [ 48%]
120kwant/physics/tests/test_symmetry.py ......                              [ 49%]
121kwant/solvers/__init__.py .                                              [ 49%]
122kwant/solvers/common.py .                                                [ 49%]
123kwant/solvers/default.py .                                               [ 50%]
124kwant/solvers/mumps.py .                                                 [ 50%]
125kwant/solvers/sparse.py .                                                [ 50%]
126kwant/solvers/tests/__init__.py .                                        [ 50%]
127kwant/solvers/tests/test_solvers.py .................................... [ 57%]
128........................................................................ [ 70%]
129.....                                                                    [ 71%]
130kwant/tests/__init__.py .                                                [ 71%]
131kwant/tests/test_builder.py .......................................F     [ 78%]
132kwant/tests/test_comprehensive.py ..                                     [ 78%]
133kwant/tests/test_kpm.py ...........................                      [ 83%]
134kwant/tests/test_lattice.py ....................                         [ 87%]
135kwant/tests/test_operator.py .................                           [ 90%]
136kwant/tests/test_plotter.py ...................                          [ 94%]
137kwant/tests/test_qsymm.py ............                                   [ 96%]
138kwant/tests/test_rmt.py ....                                             [ 96%]
139kwant/tests/test_system.py .....                                         [ 97%]
140kwant/tests/test_wraparound.py ............                              [100%]
141=================================== FAILURES ===================================
142________________________________ pyflakes-check ________________________________
143/builds/quaeritis/kwant/kwant/builder.py:1565: UndefinedName
144undefined name 'args'
145/builds/quaeritis/kwant/kwant/builder.py:1567: UndefinedName
146undefined name 'args'
147____________________________ test_add_peierls_phase ____________________________
148self = <kwant.builder.InfiniteSystem object at 0x7f928de70810>, i = 1, j = 0
149params = {'phi': functools.partial(<function _finite_wrapper at 0x7f9296188c20>, <kwant.builder.FiniteSystem object at 0x7f928d...r.InfiniteSystem object at 0x7f928de70410>, {(1, 6): (1+0j), (2, 7): (1+0j), (3, 8): (1+0j), (4, 9): (1+0j)}), 't': -1}
150args = <map object at 0x7f928b592a50>
151value = <function _add_peierls_phase.<locals>.const_hopping at 0x7f928e00bcb0>
152param_names = ('phi_lead0',)
153    def hamiltonian(self, i, j, *args, params=None):
154        if args and params:
155            raise TypeError("'args' and 'params' are mutually exclusive.")
156        if i == j:
157            value, param_names = self.onsites[i]
158            if param_names is not None:  # 'value' is callable
159                site = self.symmetry.to_fd(self.sites[i])
160                if params:
161                    # See body of _value_params_pair_cache().
162                    if isinstance(param_names, Exception):
163                        raise param_names
164                    args = map(params.__getitem__, param_names)
165                try:
166                    value = value(site, *args)
167                except Exception as exc:
168                    if isinstance(exc, KeyError) and params:
169                        missing = [p for p in param_names if p not in params]
170                        if missing:
171                            msg = ('System is missing required arguments: ',
172                                   ', '.join(map('"{}"'.format, missing)))
173                            raise TypeError(''.join(msg))
174                    _raise_user_error(exc, value)
175        else:
176            edge_id = self.graph.first_edge_id(i, j)
177            value, param_names = self.hoppings[edge_id]
178            conj = value is Other
179            if conj:
180                i, j = j, i
181                edge_id = self.graph.first_edge_id(i, j)
182                value, param_names = self.hoppings[edge_id]
183            if param_names is not None:  # 'value' is callable
184                sites = self.sites
185                site_i, site_j = self.symmetry.to_fd(sites[i], sites[j])
186                if params:
187                    # See body of _value_params_pair_cache().
188                    if isinstance(param_names, Exception):
189                        raise param_names
190                    args = map(params.__getitem__, param_names)
191                try:
192>                   value = value(site_i, site_j, *args)
193kwant/builder.py:1817: 
194_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
195a = Site(kwant.lattice.Monatomic([[1.0, 0.0], [0.0, 1.0]], [0.0, 0.0], '', 1), array([0, 1]))
196b = Site(kwant.lattice.Monatomic([[1.0, 0.0], [0.0, 1.0]], [0.0, 0.0], '', 1), array([0, 0]))
197phi = functools.partial(<function _infinite_wrapper at 0x7f9296188cb0>, <kwant.builder.InfiniteSystem object at 0x7f928de70810>, {(1, 6): (1+0j), (2, 7): (1+0j), (3, 8): (1+0j), (4, 9): (1+0j)})
198    def const_hopping(a, b, phi):
199        if signs is not None:
200            return np.dot(hop(a, b, *args), phi_matrix(phi(a, b), signs))
201        else:
202>           return hop(a, b, *args) * phi(a, b)
203E           NameError: name 'args' is not defined
204kwant/builder.py:1567: NameError
205The above exception was the direct cause of the following exception:
206    def test_add_peierls_phase():
207    
208        lat = kwant.lattice.square(norbs=1)
209        syst = kwant.Builder()
210        syst[(lat(i, j) for i in range(5) for j in range(5))] = 4
211        syst[lat.neighbors()] = lambda a, b, t: -t
212    
213        lead = kwant.Builder(kwant.TranslationalSymmetry((-1, 0)))
214        lead[(lat(0, j) for j in range(5))] = 4
215        lead[lat.neighbors()] = -1
216    
217        # System without leads
218        syst_without_lead, phase_without_lead = builder.add_peierls_phase(syst)
219    
220        assert isinstance(syst_without_lead, builder.FiniteSystem)
221    
222        params_without_lead = phase_without_lead(1)
223    
224        assert all(p in params_without_lead for p in ('phi',))
225    
226        # System with leads
227        syst.attach_lead(lead)
228        syst.attach_lead(lead.reversed())
229    
230        syst, phase = builder.add_peierls_phase(syst)
231    
232        assert isinstance(syst, builder.FiniteSystem)
233    
234        params = phase(1, 0, 0)
235    
236        assert all(p in params for p in ('phi', 'phi_lead0', 'phi_lead1'))
237    
238>       kwant.smatrix(syst, energy=0.1, params=dict(t=-1, **params))
239kwant/tests/test_builder.py:1776: 
240_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
241kwant/_common.py:73: in inner
242    return f(*args, **kwargs)
243kwant/solvers/common.py:383: in smatrix
244    params=params)
245kwant/solvers/common.py:204: in _make_linear_sys
246    prop, stab = lead.modes(energy, args, params=params)
247kwant/_common.py:73: in inner
248    return f(*args, **kwargs)
249kwant/system.py:788: in modes
250    ham = self.cell_hamiltonian(args, params=params)
251kwant/_common.py:73: in inner
252    return f(*args, **kwargs)
253kwant/system.py:905: in cell_hamiltonian
254    sparse=sparse, params=params)
255kwant/_common.py:73: in inner
256    return f(*args, **kwargs)
257kwant/_system.pyx:340: in kwant._system.hamiltonian_submatrix
258    mat = func(ham, args, params, self.graph, diag, from_sites,
259kwant/_system.pyx:190: in kwant._system.make_dense
260    h = matrix(ham(ts, fs, *args, params=params), complex)
261kwant/builder.py:2798: in hamiltonian
262    return super().hamiltonian(i, j, *args, params=params)
263kwant/builder.py:1825: in hamiltonian
264    _raise_user_error(exc, value)
265_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
266exc = NameError("name 'args' is not defined")
267func = <function _add_peierls_phase.<locals>.const_hopping at 0x7f928e00bcb0>
268    def _raise_user_error(exc, func):
269        msg = ('Error occurred in user-supplied value function "{0}".\n'
270               'See the upper part of the above backtrace for more information.')
271>       raise UserCodeError(msg.format(func.__name__)) from exc
272E       kwant._common.UserCodeError: Error occurred in user-supplied value function "const_hopping".
273E       See the upper part of the above backtrace for more information.
274kwant/builder.py:1721: UserCodeError
275=============================== warnings summary ===============================
276../../../usr/local/envs/kwant-stable/lib/python3.7/importlib/_bootstrap.py:219
277  /usr/local/envs/kwant-stable/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning:
278  
279  numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
280../../../usr/local/envs/kwant-stable/lib/python3.7/importlib/_bootstrap.py:219
281  /usr/local/envs/kwant-stable/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning:
282  
283  numpy.ufunc size changed, may indicate binary incompatibility. Expected 216, got 192
284kwant/tests/test_qsymm.py: 13 warnings
285  /usr/local/envs/kwant-stable/lib/python3.7/site-packages/numpy/lib/type_check.py:546: DeprecationWarning:
286  
287  np.asscalar(a) is deprecated since NumPy v1.16, use a.item() instead
288-- Docs: https://docs.pytest.org/en/stable/warnings.html
289------------ generated xml file: /builds/quaeritis/kwant/tests.xml -------------
290============================= slowest 10 durations =============================
2915.95s call     kwant/tests/test_qsymm.py::test_find_builder_discrete_symmetries
2924.50s call     kwant/tests/test_comprehensive.py::test_qhe
2933.83s call     kwant/tests/test_plotter.py::test_density_interpolation
2943.33s call     kwant/tests/test_plotter.py::test_plotly_plot
2952.60s call     kwant/tests/test_plotter.py::test_current
2962.39s call     kwant/physics/tests/test_leads.py::test_modes_symmetries
2972.24s call     kwant/tests/test_plotter.py::test_matplotlib_plot
2981.90s call     kwant/tests/test_plotter.py::test_current_interpolation
2991.85s call     kwant/tests/test_qsymm.py::test_inverse_transform
3001.65s call     kwant/physics/tests/test_gauge.py::test_minimal_cycle_basis[2-honeycomb-half-ring]
301============ 2 failed, 548 passed, 15 warnings in 91.87s (0:01:31) =============
302/usr/local/envs/kwant-stable/lib/python3.7/site-packages/pep8.py:110: FutureWarning: Possible nested set at position 1
303  EXTRANEOUS_WHITESPACE_REGEX = re.compile(r'[[({] | []}),;:]')
 304  Running after_script  
  00:02
 305  Uploading artifacts for failed job  
  00:02
306Authenticating with credentials from /root/.docker/config.json
307Uploading artifacts...
308tests.xml: found 1 matching files                  
309Uploading artifacts to coordinator... ok            id=157901 responseStatus=201 Created token=eQhaxHqP
310ERROR: Job failed: exit code 1