after_merge stringlengths 28 79.6k | before_merge stringlengths 20 79.6k | url stringlengths 38 71 | full_traceback stringlengths 43 922k | traceback_type stringclasses 555
values |
|---|---|---|---|---|
def spatial_shape(self):
"""Return spatial shape of first image in subject.
Consistency of spatial shapes across images in the subject is checked
first.
"""
self.check_consistent_spatial_shape()
return self.get_first_image().spatial_shape
| def spatial_shape(self):
"""Return spatial shape of first image in subject.
Consistency of shapes across images in the subject is checked first.
"""
return self.shape[1:]
| https://github.com/fepegar/torchio/issues/265 | ---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-2-6b7dc2edb3cc> in <module>
----> 1 icbm.spatial_shape
~/git/torchio/torchio/data/subject.py in spatial_shape(self)
95 Consistency of shapes acr... | ValueError |
def spacing(self):
"""Return spacing of first image in subject.
Consistency of spacings across images in the subject is checked first.
"""
self.check_consistent_attribute("spacing")
return self.get_first_image().spacing
| def spacing(self):
"""Return spacing of first image in subject.
Consistency of shapes across images in the subject is checked first.
"""
self.check_consistent_shape()
image = self.get_images(intensity_only=False)[0]
return image.spacing
| https://github.com/fepegar/torchio/issues/265 | ---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-2-6b7dc2edb3cc> in <module>
----> 1 icbm.spatial_shape
~/git/torchio/torchio/data/subject.py in spatial_shape(self)
95 Consistency of shapes acr... | ValueError |
def check_consistent_shape(self) -> None:
self.check_consistent_attribute("shape")
| def check_consistent_shape(self) -> None:
shapes_dict = {}
iterable = self.get_images_dict(intensity_only=False).items()
for image_name, image in iterable:
shapes_dict[image_name] = image.shape
num_unique_shapes = len(set(shapes_dict.values()))
if num_unique_shapes > 1:
message = (
... | https://github.com/fepegar/torchio/issues/265 | ---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-2-6b7dc2edb3cc> in <module>
----> 1 icbm.spatial_shape
~/git/torchio/torchio/data/subject.py in spatial_shape(self)
95 Consistency of shapes acr... | ValueError |
def add_image(self, image: Image, image_name: str) -> None:
self[image_name] = image
self.update_attributes()
| def add_image(self, image, image_name):
self[image_name] = image
self.update_attributes()
| https://github.com/fepegar/torchio/issues/265 | ---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-2-6b7dc2edb3cc> in <module>
----> 1 icbm.spatial_shape
~/git/torchio/torchio/data/subject.py in spatial_shape(self)
95 Consistency of shapes acr... | ValueError |
def apply_transform(self, sample: Subject) -> dict:
sample.check_consistent_spatial_shape()
params = self.get_params(
self.scales,
self.degrees,
self.translation,
self.isotropic,
)
scaling_params, rotation_params, translation_params = params
for image in self.get_imag... | def apply_transform(self, sample: Subject) -> dict:
sample.check_consistent_shape()
params = self.get_params(
self.scales,
self.degrees,
self.translation,
self.isotropic,
)
scaling_params, rotation_params, translation_params = params
for image in self.get_images(sampl... | https://github.com/fepegar/torchio/issues/265 | ---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-2-6b7dc2edb3cc> in <module>
----> 1 icbm.spatial_shape
~/git/torchio/torchio/data/subject.py in spatial_shape(self)
95 Consistency of shapes acr... | ValueError |
def apply_transform(self, sample: Subject) -> dict:
sample.check_consistent_spatial_shape()
bspline_params = self.get_params(
self.num_control_points,
self.max_displacement,
self.num_locked_borders,
)
for image in self.get_images(sample):
if image[TYPE] != INTENSITY:
... | def apply_transform(self, sample: Subject) -> dict:
sample.check_consistent_shape()
bspline_params = self.get_params(
self.num_control_points,
self.max_displacement,
self.num_locked_borders,
)
for image in self.get_images(sample):
if image[TYPE] != INTENSITY:
... | https://github.com/fepegar/torchio/issues/265 | ---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-2-6b7dc2edb3cc> in <module>
----> 1 icbm.spatial_shape
~/git/torchio/torchio/data/subject.py in spatial_shape(self)
95 Consistency of shapes acr... | ValueError |
def _get_sample_shape(sample: Subject) -> TypeTripletInt:
"""Return the shape of the first image in the sample."""
sample.check_consistent_spatial_shape()
for image_dict in sample.get_images(intensity_only=False):
data = image_dict.spatial_shape # remove channels dimension
break
return ... | def _get_sample_shape(sample: Subject) -> TypeTripletInt:
"""Return the shape of the first image in the sample."""
sample.check_consistent_shape()
for image_dict in sample.get_images(intensity_only=False):
data = image_dict.spatial_shape # remove channels dimension
break
return data
| https://github.com/fepegar/torchio/issues/265 | ---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-2-6b7dc2edb3cc> in <module>
----> 1 icbm.spatial_shape
~/git/torchio/torchio/data/subject.py in spatial_shape(self)
95 Consistency of shapes acr... | ValueError |
def __init__(
self,
num_ghosts: Union[int, Tuple[int, int]] = (4, 10),
axes: Union[int, Tuple[int, ...]] = (0, 1, 2),
intensity: Union[float, Tuple[float, float]] = (0.5, 1),
restore: float = 0.02,
p: float = 1,
seed: Optional[int] = None,
):
super().__init__(p=p, seed=seed)
if not i... | def __init__(
self,
num_ghosts: Union[int, Tuple[int, int]] = (4, 10),
axes: Union[int, Tuple[int, ...]] = (0, 1, 2),
intensity: Union[float, Tuple[float, float]] = (0.5, 1),
restore: float = 0.02,
p: float = 1,
seed: Optional[int] = None,
):
super().__init__(p=p, seed=seed)
if not i... | https://github.com/fepegar/torchio/issues/218 | Traceback (most recent call last):
File "/opt/anaconda3/lib/python3.7/site-packages/IPython/core/interactiveshell.py", line 3326, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-3-57113dda3e8e>", line 2, in <module>
tranform = torchio.transforms.RandomGhosting(num_ghosts=10, intensity... | ValueError |
def __getitem__(self, index: int) -> dict:
if not isinstance(index, int):
raise ValueError(f'Index "{index}" must be int, not {type(index)}')
subject = self.subjects[index]
sample = copy.deepcopy(subject)
sample.load()
# Apply transform (this is usually the bottleneck)
if self._transfor... | def __getitem__(self, index: int) -> dict:
if not isinstance(index, int):
raise ValueError(f'Index "{index}" must be int, not {type(index)}')
subject = self.subjects[index]
sample = copy.deepcopy(subject)
# Apply transform (this is usually the bottleneck)
if self._transform is not None:
... | https://github.com/fepegar/torchio/issues/209 | torch.Size([1, 348, 272, 108])
torch.Size([1, 348, 272, 108])
Traceback (most recent call last):
File "Code/non_local_feature_alignment/dataset_manager.py", line 88, in <module>
print(b["img"][torchio.DATA])
KeyError: 'data' | KeyError |
def load(self) -> Tuple[torch.Tensor, np.ndarray]:
r"""Load the image from disk.
The file is expected to be monomodal/grayscale and 2D or 3D.
A channels dimension is added to the tensor.
Returns:
Tuple containing a 4D data tensor of size
:math:`(1, D_{in}, H_{in}, W_{in})`
and ... | def load(self) -> Tuple[torch.Tensor, np.ndarray]:
r"""Load the image from disk.
The file is expected to be monomodal/grayscale and 2D or 3D.
A channels dimension is added to the tensor.
Returns:
Tuple containing a 4D data tensor of size
:math:`(1, D_{in}, H_{in}, W_{in})`
and ... | https://github.com/fepegar/torchio/issues/209 | torch.Size([1, 348, 272, 108])
torch.Size([1, 348, 272, 108])
Traceback (most recent call last):
File "Code/non_local_feature_alignment/dataset_manager.py", line 88, in <module>
print(b["img"][torchio.DATA])
KeyError: 'data' | KeyError |
def __init__(self, *args, **kwargs):
scene.visuals.Line.__init__(self, *args, **kwargs)
self.unfreeze()
# initialize point markers
self.markers = scene.visuals.Markers(parent=self)
self.marker_colors = np.ones((len(self.pos), 4), dtype=np.float32)
self.markers.set_data(pos=self.pos, symbol="s", ... | def __init__(self, *args, **kwargs):
scene.visuals.Line.__init__(self, *args, **kwargs)
# initialize point markers
self.markers = scene.visuals.Markers()
self.marker_colors = np.ones((len(self.pos), 4), dtype=np.float32)
self.markers.set_data(pos=self.pos, symbol="s", edge_color="red", size=6)
... | https://github.com/vispy/vispy/issues/1455 | Traceback (most recent call last):
File "/home/........../basics/visuals/line_draw.py", line 178, in <module>
win = Canvas()
File "/home/........../basics/visuals/line_draw.py", line 154, in __init__
self.pos = np.zeros((n, 3), dtype=np.float32)
File "/home/........../lib/python3.6/site-packages/vispy/util/frozen.py", ... | AttributeError |
def select_point(self, pos_scene, radius=5):
"""
Get line point close to mouse pointer and its index
Parameters
----------
event : the mouse event being processed
radius : scalar
max. distance in pixels between mouse and line point to be accepted
return: (numpy.array, int)
p... | def select_point(self, event, radius=5):
"""
Get line point close to mouse pointer and its index
Parameters
----------
event : the mouse event being processed
radius : scalar
max. distance in pixels between mouse and line point to be accepted
return: (numpy.array, int)
picke... | https://github.com/vispy/vispy/issues/1455 | Traceback (most recent call last):
File "/home/........../basics/visuals/line_draw.py", line 178, in <module>
win = Canvas()
File "/home/........../basics/visuals/line_draw.py", line 154, in __init__
self.pos = np.zeros((n, 3), dtype=np.float32)
File "/home/........../lib/python3.6/site-packages/vispy/util/frozen.py", ... | AttributeError |
def on_mouse_press(self, pos_scene):
# self.print_mouse_event(event, 'Mouse press')
# pos_scene = event.pos[:3]
# find closest point to mouse and select it
self.selected_point, self.selected_index = self.select_point(pos_scene)
# if no point was clicked add a new one
if self.selected_point is ... | def on_mouse_press(self, event):
self.print_mouse_event(event, "Mouse press")
pos_scene = event.pos[:3]
# find closest point to mouse and select it
self.selected_point, self.selected_index = self.select_point(event)
# if no point was clicked add a new one
if self.selected_point is None:
... | https://github.com/vispy/vispy/issues/1455 | Traceback (most recent call last):
File "/home/........../basics/visuals/line_draw.py", line 178, in <module>
win = Canvas()
File "/home/........../basics/visuals/line_draw.py", line 154, in __init__
self.pos = np.zeros((n, 3), dtype=np.float32)
File "/home/........../lib/python3.6/site-packages/vispy/util/frozen.py", ... | AttributeError |
def on_mouse_move(self, pos_scene):
if self.selected_point is not None:
# update selected point to new position given by mouse
self.selected_point[0] = round(pos_scene[0] / self.gridsize) * self.gridsize
self.selected_point[1] = round(pos_scene[1] / self.gridsize) * self.gridsize
sel... | def on_mouse_move(self, event):
# left mouse button
if event.button == 1:
# self.print_mouse_event(event, 'Mouse drag')
if self.selected_point is not None:
pos_scene = event.pos
# update selected point to new position given by mouse
self.selected_point[0] = ro... | https://github.com/vispy/vispy/issues/1455 | Traceback (most recent call last):
File "/home/........../basics/visuals/line_draw.py", line 178, in <module>
win = Canvas()
File "/home/........../basics/visuals/line_draw.py", line 154, in __init__
self.pos = np.zeros((n, 3), dtype=np.float32)
File "/home/........../lib/python3.6/site-packages/vispy/util/frozen.py", ... | AttributeError |
def __init__(self):
scene.SceneCanvas.__init__(self, keys="interactive", size=(800, 800))
# Create some initial points
n = 7
self.unfreeze()
self.pos = np.zeros((n, 3), dtype=np.float32)
self.pos[:, 0] = np.linspace(-50, 50, n)
self.pos[:, 1] = np.random.normal(size=n, scale=10, loc=0)
... | def __init__(self):
scene.SceneCanvas.__init__(self, keys="interactive", size=(800, 800))
# Create some initial points
n = 7
self.pos = np.zeros((n, 3), dtype=np.float32)
self.pos[:, 0] = np.linspace(-50, 50, n)
self.pos[:, 1] = np.random.normal(size=n, scale=10, loc=0)
# create new editab... | https://github.com/vispy/vispy/issues/1455 | Traceback (most recent call last):
File "/home/........../basics/visuals/line_draw.py", line 178, in <module>
win = Canvas()
File "/home/........../basics/visuals/line_draw.py", line 154, in __init__
self.pos = np.zeros((n, 3), dtype=np.float32)
File "/home/........../lib/python3.6/site-packages/vispy/util/frozen.py", ... | AttributeError |
def _use(self, backend_name=None):
"""Select a backend by name. See class docstring for details."""
# See if we're in a specific testing mode, if so DONT check to see
# if it's a valid backend. If it isn't, it's a good thing we
# get an error later because we should have decorated our test
# with re... | def _use(self, backend_name=None):
"""Select a backend by name. See class docstring for details."""
# See if we're in a specific testing mode, if so DONT check to see
# if it's a valid backend. If it isn't, it's a good thing we
# get an error later because we should have decorated our test
# with re... | https://github.com/vispy/vispy/issues/582 | RuntimeError Traceback (most recent call last)
<ipython-input-2-b622cb67980d> in <module>()
----> 1 c = app.Canvas(keys='interactive')
/usr/local/lib/python2.7/dist-packages/vispy-0.3.0-py2.7.egg/vispy/app/canvas.pyc in __init__(self, title, size, position, show, autoswap, app, create_nati... | RuntimeError |
def _set_keys(self, keys):
if keys is not None:
if isinstance(keys, string_types):
if keys != "interactive":
raise ValueError(
'keys, if string, must be "interactive", not %s' % (keys,)
)
def toggle_fs():
self.fulls... | def _set_keys(self, keys):
if keys is not None:
if isinstance(keys, string_types):
if keys != "interactive":
raise ValueError(
'keys, if string, must be "interactive", not %s' % (keys,)
)
def toggle_fs():
self.fulls... | https://github.com/vispy/vispy/issues/542 | WARNING: Traceback (most recent call last):
File ".\examples\demo\gloo\brain.py", line 156, in <module>
app.run()
File "D:\Git\vispy\vispy\app\_default_app.py", line 54, in run
return default_app.run()
File "D:\Git\vispy\vispy\app\application.py", line 88, in run
return self._backend._vispy_run()
File "D:\Git\vispy\vis... | AttributeError |
def keys_check(event):
if event.key is not None:
use_name = event.key.name.lower()
if use_name in self._keys_check:
self._keys_check[use_name]()
| def keys_check(event):
use_name = event.key.name.lower()
if use_name in self._keys_check:
self._keys_check[use_name]()
| https://github.com/vispy/vispy/issues/542 | WARNING: Traceback (most recent call last):
File ".\examples\demo\gloo\brain.py", line 156, in <module>
app.run()
File "D:\Git\vispy\vispy\app\_default_app.py", line 54, in run
return default_app.run()
File "D:\Git\vispy\vispy\app\application.py", line 88, in run
return self._backend._vispy_run()
File "D:\Git\vispy\vis... | AttributeError |
def checkerboard(grid_num=8, grid_size=32):
row_even = grid_num // 2 * [0, 1]
row_odd = grid_num // 2 * [1, 0]
Z = np.row_stack(grid_num // 2 * (row_even, row_odd)).astype(np.uint8)
return 255 * Z.repeat(grid_size, axis=0).repeat(grid_size, axis=1)
| def checkerboard(grid_num=8, grid_size=32):
row_even = grid_num / 2 * [0, 1]
row_odd = grid_num / 2 * [1, 0]
Z = np.row_stack(grid_num / 2 * (row_even, row_odd)).astype(np.uint8)
return 255 * Z.repeat(grid_size, axis=0).repeat(grid_size, axis=1)
| https://github.com/vispy/vispy/issues/525 | WARNING: normal has not been bound
WARNING: color has not been bound
WARNING: Traceback (most recent call last):
File "textured_cube.py", line 102, in <module>
c.show()
File "/home/cyrille/git/vispy/vispy/app/canvas.py", line 320, in show
return self._backend._vispy_set_visible(visible)
File "/home/cyrille/git/vispy/vi... | TypeError |
def _deactivate(self):
if self._gtype in (gl.GL_SAMPLER_2D, GL_SAMPLER_3D):
# gl.glActiveTexture(gl.GL_TEXTURE0 + self._unit)
if self.data is not None:
if isinstance(self._data, BaseTexture):
self.data.deactivate()
| def _deactivate(self):
if self._gtype in (gl.GL_SAMPLER_2D, GL_SAMPLER_3D):
# gl.glActiveTexture(gl.GL_TEXTURE0 + self._unit)
if self.data is not None:
self.data.deactivate()
| https://github.com/vispy/vispy/issues/525 | WARNING: normal has not been bound
WARNING: color has not been bound
WARNING: Traceback (most recent call last):
File "textured_cube.py", line 102, in <module>
c.show()
File "/home/cyrille/git/vispy/vispy/app/canvas.py", line 320, in show
return self._backend._vispy_set_visible(visible)
File "/home/cyrille/git/vispy/vi... | TypeError |
def on_draw(self, event):
self.framebuffer.activate()
set_viewport(0, 0, 512, 512)
clear(color=True, depth=True)
set_state(depth_test=True)
self.cube.draw("triangles", self.indices)
self.framebuffer.deactivate()
set_viewport(0, 0, *self.size)
clear(color=True)
set_state(depth_test=Fa... | def on_draw(self, event):
self.framebuffer.activate()
set_viewport(0, 0, 512, 512)
clear(color=True, depth=True)
set_state(depth_test=True)
self.cube.draw("triangles", self.indices)
self.framebuffer.deactivate()
clear(color=True)
set_state(depth_test=False)
self.quad.draw("triangle_s... | https://github.com/vispy/vispy/issues/528 | cyrille@Cyrille-ASUS:~/git/vispy/examples/demo/gloo$ python realtime_signals.py ERROR: Could not set variable 'a_position' with value [-0.0093575 0.1638512 0.15590386 ..., 0.07139178 -0.14649338
0.06221156]
Traceback (most recent call last):
File "realtime_signals.py", line 162, in <module>
c = Canvas()
File "real... | IndexError |
def __init__(self):
app.Canvas.__init__(self, title="Use your wheel to zoom!", keys="interactive")
self.program = gloo.Program(VERT_SHADER, FRAG_SHADER)
self.program["a_position"] = y.reshape(-1, 1)
self.program["a_color"] = color
self.program["a_index"] = index
self.program["u_scale"] = (1.0, 1... | def __init__(self):
app.Canvas.__init__(self, title="Use your wheel to zoom!", keys="interactive")
self.program = gloo.Program(VERT_SHADER, FRAG_SHADER)
self.program["a_position"] = y.ravel()
self.program["a_color"] = color
self.program["a_index"] = index
self.program["u_scale"] = (1.0, 1.0)
... | https://github.com/vispy/vispy/issues/528 | cyrille@Cyrille-ASUS:~/git/vispy/examples/demo/gloo$ python realtime_signals.py ERROR: Could not set variable 'a_position' with value [-0.0093575 0.1638512 0.15590386 ..., 0.07139178 -0.14649338
0.06221156]
Traceback (most recent call last):
File "realtime_signals.py", line 162, in <module>
c = Canvas()
File "real... | IndexError |
def __init__(self):
app.Canvas.__init__(self, title="Spacy", keys="interactive")
self.size = 800, 600
self.program = gloo.Program(vertex, fragment)
self.view = np.eye(4, dtype=np.float32)
self.model = np.eye(4, dtype=np.float32)
self.projection = np.eye(4, dtype=np.float32)
self.timer = ap... | def __init__(self):
app.Canvas.__init__(self, title="Spacy", keys="interactive")
self.size = 800, 600
self.program = gloo.Program(vertex, fragment)
self.view = np.eye(4, dtype=np.float32)
self.model = np.eye(4, dtype=np.float32)
self.projection = np.eye(4, dtype=np.float32)
self.timer = ap... | https://github.com/vispy/vispy/issues/528 | cyrille@Cyrille-ASUS:~/git/vispy/examples/demo/gloo$ python realtime_signals.py ERROR: Could not set variable 'a_position' with value [-0.0093575 0.1638512 0.15590386 ..., 0.07139178 -0.14649338
0.06221156]
Traceback (most recent call last):
File "realtime_signals.py", line 162, in <module>
c = Canvas()
File "real... | IndexError |
def _get_tick_frac_labels(self):
"""Get the major ticks, minor ticks, and major labels"""
minor_num = 4 # number of minor ticks per major division
if self.axis.scale_type == "linear":
domain = self.axis.domain
if domain[1] < domain[0]:
flip = True
domain = domain[::-... | def _get_tick_frac_labels(self):
# This conditional is currently unnecessary since we only support
# linear, but eventually we will support others so we leave it in
if self.axis.scale_type == "linear":
major_num = 11 # maximum number of major ticks
minor_num = 4 # maximum number of minor t... | https://github.com/vispy/vispy/issues/7 | Traceback (most recent call last):
File "oscilloscope.py", line 138, in on_paint
visual.draw(transform)
File "oscilloscope.py", line 79, in draw
self.program.uniforms['color'] = self.color
File "../vispy/oogl/program_inputs.py", line 43, in __setitem__
self._set(k, v)
File "../vispy/oogl/program_inputs.py", line 94, in... | IndexError |
def __init__(
self, nbins=10, steps=None, trim=True, integer=False, symmetric=False, prune=None
):
"""
Keyword args:
*nbins*
Maximum number of intervals; one less than max number of ticks.
*steps*
Sequence of nice numbers starting with 1 and ending with 10;
e.g., [1, 2, 4, 5,... | def __init__(self, axis):
self.axis = axis
| https://github.com/vispy/vispy/issues/7 | Traceback (most recent call last):
File "oscilloscope.py", line 138, in on_paint
visual.draw(transform)
File "oscilloscope.py", line 79, in draw
self.program.uniforms['color'] = self.color
File "../vispy/oogl/program_inputs.py", line 43, in __setitem__
self._set(k, v)
File "../vispy/oogl/program_inputs.py", line 94, in... | IndexError |
def handle_import_data(self, data):
"""Import additional data for tuning
Parameters
----------
data:
a list of dictionarys, each of which has at least two keys, 'parameter' and 'value'
Raises
------
AssertionError
data doesn't have required key 'parameter' and 'value'
"... | def handle_import_data(self, data):
"""Import additional data for tuning
Parameters
----------
data:
a list of dictionarys, each of which has at least two keys, 'parameter' and 'value'
Raises
------
AssertionError
data doesn't have required key 'parameter' and 'value'
"... | https://github.com/microsoft/nni/issues/2140 | [03/09/2020, 03:51:05 PM] INFO (nni.msg_dispatcher_base/MainThread) Start dispatcher
[03/09/2020, 03:51:05 PM] INFO (nni.tuner/MainThread) Load checkpoint ignored by tuner, checkpoint path: /home/arvoelke/nni/experiments/NdfeH2R1/checkpoint
[03/09/2020, 03:51:05 PM] INFO (nni.assessor/MainThread) Load checkpoint ignore... | TypeError |
def import_data(self, data):
"""
Import additional data for tuning.
Parameters
----------
data : list of dict
Each of which has at least two keys, ``parameter`` and ``value``.
"""
_completed_num = 0
for trial_info in data:
self.logger.info(
"Importing data, c... | def import_data(self, data):
"""
Import additional data for tuning.
Parameters
----------
data : list of dict
Each of which has at least two keys, ``parameter`` and ``value``.
"""
_completed_num = 0
for trial_info in data:
self.logger.info(
"Importing data, c... | https://github.com/microsoft/nni/issues/2140 | [03/09/2020, 03:51:05 PM] INFO (nni.msg_dispatcher_base/MainThread) Start dispatcher
[03/09/2020, 03:51:05 PM] INFO (nni.tuner/MainThread) Load checkpoint ignored by tuner, checkpoint path: /home/arvoelke/nni/experiments/NdfeH2R1/checkpoint
[03/09/2020, 03:51:05 PM] INFO (nni.assessor/MainThread) Load checkpoint ignore... | TypeError |
def _pack_parameter(
parameter_id, params, customized=False, trial_job_id=None, parameter_index=None
):
_trial_params[parameter_id] = params
ret = {
"parameter_id": parameter_id,
"parameter_source": "customized" if customized else "algorithm",
"parameters": params,
}
if trial... | def _pack_parameter(
parameter_id, params, customized=False, trial_job_id=None, parameter_index=None
):
_trial_params[parameter_id] = params
ret = {
"parameter_id": parameter_id,
"parameter_source": "customized" if customized else "algorithm",
"parameters": params,
}
if trial... | https://github.com/microsoft/nni/issues/1589 | Using TensorFlow backend.
Traceback (most recent call last):
File "test.py", line 164, in <module>
train(ARGS, RECEIVED_PARAMS)
File "test.py", line 136, in train
validation_data=(x_test, y_test), callbacks=[SendMetrics(), TensorBoard(log_dir=TENSORBOARD_DIR)])
File "/home/msalz/venv_nni_dev/lib64/python3.6/site-packag... | ValueError |
def request_next_parameter():
metric = to_json(
{
"trial_job_id": trial_env_vars.NNI_TRIAL_JOB_ID,
"type": "REQUEST_PARAMETER",
"sequence": 0,
"parameter_index": _param_index,
}
)
send_metric(metric)
| def request_next_parameter():
metric = json_tricks.dumps(
{
"trial_job_id": trial_env_vars.NNI_TRIAL_JOB_ID,
"type": "REQUEST_PARAMETER",
"sequence": 0,
"parameter_index": _param_index,
}
)
send_metric(metric)
| https://github.com/microsoft/nni/issues/1589 | Using TensorFlow backend.
Traceback (most recent call last):
File "test.py", line 164, in <module>
train(ARGS, RECEIVED_PARAMS)
File "test.py", line 136, in train
validation_data=(x_test, y_test), callbacks=[SendMetrics(), TensorBoard(log_dir=TENSORBOARD_DIR)])
File "/home/msalz/venv_nni_dev/lib64/python3.6/site-packag... | ValueError |
def report_intermediate_result(metric):
"""
Reports intermediate result to NNI.
Parameters
----------
metric:
serializable object.
"""
global _intermediate_seq
assert _params or trial_env_vars.NNI_PLATFORM is None, (
"nni.get_next_parameter() needs to be called before re... | def report_intermediate_result(metric):
"""
Reports intermediate result to NNI.
Parameters
----------
metric:
serializable object.
"""
global _intermediate_seq
assert _params or trial_env_vars.NNI_PLATFORM is None, (
"nni.get_next_parameter() needs to be called before re... | https://github.com/microsoft/nni/issues/1589 | Using TensorFlow backend.
Traceback (most recent call last):
File "test.py", line 164, in <module>
train(ARGS, RECEIVED_PARAMS)
File "test.py", line 136, in train
validation_data=(x_test, y_test), callbacks=[SendMetrics(), TensorBoard(log_dir=TENSORBOARD_DIR)])
File "/home/msalz/venv_nni_dev/lib64/python3.6/site-packag... | ValueError |
def report_final_result(metric):
"""
Reports final result to NNI.
Parameters
----------
metric:
serializable object.
"""
assert _params or trial_env_vars.NNI_PLATFORM is None, (
"nni.get_next_parameter() needs to be called before report_final_result"
)
metric = to_js... | def report_final_result(metric):
"""
Reports final result to NNI.
Parameters
----------
metric:
serializable object.
"""
assert _params or trial_env_vars.NNI_PLATFORM is None, (
"nni.get_next_parameter() needs to be called before report_final_result"
)
metric = json_... | https://github.com/microsoft/nni/issues/1589 | Using TensorFlow backend.
Traceback (most recent call last):
File "test.py", line 164, in <module>
train(ARGS, RECEIVED_PARAMS)
File "test.py", line 136, in train
validation_data=(x_test, y_test), callbacks=[SendMetrics(), TensorBoard(log_dir=TENSORBOARD_DIR)])
File "/home/msalz/venv_nni_dev/lib64/python3.6/site-packag... | ValueError |
def parse_annotation_mutable_layers(code, lineno, nas_mode):
"""Parse the string of mutable layers in annotation.
Return a list of AST Expr nodes
code: annotation string (excluding '@')
nas_mode: the mode of NAS
"""
module = ast.parse(code)
assert type(module) is ast.Module, "internal error ... | def parse_annotation_mutable_layers(code, lineno, nas_mode):
"""Parse the string of mutable layers in annotation.
Return a list of AST Expr nodes
code: annotation string (excluding '@')
nas_mode: the mode of NAS
"""
module = ast.parse(code)
assert type(module) is ast.Module, "internal error ... | https://github.com/microsoft/nni/issues/1560 | Traceback (most recent call last):
File "/data/hdd3/yugzh/ENAS_NLP/venv/lib/python3.5/site-packages/nni_annotation/specific_code_generator.py", line 355, in parse
transformer.visit(ast_tree)
File "/data/hdd3/yugzh/ENAS_NLP/venv/lib/python3.5/site-packages/nni_annotation/specific_code_generator.py", line 278, in visit
r... | AssertionError |
def _visit_string(self, node):
string = node.value.s
if string.startswith("@nni."):
self.annotated = True
else:
return node # not an annotation, ignore it
if string.startswith("@nni.get_next_parameter"):
deprecated_message = (
"'@nni.get_next_parameter' is deprecate... | def _visit_string(self, node):
string = node.value.s
if string.startswith("@nni."):
self.annotated = True
else:
return node # not an annotation, ignore it
if string.startswith("@nni.get_next_parameter"):
deprecated_message = "'@nni.get_next_parameter' is deprecated in annotatio... | https://github.com/microsoft/nni/issues/1560 | Traceback (most recent call last):
File "/data/hdd3/yugzh/ENAS_NLP/venv/lib/python3.5/site-packages/nni_annotation/specific_code_generator.py", line 355, in parse
transformer.visit(ast_tree)
File "/data/hdd3/yugzh/ENAS_NLP/venv/lib/python3.5/site-packages/nni_annotation/specific_code_generator.py", line 278, in visit
r... | AssertionError |
def log_trial(args):
"""'get trial log path"""
trial_id_path_dict = {}
trial_id_list = []
nni_config = Config(get_config_filename(args))
rest_port = nni_config.get_config("restServerPort")
rest_pid = nni_config.get_config("restServerPid")
if not detect_process(rest_pid):
print_error(... | def log_trial(args):
"""'get trial log path"""
trial_id_path_dict = {}
nni_config = Config(get_config_filename(args))
rest_port = nni_config.get_config("restServerPort")
rest_pid = nni_config.get_config("restServerPid")
if not detect_process(rest_pid):
print_error("Experiment is not runn... | https://github.com/microsoft/nni/issues/1548 | root# nnictl log trial
Traceback (most recent call last):
File "/root/.pyenv/versions/3.6.8/bin/nnictl", line 11, in <module>
sys.exit(parse_args())
File "/root/.pyenv/versions/3.6.8/lib/python3.6/site-packages/nni_cmd/nnictl.py", line 217, in parse_args
args.func(args)
File "/root/.pyenv/versions/3.6.8/lib/python3.6/s... | KeyError |
def send_email_sendgrid(sender, subject, message, recipients, image_png):
import sendgrid as sendgrid_lib
client = sendgrid_lib.SendGridAPIClient(sendgrid().apikey)
to_send = sendgrid_lib.Mail(
from_email=sender, to_emails=recipients, subject=subject
)
if email().format == "html":
... | def send_email_sendgrid(sender, subject, message, recipients, image_png):
import sendgrid as sendgrid_lib
client = sendgrid_lib.SendGridClient(
sendgrid().username, sendgrid().password, raise_errors=True
)
to_send = sendgrid_lib.Mail()
to_send.add_to(recipients)
to_send.set_from(sender)... | https://github.com/spotify/luigi/issues/1956 | Traceback (most recent call last):
File "/home/ubuntu/.virtualenvs/janrain/local/lib/python2.7/site-packages/luigi/retcodes.py", line 74, in run_with_retcodes
worker = luigi.interface._run(argv)['worker']
File "/home/ubuntu/.virtualenvs/janrain/local/lib/python2.7/site-packages/luigi/interface.py", line 237, in _run
re... | AttributeError |
def find_spec(self, name, path, target=None):
# If jvm is not started then we just check against the TLDs
if not _jpype.isStarted():
base = name.partition(".")[0]
if not base in _JDOMAINS:
return None
raise ImportError("Attempt to create Java package '%s' without jvm" % name)... | def find_spec(self, name, path, target=None):
# If jvm is not started then we just check against the TLDs
if not _jpype.isStarted():
base = name.partition(".")[0]
if not base in _JDOMAINS:
return None
raise ImportError("Attempt to create Java package '%s' without jvm" % name)... | https://github.com/jpype-project/jpype/issues/838 | $ export CLASSPATH=lib/lucene-core-8.6.0.jar
$ python
Python 3.8.2 (default, Jul 16 2020, 14:00:26)
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
import jpype
import jpype.imports
print(jpype.getDefaultJVMPath())
/usr/lib/jvm/java-14-openjdk-amd64/lib/server/libjvm.so
jpype... | AttributeError |
def find_spec(self, name, path, target=None):
# If jvm is not started then we just check against the TLDs
if not _jpype.isStarted():
base = name.partition(".")[0]
if not base in _JDOMAINS:
return None
raise ImportError("Attempt to create java modules without jvm")
# Chec... | def find_spec(self, name, path, target=None):
# If jvm is not started then we just check against the TLDs
if not _jpype.isStarted():
base = name.partition(".")[0]
if not base in _JDOMAINS:
return None
raise ImportError("Attempt to create java modules without jvm")
# Chec... | https://github.com/jpype-project/jpype/issues/748 | Traceback (most recent call last):
File "/home/nelson85/env/python-ubuntu/lib/python3.6/site-packages/JPype1-0.7.6.dev0-py3.6-linux-x86_64.egg/jpype/imports.py", line 188, in find_spec
cls = _java_lang_Class.forName(name)
NameError: name '_java_lang_Class' is not defined
The above exception was the direct cause of the... | NameError |
def build(
serviceName,
version,
http=None,
discoveryServiceUrl=DISCOVERY_URI,
developerKey=None,
model=None,
requestBuilder=HttpRequest,
credentials=None,
cache_discovery=True,
cache=None,
client_options=None,
adc_cert_path=None,
adc_key_path=None,
num_retries=1,... | def build(
serviceName,
version,
http=None,
discoveryServiceUrl=DISCOVERY_URI,
developerKey=None,
model=None,
requestBuilder=HttpRequest,
credentials=None,
cache_discovery=True,
cache=None,
client_options=None,
adc_cert_path=None,
adc_key_path=None,
num_retries=1,... | https://github.com/googleapis/google-api-python-client/issues/971 | from googleapiclient.discovery import build
build("cloudresourcemanager", version=None)
Traceback (most recent call last):
...
googleapiclient.errors.HttpError:
<HttpError 400 when requesting https://www.googleapis.com/discovery/v1/apis/cloudresourcemanager//rest
returned "Request contains an invalid argument."> | googleapiclient.errors.HttpError |
def print_table(response, title):
"""Prints out a response table.
Each row contains key(s), clicks, impressions, CTR, and average position.
Args:
response: The server response to be printed as a table.
title: The title of the table.
"""
print("\n --" + title + ":")
if "rows" not i... | def print_table(response, title):
"""Prints out a response table.
Each row contains key(s), clicks, impressions, CTR, and average position.
Args:
response: The server response to be printed as a table.
title: The title of the table.
"""
print("\n --" + title + ":")
if "rows" not i... | https://github.com/googleapis/google-api-python-client/issues/732 | Traceback (most recent call last):
File "search_analytics_api_sample.py", line 197, in <module>
main(sys.argv)
File "search_analytics_api_sample.py", line 71, in main
print_table(response, 'Available dates')
File "search_analytics_api_sample.py", line 194, in print_table
print(row_format.format(keys, row['clicks'], row... | TypeError |
def init(
argv, name, version, doc, filename, scope=None, parents=[], discovery_filename=None
):
"""A common initialization routine for samples.
Many of the sample applications do the same initialization, which has now
been consolidated into this function. This function uses common idioms found
in ... | def init(
argv, name, version, doc, filename, scope=None, parents=[], discovery_filename=None
):
"""A common initialization routine for samples.
Many of the sample applications do the same initialization, which has now
been consolidated into this function. This function uses common idioms found
in ... | https://github.com/googleapis/google-api-python-client/issues/524 | Python 3.6.5 (default, Mar 31 2018, 13:05:03)
[GCC 4.2.1 Compatible Apple LLVM 9.1.0 (clang-902.0.39.1)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
from apiclient import discovery
Traceback (most recent call last):
File "/Users/eric/projects/google-api-python-client/googleapiclient... | ModuleNotFoundError |
def encode_block(self, obj):
"""
Parameters
----------
obj : AtomGroup or Universe
"""
traj = obj.universe.trajectory
ts = traj.ts
try:
molecule = ts.data["molecule"]
except KeyError:
raise_from(
NotImplementedError("MOL2Writer cannot currently write non ... | def encode_block(self, obj):
"""
Parameters
----------
obj : AtomGroup or Universe
"""
traj = obj.universe.trajectory
ts = traj.ts
try:
molecule = ts.data["molecule"]
except KeyError:
raise_from(
NotImplementedError("MOL2Writer cannot currently write non ... | https://github.com/MDAnalysis/mdanalysis/issues/2678 | import MDAnalysis as mda
mda.__version__
'0.20.1'
from MDAnalysis.tests.datafiles import mol2_molecules
u = mda.Universe(mol2_molecules)
u.atoms[:4].write('group1.mol2') # 👍
u.atoms[:4].write('group2.mol2') # 👎
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "MDAnalysis/core/groups.py"... | IndexError |
def __init__(
self,
atomgroup,
reference=None,
select="all",
groupselections=None,
weights=None,
weights_groupselections=False,
tol_mass=0.1,
ref_frame=0,
**kwargs,
):
r"""Parameters
----------
atomgroup : AtomGroup or Universe
Group of atoms for which the RMS... | def __init__(
self,
atomgroup,
reference=None,
select="all",
groupselections=None,
weights=None,
tol_mass=0.1,
ref_frame=0,
**kwargs,
):
r"""Parameters
----------
atomgroup : AtomGroup or Universe
Group of atoms for which the RMSD is calculated. If a trajectory is... | https://github.com/MDAnalysis/mdanalysis/issues/2429 | import MDAnalysis as mda
from MDAnalysis.tests.datafiles import PSF, DCD, CRD
import MDAnalysis.analysis.rms as rms
mda.__version__
'0.20.1'
u = mda.Universe(PSF, DCD) # closed AdK (PDB ID: 1AKE)
R = rms.RMSD(u, # universe to align
... u, # reference universe or atomgroup
... select='backbo... | ValueError |
def _prepare(self):
self._n_atoms = self.mobile_atoms.n_atoms
if not self.weights_groupselections:
if not iterable(self.weights): # apply 'mass' or 'None' to groupselections
self.weights_groupselections = [self.weights] * len(self.groupselections)
else:
self.weights_grou... | def _prepare(self):
self._n_atoms = self.mobile_atoms.n_atoms
if not iterable(self.weights) and self.weights == "mass":
self.weights = self.ref_atoms.masses
if self.weights is not None:
self.weights = np.asarray(self.weights, dtype=np.float64) / np.mean(
self.weights
)
... | https://github.com/MDAnalysis/mdanalysis/issues/2429 | import MDAnalysis as mda
from MDAnalysis.tests.datafiles import PSF, DCD, CRD
import MDAnalysis.analysis.rms as rms
mda.__version__
'0.20.1'
u = mda.Universe(PSF, DCD) # closed AdK (PDB ID: 1AKE)
R = rms.RMSD(u, # universe to align
... u, # reference universe or atomgroup
... select='backbo... | ValueError |
def _single_frame(self):
mobile_com = self.mobile_atoms.center(self.weights_select).astype(np.float64)
self._mobile_coordinates64[:] = self.mobile_atoms.positions
self._mobile_coordinates64 -= mobile_com
self.rmsd[self._frame_index, :2] = self._ts.frame, self._trajectory.time
if self._groupselecti... | def _single_frame(self):
mobile_com = self.mobile_atoms.center(self.weights).astype(np.float64)
self._mobile_coordinates64[:] = self.mobile_atoms.positions
self._mobile_coordinates64 -= mobile_com
self.rmsd[self._frame_index, :2] = self._ts.frame, self._trajectory.time
if self._groupselections_ato... | https://github.com/MDAnalysis/mdanalysis/issues/2429 | import MDAnalysis as mda
from MDAnalysis.tests.datafiles import PSF, DCD, CRD
import MDAnalysis.analysis.rms as rms
mda.__version__
'0.20.1'
u = mda.Universe(PSF, DCD) # closed AdK (PDB ID: 1AKE)
R = rms.RMSD(u, # universe to align
... u, # reference universe or atomgroup
... select='backbo... | ValueError |
def _get_dh_pairs(self):
"""Finds donor-hydrogen pairs.
Returns
-------
donors, hydrogens: AtomGroup, AtomGroup
AtomGroups corresponding to all donors and all hydrogens. AtomGroups are ordered such that, if zipped, will
produce a list of donor-hydrogen pairs.
"""
# If donors_se... | def _get_dh_pairs(self):
"""Finds donor-hydrogen pairs.
Returns
-------
donors, hydrogens: AtomGroup, AtomGroup
AtomGroups corresponding to all donors and all hydrogens. AtomGroups are ordered such that, if zipped, will
produce a list of donor-hydrogen pairs.
"""
# If donors_se... | https://github.com/MDAnalysis/mdanalysis/issues/2396 | ---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
~/anaconda3/envs/py36/lib/python3.6/site-packages/MDAnalysis/core/universe.py in __getattr__(self, key)
509 try:
--> 510 segment = self._instant_sel... | KeyError |
def _single_frame(self):
box = self._ts.dimensions
# Update donor-hydrogen pairs if necessary
if self.update_selections:
self._donors, self._hydrogens = self._get_dh_pairs()
# find D and A within cutoff distance of one another
# min_cutoff = 1.0 as an atom cannot form a hydrogen bond with ... | def _single_frame(self):
box = self._ts.dimensions
# Update donor-hydrogen pairs if necessary
if self.update_selections:
self._donors, self._hydrogens = self._get_dh_pairs()
# find D and A within cutoff distance of one another
# min_cutoff = 1.0 as an atom cannot form a hydrogen bond with ... | https://github.com/MDAnalysis/mdanalysis/issues/2396 | ---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
~/anaconda3/envs/py36/lib/python3.6/site-packages/MDAnalysis/core/universe.py in __getattr__(self, key)
509 try:
--> 510 segment = self._instant_sel... | KeyError |
def __init__(self, universe, selection1, selection2, t0, tf, dtmax):
self.universe = universe
self.selection1 = selection1
self.selection2 = selection2
self.t0 = t0
self.tf = tf - 1
self.dtmax = dtmax
self.timeseries = None
| def __init__(self, universe, selection1, selection2, t0, tf, dtmax, nproc=1):
self.universe = universe
self.selection1 = selection1
self.selection2 = selection2
self.t0 = t0
self.tf = tf - 1
self.dtmax = dtmax
self.nproc = nproc
self.timeseries = None
| https://github.com/MDAnalysis/mdanalysis/issues/2511 | ts= 1
ts= 2
/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/all/lib/python3.7/site-packages/MDAnalysis/analysis/base.py:116: DeprecationWarning: Setting the following kwargs should be done in the run() method: start, stop
DeprecationWarning)
/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/al... | NameError |
def run(self, **kwargs):
"""Analyze trajectory and produce timeseries"""
h_list = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis(
self.universe, self.selection1, self.selection2, distance=3.5, angle=120.0
)
h_list.run(**kwargs)
self.timeseries = self._getGraphics(h_list.timeseries, self.t0,... | def run(self, **kwargs):
"""Analyze trajectory and produce timeseries"""
h_list = []
i = 0
if self.nproc > 1:
while i < len(self.universe.trajectory):
jobs = []
k = i
for j in range(self.nproc):
# start
print("ts=", i + 1)
... | https://github.com/MDAnalysis/mdanalysis/issues/2511 | ts= 1
ts= 2
/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/all/lib/python3.7/site-packages/MDAnalysis/analysis/base.py:116: DeprecationWarning: Setting the following kwargs should be done in the run() method: start, stop
DeprecationWarning)
/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/al... | NameError |
def _determine_method(
reference, configuration, max_cutoff, min_cutoff=None, box=None, method=None
):
"""Guesses the fastest method for capped distance calculations based on the
size of the coordinate sets and the relative size of the target volume.
Parameters
----------
reference : numpy.ndar... | def _determine_method(
reference, configuration, max_cutoff, min_cutoff=None, box=None, method=None
):
"""Guesses the fastest method for capped distance calculations based on the
size of the coordinate sets and the relative size of the target volume.
Parameters
----------
reference : numpy.ndar... | https://github.com/MDAnalysis/mdanalysis/issues/2361 | from MDAnalysis.tests.datafiles import *
pdbqt = mda.Universe(PDBQT_input)
pdb = mda.Universe(PDB)
pdb.atoms.icodes
array(['', '', '', ..., '', '', ''], dtype=object)
pdbqt.atoms.icodes
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/lily/anaconda3/envs/mdanalysis/lib/python3.7/site-... | AttributeError |
def parse(self, **kwargs):
"""Parse PSF file into Topology
Returns
-------
MDAnalysis *Topology* object
"""
# Open and check psf validity
with openany(self.filename) as psffile:
header = next(psffile)
if not header.startswith("PSF"):
err = "{0} is not valid PSF f... | def parse(self, **kwargs):
"""Parse PSF file into Topology
Returns
-------
MDAnalysis *Topology* object
"""
# Open and check psf validity
with openany(self.filename) as psffile:
header = next(psffile)
if not header.startswith("PSF"):
err = "{0} is not valid PSF f... | https://github.com/MDAnalysis/mdanalysis/issues/2232 | ---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-6-90d681257701> in <module>
----> 1 u = mda.Universe(RNA_PSF)
/Volumes/Data/oliver/Biop/Projects/Methods/MDAnalysis/mdanalysis/package/MDAnalysis/core/u... | AttributeError |
def select_atoms(self, sel, *othersel, **selgroups):
"""Select :class:`Atoms<Atom>` using a selection string.
Returns an :class:`AtomGroup` with :class:`Atoms<Atom>` sorted according
to their index in the topology (this is to ensure that there are no
duplicates, which can happen with complicated select... | def select_atoms(self, sel, *othersel, **selgroups):
"""Select :class:`Atoms<Atom>` using a selection string.
Returns an :class:`AtomGroup` with :class:`Atoms<Atom>` sorted according
to their index in the topology (this is to ensure that there are no
duplicates, which can happen with complicated select... | https://github.com/MDAnalysis/mdanalysis/issues/1926 | TypeError Traceback (most recent call last)
<ipython-input-5-ec0d294eeb2a> in <module>()
1 u = mda.Universe(PDB)
----> 2 ref = u.copy()
~/anaconda3/lib/python3.6/site-packages/MDAnalysis/core/universe.py in copy(self)
337 def copy(self):
338 """Return an independent copy of ... | TypeError |
def atoms(self):
"""An :class:`AtomGroup` of :class:`Atoms<Atom>` present in this
:class:`ResidueGroup`.
The :class:`Atoms<Atom>` are ordered locally by :class:`Residue` in the
:class:`ResidueGroup`. Duplicates are *not* removed.
"""
# If indices is an empty list np.concatenate will fail (Issu... | def atoms(self):
"""An :class:`AtomGroup` of :class:`Atoms<Atom>` present in this
:class:`ResidueGroup`.
The :class:`Atoms<Atom>` are ordered locally by :class:`Residue` in the
:class:`ResidueGroup`. Duplicates are *not* removed.
"""
ag = self.universe.atoms[np.concatenate(self.indices)]
#... | https://github.com/MDAnalysis/mdanalysis/issues/1999 | ValueError: need at least one array to concatenate
Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2878, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-5-6c6c6b22c39a>", line 1, in <module>
sel.select_atoms('resname S... | ValueError |
def atoms(self):
"""An :class:`AtomGroup` of :class:`Atoms<Atom>` present in this
:class:`SegmentGroup`.
The :class:`Atoms<Atom>` are ordered locally by :class:`Residue`, which
are further ordered by :class:`Segment` in the :class:`SegmentGroup`.
Duplicates are *not* removed.
"""
# If indic... | def atoms(self):
"""An :class:`AtomGroup` of :class:`Atoms<Atom>` present in this
:class:`SegmentGroup`.
The :class:`Atoms<Atom>` are ordered locally by :class:`Residue`, which
are further ordered by :class:`Segment` in the :class:`SegmentGroup`.
Duplicates are *not* removed.
"""
ag = self.... | https://github.com/MDAnalysis/mdanalysis/issues/1999 | ValueError: need at least one array to concatenate
Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2878, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-5-6c6c6b22c39a>", line 1, in <module>
sel.select_atoms('resname S... | ValueError |
def check_slice_indices(self, start, stop, step):
"""Check frame indices are valid and clip to fit trajectory.
The usage follows standard Python conventions for :func:`range` but see
the warning below.
Parameters
----------
start : int or None
Starting frame index (inclusive). ``None`` c... | def check_slice_indices(self, start, stop, step):
"""Check frame indices are valid and clip to fit trajectory.
The usage follows standard Python conventions for :func:`range` but see
the warning below.
Parameters
----------
start : int or None
Starting frame index (inclusive). ``None`` c... | https://github.com/MDAnalysis/mdanalysis/issues/1944 | ---------------------------------------------------------------------------
EOFError Traceback (most recent call last)
<ipython-input-6-20f70c5f75bf> in <module>()
1 print(list(range(10)[10:0:-1]))
----> 2 print([ts.frame for ts in u.trajectory[10:0:-1]])
<ipython-input-6-20f70c5f75bf>... | EOFError |
def _single_frame(self):
index = self._frame_index
mobile_com = self.mobile_atoms.center(self._weights)
mobile_coordinates = self.mobile_atoms.positions - mobile_com
mobile_atoms, self.rmsd[index] = _fit_to(
mobile_coordinates,
self._ref_coordinates,
self.mobile,
mobile_c... | def _single_frame(self):
index = self._ts.frame
mobile_com = self.mobile_atoms.center(self._weights)
mobile_coordinates = self.mobile_atoms.positions - mobile_com
mobile_atoms, self.rmsd[index] = _fit_to(
mobile_coordinates,
self._ref_coordinates,
self.mobile,
mobile_com,... | https://github.com/MDAnalysis/mdanalysis/issues/1714 | ---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
<ipython-input-5-95462d8a76b2> in <module>()
----> 1 align.AlignTraj(u, ref, select='all', step=5, filename='test.xtc').run()
~/anaconda3/lib/python3.6/site-packages/M... | IndexError |
def __init__(
self,
atomgroup,
reference=None,
select="all",
groupselections=None,
filename="rmsd.dat",
weights=None,
tol_mass=0.1,
ref_frame=0,
**kwargs,
):
r"""
Parameters
----------
atomgroup : AtomGroup or Universe
Group of atoms for which the RMSD is ... | def __init__(
self,
atomgroup,
reference=None,
select="all",
groupselections=None,
filename="rmsd.dat",
weights=None,
tol_mass=0.1,
ref_frame=0,
**kwargs,
):
r"""
Parameters
----------
atomgroup : AtomGroup or Universe
Group of atoms for which the RMSD is ... | https://github.com/MDAnalysis/mdanalysis/issues/1487 | R = MDAnalysis.analysis.rms.RMSD(atomgroup=u, reference=u, select='backbone', groupselections=['backbone and resid 1:10','backbone and resid 10:20'])
R.run()
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-i... | ValueError |
def get_weights(atoms, weights):
"""Check that a `weights` argument is compatible with `atoms`.
Parameters
----------
atoms : AtomGroup or array_like
The atoms that the `weights` should be applied to. Typically this
is a :class:`AtomGroup` but because only the length is compared,
... | def get_weights(atoms, weights):
"""Check that a `weights` argument is compatible with `atoms`.
Parameters
----------
atoms : AtomGroup or array_like
The atoms that the `weights` should be applied to. Typically this
is a :class:`AtomGroup` but because only the length is compared,
... | https://github.com/MDAnalysis/mdanalysis/issues/1487 | R = MDAnalysis.analysis.rms.RMSD(atomgroup=u, reference=u, select='backbone', groupselections=['backbone and resid 1:10','backbone and resid 10:20'])
R.run()
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-i... | ValueError |
def _single_frame(self):
mobile_com = self.mobile_atoms.center(self.weights).astype(np.float64)
self._mobile_coordinates64[:] = self.mobile_atoms.positions
self._mobile_coordinates64 -= mobile_com
self.rmsd[self._frame_index, :2] = self._ts.frame, self._trajectory.time
if self._groupselections_ato... | def _single_frame(self):
mobile_com = self.mobile_atoms.center(self.weights).astype(np.float64)
self._mobile_coordinates64[:] = self.mobile_atoms.positions
self._mobile_coordinates64 -= mobile_com
self.rmsd[self._frame_index, :2] = self._ts.frame, self._trajectory.time
if self._groupselections_ato... | https://github.com/MDAnalysis/mdanalysis/issues/1487 | R = MDAnalysis.analysis.rms.RMSD(atomgroup=u, reference=u, select='backbone', groupselections=['backbone and resid 1:10','backbone and resid 10:20'])
R.run()
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-i... | ValueError |
def __init__(self, trzfilename, n_atoms=None, **kwargs):
"""Creates a TRZ Reader
Parameters
----------
trzfilename : str
name of input file
n_atoms : int
number of atoms in trajectory, must be taken from topology file!
convert_units : bool (optional)
converts units to MD... | def __init__(self, trzfilename, n_atoms=None, **kwargs):
"""Creates a TRZ Reader
Parameters
----------
trzfilename : str
name of input file
n_atoms : int
number of atoms in trajectory, must be taken from topology file!
convert_units : bool (optional)
converts units to MD... | https://github.com/MDAnalysis/mdanalysis/issues/1424 | Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/nose/case.py", line 381, in setUp
try_run(self.inst, ('setup', 'setUp'))
File "/usr/lib/python2.7/site-packages/nose/util.py", line 471, in try_run
return func()
File "/builddir/build/BUILD/MDAnalysis-0.16.1/MDAnalysisTests-0.16.1/MDAnalysisTests... | IOError |
def _read_trz_header(self):
"""Reads the header of the trz trajectory"""
self._headerdtype = np.dtype(
[
("p1", "<i4"),
("title", "80c"),
("p2", "<2i4"),
("force", "<i4"),
("p3", "<i4"),
]
)
data = np.fromfile(self.trzfile, dtyp... | def _read_trz_header(self):
"""Reads the header of the trz trajectory"""
self._headerdtype = np.dtype(
[("p1", "i4"), ("title", "80c"), ("p2", "2i4"), ("force", "i4"), ("p3", "i4")]
)
data = np.fromfile(self.trzfile, dtype=self._headerdtype, count=1)
self.title = "".join(c.decode("utf-8") fo... | https://github.com/MDAnalysis/mdanalysis/issues/1424 | Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/nose/case.py", line 381, in setUp
try_run(self.inst, ('setup', 'setUp'))
File "/usr/lib/python2.7/site-packages/nose/util.py", line 471, in try_run
return func()
File "/builddir/build/BUILD/MDAnalysis-0.16.1/MDAnalysisTests-0.16.1/MDAnalysisTests... | IOError |
def __init__(self, filename, n_atoms, title="TRZ", convert_units=None):
"""Create a TRZWriter
Parameters
----------
filename : str
name of output file
n_atoms : int
number of atoms in trajectory
title : str (optional)
title of the trajectory; the title must be 80 charact... | def __init__(self, filename, n_atoms, title="TRZ", convert_units=None):
"""Create a TRZWriter
Parameters
----------
filename : str
name of output file
n_atoms : int
number of atoms in trajectory
title : str (optional)
title of the trajectory; the title must be 80 charact... | https://github.com/MDAnalysis/mdanalysis/issues/1424 | Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/nose/case.py", line 381, in setUp
try_run(self.inst, ('setup', 'setUp'))
File "/usr/lib/python2.7/site-packages/nose/util.py", line 471, in try_run
return func()
File "/builddir/build/BUILD/MDAnalysis-0.16.1/MDAnalysisTests-0.16.1/MDAnalysisTests... | IOError |
def _writeheader(self, title):
hdt = np.dtype(
[
("pad1", "<i4"),
("title", "80c"),
("pad2", "<i4"),
("pad3", "<i4"),
("nrec", "<i4"),
("pad4", "<i4"),
]
)
out = np.zeros((), dtype=hdt)
out["pad1"], out["pad2"] = 80,... | def _writeheader(self, title):
hdt = np.dtype(
[
("pad1", "i4"),
("title", "80c"),
("pad2", "i4"),
("pad3", "i4"),
("nrec", "i4"),
("pad4", "i4"),
]
)
out = np.zeros((), dtype=hdt)
out["pad1"], out["pad2"] = 80, 80
... | https://github.com/MDAnalysis/mdanalysis/issues/1424 | Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/nose/case.py", line 381, in setUp
try_run(self.inst, ('setup', 'setUp'))
File "/usr/lib/python2.7/site-packages/nose/util.py", line 471, in try_run
return func()
File "/builddir/build/BUILD/MDAnalysis-0.16.1/MDAnalysisTests-0.16.1/MDAnalysisTests... | IOError |
def parse(self):
"""Parse atom information from PQR file *filename*.
Returns
-------
A MDAnalysis Topology object
"""
serials = []
names = []
resnames = []
chainIDs = []
resids = []
icodes = []
charges = []
radii = []
with openany(self.filename, "r") as f:
... | def parse(self):
"""Parse atom information from PQR file *filename*.
Returns
-------
A MDAnalysis Topology object
"""
serials = []
names = []
resnames = []
chainIDs = []
resids = []
charges = []
radii = []
with openany(self.filename, "r") as f:
for line in f... | https://github.com/MDAnalysis/mdanalysis/issues/1317 | ValueError Traceback (most recent call last)
<ipython-input-92-bd129cc992c5> in <module>()
----> 1 mda.Universe('1A2C.pqr')
/nfs/homes/kreidy/.local/lib/python2.7/site-packages/MDAnalysis/core/universe.pyc in __init__(self, *args, **kwargs)
246 raise ValueError("Faile... | ValueError |
def __init__(
self,
traj,
reference=None,
select="all",
groupselections=None,
filename="rmsd.dat",
mass_weighted=False,
tol_mass=0.1,
ref_frame=0,
):
"""Setting up the RMSD analysis.
The RMSD will be computed between *select* and *reference* for
all frames in the traject... | def __init__(
self,
traj,
reference=None,
select="all",
groupselections=None,
filename="rmsd.dat",
mass_weighted=False,
tol_mass=0.1,
ref_frame=0,
):
"""Setting up the RMSD analysis.
The RMSD will be computed between *select* and *reference* for
all frames in the traject... | https://github.com/MDAnalysis/mdanalysis/issues/897 | ---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-6-be62615c3dd7> in <module>()
----> 1 R = RMSD(u, select="protein and name CA")
/nfs/homes2/oliver/Library/python/mdanalysis/package/MDAnalysis/analysis... | NameError |
def _complete_for_arg(
self,
arg_action: argparse.Action,
text: str,
line: str,
begidx: int,
endidx: int,
consumed_arg_values: Dict[str, List[str]],
*,
cmd_set: Optional[CommandSet] = None,
) -> List[str]:
"""
Tab completion routine for an argparse argument
:return: list ... | def _complete_for_arg(
self,
arg_action: argparse.Action,
text: str,
line: str,
begidx: int,
endidx: int,
consumed_arg_values: Dict[str, List[str]],
*,
cmd_set: Optional[CommandSet] = None,
) -> List[str]:
"""
Tab completion routine for an argparse argument
:return: list ... | https://github.com/python-cmd2/cmd2/issues/967 | Traceback (most recent call last):
File "/home/martin/.virtualenvs/pyos/lib/python3.8/site-packages/cmd2/cmd2.py", line 1707, in complete
self._completion_for_command(text, line, begidx, endidx, shortcut_to_restore)
File "/home/martin/.virtualenvs/pyos/lib/python3.8/site-packages/cmd2/cmd2.py", line 1592, in _completio... | TypeError |
def _initialize_history(self, hist_file):
"""Initialize history using history related attributes
This function can determine whether history is saved in the prior text-based
format (one line of input is stored as one line in the file), or the new-as-
of-version 0.9.13 pickle based format.
History ... | def _initialize_history(self, hist_file):
"""Initialize history using history related attributes
This function can determine whether history is saved in the prior text-based
format (one line of input is stored as one line in the file), or the new-as-
of-version 0.9.13 pickle based format.
History ... | https://github.com/python-cmd2/cmd2/issues/785 | Traceback (most recent call last):
File "C:\Users\mattthk4\AppData\Local\Programs\Python\Python36\lib\runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "C:\Users\mattthk4\AppData\Local\Programs\Python\Python36\lib\runpy.py", line 85, in _run_code
exec(code, run_globals)
File "C:\Users\mattthk4\cven... | ValueError |
def _get_pointer(self):
try:
if self.thisdir.files[self._pointer] != self._pointed_obj:
try:
self._pointer = self.thisdir.files.index(self._pointed_obj)
except ValueError:
self._set_pointer(self._pointer)
except (TypeError, IndexError):
pas... | def _get_pointer(self):
if (
self.thisdir is not None
and self.thisdir.files[self._pointer] != self._pointed_obj
):
try:
self._pointer = self.thisdir.files.index(self._pointed_obj)
except ValueError:
self._pointed_obj = self.thisdir.files[self._pointer]
... | https://github.com/ranger/ranger/issues/2136 | $ ranger --clean (ai)
ranger version: ranger-master
Python version: 3.8.6 (default, Sep 30 2020, 04:00:38) [GCC 10.2.0]
Locale: en_GB.UTF-8
Traceback (most recent call last):
File "/usr/lib/python3.8/site-packages/ranger/core/main.py", line 203, in main
fm.loop(... | TypeError |
def _set_pointer(self, value):
self._pointer = value
try:
self._pointed_obj = self.thisdir.files[self._pointer]
except (TypeError, IndexError):
pass
| def _set_pointer(self, value):
self._pointer = value
try:
self._pointed_obj = self.thisdir.files[self._pointer]
except TypeError:
pass
except IndexError:
pass
| https://github.com/ranger/ranger/issues/2136 | $ ranger --clean (ai)
ranger version: ranger-master
Python version: 3.8.6 (default, Sep 30 2020, 04:00:38) [GCC 10.2.0]
Locale: en_GB.UTF-8
Traceback (most recent call last):
File "/usr/lib/python3.8/site-packages/ranger/core/main.py", line 203, in main
fm.loop(... | TypeError |
def _set_pointer(self, value):
self._pointer = value
try:
self._pointed_obj = self.thisdir.files[self._pointer]
except (TypeError, IndexError):
pass
| def _set_pointer(self, value):
self._pointer = value
self._pointed_obj = self.thisdir.files[self._pointer]
| https://github.com/ranger/ranger/issues/2071 | Message Log:
21:48:19 INFO ranger version: ranger-master
21:48:19 INFO Python version: 3.8.5 (default, Jul 27 2020, 08:42:51) [GCC 10.1.0]
21:48:19 INFO Locale: en_US.UTF-8
21:48:19 INFO Process ID: 73182
21:48:25 ERRO Notification: 'NoneType' object is not subscriptable
21:48:25 ERRO 'NoneType' object is not subscript... | TypeError |
def _set_pointer(self, value):
self._pointer = value
try:
self._pointed_obj = self.thisdir.files[self._pointer]
except TypeError:
pass
except IndexError:
pass
| def _set_pointer(self, value):
self._pointer = value
try:
self._pointed_obj = self.thisdir.files[self._pointer]
except TypeError:
pass
| https://github.com/ranger/ranger/issues/2173 | ranger version: ranger-master
Python version: 3.9.0 (default, Oct 7 2020, 23:09:01) [GCC 10.2.0]
Locale: en_IN.UTF-8
Traceback (most recent call last):
File "/usr/lib/python3.9/site-packages/ranger/core/main.py", line 203, in main
fm.loop()
File "/usr/lib/python3.9/site-packages/ranger/core/fm.py", line 382, in loop
... | IndexError |
def sha512_encode(path, inode=None):
if inode is None:
inode = stat(path).st_ino
inode_path = "{0}{1}".format(str(inode), path)
if PY3:
inode_path = inode_path.encode("utf-8", "backslashreplace")
return "{0}.jpg".format(sha512(inode_path).hexdigest())
| def sha512_encode(path, inode=None):
if inode is None:
inode = stat(path).st_ino
inode_path = "{0}{1}".format(str(inode), path)
if PY3:
inode_path = inode_path.encode("utf-8", "backslashescape")
return "{0}.jpg".format(sha512(inode_path).hexdigest())
| https://github.com/ranger/ranger/issues/2119 | ranger version: ranger-master
Python version: 3.8.5 (default, Sep 5 2020, 10:50:12) [GCC 10.2.0]
Locale: de_DE.UTF-8
Current file: '/path/to/my/file/Arbeitszeitnachweis_f\udc81r Minijobber_2020_09.PDF'
Traceback (most recent call last):
File "/usr/lib/python3.8/site-packages/ranger/core/main.py", line 203, in main
fm... | LookupError |
def sha512_encode(path, inode=None):
if inode is None:
inode = stat(path).st_ino
inode_path = "{0}{1}".format(str(inode), path)
if PY3:
inode_path = inode_path.encode("utf-8", "backslashescape")
return "{0}.jpg".format(sha512(inode_path).hexdigest())
| def sha512_encode(path, inode=None):
if inode is None:
inode = stat(path).st_ino
sha = sha512("{0}{1}".format(path, str(inode)).encode("utf-8", "backslashescape"))
return "{0}.jpg".format(sha.hexdigest())
| https://github.com/ranger/ranger/issues/2054 | Current file: '/tmp/example_f\xc2\xa1le.txt'
Traceback (most recent call last):
File "/home/panta/programs/ranger/ranger/core/main.py", line 203, in main
fm.loop()
File "/home/panta/programs/ranger/ranger/core/fm.py", line 376, in loop
ui.redraw()
File "/home/panta/programs/ranger/ranger/gui/ui.py", line 343, in redra... | UnicodeDecodeError |
def enter_dir(self, path, history=True):
"""Enter given path"""
# TODO: Ensure that there is always a self.thisdir
if path is None:
return None
path = str(path)
# clear filter in the folder we're leaving
if self.fm.settings.clear_filters_on_dir_change and self.thisdir:
self.this... | def enter_dir(self, path, history=True):
"""Enter given path"""
# TODO: Ensure that there is always a self.thisdir
if path is None:
return None
path = str(path)
# clear filter in the folder we're leaving
if self.fm.settings.clear_filters_on_dir_change and self.thisdir:
self.this... | https://github.com/ranger/ranger/issues/1386 | $ ranger/ranger.py ~/.config/neofetch/config.conf
ranger version: ranger-master 1.9.2
Python version: 2.7.15+ (default, Oct 2 2018, 22:12:08) [GCC 8.2.0]
Locale: None.None
Traceback (most recent call last):
File "/home/techtonik/p/ranger/ranger/core/main.py", line 195, in main
fm.loop()
File "/home/techtonik/p/ranger... | AttributeError |
def __init__(self, env=None, fm=None): # pylint: disable=super-init-not-called
self.keybuffer = KeyBuffer()
self.keymaps = KeyMaps(self.keybuffer)
self.redrawlock = threading.Event()
self.redrawlock.set()
self.titlebar = None
self._viewmode = None
self.taskview = None
self.status = Non... | def __init__(self, env=None, fm=None): # pylint: disable=super-init-not-called
self.keybuffer = KeyBuffer()
self.keymaps = KeyMaps(self.keybuffer)
self.redrawlock = threading.Event()
self.redrawlock.set()
self.titlebar = None
self._viewmode = None
self.taskview = None
self.status = Non... | https://github.com/ranger/ranger/issues/1805 | ranger version: ranger 1.9.3
Python version: 3.7.3 (default, Apr 3 2019, 05:39:12) [GCC 8.2.0]
Locale: en_US.UTF-8
Traceback (most recent call last):
File "/home/pi/.local/lib/python3.7/site-packages/ranger/core/main.py", line 171, in main
fm.initialize()
File "/home/pi/.local/lib/python3.7/site-packages/ranger/core/... | FileNotFoundError |
def handle_multiplexer(self):
if self.settings.update_tmux_title and not self._multiplexer_title:
try:
if _in_tmux():
# Stores the automatic-rename setting
# prints out a warning if allow-rename isn't set in tmux
try:
tmux_allow... | def handle_multiplexer(self):
if self.settings.update_tmux_title:
if "TMUX" in os.environ:
# Stores the automatic-rename setting
# prints out a warning if the allow-rename in tmux is not set
tmux_allow_rename = check_output(
["tmux", "show-window-options",... | https://github.com/ranger/ranger/issues/1805 | ranger version: ranger 1.9.3
Python version: 3.7.3 (default, Apr 3 2019, 05:39:12) [GCC 8.2.0]
Locale: en_US.UTF-8
Traceback (most recent call last):
File "/home/pi/.local/lib/python3.7/site-packages/ranger/core/main.py", line 171, in main
fm.initialize()
File "/home/pi/.local/lib/python3.7/site-packages/ranger/core/... | FileNotFoundError |
def restore_multiplexer_name(self):
if self._multiplexer_title:
try:
if _in_tmux():
if self._tmux_automatic_rename:
check_output(
[
"tmux",
"set-window-option",
... | def restore_multiplexer_name(self):
try:
if "TMUX" in os.environ:
if self._tmux_automatic_rename:
check_output(
[
"tmux",
"set-window-option",
"automatic-rename",
s... | https://github.com/ranger/ranger/issues/1805 | ranger version: ranger 1.9.3
Python version: 3.7.3 (default, Apr 3 2019, 05:39:12) [GCC 8.2.0]
Locale: en_US.UTF-8
Traceback (most recent call last):
File "/home/pi/.local/lib/python3.7/site-packages/ranger/core/main.py", line 171, in main
fm.initialize()
File "/home/pi/.local/lib/python3.7/site-packages/ranger/core/... | FileNotFoundError |
def main(
# pylint: disable=too-many-locals,too-many-return-statements
# pylint: disable=too-many-branches,too-many-statements
):
"""initialize objects and run the filemanager"""
import ranger.api
from ranger.container.settings import Settings
from ranger.core.shared import FileManagerAware, Set... | def main(
# pylint: disable=too-many-locals,too-many-return-statements
# pylint: disable=too-many-branches,too-many-statements
):
"""initialize objects and run the filemanager"""
import ranger.api
from ranger.container.settings import Settings
from ranger.core.shared import FileManagerAware, Set... | https://github.com/ranger/ranger/issues/1052 | shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
Traceback (most recent call last):
File "/github/ranger/ranger.py", line 36, in <module>... | OSError |
def data_status_root(self):
statuses = set()
# Paths with status
lines = self._run(["status"]).split("\n")
lines = list(filter(None, lines))
if not lines:
return "sync"
for line in lines:
code = line[0]
if code == " ":
continue
statuses.add(self._stat... | def data_status_root(self):
statuses = set()
# Paths with status
lines = self._run(["status"]).split("\n")
if not lines:
return "sync"
for line in lines:
code = line[0]
if code == " ":
continue
statuses.add(self._status_translate(code))
for status in... | https://github.com/ranger/ranger/issues/1296 | Message Log:
11:12:54 INFO ranger version: ranger-master 1.9.1
11:12:54 INFO Python version: 3.6.5 (default, Aug 9 2018, 08:22:49) [GCC 5.5.0]
11:12:54 INFO Locale: en_GB.UTF-8
11:12:54 INFO Process ID: 27126
11:12:56 ERRO Notification: VCS Exception: View log for more info
11:12:56 ERRO string index out of range
Trac... | IndexError |
def data_status_subpaths(self):
statuses = {}
# Paths with status
lines = self._run(["status"]).split("\n")
lines = list(filter(None, lines))
for line in lines:
code, path = line[0], line[8:]
if code == " ":
continue
statuses[os.path.normpath(path)] = self._statu... | def data_status_subpaths(self):
statuses = {}
# Paths with status
lines = self._run(["status"]).split("\n")
for line in lines:
code, path = line[0], line[8:]
if code == " ":
continue
statuses[os.path.normpath(path)] = self._status_translate(code)
return statuses... | https://github.com/ranger/ranger/issues/1296 | Message Log:
11:12:54 INFO ranger version: ranger-master 1.9.1
11:12:54 INFO Python version: 3.6.5 (default, Aug 9 2018, 08:22:49) [GCC 5.5.0]
11:12:54 INFO Locale: en_GB.UTF-8
11:12:54 INFO Process ID: 27126
11:12:56 ERRO Notification: VCS Exception: View log for more info
11:12:56 ERRO string index out of range
Trac... | IndexError |
def main(
# pylint: disable=too-many-locals,too-many-return-statements
# pylint: disable=too-many-branches,too-many-statements
):
"""initialize objects and run the filemanager"""
import ranger.api
from ranger.container.settings import Settings
from ranger.core.shared import FileManagerAware, Set... | def main(
# pylint: disable=too-many-locals,too-many-return-statements
# pylint: disable=too-many-branches,too-many-statements
):
"""initialize objects and run the filemanager"""
import ranger.api
from ranger.container.settings import Settings
from ranger.core.shared import FileManagerAware, Set... | https://github.com/ranger/ranger/issues/1137 | 16:15:22 ERRO Notification: 'NoneType' object has no attribute 'unload'
16:15:22 ERRO 'NoneType' object has no attribute 'unload'
Traceback (most recent call last):
File "/usr/lib/python3.6/site-packages/ranger/core/actions.py", line 251, in execute_console
cmd.execute()
File "/usr/lib/python3.6/site-packages/ranger/co... | AttributeError |
def _get_best_study_config(self):
metadata = {
"best_trial_number": self.study.best_trial.number,
"best_trial_evaluation": self.study.best_value,
}
pipeline_config = dict()
for k, v in self.study.user_attrs.items():
if k.startswith("pykeen_"):
metadata[k[len("pykeen_... | def _get_best_study_config(self):
metadata = {
"best_trial_number": self.study.best_trial.number,
"best_trial_evaluation": self.study.best_value,
}
pipeline_config = dict()
for k, v in self.study.user_attrs.items():
if k.startswith("pykeen_"):
metadata[k[len("pykeen_... | https://github.com/pykeen/pykeen/issues/230 | Traceback (most recent call last):
File "hpo_run.py", line 80, in <module>
run_hpo_search(args)
File "hpo_run.py", line 62, in run_hpo_search
hpo_pipeline_result.save_to_directory('study')
File "/home/user/anaconda3/envs/pykeen/lib/python3.8/site-packages/pykeen/hpo/hpo.py", line 327, in save_to_directory
json.dump(sel... | TypeError |
def hpo_pipeline(
*,
# 1. Dataset
dataset: Union[None, str, Dataset, Type[Dataset]] = None,
dataset_kwargs: Optional[Mapping[str, Any]] = None,
training: Union[None, str, TriplesFactory] = None,
testing: Union[None, str, TriplesFactory] = None,
validation: Union[None, str, TriplesFactory] = ... | def hpo_pipeline(
*,
# 1. Dataset
dataset: Union[None, str, Dataset, Type[Dataset]] = None,
dataset_kwargs: Optional[Mapping[str, Any]] = None,
training: Union[None, str, TriplesFactory] = None,
testing: Union[None, str, TriplesFactory] = None,
validation: Union[None, str, TriplesFactory] = ... | https://github.com/pykeen/pykeen/issues/230 | Traceback (most recent call last):
File "hpo_run.py", line 80, in <module>
run_hpo_search(args)
File "hpo_run.py", line 62, in run_hpo_search
hpo_pipeline_result.save_to_directory('study')
File "/home/user/anaconda3/envs/pykeen/lib/python3.8/site-packages/pykeen/hpo/hpo.py", line 327, in save_to_directory
json.dump(sel... | TypeError |
def pipeline( # noqa: C901
*,
# 1. Dataset
dataset: Union[None, str, Dataset, Type[Dataset]] = None,
dataset_kwargs: Optional[Mapping[str, Any]] = None,
training: Union[None, TriplesFactory, str] = None,
testing: Union[None, TriplesFactory, str] = None,
validation: Union[None, TriplesFactor... | def pipeline( # noqa: C901
*,
# 1. Dataset
dataset: Union[None, str, Dataset, Type[Dataset]] = None,
dataset_kwargs: Optional[Mapping[str, Any]] = None,
training: Union[None, TriplesFactory, str] = None,
testing: Union[None, TriplesFactory, str] = None,
validation: Union[None, TriplesFactor... | https://github.com/pykeen/pykeen/issues/230 | Traceback (most recent call last):
File "hpo_run.py", line 80, in <module>
run_hpo_search(args)
File "hpo_run.py", line 62, in run_hpo_search
hpo_pipeline_result.save_to_directory('study')
File "/home/user/anaconda3/envs/pykeen/lib/python3.8/site-packages/pykeen/hpo/hpo.py", line 327, in save_to_directory
json.dump(sel... | TypeError |
def summary_str(self, title: Optional[str] = None, end="\n") -> str:
"""Make a summary string of all of the factories."""
rows = self._summary_rows()
n_triples = sum(count for *_, count in rows)
rows.append(("Total", "-", "-", n_triples))
t = tabulate(rows, headers=["Name", "Entities", "Relations", ... | def summary_str(self, end="\n") -> str:
"""Make a summary string of all of the factories."""
rows = self._summary_rows()
n_triples = sum(count for *_, count in rows)
rows.append(("Total", "-", "-", n_triples))
t = tabulate(rows, headers=["Name", "Entities", "Relations", "Triples"])
return f"{sel... | https://github.com/pykeen/pykeen/issues/146 | Traceback (most recent call last):
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 49, in <module>
main()
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 36, in main
testing.new_with_restriction(relations=evaluation_relation_whitelist)
File "/Users/cthoyt/dev/pykeen/src/pykeen/triples/triples_factory.py", lin... | KeyError |
def summarize(self, title: Optional[str] = None, file=None) -> None:
"""Print a summary of the dataset."""
print(self.summary_str(title=title), file=file)
| def summarize(self) -> None:
"""Print a summary of the dataset."""
print(self.summary_str())
| https://github.com/pykeen/pykeen/issues/146 | Traceback (most recent call last):
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 49, in <module>
main()
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 36, in main
testing.new_with_restriction(relations=evaluation_relation_whitelist)
File "/Users/cthoyt/dev/pykeen/src/pykeen/triples/triples_factory.py", lin... | KeyError |
def _load(self) -> None:
self._training = TriplesFactory.from_path(
path=self.training_path,
create_inverse_triples=self.create_inverse_triples,
)
self._testing = TriplesFactory.from_path(
path=self.testing_path,
entity_to_id=self._training.entity_to_id, # share entity index... | def _load(self) -> None:
self._training = TriplesFactory.from_path(
path=self.training_path,
create_inverse_triples=self.create_inverse_triples,
)
self._testing = TriplesFactory.from_path(
path=self.testing_path,
entity_to_id=self._training.entity_to_id, # share entity index... | https://github.com/pykeen/pykeen/issues/146 | Traceback (most recent call last):
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 49, in <module>
main()
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 36, in main
testing.new_with_restriction(relations=evaluation_relation_whitelist)
File "/Users/cthoyt/dev/pykeen/src/pykeen/triples/triples_factory.py", lin... | KeyError |
def _load_validation(self) -> None:
# don't call this function by itself. assumes called through the `validation`
# property and the _training factory has already been loaded
self._validation = TriplesFactory.from_path(
path=self.validation_path,
entity_to_id=self._training.entity_to_id, # ... | def _load_validation(self) -> None:
# don't call this function by itself. assumes called through the `validation`
# property and the _training factory has already been loaded
self._validation = TriplesFactory.from_path(
path=self.validation_path,
entity_to_id=self._training.entity_to_id, # ... | https://github.com/pykeen/pykeen/issues/146 | Traceback (most recent call last):
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 49, in <module>
main()
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 36, in main
testing.new_with_restriction(relations=evaluation_relation_whitelist)
File "/Users/cthoyt/dev/pykeen/src/pykeen/triples/triples_factory.py", lin... | KeyError |
def generate_triples(
num_entities: int = 33,
num_relations: int = 7,
num_triples: int = 101,
compact: bool = True,
random_state: TorchRandomHint = None,
) -> torch.LongTensor:
"""Generate random triples in a torch tensor."""
random_state = ensure_torch_random_state(random_state)
rv = t... | def generate_triples(
num_entities: int = 33,
num_relations: int = 7,
num_triples: int = 101,
compact: bool = True,
random_state: RandomHint = None,
) -> np.ndarray:
"""Generate random triples."""
random_state = ensure_random_state(random_state)
rv = np.stack(
[
rando... | https://github.com/pykeen/pykeen/issues/146 | Traceback (most recent call last):
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 49, in <module>
main()
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 36, in main
testing.new_with_restriction(relations=evaluation_relation_whitelist)
File "/Users/cthoyt/dev/pykeen/src/pykeen/triples/triples_factory.py", lin... | KeyError |
def generate_labeled_triples(
num_entities: int = 33,
num_relations: int = 7,
num_triples: int = 101,
random_state: TorchRandomHint = None,
) -> np.ndarray:
"""Generate labeled random triples."""
mapped_triples = generate_triples(
num_entities=num_entities,
num_relations=num_rela... | def generate_labeled_triples(
num_entities: int = 33,
num_relations: int = 7,
num_triples: int = 101,
random_state: RandomHint = None,
) -> np.ndarray:
"""Generate labeled random triples."""
t = generate_triples(
num_entities=num_entities,
num_relations=num_relations,
num... | https://github.com/pykeen/pykeen/issues/146 | Traceback (most recent call last):
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 49, in <module>
main()
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 36, in main
testing.new_with_restriction(relations=evaluation_relation_whitelist)
File "/Users/cthoyt/dev/pykeen/src/pykeen/triples/triples_factory.py", lin... | KeyError |
def generate_triples_factory(
num_entities: int = 33,
num_relations: int = 7,
num_triples: int = 101,
random_state: TorchRandomHint = None,
create_inverse_triples: bool = False,
) -> TriplesFactory:
"""Generate a triples factory with random triples."""
mapped_triples = generate_triples(
... | def generate_triples_factory(
num_entities: int = 33,
num_relations: int = 7,
num_triples: int = 101,
random_state: RandomHint = None,
create_inverse_triples: bool = False,
) -> TriplesFactory:
"""Generate a triples factory with random triples."""
triples = generate_labeled_triples(
... | https://github.com/pykeen/pykeen/issues/146 | Traceback (most recent call last):
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 49, in <module>
main()
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 36, in main
testing.new_with_restriction(relations=evaluation_relation_whitelist)
File "/Users/cthoyt/dev/pykeen/src/pykeen/triples/triples_factory.py", lin... | KeyError |
def __init__(
self,
triples_factory: TriplesFactory,
minimum_frequency: Optional[float] = None,
symmetric: bool = True,
):
"""Index the inverse frequencies and the inverse relations in the triples factory.
:param triples_factory: The triples factory to index.
:param minimum_frequency: The m... | def __init__(
self,
triples_factory: TriplesFactory,
minimum_frequency: Optional[float] = None,
symmetric: bool = True,
use_tqdm: bool = True,
use_multiprocessing: bool = False,
):
"""Index the inverse frequencies and the inverse relations in the triples factory.
:param triples_factory:... | https://github.com/pykeen/pykeen/issues/146 | Traceback (most recent call last):
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 49, in <module>
main()
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 36, in main
testing.new_with_restriction(relations=evaluation_relation_whitelist)
File "/Users/cthoyt/dev/pykeen/src/pykeen/triples/triples_factory.py", lin... | KeyError |
def apply(self, triples_factory: TriplesFactory) -> TriplesFactory:
"""Make a new triples factory containing neither duplicate nor inverse relationships."""
return triples_factory.new_with_restriction(
relations=self.relations_to_delete, invert_relation_selection=True
)
| def apply(self, triples_factory: TriplesFactory) -> TriplesFactory:
"""Make a new triples factory containing neither duplicate nor inverse relationships."""
return triples_factory.new_without_relations(self.relations_to_delete)
| https://github.com/pykeen/pykeen/issues/146 | Traceback (most recent call last):
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 49, in <module>
main()
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 36, in main
testing.new_with_restriction(relations=evaluation_relation_whitelist)
File "/Users/cthoyt/dev/pykeen/src/pykeen/triples/triples_factory.py", lin... | KeyError |
def unleak(
train: TriplesFactory,
*triples_factories: TriplesFactory,
n: Union[None, int, float] = None,
minimum_frequency: Optional[float] = None,
) -> Iterable[TriplesFactory]:
"""Unleak a train, test, and validate triples factory.
:param train: The target triples factory
:param triples_... | def unleak(
train: TriplesFactory,
*triples_factories: TriplesFactory,
n: Union[None, int, float] = None,
minimum_frequency: Optional[float] = None,
) -> Iterable[TriplesFactory]:
"""Unleak a train, test, and validate triples factory.
:param train: The target triples factory
:param triples_... | https://github.com/pykeen/pykeen/issues/146 | Traceback (most recent call last):
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 49, in <module>
main()
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 36, in main
testing.new_with_restriction(relations=evaluation_relation_whitelist)
File "/Users/cthoyt/dev/pykeen/src/pykeen/triples/triples_factory.py", lin... | KeyError |
def reindex(*triples_factories: TriplesFactory) -> List[TriplesFactory]:
"""Reindex a set of triples factories."""
# get entities and relations occurring in triples
all_triples = torch.cat(
[factory.mapped_triples for factory in triples_factories], dim=0
)
# generate ID translation and new ... | def reindex(*triples_factories: TriplesFactory) -> List[TriplesFactory]:
"""Reindex a set of triples factories."""
triples = np.concatenate(
[triples_factory.triples for triples_factory in triples_factories],
axis=0,
)
entity_to_id = create_entity_mapping(triples)
relation_to_id = cr... | https://github.com/pykeen/pykeen/issues/146 | Traceback (most recent call last):
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 49, in <module>
main()
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 36, in main
testing.new_with_restriction(relations=evaluation_relation_whitelist)
File "/Users/cthoyt/dev/pykeen/src/pykeen/triples/triples_factory.py", lin... | KeyError |
def _main():
"""Test unleaking FB15K.
Run with ``python -m pykeen.triples.leakage``.
"""
from pykeen.datasets import get_dataset
logging.basicConfig(format="pykeen: %(message)s", level=logging.INFO)
fb15k = get_dataset(dataset="fb15k")
fb15k.summarize()
n = 401 # magic 401 from the ... | def _main():
"""Test unleaking FB15K.
Run with ``python -m pykeen.triples.leakage``.
"""
from pykeen.datasets import get_dataset
logging.basicConfig(format="pykeen: %(message)s", level=logging.INFO)
print("Summary FB15K")
fb15k = get_dataset(dataset="fb15k")
summarize(fb15k.training, ... | https://github.com/pykeen/pykeen/issues/146 | Traceback (most recent call last):
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 49, in <module>
main()
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 36, in main
testing.new_with_restriction(relations=evaluation_relation_whitelist)
File "/Users/cthoyt/dev/pykeen/src/pykeen/triples/triples_factory.py", lin... | KeyError |
def from_labeled_triples(
cls,
triples: LabeledTriples,
create_inverse_triples: bool = False,
entity_to_id: Optional[EntityMapping] = None,
relation_to_id: Optional[RelationMapping] = None,
compact_id: bool = True,
filter_out_candidate_inverse_relations: bool = True,
) -> "TriplesFactory":
... | def from_labeled_triples(
cls,
triples: LabeledTriples,
create_inverse_triples: bool = False,
entity_to_id: Optional[EntityMapping] = None,
relation_to_id: Optional[RelationMapping] = None,
compact_id: bool = True,
) -> "TriplesFactory":
"""
Create a new triples factory from label-based ... | https://github.com/pykeen/pykeen/issues/146 | Traceback (most recent call last):
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 49, in <module>
main()
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 36, in main
testing.new_with_restriction(relations=evaluation_relation_whitelist)
File "/Users/cthoyt/dev/pykeen/src/pykeen/triples/triples_factory.py", lin... | KeyError |
def num_relations(self) -> int: # noqa: D401
"""The number of unique relations."""
if self.create_inverse_triples:
return 2 * self.real_num_relations
return self.real_num_relations
| def num_relations(self) -> int: # noqa: D401
"""The number of unique relations."""
return len(self.relation_to_id)
| https://github.com/pykeen/pykeen/issues/146 | Traceback (most recent call last):
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 49, in <module>
main()
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 36, in main
testing.new_with_restriction(relations=evaluation_relation_whitelist)
File "/Users/cthoyt/dev/pykeen/src/pykeen/triples/triples_factory.py", lin... | KeyError |
def triples(self) -> np.ndarray: # noqa: D401
"""The labeled triples, a 3-column matrix where each row are the head label, relation label, then tail label."""
logger.warning(
"Reconstructing all label-based triples. This is expensive and rarely needed."
)
return self.label_triples(self.mapped_t... | def triples(self) -> np.ndarray: # noqa: D401
"""The labeled triples."""
# TODO: Deprecation warning. Will be replaced by re-constructing them from ID-based + mapping soon.
return self._triples
| https://github.com/pykeen/pykeen/issues/146 | Traceback (most recent call last):
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 49, in <module>
main()
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 36, in main
testing.new_with_restriction(relations=evaluation_relation_whitelist)
File "/Users/cthoyt/dev/pykeen/src/pykeen/triples/triples_factory.py", lin... | KeyError |
def get_inverse_relation_id(self, relation: Union[str, int]) -> int:
"""Get the inverse relation identifier for the given relation."""
if not self.create_inverse_triples:
raise ValueError("Can not get inverse triple, they have not been created.")
relation = next(iter(self.relations_to_ids(relations=... | def get_inverse_relation_id(self, relation: str) -> int:
"""Get the inverse relation identifier for the given relation."""
if not self.create_inverse_triples:
raise ValueError("Can not get inverse triple, they have not been created.")
inverse_relation = self.relation_to_inverse[relation]
return ... | https://github.com/pykeen/pykeen/issues/146 | Traceback (most recent call last):
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 49, in <module>
main()
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 36, in main
testing.new_with_restriction(relations=evaluation_relation_whitelist)
File "/Users/cthoyt/dev/pykeen/src/pykeen/triples/triples_factory.py", lin... | KeyError |
def create_slcwa_instances(self) -> Instances:
"""Create sLCWA instances for this factory's triples."""
return SLCWAInstances(
mapped_triples=self._add_inverse_triples_if_necessary(
mapped_triples=self.mapped_triples
)
)
| def create_slcwa_instances(self) -> Instances:
"""Create sLCWA instances for this factory's triples."""
return SLCWAInstances(mapped_triples=self.mapped_triples)
| https://github.com/pykeen/pykeen/issues/146 | Traceback (most recent call last):
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 49, in <module>
main()
File "/Users/cthoyt/dev/pykeen/scratch/tst.py", line 36, in main
testing.new_with_restriction(relations=evaluation_relation_whitelist)
File "/Users/cthoyt/dev/pykeen/src/pykeen/triples/triples_factory.py", lin... | KeyError |
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