text:
Errors during opening certain EDF files

with mne.io.read_raw_edf(file, preload=False)
I got the following error:
EDF file detected
Setting channel info structure...
Creating raw.info structure...

<ipython-input-15-1c792ee67613>:21: RuntimeWarning: 6 channel names are too long, have been truncated to 15 characters:
['Sensor-E:EDA (Ha', '[A] EEG (1-45 Hz', '[B] EEG (1-45 Hz', '[C] EEG (1-45 Hz', '[D] EEG (1-45 Hz', '[G] HRV-LF / HRV']
  raw.append(mne.io.read_raw_edf(file, preload=False))

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-15-1c792ee67613> in <module>()
     19 for file in file_list:
     20     file = os.path.join(path,file)
---> 21     raw.append(mne.io.read_raw_edf(file, preload=False))
     22     #raw.append(mne.io.read_raw_edf(file, preload=True, stim_channel=None))

C:\ProgramData\Anaconda3\lib\site-packages\mne\io\edf\edf.py in read_raw_edf(input_fname, montage, eog, misc, stim_channel, exclude, preload, verbose)
   1171     return RawEDF(input_fname=input_fname, montage=montage, eog=eog, misc=misc,
   1172                   stim_channel=stim_channel, exclude=exclude, preload=preload,
-> 1173                   verbose=verbose)
   1174
   1175

<C:\ProgramData\Anaconda3\lib\site-packages\mne\externals\decorator.py:decorator-gen-157> in __init__(self, input_fname, montage, eog, misc, stim_channel, exclude, preload, verbose)

C:\ProgramData\Anaconda3\lib\site-packages\mne\utils\_logging.py in wrapper(*args, **kwargs)
     88             with use_log_level(verbose_level):
     89                 return function(*args, **kwargs)
---> 90         return function(*args, **kwargs)
     91     return FunctionMaker.create(
     92         function, 'return decfunc(%(signature)s)',

C:\ProgramData\Anaconda3\lib\site-packages\mne\io\edf\edf.py in __init__(self, input_fname, montage, eog, misc, stim_channel, exclude, preload, verbose)
    130             # Read TAL data exploiting the header info (no regexp)
    131             tal_data = self._read_segment_file([], [], 0, 0, int(self.n_times),
--> 132                                                None, None)
    133             onset, duration, desc = _read_annotations_edf(tal_data[0])
    134

<C:\ProgramData\Anaconda3\lib\site-packages\mne\externals\decorator.py:decorator-gen-158> in _read_segment_file(self, data, idx, fi, start, stop, cals, mult)

C:\ProgramData\Anaconda3\lib\site-packages\mne\utils\_logging.py in wrapper(*args, **kwargs)
     88             with use_log_level(verbose_level):
     89                 return function(*args, **kwargs)
---> 90         return function(*args, **kwargs)
     91     return FunctionMaker.create(
     92         function, 'return decfunc(%(signature)s)',

C:\ProgramData\Anaconda3\lib\site-packages\mne\io\edf\edf.py in _read_segment_file(self, data, idx, fi, start, stop, cals, mult)
    143         return _read_segment_file(data, idx, fi, start, stop,
    144                                   self._raw_extras[fi], self.info['chs'],
--> 145                                   self._filenames[fi])
    146
    147

C:\ProgramData\Anaconda3\lib\site-packages\mne\io\edf\edf.py in _read_segment_file(data, idx, fi, start, stop, raw_extras, chs, filenames)
    319                             npad=0, axis=-1)
    320                 assert ch_data.shape == (len(ch_data), buf_len)
--> 321                 data[ii, d_sidx:d_eidx] = ch_data.ravel()[r_sidx:r_eidx]
    322
    323     # only try to read the stim channel if it's not None and it's

TypeError: list indices must be integers or slices, not tuple

with mne.io.read_raw_edf(file, preload=True)
I got a different error:
EDF file detected
Setting channel info structure...
Creating raw.info structure...
Reading 0 ... 184319  =      0.000 ...   719.996 secs...

<ipython-input-16-40cad0d0f48b>:22: RuntimeWarning: 6 channel names are too long, have been truncated to 15 characters:
['Sensor-E:EDA (Ha', '[A] EEG (1-45 Hz', '[B] EEG (1-45 Hz', '[C] EEG (1-45 Hz', '[D] EEG (1-45 Hz', '[G] HRV-LF / HRV']
  raw.append(mne.io.read_raw_edf(file, preload=True))

---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
<ipython-input-16-40cad0d0f48b> in <module>()
     20     file = os.path.join(path,file)
     21     #raw.append(mne.io.read_raw_edf(file, preload=False))
---> 22     raw.append(mne.io.read_raw_edf(file, preload=True))

C:\ProgramData\Anaconda3\lib\site-packages\mne\io\edf\edf.py in read_raw_edf(input_fname, montage, eog, misc, stim_channel, exclude, preload, verbose)
   1171     return RawEDF(input_fname=input_fname, montage=montage, eog=eog, misc=misc,
   1172                   stim_channel=stim_channel, exclude=exclude, preload=preload,
-> 1173                   verbose=verbose)
   1174
   1175

<C:\ProgramData\Anaconda3\lib\site-packages\mne\externals\decorator.py:decorator-gen-157> in __init__(self, input_fname, montage, eog, misc, stim_channel, exclude, preload, verbose)

C:\ProgramData\Anaconda3\lib\site-packages\mne\utils\_logging.py in wrapper(*args, **kwargs)
     88             with use_log_level(verbose_level):
     89                 return function(*args, **kwargs)
---> 90         return function(*args, **kwargs)
     91     return FunctionMaker.create(
     92         function, 'return decfunc(%(signature)s)',

C:\ProgramData\Anaconda3\lib\site-packages\mne\io\edf\edf.py in __init__(self, input_fname, montage, eog, misc, stim_channel, exclude, preload, verbose)
    123                          raw_extras=[edf_info], last_samps=last_samps,
    124                          orig_format='int', orig_units=orig_units,
--> 125                          verbose=verbose)
    126
    127         # Read annotations from file and set it

<C:\ProgramData\Anaconda3\lib\site-packages\mne\externals\decorator.py:decorator-gen-138> in __init__(self, info, preload, first_samps, last_samps, filenames, raw_extras, orig_format, dtype, buffer_size_sec, orig_units, verbose)

C:\ProgramData\Anaconda3\lib\site-packages\mne\utils\_logging.py in wrapper(*args, **kwargs)
     88             with use_log_level(verbose_level):
     89                 return function(*args, **kwargs)
---> 90         return function(*args, **kwargs)
     91     return FunctionMaker.create(
     92         function, 'return decfunc(%(signature)s)',

C:\ProgramData\Anaconda3\lib\site-packages\mne\io\base.py in __init__(self, info, preload, first_samps, last_samps, filenames, raw_extras, orig_format, dtype, buffer_size_sec, orig_units, verbose)
    422         self._update_times()
    423         if load_from_disk:
--> 424             self._preload_data(preload)
    425         self._init_kwargs = _get_argvalues()
    426

<C:\ProgramData\Anaconda3\lib\site-packages\mne\externals\decorator.py:decorator-gen-141> in _preload_data(self, preload, verbose)

C:\ProgramData\Anaconda3\lib\site-packages\mne\utils\_logging.py in wrapper(*args, **kwargs)
     88             with use_log_level(verbose_level):
     89                 return function(*args, **kwargs)
---> 90         return function(*args, **kwargs)
     91     return FunctionMaker.create(
     92         function, 'return decfunc(%(signature)s)',

C:\ProgramData\Anaconda3\lib\site-packages\mne\io\base.py in _preload_data(self, preload, verbose)
    667         logger.info('Reading %d ... %d  =  %9.3f ... %9.3f secs...' %
    668                     (0, len(self.times) - 1, 0., self.times[-1]))
--> 669         self._data = self._read_segment(data_buffer=data_buffer)
    670         assert len(self._data) == self.info['nchan']
    671         self.preload = True

C:\ProgramData\Anaconda3\lib\site-packages\mne\io\base.py in _read_segment(self, start, stop, sel, data_buffer, projector, verbose)
    566             self._read_segment_file(data[:, this_sl], idx, fi,
    567                                     int(start_file), int(stop_file),
--> 568                                     cals, mult)
    569             offset += n_read
    570         return data

<C:\ProgramData\Anaconda3\lib\site-packages\mne\externals\decorator.py:decorator-gen-158> in _read_segment_file(self, data, idx, fi, start, stop, cals, mult)

C:\ProgramData\Anaconda3\lib\site-packages\mne\utils\_logging.py in wrapper(*args, **kwargs)
     88             with use_log_level(verbose_level):
     89                 return function(*args, **kwargs)
---> 90         return function(*args, **kwargs)
     91     return FunctionMaker.create(
     92         function, 'return decfunc(%(signature)s)',

C:\ProgramData\Anaconda3\lib\site-packages\mne\io\edf\edf.py in _read_segment_file(self, data, idx, fi, start, stop, cals, mult)
    143         return _read_segment_file(data, idx, fi, start, stop,
    144                                   self._raw_extras[fi], self.info['chs'],
--> 145                                   self._filenames[fi])
    146
    147

C:\ProgramData\Anaconda3\lib\site-packages\mne\io\edf\edf.py in _read_segment_file(data, idx, fi, start, stop, raw_extras, chs, filenames)
    319                             npad=0, axis=-1)
    320                 assert ch_data.shape == (len(ch_data), buf_len)
--> 321                 data[ii, d_sidx:d_eidx] = ch_data.ravel()[r_sidx:r_eidx]
    322
    323     # only try to read the stim channel if it's not None and it's

IndexError: index 11 is out of bounds for axis 0 with size 10

Can anyone help me with this?

can you share a problematic file?

In addition, could you please check if the problematic file passes the validation in EDFbrowser (https://www.teuniz.net/edfbrowser/EDFbrowser manual.html#EDF_and_BDF_compatibility_checker)?

In addition, could you please check if the problematic file passes the validation in EDFbrowser (https://www.teuniz.net/edfbrowser/EDFbrowser manual.html#EDF_and_BDF_compatibility_checker)?

This is really a nice useful tool. I checked the file with this tool, unfortunately the file cannot be opened either. The problem would be the file and I'll have the file fixed first then. Thanks a lot!

In addition, could you please check if the problematic file passes the validation in EDFbrowser (https://www.teuniz.net/edfbrowser/EDFbrowser manual.html#EDF_and_BDF_compatibility_checker)?

The file was fixed and EDFbrowser can open this file now, but I still get the same error while opening it in MNE.
Since I do not wish to make this file public, shall I share this privately e.g. via email?

What did you do to fix the file? Sure, just send me a link to the file (since I assume it will be too large to attach directly).

What did you do to fix the file? Sure, just send me a link to the file (since I assume it will be too large to attach directly).

I did not fix the file by myself. I got another exported file from the same recording. The file is here: https://drive.google.com/drive/folders/1j32lv4g4brHuqOYnchr6cPZIDeh94S0x?usp=sharing

Thanks, I'll take a look.

This file works with 0.20 - can you try with that latest version?

This file works with 0.20 - can you try with that latest version?

I updated my MNE to 0.20 and could read the file. Thanks a lot.

authors: agramfort cbrnr datalw


text:
Accessing data after applying gradient compensation & picking doesn't work

Steps to reproduce
import os.path as op
from mne.io import read_raw_fif

base_dir = op.join('/Users/hoechenberger/Development/mne-python/mne', 'io',
                   'tests', 'data')
raw_ctf_fname = op.join(base_dir, 'test_ctf_raw.fif')

raw = read_raw_fif(raw_ctf_fname, preload=False)
raw.apply_gradient_compensation(3)
raw.copy().pick_types(meg=True).get_data()

Expected results
Opening raw data file /Users/hoechenberger/Development/mne-python/mne/io/tests/data/test_ctf_raw.fif...
    Read 5 compensation matrices
    Range : 24000 ... 31200 =     10.000 ...    13.000 secs
Ready.
Current compensation grade : 0
Reading 0 ... 7200  =      0.000 ...     3.000 secs...
Compensator constructed to change 0 -> 3
Applying compensator to loaded data

Actual results
Opening raw data file /Users/hoechenberger/Development/mne-python/mne/io/tests/data/test_ctf_raw.fif...
    Read 5 compensation matrices
    Range : 24000 ... 31200 =     10.000 ...    13.000 secs
Ready.
Current compensation grade : 0
Compensator constructed to change 0 -> 3
Traceback (most recent call last):
  File "/private/tmp/mwe.py", line 10, in <module>
    raw.copy().pick_types(meg=True).get_data()
  File "<decorator-gen-166>", line 21, in get_data
  File "/Users/hoechenberger/Development/mne-python/mne/io/base.py", line 823, in get_data
    data, times = self[picks, start:stop]
  File "/Users/hoechenberger/Development/mne-python/mne/io/base.py", line 772, in __getitem__
    data = self._read_segment(start=start, stop=stop, sel=sel,
  File "<decorator-gen-163>", line 21, in _read_segment
  File "/Users/hoechenberger/Development/mne-python/mne/io/base.py", line 375, in _read_segment
    mult = self._comp[idx] * cals
ValueError: operands could not be broadcast together with shapes (304,309) (1,304)

Additional information
If the data is preloaded:
raw = read_raw_fif(raw_ctf_fname, preload=True)

the problem does not occur.
Also if I skip the pick_types() it does work.
NumPy is 1.19.1.

I can look into this in the coming days

source: gharchive/issue

authors: hoechenberger larsoner

repo: mne-tools/mne-python

license_type: permissive

license_source: github-api


text:
Add methods to render bem, add html str to report

Addresses #1793.

It would be good to have a test at least for the HTML-adding functionality. The BEM would be nice, too, but it's only a one-line wrapper so probably overkill.

test added and travis et al are happy again

Nice, thanks!

source: gharchive/pull-request


text:
Solving issue related with infomax when weights in not None

@Eric89GXL , @agramfort (this is the bug that I talked to you this week)
This pull request aims to solve an issue related with infomax when weights in not None.
The current infomax implementation does all its calculations using a transposed version of the weights matrix, and at the end it returns weights.T. But, if the user gives as input a weights matrix, infomax will take it as it is, that is, it will not transpose it, which results in a subtle error:
the algorithm will run, but the result will not be correct because it has not used the correct initial weights matrix.
Reproducibilitiy of this subtle error:
If we run infomax using max_iter=0, the resulting weights matrix should be the same initial weights matrix provided by the user:

import numpy as np
from mne.preprocessing.infomax_ import infomax
X = np.random.random((3, 100))
weights = np.array([[1,2,3],[4,5,6],[7,8,9]], dtype=np.float64)
w1 = infomax(X, max_iter=0, weights=weights, extended=True)
w2 = infomax(X, max_iter=0, weights=weights, extended=False)
Here we can see that the resulting weights matrix is the transposed version of the weights matrix provided by the user, which is an error.
This pull request contains the solution to this issue, as well as the corresponding test.

Current coverage is 87.29% (diff: 100%)

Merging #3614 into master will increase coverage by 4.45%

@@             master      #3614   diff @@
==========================================
  Files           341        341
  Lines         60542      60550      +8
  Methods           0          0
  Messages          0          0
  Branches       9271       9271
==========================================
+ Hits          50150      52855   +2705
+ Misses         7745       4937   -2808
- Partials       2647       2758    +111

Powered by Codecov. Last update e9dd187...9ff4ffc

@jmontoyam thanks heaps
can you update what's new bug section?
thx

@agramfort I have updated what's new bug section.

Thx !

authors: agramfort codecov-io jmontoyam


text:
ENH: Adding support of GridSearchCV for mne.decoding.LinearModel

Reference issue
Example: Fixes #7027 .
What does this implement/fix?
This PR adds the support of GridSearchCV for LinearModel. I also ran the decoding/tests/test_base.py and got the 3 passed.

@iamsc can you please add a new test in  https://github.com/mne-tools/mne-python/blob/master/mne/decoding/tests/test_base.py ? thx

@iamsc can you please add a new test in https://github.com/mne-tools/mne-python/blob/master/mne/decoding/tests/test_base.py ? thx

No problem~ I have modified some tests in test_base.py.
Because the original test_get_coef function in test_base.py only focused on the regression estimator tests, I added some new tests which considers some possible types of estimators, likes classification, regression, classification with GridSearchCV, regression with GridSearchCV.
Moreover, in test_linearmodel function, I also added the classification/regression with GridSearchCV tests.

@iamsc you have some flake8 errors. Run make pep or flake8 on your files to see what's wrong

@iamsc you have some flake8 errors. Run make pep or flake8 on your files to see what's wrong

Sorry for those errors. I have already fixed those errors on my files using make pep.
However, there are still some other errors from make pep, likes mne/tests/test_docstring_parameters.py. I just ignored this kind of errors because I have not modified those files in this PR.

tests should be as fast as possible. Can you report how long it takes to run now compared to before?

If it only sets cv as 2, the test duration will decrease 77.17 seconds compared to before.
========================================================================== slowest 20 test durations ===========================================================================
180.56s call     mne/decoding/tests/test_base.py::test_get_coef
3.36s setup    mne/decoding/tests/test_base.py::test_get_coef
0.50s call     mne/decoding/tests/test_base.py::test_cross_val_multiscore
0.08s call     mne/decoding/tests/test_base.py::test_linearmodel
0.00s setup    mne/decoding/tests/test_base.py::test_linearmodel
0.00s setup    mne/decoding/tests/test_base.py::test_cross_val_multiscore
0.00s teardown mne/decoding/tests/test_base.py::test_get_coef
0.00s teardown mne/decoding/tests/test_base.py::test_cross_val_multiscore
0.00s teardown mne/decoding/tests/test_base.py::test_linearmodel

Results (184.80s):
       3 passed

If I remove 1000 from C list in parameter grids and set cv  as 2, the test duration will decrease to 15.92 seconds.
========================================================================== slowest 20 test durations ===========================================================================
11.61s call     mne/decoding/tests/test_base.py::test_get_coef
3.60s setup    mne/decoding/tests/test_base.py::test_get_coef
0.19s call     mne/decoding/tests/test_base.py::test_cross_val_multiscore
0.03s call     mne/decoding/tests/test_base.py::test_linearmodel
0.00s setup    mne/decoding/tests/test_base.py::test_linearmodel
0.00s setup    mne/decoding/tests/test_base.py::test_cross_val_multiscore
0.00s teardown mne/decoding/tests/test_base.py::test_cross_val_multiscore
0.00s teardown mne/decoding/tests/test_base.py::test_get_coef
0.00s teardown mne/decoding/tests/test_base.py::test_linearmodel

Results (15.69s):
       3 passed

I will re-commit the second one later.

Even 11 sec is quite long for a test. How long is it in master? Ideally these changes wouldn't add more than 0.1 sec or so. We run a lot of tests, and a lot that do much more complex processing than this, so we need to keep test times to a minimum.
If you need help speeding it up let me know and I can look at tweaking the test to get the time down

Even 11 sec is quite long for a test. How long is it in master? Ideally these changes wouldn't add more than 0.1 sec or so. We run a lot of tests, and a lot that do much more complex processing than this, so we need to keep test times to a minimum.
If you need help speeding it up let me know and I can look at tweaking the test to get the time down

Here is the time duration results of master:
========================================================================== slowest 20 test durations ===========================================================================
3.59s setup    mne/decoding/tests/test_base.py::test_get_coef
0.70s call     mne/decoding/tests/test_base.py::test_get_coef
0.23s call     mne/decoding/tests/test_base.py::test_cross_val_multiscore
0.01s call     mne/decoding/tests/test_base.py::test_linearmodel
0.00s setup    mne/decoding/tests/test_base.py::test_linearmodel
0.00s teardown mne/decoding/tests/test_base.py::test_cross_val_multiscore
0.00s teardown mne/decoding/tests/test_base.py::test_get_coef
0.00s setup    mne/decoding/tests/test_base.py::test_cross_val_multiscore
0.00s teardown mne/decoding/tests/test_base.py::test_linearmodel

Results (4.82s):
       3 passed

I also tried to remove 100 from C list further, the results are as follows:
========================================================================== slowest 20 test durations ===========================================================================
4.07s setup    mne/decoding/tests/test_base.py::test_get_coef
1.32s call     mne/decoding/tests/test_base.py::test_get_coef
0.21s call     mne/decoding/tests/test_base.py::test_cross_val_multiscore
0.02s call     mne/decoding/tests/test_base.py::test_linearmodel
0.00s setup    mne/decoding/tests/test_base.py::test_linearmodel
0.00s teardown mne/decoding/tests/test_base.py::test_cross_val_multiscore
0.00s setup    mne/decoding/tests/test_base.py::test_cross_val_multiscore
0.00s teardown mne/decoding/tests/test_base.py::test_linearmodel
0.00s teardown mne/decoding/tests/test_base.py::test_get_coef

Results (6.03s):
       3 passed

It seems like to close to the time duration in master. I come up with some possible directions I can try with, such as reducing the testing sample size, removing some tests for the possible types of estimators, etc. @larsoner do you have other suggestions that I can also try with?

I would try those, plus reducing the number of samples and/or features.
If the regressors/estimators you are iterating over are sklearn estimators, you probably don't need to do more than one. We can trust them to adhere to their own API requirements, so testing a single one should work.

Thanks @larsoner for your suggestions. I have tweaked some tests, including removing some estimators, reducing the parameter space, and reducing the number of samples.
Here is the new time duration:
========================================================================== slowest 20 test durations ===========================================================================
3.22s setup    mne/decoding/tests/test_base.py::test_get_coef
0.79s call     mne/decoding/tests/test_base.py::test_get_coef
0.21s call     mne/decoding/tests/test_base.py::test_cross_val_multiscore
0.02s call     mne/decoding/tests/test_base.py::test_linearmodel
0.00s setup    mne/decoding/tests/test_base.py::test_linearmodel
0.00s setup    mne/decoding/tests/test_base.py::test_cross_val_multiscore
0.00s teardown mne/decoding/tests/test_base.py::test_cross_val_multiscore
0.00s teardown mne/decoding/tests/test_base.py::test_linearmodel
0.00s teardown mne/decoding/tests/test_base.py::test_get_coef

Results (4.43s):
       3 passed

OK~ No problem.

Thx @iamsc !

I’m happy to contribute to MNE and learn from you folks. Thanks @agramfort and @larsoner .
Sent with GitHawk

looking forward to your next PRs :)
thanks for contributing

authors: agramfort iamsc larsoner


text:
Update download URL to pyvistaqt main branch

Follows https://github.com/mne-tools/mne-python/pull/9497/files and https://github.com/pyvista/pyvistaqt/pull/120, the PR updates the branch name of pyvistaqt.

Please merge once CIs come back happy!

I manually downloaded the file so I'll try to save the CIs some cycles here

authors: GuillaumeFavelier larsoner


text:
Zoom/Pan a Viewgroup (RelativeLayout/Framelayout) containing multiple child views inside it.

Hello,
Nice work.
Was just wondering how can I achieve zoom/pan on an entire Viewgroup which contains multiple child views (buttons, imageviews etc) altogether. So basically I want to zoom/pan the entire Activity (the activity layout, excluding actionbar/title-bar).
Can I use ZoomPanLayout class in the project for the use-case I have mentioned above.
Thanks!

Yes, the ZoomPanLayout should work for your needs, but you'll have to implement scaling explicitly (I've posted a sample several times in this repo's wiki - seach for "ScalingLayout") - ZoomPanLayout pans and will report a scaled value, but it's up to the implementation to manage that (e.g., some implementations might want to scale a background but just reposition markers, like Google Maps, while others might want to scale everything, etc).
HTH

repo: moagrius/TileView

license: mit

license_source: bigquery


text:
Open up project on browser from the push of a button

Open up a project from the push of a button for the selected project.

Because of the different types of boards, as well as the missing id from jira rest api, this will be in a later version.


text:
Make file description of main executlabe configurable

The file description can show up in dialogs such as this one:

According to https://learn.microsoft.com/en-us/windows/win32/menurc/versioninfo-resource:

FileDescription
File description to be presented to users. This string may be displayed in a list box when the user is choosing files to install—for example, Keyboard Driver for AT-Style Keyboards. This string is required.

Currently, we're setting this to the packageDescription which might not be a good fit to describe the app as a whole with out the packageName visible. Instead of merging the two automatically, the user should be able to set a separate string.

Fixed via 87137603740758b4fec20b4783744e855122c099, I'd guess?

Indeed 👍

authors: ialokim sebkur

repo: mobanisto/pinpit-gradle-plugin


text:
forward cache_dir in HQQWrapper.from_quantized()

As I have been discussing with @mobicham in #37 a small PR to forward cache_dir in HQQWrapper.from_quantized() to BaseHQQModel.try_snapshot_download(); as well as add NoneType hints to allow more deliberate matching to the HuggingFace default cache_dir value

Thanks @MarkBenjamin , sorry for the delay, I will try to test it this week hopefully

authors: MarkBenjamin mobicham

repo: mobiusml/hqq


text:
Add tests for loading reporters w/ relative/absolute paths

I'd like to have tests for the new feature added in #2659.
Gonna do this today after I review the rest of the un-released commits. Let me know if you want to tackle it for me.

I can help with writing a test to cover #2659 if you give me some pointers on what to cover in the test.

@sul4bh Thanks!
It should cover:

using a relative path as the argument for the reporter option
using an absolute path as the argument for the reporter option

So maybe write a very short and useless reporter, and use this helper to execute the mocha binary, and check its output and that there haven't been any error: https://github.com/mochajs/mocha/blob/7a05a6c8c196bb9a8dcfb156499507238f6f7e5a/test/integration/helpers.js#L44-L83.
Ping me on Gitter if anything! :)

Awesome. I am on it!

@sul4bh ❤

Closed via #2773.

repo: mochajs/mocha

license: MIT


text:
can Mocha.run() by add code, not by addFile before?

Prerequisites

[x] Checked that your issue hasn't already been filed by cross-referencing [issues with the faq label](https://github.com/mochajs/mocha/issues?

Description

I hope that mocha could run the code for testing immediately, not by addFill before.
because our web can help users edit online code， it only save the code for testing.
now the only way the users could run testing code online is that we build testing files from the code, and addFile , run file with Mocha.
so, is there a  immediate way to run the code for testing with Mocha? thx

Cannot understand what you're asking here. You can run Mocha by CLI or programmatically. You have to write your own tests. Once those exist, maybe use temp files for Mocha invocation.

ok, thx.
i got it.  I want to run Mocha by Progrommatically.


text:
Ignore asynchronous failures after spec resolution

This improves on https://github.com/mochajs/mocha/pull/1540 From that thread:
Given the following test, which only has one spec:
it('fails exactly once when a global error is thrown first', function(done) {
  setTimeout(function() {
    throw new Error('global error');

    setTimeout(function() {
      done(new Error('test error'));
    }, 0);
  }, 0);
});

You get two two failures:
$ ./bin/mocha pr1540.js

  ․․

  0 passing (6ms)
  2 failing

  1)  fails exactly once:
     Error: test error
      at null._onTimeout (/Users/danielstjules/git/mocha/pr1540.js:10:12)
      at Timer.listOnTimeout [as ontimeout] (timers.js:110:15)
      at timers.js:117:18
      at process._tickCallback (node.js:415:13)
      at process._tickFromSpinner (node.js:390:15)

  2)  fails exactly once:
     Error: test error
      at null._onTimeout (/Users/danielstjules/git/mocha/pr1540.js:10:12)
      at Timer.listOnTimeout [as ontimeout] (timers.js:110:15)
      at timers.js:117:18
      at process._tickCallback (node.js:415:13)
      at process._tickFromSpinner (node.js:390:15)

But after this PR, it correctly only shows one failure, and highlights the error thrown first ("global error"):
$ ./bin/mocha pr1540.js

  ․

  0 passing (6ms)
  1 failing

  1)  fails exactly once:
     Uncaught Error: global error
      at null._onTimeout (/Users/danielstjules/git/mocha/pr1540.js:12:11)
      at Timer.listOnTimeout [as ontimeout] (timers.js:110:15)

In addition to the above fix, this PR improves on #1540 by also correctly handling the following test case:
it('fails exactly once when a global error is thrown second', function(done) {
  setTimeout(function() {
    done(new Error('test error'));
  }, 0);

  setTimeout(function() {
    throw new Error('global error');
  }, 0);
});

It now also only reports a single failing spec, rather than two.

Awesome! Thanks

No problem! :)

authors: danielstjules travisjeffery


text:
ignore lockfiles for now

This ensures we don't have to deal with package-lock.json and yarn.lock for now.

@ScottFreeCode It makes sense for "apps".

Coverage remained the same at 88.288% when pulling 8441d46b519ab9127a23abd93b48a5e71b65e20b on lockfiles into 10e5ada8407eeb3081061ee5c6b53c5b8f5241c6 on master.

authors: boneskull coveralls


text:
【BUG】Server Close() Panic

Hi @wwhai , are you using this as an embedded module in your application? If so, check if you're calling the server.Close() more than once.

authors: thedevop wwhai

repo: mochi-mqtt/server


text:
Golang smtpmock v1.5.0

Golang smtpmock v1.5.0

Codecov Report

Merging #78 (cf277b0) into master (7537743) will not change coverage.
The diff coverage is 100.00%.

@@            Coverage Diff            @@
##            master       #78   +/-   ##
=========================================
  Coverage   100.00%   100.00%
=========================================
  Files           15        15
  Lines          602       613   +11
=========================================
+ Hits           602       613   +11

Impacted Files
Coverage Δ

cmd/main.go
100.00% <100.00%> (ø)

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 7537743...cf277b0. Read the comment docs.

authors: bestwebua codecov-commenter

repo: mocktools/go-smtp-mock


text:
Fix CI by running linter & replacing deprecated fn

Replace deprecated .copy -> .copy_mount to fix PyTest

Run black to fix my earlier PR

Before

After

Type of Change

[ ] New Example
[ ] Example updates (Bug fixes, new features, etc.)
[x] Other (changes to the codebase, but not to examples)

Checklist

[x] Example is testable in synthetic monitoring system, or lambda-test: false is added to example frontmatter
[x] Example does not require third-party dependencies to be installed locally
[x] Example is documented with comments throughout, in a Literate Programming style.

Outside contributors
You're great! Thanks for your contribution.

forgot that github actions arent enabled by default when forking so i missed the black linter check, so definitely wanted to fix that. figured id be a good samaritan by also fixing PyTest

Nice, thanks for doing this!!

repo: modal-labs/modal-examples


text:
Rewrite loops with multiple back edges to having a single back edge only

This is a re-creation of #900 after the Kani history rewrite. I can't force-push to that branch to do the rebase, so I'm just recreating it.
Description of changes:
rustc reasonably translates if statements at end of a loop body to
backwards jumps to the loop head. This, however, causes CBMC's symbolic
execution to spuriously treat these as nested loops. This commit now
enables a rewrite step that had previously been built for exactly such
cases.
Resolved issues:
Resolves #1046
Call-outs:

Testing:

How is this change tested?

Is this a refactor change?

Checklist

[ ] Each commit message has a non-empty body, explaining why the change was made
[ ] Methods or procedures are documented
[ ] Regression or unit tests are included, or existing tests cover the modified code
[ ] My PR is restricted to a single feature or bugfix

By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 and MIT licenses.

Discussed with @tautschnig. This rewrite has no known soundness issues. The only relevent effect is that it affects how CBMC counts loop unwindings, which is what was causing the test failure.

Interesting, do we have any idea when that's the case? It doesn't seem to affect all loop unwinding.
BTW, I don't see this option documented anywhere in their public documents or goto-instrument --help. Do we know why that's not customer visible? @tautschnig
Is this transformation pass similar to LoopSimplify in LLVM?

I believe its cases where the final statement of the loop body is an if with no matching else: CBMC was previously misidentifying them as nested loops, instead of as a single loop with multiple back-edges

Discussed with @tautschnig. This rewrite has no known soundness issues. The only relevent effect is that it affects how CBMC counts loop unwindings, which is what was causing the test failure.

Interesting, do we have any idea when that's the case? It doesn't seem to affect all loop unwinding.

It was really only a problem when there were multiple back-edges in a loop. This is entirely reasonable for a compiler to generate, but it catches CBMC's symbolic execution off guard for CBMC's C front-end (and goto conversion) will never generate this. (The choice is for what to do with continue instructions: a compiler could either choose to generate a jump to the backwards goto at the end of a loop, or directly jump back to the loop head. CBMC's goto conversion does the former, but apparently rustc at least sometimes does the latter. And presumably javac also does the latter at times.)

BTW, I don't see this option documented anywhere in their public documents or goto-instrument --help. Do we know why that's not customer visible? @tautschnig

I'm pretty sure it just was forgotten about when it was built. Presumably it was built to deal with code originating from javac. We should fix the documentation problem, but there already is an item on my todo list to include automated checks in CI that all options are documented (unless intentionally left undocumented). So I'll get to this eventually...

Is this transformation pass similar to LoopSimplify in LLVM?

It's not quite as elaborate, it does only one part of it, the "This pass also guarantees that loops will have exactly one backedge."

Added #1046 to "Resolved issues".

authors: adpaco-aws celinval danielsn tautschnig tedinski

repo: model-checking/kani


text:
Protobuf extension breaks if protobuf message variables contain underscore

Rewrite for clarity:
The protobuf extension only works for gRPC messages with one word variables. It breaks if there are multiple words in a variable, separated by underscores (which is the standard naming convention for protobuf lanaguage, see https://developers.google.com/protocol-buffers/docs/proto3).

Can you provide your proto file? Thanks.

Proto:
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I guessed this issue had bean fixed by #466

I think it was partially fixed, but validate() doesn't work if you add custom field mappings. The mapping is successful, but validate() will throw an exception listing the overridden properties in snake_case form.

authors: ShawnStrong chhsiao90 internetstaff

repo: modelmapper/modelmapper


text:
Recommended threshold of cosine distance of two speeches

Is there recommended "cosine distance threshold" for predicting two speeches belong or not belong to same person? Thanks a lot!

The threshold is determined by the test set, so there isn't a universal value. If a specific number must be set, consider establishing it around 0.5.

authors: hkingtswcbyy yfchenlucky


text:
Need some tutorials or examples to let dialog agent answer question based on knowledge base.

I'm working on the RAG multi-agent example. Now I have finished text embedding by importing external pdf files to the knowledge base. Then, I know that another dialog agent is required to get knowledge from the base and answer my question based on such knowledge.
I'm confused that how can I add a dialog agent to get the knowledge and answer my question.

@ZiTao-Li @FredericW Please check this issue.

authors: DavdGao LotusPhilip

repo: modelscope/agentscope


text:
Missing 'title' method in StringMethods object

System information

**OS Platform and Distribution: Linux Ubuntu 16.04
Modin installed from (source or binary): binary
Modin version: 0.6.3
Python version: 3.6.8
Exact command to reproduce:

Describe the problem
Got AttributeError: 'StringMethods' object has no attribute 'title' when I was trying to execute a line of code contains series.str.title().
I have checked the code in modin/pandas/series.py, method 'title' isn't there. Can you add it in or introduce a workaround? Thanks a lot!
Source code / logs
modin/pandas/series.py

Hi @jh-wu, thanks for posting!
I will get this fixed before the next release, it shouldn't take long to implement. As a temporary workaround, you can do series.apply(str.title).

authors: devin-petersohn jh-wu

repo: modin-project/modin


text:
Update to Beta 6 - Delete useless images

This PR update dependencies  to 2.0.0 beta-6 and delete unused images

Ready for review.

Version was updated to beta 8

repo: modrinth/docs


text:
🛑 STATUS.MOFE.IO is down

In d63666c, STATUS.MOFE.IO (https://status.mofe.io) was down:

HTTP code: 0
Response time: 0 ms

Resolved: STATUS.MOFE.IO is back up in 35d21dc.

repo: mofelee/upptime


text:
Avoid uninitialised variable warning for io_console check

In newer Rubys, io_console should be available, and hence $no_io_console may be an uninitialised variable.
Just set it to false and change to true if we can't find io_console.

Thanks!

Thank you!

authors: mogest thesamesam

repo: mogest/unix-crypt


text:
Possible fix for LIMIT issue

https://github.com/mogui/pyorient/issues/153

Coverage decreased (-0.02%) to 79.706% when pulling dc8205c75e6ece42a2948e7cb4ec2eb19aec5f08 on Ostico:possible_fix_limit into 0bedd751beebd9d61419cb9619060a0c5123c24e on mogui:develop.

Coverage increased (+0.02%) to 79.756% when pulling 4d90344ed966544cd82a1009f031361dc538fdc4 on Ostico:possible_fix_limit into 0bedd751beebd9d61419cb9619060a0c5123c24e on mogui:develop.

authors: Ostico coveralls

repo: mogui/pyorient


text:
Switch from JSHint to ESLint

JSHint doesn't really work well with ES6, we should switch to ESLint which has much better ES6 support (and even a bunch of ES6-specific options) plus in general much more configurable.
If there are no counterarguments, I'll do the switch.

Switched to ESLint and enabled most of the ESLint rules. Most I could just enable, for others I had to make a few tweaks to the code to make it conform.
Tried to keep all our existing JSHint rules, but not all rules had equivalent ESLint rules and JSHint also has bunch of rules that it enabled by default. Tried to make the best of this.

repo: mohebifar/lebab


text:
Update misp_tie.py

Added SHA1 and SHA256

Had a error in the for loop. Another pull request coming.

repo: mohlcyber/MISP-TIE


text:
when i use "npm run build",error happend!

0 info it worked if it ends with ok
1 verbose cli [ 'C:\Program Files\nodejs\node.exe',
1 verbose cli   'C:\Program Files\nodejs\node_modules\npm\bin\npm-cli.js',
1 verbose cli   'run',
1 verbose cli   'deploy' ]
2 info using npm@3.10.8
3 info using node@v6.9.1
4 verbose run-script [ 'predeploy', 'deploy', 'postdeploy' ]
5 info lifecycle angular2-express-mongo@1.0.0~predeploy: angular2-express-mongo@1.0.0
6 silly lifecycle angular2-express-mongo@1.0.0~predeploy: no script for predeploy, continuing
7 info lifecycle angular2-express-mongo@1.0.0~deploy: angular2-express-mongo@1.0.0
8 verbose lifecycle angular2-express-mongo@1.0.0~deploy: unsafe-perm in lifecycle true
9 verbose lifecycle angular2-express-mongo@1.0.0~deploy: PATH: C:\Program Files\nodejs\node_modules\npm\bin\node-gyp-bin;C:\Users\jyj\Angular2-express-mongoose-gulp-node-typescript-master\node_modules.bin;C:\Program Files (x86)\Intel\iCLS Client;C:\Program Files\Intel\iCLS Client;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0;C:\Program Files\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files\Intel\Intel(R) Management Engine Components\IPT;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\IPT;C:\Program Files\Intel\WiFi\bin;C:\Program Files\Common Files\Intel\WirelessCommon;C:\Program Files (x86)\Common Files\lenovo\easyplussdk\bin;C:\Program Files (x86)\Lenovo\Lenovo Home;C:\Program Files\nodejs;C:\Program Files\TortoiseSVN\bin;D:\JDK1.8\bin;D:\androidsdk\platform-tools;D:\androidsdk\tools;C:\Users\jyj\AppData\Roaming\npm;C:\Program Files (x86)\Microsoft VS Code\bin
10 verbose lifecycle angular2-express-mongo@1.0.0~deploy: CWD: C:\Users\jyj\Angular2-express-mongoose-gulp-node-typescript-master
11 silly lifecycle angular2-express-mongo@1.0.0~deploy: Args: [ '/d /s /c',
11 silly lifecycle   'concurrently --kill-others "gulp watch" "node ./dist/server/bin/www"' ]
12 silly lifecycle angular2-express-mongo@1.0.0~deploy: Returned: code: 1  signal: null
13 info lifecycle angular2-express-mongo@1.0.0~deploy: Failed to exec deploy script
14 verbose stack Error: angular2-express-mongo@1.0.0 deploy: concurrently --kill-others "gulp watch" "node ./dist/server/bin/www"
14 verbose stack Exit status 1
14 verbose stack     at EventEmitter. (C:\Program Files\nodejs\node_modules\npm\lib\utils\lifecycle.js:255:16)
14 verbose stack     at emitTwo (events.js:106:13)
14 verbose stack     at EventEmitter.emit (events.js:191:7)
14 verbose stack     at ChildProcess. (C:\Program Files\nodejs\node_modules\npm\lib\utils\spawn.js:40:14)
14 verbose stack     at emitTwo (events.js:106:13)
14 verbose stack     at ChildProcess.emit (events.js:191:7)
14 verbose stack     at maybeClose (internal/child_process.js:877:16)
14 verbose stack     at Process.ChildProcess._handle.onexit (internal/child_process.js:226:5)
15 verbose pkgid angular2-express-mongo@1.0.0
16 verbose cwd C:\Users\jyj\Angular2-express-mongoose-gulp-node-typescript-master
17 error Windows_NT 6.1.7601
18 error argv "C:\Program Files\nodejs\node.exe" "C:\Program Files\nodejs\node_modules\npm\bin\npm-cli.js" "run" "deploy"
19 error node v6.9.1
20 error npm  v3.10.8
21 error code ELIFECYCLE
22 error angular2-express-mongo@1.0.0 deploy: concurrently --kill-others "gulp watch" "node ./dist/server/bin/www"
22 error Exit status 1
23 error Failed at the angular2-express-mongo@1.0.0 deploy script 'concurrently --kill-others "gulp watch" "node ./dist/server/bin/www"'.
23 error Make sure you have the latest version of node.js and npm installed.
23 error If you do, this is most likely a problem with the angular2-express-mongo package,
23 error not with npm itself.
23 error Tell the author that this fails on your system:
23 error     concurrently --kill-others "gulp watch" "node ./dist/server/bin/www"
23 error You can get information on how to open an issue for this project with:
23 error     npm bugs angular2-express-mongo
23 error Or if that isn't available, you can get their info via:
23 error     npm owner ls angular2-express-mongo
23 error There is likely additional logging output above.
24 verbose exit [ 1, true ]

what were your build steps ?


text:
fix symlinks action

A quick fix to the existing action that runs the symlinks file. It's currently disabled, but I figured I might as well fix it up in case it is desired at some point.
You can see it's working here. I deleted the spark scripts to check it's all working as expected.
Happy to rm the action if either of you feels it's unnecessary.
At the very least, it's a useful template for run a bash script and then committing and changes.

@ADBond, @RossKen on actions, does it make sense to combine our black and ruff checks into a singular action? They both perform the same purpose.
If Y, shall I implement an auto-lint using ruff so we can automatically capture and resolve as many issues as possible?

@ADBond, @RossKen on actions, does it make sense to combine our black and ruff checks into a singular action? They both perform the same purpose.
If Y, shall I implement an auto-lint using ruff so we can automatically capture and resolve as many issues as possible?

I think it seems reasonable to have them in the same workflow as there isn't really any meaningful difference in what they are doing for us, and using autofix for ruff also seems like a sensible choice (although I think that still leaves a few we need to manually do. But we're doing that anyway).
I think though it would be good if they would both run and make any changes before committing, but also allowing the separate outputs to be seen easily if there's stuff that needs to be sorted by the dev

https://github.com/moj-analytical-services/splink/pull/1324#pullrequestreview-1476623547
Ah, so the extra layer appears to have paid dividends already...
https://github.com/moj-analytical-services/splink/commit/24745cc14521b706f35ac3a6747e06c9d75179d6

authors: ADBond ThomasHepworth

repo: moj-analytical-services/splink


text:
发现一个页面方法调用两次

我发现博客运行的时候，比如首页，我在/common/models/Content.php的find()方法，打印一个东西出来，你看刷新页面的时候，会发现打印两次，其他地方也是这样，刷新一次页面调用两次方法。是因为其他地方也调用了find吗。
我还觉得页面响应速度好慢。

打印两次 是因为他有子类  Content是个抽象类，不建议直接用 而是用他的之类Post Page Attachment

return new ContentQuery(get_called_class(),['contentType'=>static::TYPE]);
我不是很明白这句话，get_called_class的值是models/post，后面是contentType也是post，但是在ContentQuery类里面没看到接收这两个参数的地方啊，找了父类没有，我是初学Yii，请赐教，谢谢！

http://apidoc.yii2.cn/guide-db-active-record.html  看最下面那个作用域， 至于没找到接收参数的地方，应该看她的父类ActiveQuery类

authors: mojifan tanteng

repo: mojifan/MoBlog


text:
test: test debug

Resolves #

Pull Request Test Coverage Report for Build 6300105061

0 of 0   changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage remained the same at 64.062%

Totals

Change from base Build 6294480009:
0.0%

Covered Lines:
936

Relevant Lines:
1391

💛  - Coveralls


text:
Improve kbd navigation; accessibility

While tab-nav is actually surprisingly decent, 90% of all of the UI is not set up to display an outline when it is focused lol
also, we should probably figure out how to improve accessibility

Just noticed the upload and clone url buttons have no focus-visible style so probably should go do that

repo: mollersuite/monofile

license: Unlicense