I'm struggling to get the deap.tools.mutUniformInt mutation function to work. To isolate the issue for this SO question, I changed line 62 of examples/ga/onemax.py from
toolbox.register("mutate", tools.mutFlipBit, indpb=0.05)
to
toolbox.register("mutate", tools.mutUniformInt, 0, 1, indpb=0.05)
The onemax.py example now fails:
C:\Users\mshiv\DEAP>python onemax.py
Start of evolution
Evaluated 300 individuals
-- Generation 1 --
Traceback (most recent call last):
File "C:\Users\mshiv\DEAP\onemax.py", line 161, in <module>
main()
File "C:\Users\mshiv\DEAP\onemax.py", line 128, in main
toolbox.mutate(mutant)
File "C:\Users\mshiv\AppData\Local\Programs\Python\Python39\lib\site-packages\deap\tools\mutation.py", line 159, in mutUniformInt
size = len(individual)
TypeError: object of type 'int' has no len()
Both mutators should operate on an Individual, which is defined in onemax.py to be a list, so why does mutFlipBit work, but mutUniformInt seems to receive the Individual parameter as an int, not a list?
Poking around in the DEAP code, I found that mutUniformInt receives the parameters out of order, i.e. they are passed in as (low, up, individual, indpb) whereas the function itself is defined as
def mutUniformInt(individual, low, up, indpb):
Am I registering this mutation function incorrectly?
Source of the onemax example I altered:
https://github.com/DEAP/deap/blob/master/examples/ga/onemax.py
NVM - found the answer here:
https://groups.google.com/g/deap-users/c/4sw2_Al4YFI/m/EvUiq70IBAAJ
The correct syntax should have been:
toolbox.register("mutate", tools.mutUniformInt, low=0, up=1, indpb=0.05)
Related
I've just started learning my way around Biopython and I'm trying to use ExPASy to retrieve SwissProt records, just like described in page 180 of the Biopython tutorial (http://biopython.org/DIST/docs/tutorial/Tutorial.pdf), but also in a relevant ROSALIND exercise (http://rosalind.info/problems/dbpr/ - click to expand the "Programming shortcut" section).
The code I'm using is basically the same as in the ROSALIND exercise:
from Bio import ExPASy
from Bio import SwissProt
handle = ExPASy.get_sprot_raw('Q5SLP9')
record = SwissProt.read(handle)
However, the SwissProt.read function gives the following error messages (I've trimmed some of the filepaths):
Traceback (most recent call last): File "code.py", line 4, in <module>
record = SwissProt.read(handle) File "lib\site-packages\Bio\SwissProt\__init__.py", line 151, in read
record = _read(handle) File "lib\site-packages\Bio\SwissProt\__init__.py", line 255, in _read
_read_ft(record, line) File "lib\site-packages\Bio\SwissProt\__init__.py", line 594, in _read_ft
assert not from_res and not to_res, line AssertionError: /note="Single-stranded DNA-binding protein"
I found this has been reported in GitHub (https://github.com/biopython/biopython/issues/2417), so I'm not the first one who gets this, but I don't really find any updated version of the package or any way to fix the issue. Maybe it's because I'm very new to using packages. Could someone help me please?
Please update your BioPython to version 1.77. The issue has been fixed with pull request 2484.
python3.8
My code:
from googleads import adwords
def execute_request():
adwords_client = adwords.AdWordsClient.LoadFromStorage(path="google_general/googleads.yaml")
campaign_service = adwords_client.GetService('CampaignService', version='v201809')
pass
context["dict_list"] = execute_request()
Traceback:
Traceback (most recent call last):
File "/home/michael/pycharm-community-2019.3.2/plugins/python-ce/helpers/pydev/_pydevd_bundle/pydevd_xml.py", line 282, in frame_vars_to_xml
xml += var_to_xml(v, str(k), evaluate_full_value=eval_full_val)
File "/home/michael/pycharm-community-2019.3.2/plugins/python-ce/helpers/pydev/_pydevd_bundle/pydevd_xml.py", line 369, in var_to_xml
elif hasattr(v, "__len__") and not is_string(v):
File "/home/michael/PycharmProjects/ads3/venv/lib/python3.8/site-packages/googleads/common.py", line 694, in __getattr__
raise googleads.errors.GoogleAdsValueError('Service %s not found' % attr)
googleads.errors.GoogleAdsValueError: Service __len__ not found
Unexpected error, recovered safely.
googleads.yaml about logging
logging:
version: 1
disable_existing_loggers: False
formatters:
default_fmt:
format: ext://googleads.util.LOGGER_FORMAT
handlers:
default_handler:
class: logging.StreamHandler
formatter: default_fmt
level: DEBUG
loggers:
# Configure root logger
"":
handlers: [default_handler]
level: DEBUG
I've just started studying the API.
Namely, I'm trying to execute my first request (https://developers.google.com/adwords/api/docs/guides/first-api-call#make_your_first_api_call)
Could you help me with this problem? At least how to localize it more precisely.
This seems to be a problem which results from the way the PyCharm debugger inspects live objects during debugging.
Specifically, it checks if a given object has the __len__ attribute/method in the code of var_to_xml, most likely to determine an appropriate representation of the object for the debugger interface (which seems to require constructing an XML representation).
googleads service objects such as your campaign_service, however, use some magic to be able to call the defined SOAP methods on them without requiring to hard-code all of them. The code looks like this:
def __getattr__(self, attr):
"""Support service.method() syntax."""
if self._WsdlHasMethod(attr):
if attr not in self._method_proxies:
self._method_proxies[attr] = self._CreateMethod(attr)
return self._method_proxies[attr]
else:
raise googleads.errors.GoogleAdsValueError('Service %s not found' % attr)
This means that the debugger's check for a potential __len__ attribute is intercepted, and because the CampaignService does not have a SOAP operation called __len__, an exception is raised.
You can validate this by running your snippet in the regular way (i.e. not debugging it) and checking if that works.
An actual fix would seem to either require that PyCharm's debugger changes the way it inspects objects (not calling hasattr(v, "__len__")) or that googleads modifies the way it implements __getattr__, for example by actually implementing a __len__ method that just raises AttributeError.
I am using a Flask server to handle requests for some image-processing tasks.
The processing relies extensively on OpenCV and I would now like to trivially-parallelize some of the slower steps.
I have a preference for multiprocessing rather than multithreading (please assume the former in your answers).
But multiprocessing with opencv is apparently broken (I am on Python 2.7 + macOS): https://github.com/opencv/opencv/issues/5150
One solution (see https://github.com/opencv/opencv/issues/5150#issuecomment-400727184) is to use the excellent Loky (https://github.com/tomMoral/loky)
[Question: What other working solutions exist apart from concurrent.futures, loky, joblib..?]
But Loky leads me to the following stacktrace:
a,b = f.result()
File "/anaconda2/lib/python2.7/site-packages/loky/_base.py", line 433, in result
return self.__get_result()
File "/anaconda2/lib/python2.7/site-packages/loky/_base.py", line 381, in __get_result
raise self._exception
BrokenProcessPool: A task has failed to un-serialize. Please ensure that the arguments of the function are all picklable.
This was caused directly by
'''
Traceback (most recent call last):
File "/anaconda2/lib/python2.7/site-packages/loky/process_executor.py", line 391, in _process_worker
call_item = call_queue.get(block=True, timeout=timeout)
File "/anaconda2/lib/python2.7/multiprocessing/queues.py", line 135, in get
res = self._recv()
File "myfile.py", line 44, in <module>
app.config['EXECUTOR_MAX_WORKERS'] = 5
File "/anaconda2/lib/python2.7/site-packages/werkzeug/local.py", line 348, in __getattr__
return getattr(self._get_current_object(), name)
File "/anaconda2/lib/python2.7/site-packages/werkzeug/local.py", line 307, in _get_current_object
return self.__local()
File "/anaconda2/lib/python2.7/site-packages/flask/globals.py", line 52, in _find_app
raise RuntimeError(_app_ctx_err_msg)
RuntimeError: Working outside of application context.
This typically means that you attempted to use functionality that needed
to interface with the current application object in some way. To solve
this, set up an application context with app.app_context(). See the
documentation for more information.
'''
The functions to be parallelized are not being called from app/main.py, but rather from an abitrarily-deep submodule.
I have tried the similarly-useful-looking https://flask-executor.readthedocs.io/en/latest, also so far in vain.
So the question is:
How can I safely pass the application context through to the workers or otherwise get multiprocessing working (without recourse to multithreading)?
I can build out this question if you need more information. Many thanks as ever.
Related resources:
Copy flask request/app context to another process
Flask Multiprocessing
Update:
Non-opencv calls work fine with flask-executor (no Loky) :)
The problem comes when trying to call an opencv function like knnMatch.
If Loky fixes the opencv issue, I wonder if it can be made to work with flask-executor (not for me, so far).
While running the PyBBIO examples phant_test.py and analog_test.py I received the following error (I believe 'could' is a typo meant to be 'could not'):
Traceback (most recent call last):
File "analog_test.py", line 47, in <module>
run(setup, loop)
File "/usr/lib/python2.7/site-packages/PyBBIO-0.9-py2.7-linux-armv7l.egg/bbio/bbio.py", line 63, in run
loop()
File "analog_test.py", line 37, in loop
val1 = analogRead(pot1)
File "/usr/lib/python2.7/site-packages/PyBBIO-0.9-py2.7-linux-armv7l.egg/bbio/platform/beaglebone/bone_3_8/adc.py", line 46, in analogRead
raise Exception('*Could load overlay for adc_pin: %s' % adc_pin)
Exception: *Could load overlay for adc_pin: ['/sys/devices/ocp.2/PyBBIO-AIN0.*/AIN0', 'PyBBIO-AIN0', 'P9.39']
I have tried restarting the BeagleBone (rev A6 running Angstrom with a 3.8 kernel, with no capes connected) to clear the /sys/devices/bone_capemgr.7/slots file, but that did not work. It seems PyBBIO is accessing the slots file and adding overlays because the slots file looks like this after the example program runs:
0: 54:PF---
1: 55:PF---
2: 56:PF---
3: 57:PF---
4: ff:P-O-L Override Board Name,00A0,Override Manuf,PyBBIO-ADC
5: ff:P-O-L Override Board Name,00A0,Override Manuf,PyBBIO-AIN0
Since there were some changes being made to the slots file I checked what files the analog_read(adc_pin) function in the adc.py file of PyBBIO was retrieving. With some print statements I figured out the root problem was that the /sys/devices/ocp.2/PyBBIO-AIN0.*/AIN0 file, which apparently stores the analog read values, does not exist. The glob.glob function returns a null array, and ls /sys/devices/ocp.2/PyBBIO-AIN0.10/ shows modalias power subsystem uevent as the only contents. Is there something wrong in the overlay file? Or could there be another program or problem that is preventing the BeagleBone from writing the AIN0 file that PyBBIO is trying to read? The python code seems to be logically correct, but the overlay is working incorrectly or being blocked in some way.
I am trying to follow the sample code of the book "Mining the social web", 1-3.
I know its old so I follow the new sample from the web page enter link description here
BUT, SOMETIMES, I will suffer a Error info when I implement the code:
[ trend.decode('utf-8') for trend in world_trends()[0]['trends'] ]
And the error info is like this:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "build/bdist.macosx-10.6-universal/egg/twitter/api.py", line 167, in __call__
File "build/bdist.macosx-10.6-universal/egg/twitter/api.py", line 173, in _handle_response
File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/encodings/utf_8.py", line 16, in decode
return codecs.utf_8_decode(input, errors, True)
UnicodeDecodeError: 'utf8' codec can't decode byte 0x8b in position 1: unexpected code byte
It doesnt always happen, but I think no programmer likes such a "random" case.
So could anyone help me on this issue? Whats the problem and how I can solve this?
Great thanks~
byte 0x8b in position 1 usually signals that the data stream is gzipped. For similar problems, see here and here.
To unzip the data stream:
buf = StringIO.StringIO(<response object>.content)
gzip_f = gzip.GzipFile(fileobj=buf)
content = gzip_f.read()
By default decode() will throw an error if it encounters a byte that it doesn't know how to decode.
You can use trend.decode('utf-8', 'replace') or trend.decode('utf-8', 'ignore') to not throw an error and silently ignore it.
Documentation on decode() here.