Fixed error where filter args was consuming kwargs #750

collijk · 2018-08-21T03:34:00Z

Anytime unique args were treated as kwargs, joblib was failing. For instance

from joblib import Memory

m = Memory(location='joblib_cache')

@m.cache
def plus_one(a):
    return a + 1

>>> plus_one(1)
[Memory] Calling __main__--home-james-<stdin>.plus_one...
plus_one(1)
_________________________________________________________plus_one - 1.3s, 0.0min
2
>>>plus_one(a=1)
2
>>>plus_one(a=2)
[Memory] Calling __main__--home-james-<stdin>.plus_one...
plus_one(a=2)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/james/miniconda3/envs/vivarium/lib/python3.6/site-packages/joblib/memory.py", line 511, in __call__
    return self._cached_call(args, kwargs)[0]
  File "/home/james/miniconda3/envs/vivarium/lib/python3.6/site-packages/joblib/memory.py", line 455, in _cached_call
    out, metadata = self.call(*args, **kwargs)
  File "/home/james/miniconda3/envs/vivarium/lib/python3.6/site-packages/joblib/memory.py", line 675, in call
    func_id, args_id = self._get_output_identifiers(*args, **kwargs)
  File "/home/james/miniconda3/envs/vivarium/lib/python3.6/site-packages/joblib/memory.py", line 717, in _persist_input
    func_id, args_id = self._get_output_identifiers(*args, **kwargs)
  File "/home/james/miniconda3/envs/vivarium/lib/python3.6/site-packages/joblib/memory.py", line 532, in _get_output_identifiers
    argument_hash = self._get_argument_hash(*args, **kwargs)
  File "/home/james/miniconda3/envs/vivarium/lib/python3.6/site-packages/joblib/memory.py", line 526, in _get_argument_hash
    return hashing.hash(filter_args(self.func, self.ignore, args, kwargs),
  File "/home/james/miniconda3/envs/vivarium/lib/python3.6/site-packages/joblib/func_inspect.py", line 288, in filter_args
    _function_called_str(name, args, kwargs))
ValueError: Wrong number of arguments for plus_one(a):
     plus_one(, ) was called.
Wrong number of arguments for plus_one(a):
     plus_one(, ) was called.

This fixes the error by not consuming kwargs during func_inspect.filter_args.

codecov · 2018-08-21T03:46:45Z

Codecov Report

Merging #750 into master will increase coverage by 0.1%.
The diff coverage is 100%.

@@            Coverage Diff            @@
##           master     #750     +/-   ##
=========================================
+ Coverage   95.25%   95.36%   +0.1%     
=========================================
  Files          43       43             
  Lines        6197     6208     +11     
=========================================
+ Hits         5903     5920     +17     
+ Misses        294      288      -6

Impacted Files	Coverage Δ
joblib/func_inspect.py	`95.45% <100%> (+0.56%)`	⬆️
joblib/test/test_memory.py	`98.08% <100%> (+0.02%)`	⬆️
joblib/test/test_func_inspect.py	`91.86% <100%> (+0.27%)`	⬆️
joblib/_parallel_backends.py	`96% <0%> (-1.21%)`	⬇️
joblib/test/test_numpy_pickle.py	`98.35% <0%> (+0.65%)`	⬆️
joblib/test/test_dask.py	`98.11% <0%> (+2.51%)`	⬆️

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 c492cf3...61f407f. Read the comment docs.

lesteve · 2018-08-21T12:14:14Z

Good point, I ran a git bisect and it is another regression in 0.12 following the Memory store backend refactoring in #397. Would you be kind enough to add a test in joblib/test/test_memory.py and maybe one in joblib/test/test_func_inspect.py (to make sure that filter_args does not have a side effect on its kwargs parameter?

I have to say I don't really understand why filter_args was modifying its kwargs parameter but this may require a closer look at the changes that went into #397.

collijk · 2018-08-21T15:12:55Z

Yep. I'll take a look later today at the tests.

collijk · 2018-08-23T04:14:08Z

Now with regression tests against the end-to-end Memory usage and one particular use case of filter_args.

pytest output before fix:

======================================================================================= test session starts ========================================================================================
platform linux -- Python 3.6.6, pytest-3.7.2, py-1.5.4, pluggy-0.7.1
rootdir: /home/james/code/external_tools/joblib, inifile: setup.cfg
collected 1070 items / 2 skipped                                                                                                                                                                   

joblib/__init__.py s                                                                                                                                                                         [  0%]
joblib/parallel.py ss                                                                                                                                                                        [  0%]
joblib/test/test_backports.py s....                                                                                                                                                          [  0%]
joblib/test/test_disk.py .........                                                                                                                                                           [  1%]
joblib/test/test_format_stack.py s...                                                                                                                                                        [  1%]
joblib/test/test_func_inspect.py s.............................F......                                                                                                                       [  5%]
joblib/test/test_hashing.py sssssssssss..................................................................................................................................................... [ 20%]
............................................................................................................................................................................................ [ 37%]
....................................................................................................................................................ss.............                          [ 53%]
joblib/test/test_logger.py .                                                                                                                                                                 [ 53%]
joblib/test/test_memmapping.py ssssssssssssss..                                                                                                                                              [ 54%]
joblib/test/test_memory.py ss............F............................                                                                                                                       [ 58%]
joblib/test/test_my_exceptions.py ...                                                                                                                                                        [ 59%]
joblib/test/test_numpy_pickle.py sssssssssssssssssssss................................................................................s.                                                     [ 68%]
joblib/test/test_numpy_pickle_compat.py .                                                                                                                                                    [ 68%]
joblib/test/test_numpy_pickle_utils.py ..                                                                                                                                                    [ 68%]
joblib/test/test_parallel.py sssss.......................................................................................................................................................... [ 83%]
..................................................................................................................................................................ss                         [ 99%]
joblib/test/test_store_backends.py ...                                                                                                                                                       [ 99%]
joblib/test/test_testing.py .....                                                                                                                                                            [ 99%]
joblib/test/data/create_numpy_pickle.py s                                                                                                                                                    [100%]

============================================================================================= FAILURES =============================================================================================
_______________________________________________________________________________ test_filter_args_kwargs_consumption ________________________________________________________________________________

    def test_filter_args_kwargs_consumption():
        """Regression test against 0.12.0 changes.
    
        Make sure filter args doesn't consume the kwargs dict that gets passed to it.
        """
        kwargs = {'x': 0}
        filter_args(g, [], [], kwargs)
>       assert kwargs == {'x': 0}
E       AssertionError: assert {} == {'x': 0}
E         Right contains more items:
E         {'x': 0}
E         Use -v to get the full diff

joblib/test/test_func_inspect.py:233: AssertionError
____________________________________________________________________________________ test_memory_args_as_kwargs ____________________________________________________________________________________

func = <function test_memory_args_as_kwargs.<locals>.plus_one at 0x7f0d9fdd67b8>, ignore_lst = [], args = [], kwargs = {}

    def filter_args(func, ignore_lst, args=(), kwargs=dict()):
        """ Filters the given args and kwargs using a list of arguments to
            ignore, and a function specification.
    
            Parameters
            ----------
            func: callable
                Function giving the argument specification
            ignore_lst: list of strings
                List of arguments to ignore (either a name of an argument
                in the function spec, or '*', or '**')
            *args: list
                Positional arguments passed to the function.
            **kwargs: dict
                Keyword arguments passed to the function
    
            Returns
            -------
            filtered_args: list
                List of filtered positional and keyword arguments.
        """
        args = list(args)
        if isinstance(ignore_lst, _basestring):
            # Catch a common mistake
            raise ValueError(
                'ignore_lst must be a list of parameters to ignore '
                '%s (type %s) was given' % (ignore_lst, type(ignore_lst)))
        # Special case for functools.partial objects
        if (not inspect.ismethod(func) and not inspect.isfunction(func)):
            if ignore_lst:
                warnings.warn('Cannot inspect object %s, ignore list will '
                              'not work.' % func, stacklevel=2)
            return {'*': args, '**': kwargs}
        arg_spec = getfullargspec(func)
        arg_names = arg_spec.args + arg_spec.kwonlyargs
        arg_defaults = arg_spec.defaults or ()
        if arg_spec.kwonlydefaults:
            arg_defaults = arg_defaults + tuple(arg_spec.kwonlydefaults[k]
                                                for k in arg_spec.kwonlyargs
                                                if k in arg_spec.kwonlydefaults)
        arg_varargs = arg_spec.varargs
        arg_varkw = arg_spec.varkw
    
        if inspect.ismethod(func):
            # First argument is 'self', it has been removed by Python
            # we need to add it back:
            args = [func.__self__, ] + args
        # XXX: Maybe I need an inspect.isbuiltin to detect C-level methods, such
        # as on ndarrays.
    
        _, name = get_func_name(func, resolv_alias=False)
        arg_dict = dict()
        arg_position = -1
        for arg_position, arg_name in enumerate(arg_names):
            if arg_position < len(args):
                # Positional argument or keyword argument given as positional
                if arg_name not in arg_spec.kwonlyargs:
                    arg_dict[arg_name] = args[arg_position]
                else:
                    raise ValueError(
                        "Keyword-only parameter '%s' was passed as "
                        'positional parameter for %s:\n'
                        '     %s was called.'
                        % (arg_name,
                           _signature_str(name, arg_spec),
                           _function_called_str(name, args, kwargs))
                    )
    
            else:
                position = arg_position - len(arg_names)
                if arg_name in kwargs:
                    arg_dict[arg_name] = kwargs.pop(arg_name)
                else:
                    try:
>                       arg_dict[arg_name] = arg_defaults[position]
E                       IndexError: tuple index out of range

joblib/func_inspect.py:281: IndexError

During handling of the above exception, another exception occurred:

tmpdir = local('/tmp/pytest-of-james/pytest-13/test_memory_args_as_kwargs0')

    def test_memory_args_as_kwargs(tmpdir):
        """Regression test against 0.12.0 changes."""
        memory = Memory(location=tmpdir.strpath, verbose=0)
    
        @memory.cache
        def plus_one(a):
            return a + 1
    
        # This would (and should) pass before the patch.
        assert plus_one(1) == 2
        assert plus_one(a=1) == 2
    
        # However, a positional argument that joblib hadn't seen
        # before would cause a failure if it was passed as a kwarg
>       assert plus_one(a=2) == 3

joblib/test/test_memory.py:362: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
joblib/memory.py:514: in __call__
    return self._cached_call(args, kwargs)[0]
joblib/memory.py:458: in _cached_call
    out, metadata = self.call(*args, **kwargs)
joblib/memory.py:685: in call
    metadata = self._persist_input(duration, args, kwargs)
joblib/memory.py:719: in _persist_input
    func_id, args_id = self._get_output_identifiers(*args, **kwargs)
joblib/memory.py:535: in _get_output_identifiers
    argument_hash = self._get_argument_hash(*args, **kwargs)
joblib/memory.py:529: in _get_argument_hash
    return hashing.hash(filter_args(self.func, self.ignore, args, kwargs),
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

func = <function test_memory_args_as_kwargs.<locals>.plus_one at 0x7f0d9fdd67b8>, ignore_lst = [], args = [], kwargs = {}

    def filter_args(func, ignore_lst, args=(), kwargs=dict()):
        """ Filters the given args and kwargs using a list of arguments to
            ignore, and a function specification.
    
            Parameters
            ----------
            func: callable
                Function giving the argument specification
            ignore_lst: list of strings
                List of arguments to ignore (either a name of an argument
                in the function spec, or '*', or '**')
            *args: list
                Positional arguments passed to the function.
            **kwargs: dict
                Keyword arguments passed to the function
    
            Returns
            -------
            filtered_args: list
                List of filtered positional and keyword arguments.
        """
        args = list(args)
        if isinstance(ignore_lst, _basestring):
            # Catch a common mistake
            raise ValueError(
                'ignore_lst must be a list of parameters to ignore '
                '%s (type %s) was given' % (ignore_lst, type(ignore_lst)))
        # Special case for functools.partial objects
        if (not inspect.ismethod(func) and not inspect.isfunction(func)):
            if ignore_lst:
                warnings.warn('Cannot inspect object %s, ignore list will '
                              'not work.' % func, stacklevel=2)
            return {'*': args, '**': kwargs}
        arg_spec = getfullargspec(func)
        arg_names = arg_spec.args + arg_spec.kwonlyargs
        arg_defaults = arg_spec.defaults or ()
        if arg_spec.kwonlydefaults:
            arg_defaults = arg_defaults + tuple(arg_spec.kwonlydefaults[k]
                                                for k in arg_spec.kwonlyargs
                                                if k in arg_spec.kwonlydefaults)
        arg_varargs = arg_spec.varargs
        arg_varkw = arg_spec.varkw
    
        if inspect.ismethod(func):
            # First argument is 'self', it has been removed by Python
            # we need to add it back:
            args = [func.__self__, ] + args
        # XXX: Maybe I need an inspect.isbuiltin to detect C-level methods, such
        # as on ndarrays.
    
        _, name = get_func_name(func, resolv_alias=False)
        arg_dict = dict()
        arg_position = -1
        for arg_position, arg_name in enumerate(arg_names):
            if arg_position < len(args):
                # Positional argument or keyword argument given as positional
                if arg_name not in arg_spec.kwonlyargs:
                    arg_dict[arg_name] = args[arg_position]
                else:
                    raise ValueError(
                        "Keyword-only parameter '%s' was passed as "
                        'positional parameter for %s:\n'
                        '     %s was called.'
                        % (arg_name,
                           _signature_str(name, arg_spec),
                           _function_called_str(name, args, kwargs))
                    )
    
            else:
                position = arg_position - len(arg_names)
                if arg_name in kwargs:
                    arg_dict[arg_name] = kwargs.pop(arg_name)
                else:
                    try:
                        arg_dict[arg_name] = arg_defaults[position]
                    except (IndexError, KeyError):
                        # Missing argument
                        raise ValueError(
                            'Wrong number of arguments for %s:\n'
                            '     %s was called.'
                            % (_signature_str(name, arg_spec),
>                              _function_called_str(name, args, kwargs))
                        )
E                       ValueError: Wrong number of arguments for plus_one(a):
E                            plus_one(, ) was called.

joblib/func_inspect.py:288: ValueError
======================================================================== 2 failed, 1003 passed, 67 skipped in 54.76 seconds ========================================================================
[INFO:MainProcess:MainThread] process shutting down
[DEBUG:MainProcess:MainThread] running all "atexit" finalizers with priority >= 0
[DEBUG:MainProcess:MainThread] Interpreter shutting down. Waking up queue_manager_threads [(<Thread(QueueManagerThread, started daemon 139695514167040)>, <joblib.externals.loky.process_executor._ThreadWakeup object at 0x7f0d9cf0c6a0>)]
[DEBUG:MainProcess:QueueManagerThread] queue management thread shutting down
[DEBUG:MainProcess:QueueManagerThread] closing call_queue
[DEBUG:MainProcess:QueueManagerThread] telling queue thread to quit
[DEBUG:MainProcess:QueueManagerThread] joining processes
[DEBUG:MainProcess:QueueFeederThread] feeder thread got sentinel -- exiting
[DEBUG:MainProcess:QueueManagerThread] queue management thread clean shutdown of worker processes: []
[DEBUG:MainProcess:MainThread] running the remaining "atexit" finalizers

pytest output after fix:

======================================================================================= test session starts ========================================================================================
platform linux -- Python 3.6.6, pytest-3.7.2, py-1.5.4, pluggy-0.7.1
rootdir: /home/james/code/external_tools/joblib, inifile: setup.cfg
collected 1070 items / 2 skipped                                                                                                                                                                   

joblib/__init__.py s                                                                                                                                                                         [  0%]
joblib/parallel.py ss                                                                                                                                                                        [  0%]
joblib/test/test_backports.py s....                                                                                                                                                          [  0%]
joblib/test/test_disk.py .........                                                                                                                                                           [  1%]
joblib/test/test_format_stack.py s...                                                                                                                                                        [  1%]
joblib/test/test_func_inspect.py s....................................                                                                                                                       [  5%]
joblib/test/test_hashing.py sssssssssss..................................................................................................................................................... [ 20%]
............................................................................................................................................................................................ [ 37%]
....................................................................................................................................................ss.............                          [ 53%]
joblib/test/test_logger.py .                                                                                                                                                                 [ 53%]
joblib/test/test_memmapping.py ssssssssssssss..                                                                                                                                              [ 54%]
joblib/test/test_memory.py ss.........................................                                                                                                                       [ 58%]
joblib/test/test_my_exceptions.py ...                                                                                                                                                        [ 59%]
joblib/test/test_numpy_pickle.py sssssssssssssssssssss................................................................................s.                                                     [ 68%]
joblib/test/test_numpy_pickle_compat.py .                                                                                                                                                    [ 68%]
joblib/test/test_numpy_pickle_utils.py ..                                                                                                                                                    [ 68%]
joblib/test/test_parallel.py sssss.......................................................................................................................................................... [ 83%]
..................................................................................................................................................................ss                         [ 99%]
joblib/test/test_store_backends.py ...                                                                                                                                                       [ 99%]
joblib/test/test_testing.py .....                                                                                                                                                            [ 99%]
joblib/test/data/create_numpy_pickle.py s                                                                                                                                                    [100%]

============================================================================= 1005 passed, 67 skipped in 52.61 seconds =============================================================================
[INFO:MainProcess:MainThread] process shutting down
[DEBUG:MainProcess:MainThread] running all "atexit" finalizers with priority >= 0
[DEBUG:MainProcess:MainThread] Interpreter shutting down. Waking up queue_manager_threads [(<Thread(QueueManagerThread, started daemon 139697284175616)>, <joblib.externals.loky.process_executor._ThreadWakeup object at 0x7f0df8e796d8>)]
[DEBUG:MainProcess:QueueManagerThread] queue management thread shutting down
[DEBUG:MainProcess:QueueManagerThread] closing call_queue
[DEBUG:MainProcess:QueueManagerThread] telling queue thread to quit
[DEBUG:MainProcess:QueueManagerThread] joining processes
[DEBUG:MainProcess:QueueFeederThread] feeder thread got sentinel -- exiting
[DEBUG:MainProcess:QueueManagerThread] queue management thread clean shutdown of worker processes: []
[DEBUG:MainProcess:MainThread] running the remaining "atexit" finalizers

collijk · 2018-08-23T04:14:58Z

I'd have written some more extensive tests, but filter_args is a pretty hairy and hard to test function.

ogrisel

Thanks for the non-regression tests. I have reworded them a bit and added an entry to the changelog. I will merge as soon as CI is green.

* tag '0.12.3': (23 commits) Release 0.12.3 Loky 2.2.1 (joblib#760) FIX: FileSystemStoreBackend string representation only returning location (path) (joblib#765) Add optional dependency on psutil MAINT remove brittle time based assertion in test (joblib#761) Fix a bug in nesting level computation with FallbackToBackend(SequentialBackend()) (joblib#759) Make docstring more consistent with project style Improved performance of call_and_shelve (joblib#757) Better test name Fix default context handling (joblib#754) cloudpickle 0.5.5 (joblib#756) Fixed error where filter args was consuming kwargs (joblib#750) FIX pickle roundtrip for Memory and related classes. (joblib#746) test that passes but timeout appveyor because of unclosed semaphore tracker (joblib#676) DOC: fine tune compressor example dataset size for ReadTheDocs (joblib#753) FIX: MemorizedResult not picklable (joblib#752) [MRG] Better message with py27 when lz4 is not installed (joblib#740) MNT remove mutable default value for backend_options parameter (joblib#748) MNT create test file for _store_backends module (joblib#749) DOC consistently use memory rather than mem in memory.rst (joblib#744) ...

* releases: (23 commits) Release 0.12.3 Loky 2.2.1 (joblib#760) FIX: FileSystemStoreBackend string representation only returning location (path) (joblib#765) Add optional dependency on psutil MAINT remove brittle time based assertion in test (joblib#761) Fix a bug in nesting level computation with FallbackToBackend(SequentialBackend()) (joblib#759) Make docstring more consistent with project style Improved performance of call_and_shelve (joblib#757) Better test name Fix default context handling (joblib#754) cloudpickle 0.5.5 (joblib#756) Fixed error where filter args was consuming kwargs (joblib#750) FIX pickle roundtrip for Memory and related classes. (joblib#746) test that passes but timeout appveyor because of unclosed semaphore tracker (joblib#676) DOC: fine tune compressor example dataset size for ReadTheDocs (joblib#753) FIX: MemorizedResult not picklable (joblib#752) [MRG] Better message with py27 when lz4 is not installed (joblib#740) MNT remove mutable default value for backend_options parameter (joblib#748) MNT create test file for _store_backends module (joblib#749) DOC consistently use memory rather than mem in memory.rst (joblib#744) ...

Fixed error where filter args was consuming kwargs

a2418f1

collijk mentioned this pull request Aug 21, 2018

Caching breaks when new (uncached) args are treated as kwargs. #751

Closed

Added in regression tests

b9ad5c5

collijk and others added 4 commits August 22, 2018 21:47

Fix flake8 error

db10a32

Wording

3ddeac4

Merge remote-tracking branch 'origin/master' into pr/750

cb8a2b1

Add entry to the changelog

61f407f

ogrisel approved these changes Aug 23, 2018

View reviewed changes

ogrisel merged commit 370dca7 into joblib:master Aug 23, 2018

jason-neal mentioned this pull request Aug 29, 2018

Resolution Convolution value/index error jason-neal/eniric#94

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

Fixed error where filter args was consuming kwargs #750

Fixed error where filter args was consuming kwargs #750

Uh oh!

collijk commented Aug 21, 2018 •

edited by lesteve

Loading

Uh oh!

codecov bot commented Aug 21, 2018 •

edited

Loading

Uh oh!

lesteve commented Aug 21, 2018

Uh oh!

collijk commented Aug 21, 2018

Uh oh!

collijk commented Aug 23, 2018

Uh oh!

collijk commented Aug 23, 2018

Uh oh!

ogrisel left a comment

Uh oh!

Uh oh!

Fixed error where filter args was consuming kwargs #750

Fixed error where filter args was consuming kwargs #750

Uh oh!

Conversation

collijk commented Aug 21, 2018 • edited by lesteve Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

codecov bot commented Aug 21, 2018 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

lesteve commented Aug 21, 2018

Uh oh!

collijk commented Aug 21, 2018

Uh oh!

collijk commented Aug 23, 2018

Uh oh!

collijk commented Aug 23, 2018

Uh oh!

ogrisel left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

collijk commented Aug 21, 2018 •

edited by lesteve

Loading

codecov bot commented Aug 21, 2018 •

edited

Loading