ValueError: Unable to configure handler 'file_default'

[levzilber2004]

Describe the bug
When I only import pyswarms it crashes on init

To Reproduce
Create an android application with com.chaquo.python
as a python compiler,
in the default config install pyswarms (which will install all the other libraries)
chaquopy {
defaultConfig {
pip {
install("pyswarms==1.3.0")
}
}

then if you run a python method with chaquopy, on import it would throw out this error
com.chaquo.python.PyException: ValueError: Unable to configure handler 'file_default'
at .logging.config.configure(config.py:570)
at .logging.config.dictConfig(config.py:808)
at .pyswarms.utils.reporter.reporter._load_defaults(reporter.py:188)
at .pyswarms.utils.reporter.reporter._setup_logger(reporter.py:184)
at .pyswarms.utils.reporter.reporter.init(reporter.py:118)
at .pyswarms.backend.generators.(generators.py:21)
at .java.chaquopy.import_override(import.pxi:26)
at .pyswarms.backend.(init.py:7)
at .java.chaquopy.import_override(import.pxi:26)
at .pyswarms.single.global_best.(global_best.py:65)
at .java.chaquopy.import_override(import.pxi:26)
at .pyswarms.single.(init.py:17)
at .java.chaquopy.import_override(import.pxi:26)
at .pyswarms.(init.py:17)
at .java.chaquopy.import_override(import.pxi:26)

Expected behavior
Expected to not crash at import

Environment (please complete the following information):

• Android
• Version: minSDK 21, targetSDK 34
• PySwarms Version 1.3..0
• Python Version 3.8

[JohnGoertz]

I have this same issue, but in a different context. I believe the root issue is that pyswarms is trying to configure a logger that outputs to a local file at init, but if the process doesn't have write permissions to the working directory then it fails.

Personally, I find the logger defaults more annoying than helpful, particularly given that it preemptively creates a log file at init, rather than when the optimization routine is begun. I think this issue could be closed simply by making that move. Similarly, toggling the progress bar and the log file during optimization should be independent, not coupled together via verbose.

My full traceback below, note the PermissionError in the middle:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
File /home/mambaforge/envs/sbdb-dev/lib/python3.11/site-packages/pyswarms/utils/reporter/reporter.py:180, in Reporter._setup_logger(self, path)
    179 try:
--> 180     with open(value, "rt") as f:
    181         config = yaml.safe_load(f.read())

TypeError: expected str, bytes or os.PathLike object, not NoneType

During handling of the above exception, another exception occurred:

PermissionError                           Traceback (most recent call last)
File /home/mambaforge/envs/sbdb-dev/lib/python3.11/logging/config.py:573, in DictConfigurator.configure(self)
    572 try:
--> 573     handler = self.configure_handler(handlers[name])
    574     handler.name = name

File /home/mambaforge/envs/sbdb-dev/lib/python3.11/logging/config.py:758, in DictConfigurator.configure_handler(self, config)
    757 try:
--> 758     result = factory(**kwargs)
    759 except TypeError as te:

File /home/mambaforge/envs/sbdb-dev/lib/python3.11/logging/handlers.py:155, in RotatingFileHandler.__init__(self, filename, mode, maxBytes, backupCount, encoding, delay, errors)
    154     encoding = io.text_encoding(encoding)
--> 155 BaseRotatingHandler.__init__(self, filename, mode, encoding=encoding,
    156                              delay=delay, errors=errors)
    157 self.maxBytes = maxBytes

File /home/mambaforge/envs/sbdb-dev/lib/python3.11/logging/handlers.py:58, in BaseRotatingHandler.__init__(self, filename, mode, encoding, delay, errors)
     55 """
     56 Use the specified filename for streamed logging
     57 """
---> 58 logging.FileHandler.__init__(self, filename, mode=mode,
     59                              encoding=encoding, delay=delay,
     60                              errors=errors)
     61 self.mode = mode

File /home/mambaforge/envs/sbdb-dev/lib/python3.11/logging/__init__.py:1181, in FileHandler.__init__(self, filename, mode, encoding, delay, errors)
   1180 else:
-> 1181     StreamHandler.__init__(self, self._open())

File /home/mambaforge/envs/sbdb-dev/lib/python3.11/logging/__init__.py:1213, in FileHandler._open(self)
   1212 open_func = self._builtin_open
-> 1213 return open_func(self.baseFilename, self.mode,
   1214                  encoding=self.encoding, errors=self.errors)

PermissionError: [Errno 13] Permission denied: '/home/report.log'

The above exception was the direct cause of the following exception:

ValueError                                Traceback (most recent call last)
Cell In[1], line 1
----> 1 import sbdb

File /home/projects/sbdb/sbdb/__init__.py:9
      7 from .librarian import *
      8 from .liquid_handling import *
----> 9 from .optimization import *
     10 from .processing import *
     11 from .schema import *

File /home/projects/sbdb/sbdb/optimization/__init__.py:1
----> 1 from .assay_optimizer import *
      2 from .denovo_probes import DeNovoProbes
      3 from .mutable_primers import MutablePrimers

File /home/projects/sbdb/sbdb/optimization/assay_optimizer.py:14
     12 from scipy.special import erfcx
     13 from scipy.stats.qmc import Sobol, LatinHypercube
---> 14 import pyswarms as ps
     15 import pytensor.tensor as pt
     16 import pytensor.gradient as pg

File /home/mambaforge/envs/sbdb-dev/lib/python3.11/site-packages/pyswarms/__init__.py:17
     14 __email__ = "ljvmiranda@gmail.com"
     15 __version__ = "1.3.0"
---> 17 from .single import global_best, local_best, general_optimizer
     18 from .discrete import binary
     19 from .utils.decorators import cost

File /home/mambaforge/envs/sbdb-dev/lib/python3.11/site-packages/pyswarms/single/__init__.py:17
      1 """
      2 The :mod:`pyswarms.single` module implements various techniques in
      3 continuous single-objective optimization. These require only one
   (...)
     14     multiplication can lead to an :code:`OverflowError`.
     15 """
---> 17 from .global_best import GlobalBestPSO
     18 from .local_best import LocalBestPSO
     19 from .general_optimizer import GeneralOptimizerPSO

File /home/mambaforge/envs/sbdb-dev/lib/python3.11/site-packages/pyswarms/single/global_best.py:67
     63 import multiprocessing as mp
     65 from collections import deque
---> 67 from ..backend.operators import compute_pbest, compute_objective_function
     68 from ..backend.topology import Star
     69 from ..backend.handlers import BoundaryHandler, VelocityHandler, OptionsHandler

File /home/mambaforge/envs/sbdb-dev/lib/python3.11/site-packages/pyswarms/backend/__init__.py:7
      1 """
      2 The :code:`pyswarms.backend` module abstracts various operations
      3 for swarm optimization: generating boundaries, updating positions, etc.
      4 You can use the methods implemented here to build your own PSO implementations.
      5 """
----> 7 from .generators import *
      8 from .handlers import *
      9 from .operators import *

File /home/mambaforge/envs/sbdb-dev/lib/python3.11/site-packages/pyswarms/backend/generators.py:21
     18 from ..utils.reporter import Reporter
     19 from .swarms import Swarm
---> 21 rep = Reporter(logger=logging.getLogger(__name__))
     24 def generate_swarm(
     25     n_particles, dimensions, bounds=None, center=1.00, init_pos=None
     26 ):
     27     """Generate a swarm
     28 
     29     Parameters
   (...)
     58         When the argument passed to bounds is not an iterable.
     59     """

File /home/mambaforge/envs/sbdb-dev/lib/python3.11/site-packages/pyswarms/utils/reporter/reporter.py:118, in Reporter.__init__(self, log_path, config_path, logger, printer)
     85 self._env_key = "LOG_CFG"
     86 self._default_config = {
     87     "version": 1,
     88     "disable_existing_loggers": False,
   (...)
    116     },
    117 }
--> 118 self._setup_logger(config_path)

File /home/mambaforge/envs/sbdb-dev/lib/python3.11/site-packages/pyswarms/utils/reporter/reporter.py:184, in Reporter._setup_logger(self, path)
    182     logging.config.dictConfig(config)
    183 except (TypeError, FileNotFoundError):
--> 184     self._load_defaults()

File /home/mambaforge/envs/sbdb-dev/lib/python3.11/site-packages/pyswarms/utils/reporter/reporter.py:188, in Reporter._load_defaults(self)
    186 def _load_defaults(self):
    187     """Load default logging configuration"""
--> 188     logging.config.dictConfig(self._default_config)

File /home/mambaforge/envs/sbdb-dev/lib/python3.11/logging/config.py:823, in dictConfig(config)
    821 def dictConfig(config):
    822     """Configure logging using a dictionary."""
--> 823     dictConfigClass(config).configure()

File /home/mambaforge/envs/sbdb-dev/lib/python3.11/logging/config.py:580, in DictConfigurator.configure(self)
    578             deferred.append(name)
    579         else:
--> 580             raise ValueError('Unable to configure handler '
    581                              '%r' % name) from e
    583 # Now do any that were deferred
    584 for name in deferred:

ValueError: Unable to configure handler 'file_default'

[levzilber2004]

Hi, I managed to solve the problem by changing the source code and ## the lines which made it crash, it seems that the problem was the way pyswarms was using the logger everything else seems to work

…

On Mon, Jun 17, 2024, 22:08 John Goertz ***@***.***> wrote: I have this same issue, but in a different context. I believe the root issue is that pyswarms is trying to configure a logger that outputs to a local file at init, but if the process doesn't have write permissions to the working directory then it fails. Personally, I find the logger defaults more annoying than helpful, particularly given that it *preemptively* creates a log file at init, rather than when the optimization routine is begun. I think this issue could be closed simply by making that move. Similarly, toggling the progress bar and the log file during optimization should be independent, not coupled together via verbose. My full traceback below, note the PermissionError in the middle: ---------------------------------------------------------------------------TypeError Traceback (most recent call last)File /home/mambaforge/envs/sbdb-dev/lib/python3.11/site-packages/pyswarms/utils/reporter/reporter.py:180, in Reporter._setup_logger(self, path) 179 try:--> 180 with open(value, "rt") as f: 181 config = yaml.safe_load(f.read()) TypeError: expected str, bytes or os.PathLike object, not NoneType During handling of the above exception, another exception occurred: PermissionError Traceback (most recent call last)File /home/mambaforge/envs/sbdb-dev/lib/python3.11/logging/config.py:573, in DictConfigurator.configure(self) 572 try:--> 573 handler = self.configure_handler(handlers[name]) 574 handler.name = name File /home/mambaforge/envs/sbdb-dev/lib/python3.11/logging/config.py:758, in DictConfigurator.configure_handler(self, config) 757 try:--> 758 result = factory(**kwargs) 759 except TypeError as te: File /home/mambaforge/envs/sbdb-dev/lib/python3.11/logging/handlers.py:155, in RotatingFileHandler.__init__(self, filename, mode, maxBytes, backupCount, encoding, delay, errors) 154 encoding = io.text_encoding(encoding)--> 155 BaseRotatingHandler.__init__(self, filename, mode, encoding=encoding, 156 delay=delay, errors=errors) 157 self.maxBytes = maxBytes File /home/mambaforge/envs/sbdb-dev/lib/python3.11/logging/handlers.py:58, in BaseRotatingHandler.__init__(self, filename, mode, encoding, delay, errors) 55 """ 56 Use the specified filename for streamed logging 57 """---> 58 logging.FileHandler.__init__(self, filename, mode=mode, 59 encoding=encoding, delay=delay, 60 errors=errors) 61 self.mode = mode File /home/mambaforge/envs/sbdb-dev/lib/python3.11/logging/__init__.py:1181, in FileHandler.__init__(self, filename, mode, encoding, delay, errors) 1180 else:-> 1181 StreamHandler.__init__(self, self._open()) File /home/mambaforge/envs/sbdb-dev/lib/python3.11/logging/__init__.py:1213, in FileHandler._open(self) 1212 open_func = self._builtin_open-> 1213 return open_func(self.baseFilename, self.mode, 1214 encoding=self.encoding, errors=self.errors) PermissionError: [Errno 13] Permission denied: '/home/report.log' The above exception was the direct cause of the following exception: ValueError Traceback (most recent call last)Cell In[1], line 1----> 1 import sbdb File /home/projects/sbdb/sbdb/__init__.py:9 7 from .librarian import * 8 from .liquid_handling import *----> 9 from .optimization import * 10 from .processing import * 11 from .schema import * File /home/projects/sbdb/sbdb/optimization/__init__.py:1----> 1 from .assay_optimizer import * 2 from .denovo_probes import DeNovoProbes 3 from .mutable_primers import MutablePrimers File /home/projects/sbdb/sbdb/optimization/assay_optimizer.py:14 12 from scipy.special import erfcx 13 from scipy.stats.qmc import Sobol, LatinHypercube---> 14 import pyswarms as ps 15 import pytensor.tensor as pt 16 import pytensor.gradient as pg File /home/mambaforge/envs/sbdb-dev/lib/python3.11/site-packages/pyswarms/__init__.py:17 14 __email__ = ***@***.***" 15 __version__ = "1.3.0"---> 17 from .single import global_best, local_best, general_optimizer 18 from .discrete import binary 19 from .utils.decorators import cost File /home/mambaforge/envs/sbdb-dev/lib/python3.11/site-packages/pyswarms/single/__init__.py:17 1 """ 2 The :mod:`pyswarms.single` module implements various techniques in 3 continuous single-objective optimization. These require only one (...) 14 multiplication can lead to an :code:`OverflowError`. 15 """---> 17 from .global_best import GlobalBestPSO 18 from .local_best import LocalBestPSO 19 from .general_optimizer import GeneralOptimizerPSO File /home/mambaforge/envs/sbdb-dev/lib/python3.11/site-packages/pyswarms/single/global_best.py:67 63 import multiprocessing as mp 65 from collections import deque---> 67 from ..backend.operators import compute_pbest, compute_objective_function 68 from ..backend.topology import Star 69 from ..backend.handlers import BoundaryHandler, VelocityHandler, OptionsHandler File /home/mambaforge/envs/sbdb-dev/lib/python3.11/site-packages/pyswarms/backend/__init__.py:7 1 """ 2 The :code:`pyswarms.backend` module abstracts various operations 3 for swarm optimization: generating boundaries, updating positions, etc. 4 You can use the methods implemented here to build your own PSO implementations. 5 """----> 7 from .generators import * 8 from .handlers import * 9 from .operators import * File /home/mambaforge/envs/sbdb-dev/lib/python3.11/site-packages/pyswarms/backend/generators.py:21 18 from ..utils.reporter import Reporter 19 from .swarms import Swarm---> 21 rep = Reporter(logger=logging.getLogger(__name__)) 24 def generate_swarm( 25 n_particles, dimensions, bounds=None, center=1.00, init_pos=None 26 ): 27 """Generate a swarm 28 29 Parameters (...) 58 When the argument passed to bounds is not an iterable. 59 """ File /home/mambaforge/envs/sbdb-dev/lib/python3.11/site-packages/pyswarms/utils/reporter/reporter.py:118, in Reporter.__init__(self, log_path, config_path, logger, printer) 85 self._env_key = "LOG_CFG" 86 self._default_config = { 87 "version": 1, 88 "disable_existing_loggers": False, (...) 116 }, 117 }--> 118 self._setup_logger(config_path) File /home/mambaforge/envs/sbdb-dev/lib/python3.11/site-packages/pyswarms/utils/reporter/reporter.py:184, in Reporter._setup_logger(self, path) 182 logging.config.dictConfig(config) 183 except (TypeError, FileNotFoundError):--> 184 self._load_defaults() File /home/mambaforge/envs/sbdb-dev/lib/python3.11/site-packages/pyswarms/utils/reporter/reporter.py:188, in Reporter._load_defaults(self) 186 def _load_defaults(self): 187 """Load default logging configuration"""--> 188 logging.config.dictConfig(self._default_config) File /home/mambaforge/envs/sbdb-dev/lib/python3.11/logging/config.py:823, in dictConfig(config) 821 def dictConfig(config): 822 """Configure logging using a dictionary."""--> 823 dictConfigClass(config).configure() File /home/mambaforge/envs/sbdb-dev/lib/python3.11/logging/config.py:580, in DictConfigurator.configure(self) 578 deferred.append(name) 579 else:--> 580 raise ValueError('Unable to configure handler ' 581 '%r' % name) from e 583 # Now do any that were deferred 584 for name in deferred: ValueError: Unable to configure handler 'file_default' — Reply to this email directly, view it on GitHub <#526 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BHVPJGITUXHRE6W57UOHM4DZH4XZDAVCNFSM6AAAAABHDJJBQ2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNZUGIZDONBUGQ> . 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