wywongbd / autocluster Goto Github PK

I am getting this error
AttributeError: module 'pynisher' has no attribute 'enforce_limits'

matplotlib/matplotlib#13555

When running a base pip install I am consistently having the same issue.

` pip3 --no-cache-dir install autocluster
Looking in indexes: https://pypi.org/simple, https://1205d49dc47b4644d672f57e74f850e6342693e3f0b8cf0b:****@packagecloud.io/agrible/internal/pypi/simple
Collecting autocluster
Downloading autocluster-0.5.2-py3-none-any.whl (35 kB)
Requirement already satisfied: six>=1.5.0 in /usr/lib/python3/dist-packages (from autocluster) (1.14.0)
Collecting matplotlib==3.0.3
Downloading matplotlib-3.0.3.tar.gz (36.6 MB)
|████████████████████████████████| 36.6 MB 3.1 MB/s
ERROR: Command errored out with exit status 1:
command: /usr/bin/python3 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ecu3m8rg/matplotlib/setup.py'"'"'; file='"'"'/tmp/pip-install-ecu3m8rg/matplotlib/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-install-ecu3m8rg/matplotlib/pip-egg-info
cwd: /tmp/pip-install-ecu3m8rg/matplotlib/
Complete output (48 lines):
Traceback (most recent call last):
File "", line 1, in
File "/tmp/pip-install-ecu3m8rg/matplotlib/setup.py", line 225, in
msg = pkg.install_help_msg()
File "/tmp/pip-install-ecu3m8rg/matplotlib/setupext.py", line 650, in install_help_msg
release = platform.linux_distribution()[0].lower()
AttributeError: module 'platform' has no attribute 'linux_distribution'
============================================================================
Edit setup.cfg to change the build options

BUILDING MATPLOTLIB
            matplotlib: yes [3.0.3]
                python: yes [3.8.2 (default, Apr 27 2020, 15:53:34)  [GCC
                        9.3.0]]
              platform: yes [linux]

REQUIRED DEPENDENCIES AND EXTENSIONS
                 numpy: yes [version 1.18.5]
      install_requires: yes [handled by setuptools]
                libagg: yes [pkg-config information for 'libagg' could not
                        be found. Using local copy.]
              freetype: no  [The C/C++ header for freetype2 (ft2build.h)
                        could not be found.  You may need to install the
                        development package.]
                   png: no  [pkg-config information for 'libpng' could not
                        be found.]
                 qhull: yes [pkg-config information for 'libqhull' could not
                        be found. Using local copy.]

OPTIONAL SUBPACKAGES
           sample_data: yes [installing]
              toolkits: yes [installing]
                 tests: no  [skipping due to configuration]
        toolkits_tests: no  [skipping due to configuration]

OPTIONAL BACKEND EXTENSIONS
                   agg: yes [installing]
                 tkagg: yes [installing; run-time loading from Python Tcl /
                        Tk]
                macosx: no  [Mac OS-X only]
             windowing: no  [Microsoft Windows only]

OPTIONAL PACKAGE DATA
                  dlls: no  [skipping due to configuration]

============================================================================
                        * The following required packages can not be built:
                        * freetype, png
----------------------------------------

ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.`

https://automl.github.io/SMAC3/stable/installation.html

This link is dead

Due to the old versions of the dependencies, installation fails with tons of errors and red text.

When trying to install autocluster I get this error and can't continue with the installation:

Collecting sklearn
  Downloading sklearn-0.0.post11.tar.gz (3.6 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'error'
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [18 lines of output]
      The 'sklearn' PyPI package is deprecated, use 'scikit-learn'
      rather than 'sklearn' for pip commands.
      
      Here is how to fix this error in the main use cases:
      - use 'pip install scikit-learn' rather than 'pip install sklearn'
      - replace 'sklearn' by 'scikit-learn' in your pip requirements files
        (requirements.txt, setup.py, setup.cfg, Pipfile, etc ...)
      - if the 'sklearn' package is used by one of your dependencies,
        it would be great if you take some time to track which package uses
        'sklearn' instead of 'scikit-learn' and report it to their issue tracker
      - as a last resort, set the environment variable
        SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True to avoid this error
      
      More information is available at
      https://github.com/scikit-learn/sklearn-pypi-package
      
      If the previous advice does not cover your use case, feel free to report it at
      https://github.com/scikit-learn/sklearn-pypi-package/issues/new
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

Also, when attempting to the run the system at all I am consistently running into a core dump issue:

`>>> from autocluster import AutoCluster, get_evaluator

X, y = datasets.make_blobs(n_samples=1000,
... n_features=2,
... centers=6,
... cluster_std=0.5,
... shuffle=True, random_state=27)
dummy_df = pd.DataFrame(X)
dummy_df.head(5)
0 1
0 7.742343 -6.603815
1 8.726121 6.433689
2 -1.427522 5.393546
3 8.801468 -5.185687
4 -1.404321 9.526536
cluster = AutoCluster(logger=None)
fit_params = {
... "df": dummy_df,
... "cluster_alg_ls": [
... 'KMeans', 'GaussianMixture', 'MiniBatchKMeans'
... ],
... "dim_reduction_alg_ls": [
... 'NullModel'
... ],
... "optimizer": 'smac',
... "n_evaluations": 40,
... "run_obj": 'quality',
... "seed": 27,
... "cutoff_time": 10,
... "preprocess_dict": {
... "numeric_cols": list(range(2)),
... "categorical_cols": [],
... "ordinal_cols": [],
... "y_col": []
... },
... "evaluator": get_evaluator(evaluator_ls = ['silhouetteScore',
... 'daviesBouldinScore',
... 'calinskiHarabaszScore'],
... weights = [1, 1, 1],
... clustering_num = None,
... min_proportion = .01,
... min_relative_proportion='default'),
... "n_folds": 3,
... "warmstart": False,
... "verbose_level": 1,
... }
result_dict = cluster.fit(**fit_params)
/home/wolvez/.local/lib/python3.8/site-packages/sklearn/ensemble/_iforest.py:252: FutureWarning: 'behaviour' is deprecated in 0.22 and will be removed in 0.24. You should not pass or set this parameter.
warn(
664/1000 datapoints remaining after outlier removal
Truncated n_evaluations: 40
Segmentation fault (core dumped)`

Using the AutoCluster module on Anaconda (Anaconda3-2019.03-Windows-x86_64) with Spyder (5.3.4) and Python (3.11.5) on Windows, I encountered this problem. How could I resolve this issue Please ?

File ~\anaconda3\Lib\site-packages\spyder_kernels\py3compat.py:357 in compat_exec
exec(code, globals, locals)

File c:********** result_dict = cluster.fit(**fit_params)

File ~\anaconda3\Lib\site-packages\autocluster\autocluster.py:305 in fit
optimal_config = self._smac_obj.optimize()

File ~\anaconda3\Lib\site-packages\smac\facade\smac_facade.py:400 in optimize
incumbent = self.solver.run()

File ~\anaconda3\Lib\site-packages\smac\optimizer\smbo.py:165 in run
self.start()

File ~\anaconda3\Lib\site-packages\smac\optimizer\smbo.py:138 in start
self.incumbent = self.initial_design.run()

File ~\anaconda3\Lib\site-packages\smac\initial_design\single_config_initial_design.py:80 in run
status, cost, runtime, additional_info = self.tae_runner.start(

File ~\anaconda3\Lib\site-packages\smac\tae\execute_ta_run.py:164 in start
status, cost, runtime, additional_info = self.run(config=config,

File ~\anaconda3\Lib\site-packages\smac\tae\execute_func.py:134 in run
rval = self._call_ta(obj, config, **obj_kwargs)

File ~\anaconda3\Lib\site-packages\smac\tae\execute_func.py:213 in _call_ta
return obj(config, **kwargs)

File ~\anaconda3\Lib\site-packages\pynisher\limit_function_call.py:198 in call
subproc.start()

File ~\anaconda3\Lib\multiprocessing\process.py:121 in start
self._popen = self._Popen(self)

File ~\anaconda3\Lib\multiprocessing\context.py:224 in _Popen
return _default_context.get_context().Process._Popen(process_obj)

File ~\anaconda3\Lib\multiprocessing\context.py:336 in _Popen
return Popen(process_obj)

File ~\anaconda3\Lib\multiprocessing\popen_spawn_win32.py:94 in init
reduction.dump(process_obj, to_child)

File ~\anaconda3\Lib\multiprocessing\reduction.py:61 in dump
ForkingPickler(file, protocol).dump(obj)

AttributeError: Can't pickle local object 'AutoCluster.fit..evaluate_model'

What does metaknowledge mean in this repository ?

Bravo !
Hao Wang

This is the first google result that comes up when I searched for "python automl clustering" and is frankly a really great library. However, it's not maintained and installation has broken.

See

https://github.com/renxida/autocluster

for a version that works as of Jan 23 2023.

I have also submitted pull requests in the hope that the author comes back, and will gladly close this issue if this repo gets some love.