TPOT underpopulates a class, but manual sklearn does not about tpot

[perib]

what version of tpot are you using? I was able to reproduce the issue in version 0.12.0, but not 0.12.2 (yet). I haven't nailed down exactly what the issue was but it seems to work for me on the latest version.

[jecorn]

This was with tpot 0.12.1. I just grabbed tpot 1.12.2 and will update when I get a chance to try it out it.

[jecorn]

This was with tpot 0.12.1. I just grabbed tpot 1.12.2 and will update when I get a chance to try it out it.

tpot 0.12.2 can now get past the error. Thanks!

Unfortunately, now there's a different error that I think might be hard to troubleshoot. Running on a single core, tpot starts going through pipelines. But when parallelizing one of the works throws an exception. It might be during a later pipelines (since it doesn't happen on a single core). I'll try to do some digging.

"""
Traceback (most recent call last):
  File "/home/cornlab/miniconda3/envs/jcorn/lib/python3.10/site-packages/joblib/externals/loky/process_executor.py", line 463, in _process_worker
    r = call_item()
  File "/home/cornlab/miniconda3/envs/jcorn/lib/python3.10/site-packages/joblib/externals/loky/process_executor.py", line 291, in __call__
    return self.fn(*self.args, **self.kwargs)
  File "/home/cornlab/miniconda3/envs/jcorn/lib/python3.10/site-packages/joblib/parallel.py", line 589, in __call__
    return [func(*args, **kwargs)
  File "/home/cornlab/miniconda3/envs/jcorn/lib/python3.10/site-packages/joblib/parallel.py", line 589, in <listcomp>
    return [func(*args, **kwargs)
  File "/home/cornlab/miniconda3/envs/jcorn/lib/python3.10/site-packages/stopit/utils.py", line 145, in wrapper
    result = func(*args, **kwargs)
  File "/home/cornlab/miniconda3/envs/jcorn/lib/python3.10/site-packages/tpot/gp_deap.py", line 424, in _wrapped_cross_val_score
    cv_iter = list(cv.split(features, target, groups))
  File "/home/cornlab/miniconda3/envs/jcorn/lib/python3.10/site-packages/sklearn/model_selection/_split.py", line 808, in split
    y = check_array(y, input_name="y", ensure_2d=False, dtype=None)
  File "/home/cornlab/miniconda3/envs/jcorn/lib/python3.10/site-packages/sklearn/utils/validation.py", line 1097, in check_array
    array.flags.writeable = True
ValueError: cannot set WRITEABLE flag to True of this array
"""

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

Traceback (most recent call last):
  File "/home/cornlab/miniconda3/envs/jcorn/lib/python3.10/site-packages/tpot/base.py", line 817, in fit
    self._pop, _ = eaMuPlusLambda(
  File "/home/cornlab/miniconda3/envs/jcorn/lib/python3.10/site-packages/tpot/gp_deap.py", line 232, in eaMuPlusLambda
    population[:] = toolbox.evaluate(population)
  File "/home/cornlab/miniconda3/envs/jcorn/lib/python3.10/site-packages/tpot/base.py", line 1575, in _evaluate_individuals
    tmp_result_scores = parallel(
  File "/home/cornlab/miniconda3/envs/jcorn/lib/python3.10/site-packages/joblib/parallel.py", line 1952, in __call__
    return output if self.return_generator else list(output)
  File "/home/cornlab/miniconda3/envs/jcorn/lib/python3.10/site-packages/joblib/parallel.py", line 1595, in _get_outputs
    yield from self._retrieve()
  File "/home/cornlab/miniconda3/envs/jcorn/lib/python3.10/site-packages/joblib/parallel.py", line 1699, in _retrieve
    self._raise_error_fast()
  File "/home/cornlab/miniconda3/envs/jcorn/lib/python3.10/site-packages/joblib/parallel.py", line 1734, in _raise_error_fast
    error_job.get_result(self.timeout)
  File "/home/cornlab/miniconda3/envs/jcorn/lib/python3.10/site-packages/joblib/parallel.py", line 736, in get_result
    return self._return_or_raise()
  File "/home/cornlab/miniconda3/envs/jcorn/lib/python3.10/site-packages/joblib/parallel.py", line 754, in _return_or_raise
    raise self._result
ValueError: cannot set WRITEABLE flag to True of this array

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/mnt/data/jcorn/autodisco/scripts/auto_tpot.py", line 39, in <module>
    pipeline_optimizer.fit(X, y)
  File "/home/cornlab/miniconda3/envs/jcorn/lib/python3.10/site-packages/tpot/base.py", line 864, in fit
    raise e
  File "/home/cornlab/miniconda3/envs/jcorn/lib/python3.10/site-packages/tpot/base.py", line 855, in fit
    self._update_top_pipeline()
  File "/home/cornlab/miniconda3/envs/jcorn/lib/python3.10/site-packages/tpot/base.py", line 963, in _update_top_pipeline
    raise RuntimeError(
RuntimeError: A pipeline has not yet been optimized. Please call fit() first.

[perib]

I've come across this error at some point too, but it seems to be working on my machine now. IIRC it was due to a package version issue. Try updating the packages, I think my issue was with an outdated version of pandas or numpy?