OneHotEncoder Failure: Simple example failure

[chclam]

An error occurs when I'm trying to run the following simple example from the main page:

from sklearn.datasets import load_breast_cancer
from sklearn.model_selection import train_test_split
from sklearn.metrics import log_loss, accuracy_score
from gama import GamaClassifier

if __name__ == '__main__':
    X, y = load_breast_cancer(return_X_y=True)
    X_train, X_test, y_train, y_test = train_test_split(X, y, stratify=y, random_state=0)

    automl = GamaClassifier(max_total_time=180, store="nothing")
    print("Starting `fit` which will take roughly 3 minutes.")
    automl.fit(X_train, y_train)

    label_predictions = automl.predict(X_test)
    probability_predictions = automl.predict_proba(X_test)

    print('accuracy:', accuracy_score(y_test, label_predictions))
    print('log loss:', log_loss(y_test, probability_predictions))
    # the `score` function outputs the score on the metric optimized towards (by default, `log_loss`)
    print('log_loss', automl.score(X_test, y_test))

The error that I get:

Traceback (most recent call last):
  File "/Users/chris/Development/gradproject/issues/gama/gama/./test.py", line 13, in <module>
    automl.fit(X_train, y_train)
  File "/Users/chris/Development/gradproject/issues/gama/gama/gama/GamaClassifier.py", line 134, in fit
    super().fit(x, y, *args, **kwargs)
  File "/Users/chris/Development/gradproject/issues/gama/gama/gama/gama.py", line 502, in fit
    self._x, self._basic_encoding_pipeline = basic_encoding(
  File "/Users/chris/Development/gradproject/issues/gama/gama/gama/utilities/preprocessing.py", line 63, in basic_encoding
    x_enc = encoding_pipeline.fit_transform(x, y=None)  # Is this dangerous?
  File "/usr/local/lib/python3.9/site-packages/sklearn/pipeline.py", line 434, in fit_transform
    return last_step.fit_transform(Xt, y, **fit_params_last_step)
  File "/usr/local/lib/python3.9/site-packages/sklearn/base.py", line 847, in fit_transform
    return self.fit(X, **fit_params).transform(X)
  File "/usr/local/lib/python3.9/site-packages/category_encoders/one_hot.py", line 152, in fit
    oe_missing_strat = {
KeyError: 'ignore'

It seems to be caused by assigning an invalid keyword to the handle_missing function parameter to OneHotEncoder in the dependency category_encoders.
According to the docs, the valid keywords are as follows: error, return_nan, value, and indicator, where value is the default.

[PGijsbers]

Hi, thanks for opening the issue and providing a solution 👍
It looks like this is specific to the latest release (and was undocumented and without deprecation warnings) :)

For those that run into this issue until a new gama PyPI release is available: please downgrade category encoders to 2.3:
pip install category-encoders==2.3

[chclam]

Hey, I'm glad to be of any help 👍

[alanwilter]

I'm hitting this same problem right now and I need it in docker.

If you don't have a linux, try with gitpod.io with https://github.com/openml/automlbenchmark

yes | python runbenchmark.py gama:latest example test -m docker -s force
...
Collecting liac-arff>=2.2.2
  Downloading liac-arff-2.5.0.tar.gz (13 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: psutil in ./frameworks/GAMA/venv/lib/python3.7/site-packages (from gama==22.0.1.dev0) (5.8.0)
ERROR: Ignored the following versions that require a different python version: 1.1.0 Requires-Python >=3.8; 1.1.0rc1 Requires-Python >=3.8; 1.1.1 Requires-Python >=3.8; 1.1.2 Requires-Python >=3.8; 1.4.0 Requires-Python >=3.8; 1.4.0rc0 Requires-Python >=3.8; 1.4.1 Requires-Python >=3.8; 1.4.2 Requires-Python >=3.8; 1.4.3 Requires-Python >=3.8; 1.4.4 Requires-Python >=3.8; 1.5.0rc0 Requires-Python >=3.8; 1.8.0 Requires-Python >=3.8,<3.11; 1.8.0rc1 Requires-Python >=3.8,<3.11; 1.8.0rc2 Requires-Python >=3.8,<3.11; 1.8.0rc3 Requires-Python >=3.8,<3.11; 1.8.0rc4 Requires-Python >=3.8,<3.11; 1.8.1 Requires-Python >=3.8,<3.11; 1.9.0 Requires-Python >=3.8,<3.12; 1.9.0rc1 Requires-Python >=3.8,<3.12; 1.9.0rc2 Requires-Python >=3.8,<3.12; 1.9.0rc3 Requires-Python >=3.8,<3.12; 1.9.1 Requires-Python >=3.8,<3.12
ERROR: Could not find a version that satisfies the requirement scikit-learn>=1.1.0 (from gama) (from versions: 0.9, 0.10, 0.11, 0.12, 0.12.1, 0.13, 0.13.1, 0.14, 0.14.1, 0.15.0b1, 0.15.0b2, 0.15.0, 0.15.1, 0.15.2, 0.16b1, 0.16.0, 0.16.1, 0.17b1, 0.17, 0.17.1, 0.18, 0.18.1, 0.18.2, 0.19b2, 0.19.0, 0.19.1, 0.19.2, 0.20rc1, 0.20.0, 0.20.1, 0.20.2, 0.20.3, 0.20.4, 0.21rc2, 0.21.0, 0.21.1, 0.21.2, 0.21.3, 0.22rc2.post1, 0.22rc3, 0.22, 0.22.1, 0.22.2, 0.22.2.post1, 0.23.0rc1, 0.23.0, 0.23.1, 0.23.2, 0.24.dev0, 0.24.0rc1, 0.24.0, 0.24.1, 0.24.2, 1.0rc1, 1.0rc2, 1.0, 1.0.1, 1.0.2)
ERROR: No matching distribution found for scikit-learn>=1.1.0
Traceback (most recent call last):

  File "<string>", line 1, in <module>

ModuleNotFoundError: No module named 'gama'



Cloning into '/bench/frameworks/GAMA/lib/gama'...
ERROR: Ignored the following versions that require a different python version: 1.1.0 Requires-Python >=3.8; 1.1.0rc1 Requires-Python >=3.8; 1.1.1 Requires-Python >=3.8; 1.1.2 Requires-Python >=3.8; 1.4.0 Requires-Python >=3.8; 1.4.0rc0 Requires-Python >=3.8; 1.4.1 Requires-Python >=3.8; 1.4.2 Requires-Python >=3.8; 1.4.3 Requires-Python >=3.8; 1.4.4 Requires-Python >=3.8; 1.5.0rc0 Requires-Python >=3.8; 1.8.0 Requires-Python >=3.8,<3.11; 1.8.0rc1 Requires-Python >=3.8,<3.11; 1.8.0rc2 Requires-Python >=3.8,<3.11; 1.8.0rc3 Requires-Python >=3.8,<3.11; 1.8.0rc4 Requires-Python >=3.8,<3.11; 1.8.1 Requires-Python >=3.8,<3.11; 1.9.0 Requires-Python >=3.8,<3.12; 1.9.0rc1 Requires-Python >=3.8,<3.12; 1.9.0rc2 Requires-Python >=3.8,<3.12; 1.9.0rc3 Requires-Python >=3.8,<3.12; 1.9.1 Requires-Python >=3.8,<3.12
ERROR: Could not find a version that satisfies the requirement scikit-learn>=1.1.0 (from gama) (from versions: 0.9, 0.10, 0.11, 0.12, 0.12.1, 0.13, 0.13.1, 0.14, 0.14.1, 0.15.0b1, 0.15.0b2, 0.15.0, 0.15.1, 0.15.2, 0.16b1, 0.16.0, 0.16.1, 0.17b1, 0.17, 0.17.1, 0.18, 0.18.1, 0.18.2, 0.19b2, 0.19.0, 0.19.1, 0.19.2, 0.20rc1, 0.20.0, 0.20.1, 0.20.2, 0.20.3, 0.20.4, 0.21rc2, 0.21.0, 0.21.1, 0.21.2, 0.21.3, 0.22rc2.post1, 0.22rc3, 0.22, 0.22.1, 0.22.2, 0.22.2.post1, 0.23.0rc1, 0.23.0, 0.23.1, 0.23.2, 0.24.dev0, 0.24.0rc1, 0.24.0, 0.24.1, 0.24.2, 1.0rc1, 1.0rc2, 1.0, 1.0.1, 1.0.2)
ERROR: No matching distribution found for scikit-learn>=1.1.0
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'gama'

Command '['/bench/frameworks/GAMA/setup.sh', 'latest']' returned non-zero exit status 1.
The command '/bin/sh -c $PY runbenchmark.py gama:latest -s only' returned a non-zero code: 2
Traceback (most recent call last):

  File "runbenchmark.py", line 182, in <module>

    bench.setup(amlb.SetupMode[args.setup])

  File "/bench/amlb/benchmark.py", line 126, in setup

    _activity_timeout_=rconfig().setup.activity_timeout)

  File "/bench/frameworks/GAMA/__init__.py", line 7, in setup

    call_script_in_same_dir(__file__, "setup.sh", *args, **kwargs)

  File "/bench/amlb/utils/process.py", line 259, in call_script_in_same_dir

    return run_script(script_path, *args, **kwargs)

  File "/bench/amlb/utils/process.py", line 253, in run_script

    return run_cmd(script_path, *args, **kwargs)

  File "/bench/amlb/utils/process.py", line 247, in run_cmd

    raise e

  File "/bench/amlb/utils/process.py", line 234, in run_cmd

    preexec_fn=params.preexec_fn)

  File "/bench/amlb/utils/process.py", line 77, in run_subprocess

    raise subprocess.CalledProcessError(retcode, process.args, output=stdout, stderr=stderr)

subprocess.CalledProcessError: Command '['/bench/frameworks/GAMA/setup.sh', 'latest']' returned non-zero exit status 1.






The command '/bin/sh -c $PY runbenchmark.py gama:latest -s only' returned a non-zero code: 2

Command 'docker build --no-cache -t automlbenchmark/gama:latest-dev -f /workspace/automlbenchmark/frameworks/GAMA/.setup/Dockerfile .' returned non-zero exit status 2.
Traceback (most recent call last):
  File "runbenchmark.py", line 182, in <module>
    bench.setup(amlb.SetupMode[args.setup])
  File "/workspace/automlbenchmark/amlb/runners/container.py", line 80, in setup
    self.image = self._build_image(cache=(mode != SetupMode.force))
  File "/workspace/automlbenchmark/amlb/runners/container.py", line 194, in _build_image
    self._run_container_build_command(image, cache)
  File "/workspace/automlbenchmark/amlb/runners/docker.py", line 98, in _run_container_build_command
    run_cmd("docker build {options} -t {container} -f {script} .".format(
  File "/workspace/automlbenchmark/amlb/utils/process.py", line 247, in run_cmd
    raise e
  File "/workspace/automlbenchmark/amlb/utils/process.py", line 221, in run_cmd
    completed = run_subprocess(str_cmd if params.shell else full_cmd,
  File "/workspace/automlbenchmark/amlb/utils/process.py", line 77, in run_subprocess
    raise subprocess.CalledProcessError(retcode, process.args, output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command 'docker build --no-cache -t automlbenchmark/gama:latest-dev -f /workspace/automlbenchmark/frameworks/GAMA/.setup/Dockerfile .' returned non-zero exit status 2.

If I run local, it works, but only because my local python is 3.8.

[alanwilter]

Never mind, changed in resources/config.yaml to python: 3.8 and it worked.

[PGijsbers]

As expected: the latest GAMA release (22.0.0) is only available for Py 3.8+