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anuprulezAnup Kumar
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Anup Kumar
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Fix linting and tool tests for scikit-learn tool suite (bgruening#1817)
* fix clf_metrics tool * fix linting errors and tests * add conditional tags * update tests * update discriminant tool * add pairwise tool * update sparse tool * update tests for ensemble * updatetests for feature selection * update tests for model_prediction, pairwise_metrics, regression_metrics, model_fit * update tests for sklearn_fitted_model_eval and sklearn_generalized_linear * update tests for lightgbm.xml ml_visualization_ex.xml model_validation.xml nn_classifier.xml numeric_clustering.xml * svm search model validation * update tests form keras_batch_ models.xml keras_model_builder.xml pca.xml pipeline.xml sample_generator.xml train_test_eval.xml * update test for keras_train_eval.xml * update tests and test data for sparse.xml * fix tests for preprocessing tool * update test data for preprocessing tools * bump suite version * update tool version * remove unique_param * update suite name * Keras>=2.10 and <2.11 work with Python=3.10 or maybe Python=3.11 * Change python=3.10 * revert the Python=3.9 version * update test files E format --------- Co-authored-by: Anup Kumar <anuprulez@gmail.com>
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‎tools/sklearn/.shed.yml‎

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@@ -20,7 +20,7 @@ auto_tool_repositories:
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name_template: "{{ tool_id }}"
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description_template: "Wrapper for scikit learn tool: {{ tool_name }}"
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suite:
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name: "sklearn_suite"
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name: "suite_sklearn"
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description: "A suite of Galaxy tools for Machine Learning algorithms such as classification, regression, and clustering"
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long_description: |

‎tools/sklearn/clf_metrics.xml‎

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‎tools/sklearn/discriminant.xml‎

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@@ -92,52 +92,92 @@ dump_model_to_h5(classifier_object, '$outfile_fit')
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</inputs>
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<expand macro="output" />
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<tests>
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<test>
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<param name="infile1" value="train.tabular" ftype="tabular" />
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<param name="infile2" value="train.tabular" ftype="tabular" />
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<param name="col1" value="1,2,3,4" />
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<param name="col2" value="5" />
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<param name="selected_task" value="train" />
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<param name="selected_algorithm" value="LinearDiscriminantAnalysis" />
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<param name="solver" value="svd" />
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<param name="store_covariance" value="True" />
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<test expect_num_outputs="1">
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<conditional name="selected_tasks">
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<param name="selected_task" value="train" />
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<conditional name="selected_algorithms">
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<param name="selected_algorithm" value="LinearDiscriminantAnalysis" />
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<conditional name="input_options">
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<param name="infile1" value="train.tabular" ftype="tabular" />
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<param name="infile2" value="train.tabular" ftype="tabular" />
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<conditional name="column_selector_options_1">
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<param name="col1" value="1,2,3,4" />
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</conditional>
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<conditional name="column_selector_options_2">
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<param name="col2" value="5" />
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</conditional>
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</conditional>
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<section name="options">
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<param name="solver" value="svd" />
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<param name="store_covariance" value="True" />
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</section>
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</conditional>
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</conditional>
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<output name="outfile_fit" file="lda_model01" compare="sim_size" delta="1" />
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</test>
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<test>
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<param name="infile1" value="train.tabular" ftype="tabular" />
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<param name="infile2" value="train.tabular" ftype="tabular" />
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<param name="col1" value="1,2,3,4" />
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<param name="col2" value="5" />
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<param name="selected_task" value="train" />
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<param name="selected_algorithm" value="LinearDiscriminantAnalysis" />
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<param name="solver" value="lsqr" />
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<test expect_num_outputs="1">
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<conditional name="selected_tasks">
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<param name="selected_task" value="train" />
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<conditional name="selected_algorithms">
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<param name="selected_algorithm" value="LinearDiscriminantAnalysis" />
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<conditional name="input_options">
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<param name="infile1" value="train.tabular" ftype="tabular" />
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<param name="infile2" value="train.tabular" ftype="tabular" />
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<conditional name="column_selector_options_1">
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<param name="col1" value="1,2,3,4" />
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</conditional>
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<conditional name="column_selector_options_2">
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<param name="col2" value="5" />
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</conditional>
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</conditional>
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<section name="options">
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<param name="solver" value="lsqr" />
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</section>
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</conditional>
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</conditional>
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<output name="outfile_fit" file="lda_model02" compare="sim_size" delta="1" />
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</test>
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<test>
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<param name="infile1" value="train.tabular" ftype="tabular" />
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<param name="infile2" value="train.tabular" ftype="tabular" />
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<param name="col1" value="1,2,3,4" />
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<param name="col2" value="5" />
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<param name="selected_task" value="train" />
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<param name="selected_algorithm" value="QuadraticDiscriminantAnalysis" />
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<test expect_num_outputs="1">
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<conditional name="selected_tasks">
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<param name="selected_task" value="train" />
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<conditional name="selected_algorithms">
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<param name="selected_algorithm" value="QuadraticDiscriminantAnalysis" />
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<conditional name="input_options">
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<param name="infile1" value="train.tabular" ftype="tabular" />
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<param name="infile2" value="train.tabular" ftype="tabular" />
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<conditional name="column_selector_options_1">
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<param name="col1" value="1,2,3,4" />
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</conditional>
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<conditional name="column_selector_options_2">
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<param name="col2" value="5" />
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</conditional>
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</conditional>
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</conditional>
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</conditional>
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<output name="outfile_fit" file="qda_model01" compare="sim_size" delta="1" />
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</test>
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<test>
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<param name="infile_model" value="lda_model01" ftype="h5mlm" />
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<param name="infile_data" value="test.tabular" ftype="tabular" />
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<param name="selected_task" value="load" />
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<test expect_num_outputs="1">
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<conditional name="selected_tasks">
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<param name="selected_task" value="load" />
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<param name="infile_model" value="lda_model01" ftype="h5mlm" />
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<param name="infile_data" value="test.tabular" ftype="tabular" />
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</conditional>
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<output name="outfile_predict" file="lda_prediction_result01.tabular" />
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</test>
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<test>
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<param name="infile_model" value="lda_model02" ftype="h5mlm" />
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<param name="infile_data" value="test.tabular" ftype="tabular" />
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<param name="selected_task" value="load" />
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<test expect_num_outputs="1">
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<conditional name="selected_tasks">
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<param name="selected_task" value="load" />
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<param name="infile_model" value="lda_model02" ftype="h5mlm" />
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<param name="infile_data" value="test.tabular" ftype="tabular" />
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</conditional>
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<output name="outfile_predict" file="lda_prediction_result02.tabular" />
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</test>
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<test>
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<param name="infile_model" value="qda_model01" ftype="h5mlm" />
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<param name="infile_data" value="test.tabular" ftype="tabular" />
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<param name="selected_task" value="load" />
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<test expect_num_outputs="1">
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<conditional name="selected_tasks">
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<param name="selected_task" value="load" />
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<param name="infile_model" value="qda_model01" ftype="h5mlm" />
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<param name="infile_data" value="test.tabular" ftype="tabular" />
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</conditional>
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<output name="outfile_predict" file="qda_prediction_result01.tabular" />
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</test>
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</tests>

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