move Metric.py to ml_metrics package & update version

immuneML/dsl/instruction_parsers/TrainMLModelParser.py

@@ -1,5 +1,4 @@
 import hashlib
-import warnings
 from inspect import signature
 from pathlib import Path
 from typing import Tuple
@@ -11,13 +10,13 @@
 from immuneML.dsl.symbol_table.SymbolTable import SymbolTable
 from immuneML.environment.EnvironmentSettings import EnvironmentSettings
 from immuneML.environment.LabelConfiguration import LabelConfiguration
-from immuneML.environment.Metric import Metric
 from immuneML.hyperparameter_optimization.HPSetting import HPSetting
 from immuneML.hyperparameter_optimization.config.LeaveOneOutConfig import LeaveOneOutConfig
 from immuneML.hyperparameter_optimization.config.ManualSplitConfig import ManualSplitConfig
 from immuneML.hyperparameter_optimization.config.ReportConfig import ReportConfig
 from immuneML.hyperparameter_optimization.config.SplitConfig import SplitConfig
 from immuneML.hyperparameter_optimization.config.SplitType import SplitType
+from immuneML.ml_metrics.Metric import Metric
 from immuneML.reports.train_ml_model_reports.TrainMLModelReport import TrainMLModelReport
 from immuneML.util.ParameterValidator import ParameterValidator
 from immuneML.util.ReflectionHandler import ReflectionHandler

immuneML/environment/Constants.py

@@ -1,6 +1,6 @@
 class Constants:
 
-    VERSION = "2.0.5"
+    VERSION = "2.0.6"
 
     # encoding constants
     FEATURE_DELIMITER = "///"

immuneML/hyperparameter_optimization/states/TrainMLModelState.py

@@ -4,12 +4,12 @@
 
 from immuneML.data_model.dataset.Dataset import Dataset
 from immuneML.environment.LabelConfiguration import LabelConfiguration
-from immuneML.environment.Metric import Metric
 from immuneML.hyperparameter_optimization.HPSetting import HPSetting
 from immuneML.hyperparameter_optimization.config.SplitConfig import SplitConfig
 from immuneML.hyperparameter_optimization.states.HPAssessmentState import HPAssessmentState
 from immuneML.hyperparameter_optimization.states.HPItem import HPItem
 from immuneML.hyperparameter_optimization.strategy.HPOptimizationStrategy import HPOptimizationStrategy
+from immuneML.ml_metrics.Metric import Metric
 from immuneML.reports.ReportResult import ReportResult
 
 

immuneML/presentation/html/HPHTMLBuilder.py

@@ -7,14 +7,14 @@
 
 from immuneML.environment.Constants import Constants
 from immuneML.environment.EnvironmentSettings import EnvironmentSettings
-from immuneML.environment.Metric import Metric
 from immuneML.hyperparameter_optimization.config.SplitType import SplitType
 from immuneML.hyperparameter_optimization.states.HPAssessmentState import HPAssessmentState
 from immuneML.hyperparameter_optimization.states.HPItem import HPItem
 from immuneML.hyperparameter_optimization.states.HPLabelState import HPLabelState
 from immuneML.hyperparameter_optimization.states.HPSelectionState import HPSelectionState
 from immuneML.hyperparameter_optimization.states.TrainMLModelState import TrainMLModelState
 from immuneML.ml_methods.util.Util import Util as MLUtil
+from immuneML.ml_metrics.Metric import Metric
 from immuneML.presentation.TemplateParser import TemplateParser
 from immuneML.presentation.html.Util import Util
 from immuneML.reports.ReportResult import ReportResult

immuneML/reports/ml_reports/TrainingPerformance.py

@@ -8,10 +8,10 @@
 from sklearn.preprocessing import label_binarize
 
 from immuneML.data_model.dataset.Dataset import Dataset
-from immuneML.environment.Metric import Metric
 from immuneML.hyperparameter_optimization import HPSetting
 from immuneML.ml_methods.MLMethod import MLMethod
 from immuneML.ml_metrics import ml_metrics
+from immuneML.ml_metrics.Metric import Metric
 from immuneML.reports.ReportOutput import ReportOutput
 from immuneML.reports.ReportResult import ReportResult
 from immuneML.reports.ml_reports.MLReport import MLReport

immuneML/workflows/instructions/MLProcess.py

@@ -5,10 +5,10 @@
 
 from immuneML.data_model.dataset.Dataset import Dataset
 from immuneML.environment.LabelConfiguration import LabelConfiguration
-from immuneML.environment.Metric import Metric
 from immuneML.hyperparameter_optimization.HPSetting import HPSetting
 from immuneML.hyperparameter_optimization.core.HPUtil import HPUtil
 from immuneML.hyperparameter_optimization.states.HPItem import HPItem
+from immuneML.ml_metrics.Metric import Metric
 from immuneML.reports.ReportUtil import ReportUtil
 from immuneML.reports.ml_reports.MLReport import MLReport
 from immuneML.util.PathBuilder import PathBuilder

immuneML/workflows/instructions/TrainMLModelInstruction.py

@@ -6,13 +6,13 @@
 
 from immuneML.IO.ml_method.MLExporter import MLExporter
 from immuneML.environment.LabelConfiguration import LabelConfiguration
-from immuneML.environment.Metric import Metric
 from immuneML.hyperparameter_optimization.config.SplitConfig import SplitConfig
 from immuneML.hyperparameter_optimization.config.SplitType import SplitType
 from immuneML.hyperparameter_optimization.core.HPAssessment import HPAssessment
 from immuneML.hyperparameter_optimization.core.HPUtil import HPUtil
 from immuneML.hyperparameter_optimization.states.TrainMLModelState import TrainMLModelState
 from immuneML.hyperparameter_optimization.strategy.HPOptimizationStrategy import HPOptimizationStrategy
+from immuneML.ml_metrics.Metric import Metric
 from immuneML.reports.train_ml_model_reports.TrainMLModelReport import TrainMLModelReport
 from immuneML.util.ReflectionHandler import ReflectionHandler
 from immuneML.workflows.instructions.Instruction import Instruction

immuneML/workflows/steps/MLMethodAssessment.py

@@ -5,10 +5,10 @@
 import pandas as pd
 from sklearn import metrics
 
-from immuneML.environment.Metric import Metric
 from immuneML.ml_methods.MLMethod import MLMethod
 from immuneML.ml_methods.util.Util import Util
 from immuneML.ml_metrics import ml_metrics
+from immuneML.ml_metrics.Metric import Metric
 from immuneML.util.PathBuilder import PathBuilder
 from immuneML.workflows.steps.MLMethodAssessmentParams import MLMethodAssessmentParams
 from immuneML.workflows.steps.Step import Step

immuneML/workflows/steps/MLMethodAssessmentParams.py

@@ -1,8 +1,8 @@
 from pathlib import Path
 
 from immuneML.data_model.dataset.Dataset import Dataset
-from immuneML.environment.Metric import Metric
 from immuneML.ml_methods.MLMethod import MLMethod
+from immuneML.ml_metrics.Metric import Metric
 from immuneML.workflows.steps.StepParams import StepParams
 
 

test/dsl/semantic_model/test_semanticModel.py

@@ -10,13 +10,13 @@
 from immuneML.environment.Constants import Constants
 from immuneML.environment.EnvironmentSettings import EnvironmentSettings
 from immuneML.environment.LabelConfiguration import LabelConfiguration
-from immuneML.environment.Metric import Metric
 from immuneML.hyperparameter_optimization.HPSetting import HPSetting
 from immuneML.hyperparameter_optimization.config.ReportConfig import ReportConfig
 from immuneML.hyperparameter_optimization.config.SplitConfig import SplitConfig
 from immuneML.hyperparameter_optimization.config.SplitType import SplitType
 from immuneML.hyperparameter_optimization.strategy.GridSearch import GridSearch
 from immuneML.ml_methods.LogisticRegression import LogisticRegression
+from immuneML.ml_metrics.Metric import Metric
 from immuneML.util.PathBuilder import PathBuilder
 from immuneML.util.RepertoireBuilder import RepertoireBuilder
 from immuneML.workflows.instructions.TrainMLModelInstruction import TrainMLModelInstruction

test/integration_tests/test_receptorClassification.py

@@ -10,14 +10,14 @@
 from immuneML.environment.Constants import Constants
 from immuneML.environment.EnvironmentSettings import EnvironmentSettings
 from immuneML.environment.LabelConfiguration import LabelConfiguration
-from immuneML.environment.Metric import Metric
 from immuneML.environment.SequenceType import SequenceType
 from immuneML.hyperparameter_optimization.HPSetting import HPSetting
 from immuneML.hyperparameter_optimization.config.ReportConfig import ReportConfig
 from immuneML.hyperparameter_optimization.config.SplitConfig import SplitConfig
 from immuneML.hyperparameter_optimization.config.SplitType import SplitType
 from immuneML.hyperparameter_optimization.strategy.GridSearch import GridSearch
 from immuneML.ml_methods.LogisticRegression import LogisticRegression
+from immuneML.ml_metrics.Metric import Metric
 from immuneML.simulation.dataset_generation.RandomDatasetGenerator import RandomDatasetGenerator
 from immuneML.workflows.instructions.TrainMLModelInstruction import TrainMLModelInstruction
 

test/integration_tests/test_sequenceClassification.py

@@ -10,14 +10,14 @@
 from immuneML.environment.Constants import Constants
 from immuneML.environment.EnvironmentSettings import EnvironmentSettings
 from immuneML.environment.LabelConfiguration import LabelConfiguration
-from immuneML.environment.Metric import Metric
 from immuneML.environment.SequenceType import SequenceType
 from immuneML.hyperparameter_optimization.HPSetting import HPSetting
 from immuneML.hyperparameter_optimization.config.ReportConfig import ReportConfig
 from immuneML.hyperparameter_optimization.config.SplitConfig import SplitConfig
 from immuneML.hyperparameter_optimization.config.SplitType import SplitType
 from immuneML.hyperparameter_optimization.strategy.GridSearch import GridSearch
 from immuneML.ml_methods.LogisticRegression import LogisticRegression
+from immuneML.ml_metrics.Metric import Metric
 from immuneML.simulation.dataset_generation.RandomDatasetGenerator import RandomDatasetGenerator
 from immuneML.workflows.instructions.TrainMLModelInstruction import TrainMLModelInstruction
 

test/reports/analysis_reports/test_CVFeaturePerformance.py

@@ -7,7 +7,6 @@
 from immuneML.environment.EnvironmentSettings import EnvironmentSettings
 from immuneML.environment.Label import Label
 from immuneML.environment.LabelConfiguration import LabelConfiguration
-from immuneML.environment.Metric import Metric
 from immuneML.hyperparameter_optimization.HPSetting import HPSetting
 from immuneML.hyperparameter_optimization.config.SplitConfig import SplitConfig
 from immuneML.hyperparameter_optimization.config.SplitType import SplitType
@@ -18,6 +17,7 @@
 from immuneML.hyperparameter_optimization.states.TrainMLModelState import TrainMLModelState
 from immuneML.hyperparameter_optimization.strategy.GridSearch import GridSearch
 from immuneML.ml_methods.ProbabilisticBinaryClassifier import ProbabilisticBinaryClassifier
+from immuneML.ml_metrics.Metric import Metric
 from immuneML.reports.ReportResult import ReportResult
 from immuneML.reports.train_ml_model_reports.CVFeaturePerformance import CVFeaturePerformance
 

test/reports/ml_reports/test_TrainingPerformance.py

@@ -9,11 +9,11 @@
 from immuneML.data_model.encoded_data.EncodedData import EncodedData
 from immuneML.environment.Constants import Constants
 from immuneML.environment.EnvironmentSettings import EnvironmentSettings
-from immuneML.environment.Metric import Metric
 from immuneML.ml_methods.LogisticRegression import LogisticRegression
 from immuneML.reports.ReportResult import ReportResult
 from immuneML.reports.ml_reports.TrainingPerformance import TrainingPerformance
 
+
 class TestEvaluation(unittest.TestCase):
 
     def setUp(self) -> None:
@@ -29,7 +29,6 @@ def _create_dummy_lr_model(self):
         return dummy_lr, encoded_tr
 
     def _create_report(self, path):
-
         report = TrainingPerformance.build_object(name='testcase')
 
         report.train_dataset = Dataset()

test/reports/ml_reports/test_mLSettingsPerformance.py

@@ -12,12 +12,12 @@
 from immuneML.environment.EnvironmentSettings import EnvironmentSettings
 from immuneML.environment.Label import Label
 from immuneML.environment.LabelConfiguration import LabelConfiguration
-from immuneML.environment.Metric import Metric
 from immuneML.hyperparameter_optimization.HPSetting import HPSetting
 from immuneML.hyperparameter_optimization.config.SplitConfig import SplitConfig
 from immuneML.hyperparameter_optimization.config.SplitType import SplitType
 from immuneML.hyperparameter_optimization.strategy.GridSearch import GridSearch
 from immuneML.ml_methods.LogisticRegression import LogisticRegression
+from immuneML.ml_metrics.Metric import Metric
 from immuneML.reports.ReportResult import ReportResult
 from immuneML.reports.train_ml_model_reports.MLSettingsPerformance import MLSettingsPerformance
 from immuneML.util.PathBuilder import PathBuilder

test/workflows/instructions/test_HPOptimizationInstruction.py

@@ -10,7 +10,6 @@
 from immuneML.environment.EnvironmentSettings import EnvironmentSettings
 from immuneML.environment.Label import Label
 from immuneML.environment.LabelConfiguration import LabelConfiguration
-from immuneML.environment.Metric import Metric
 from immuneML.hyperparameter_optimization.HPSetting import HPSetting
 from immuneML.hyperparameter_optimization.config.ReportConfig import ReportConfig
 from immuneML.hyperparameter_optimization.config.SplitConfig import SplitConfig
@@ -19,6 +18,7 @@
 from immuneML.hyperparameter_optimization.strategy.GridSearch import GridSearch
 from immuneML.ml_methods.LogisticRegression import LogisticRegression
 from immuneML.ml_methods.SVM import SVM
+from immuneML.ml_metrics.Metric import Metric
 from immuneML.preprocessing.filters.ClonesPerRepertoireFilter import ClonesPerRepertoireFilter
 from immuneML.reports.data_reports.SequenceLengthDistribution import SequenceLengthDistribution
 from immuneML.util.PathBuilder import PathBuilder

test/workflows/steps/test_MLMethodAssessment.py

@@ -11,8 +11,8 @@
 from immuneML.environment.Constants import Constants
 from immuneML.environment.EnvironmentSettings import EnvironmentSettings
 from immuneML.environment.LabelConfiguration import LabelConfiguration
-from immuneML.environment.Metric import Metric
 from immuneML.ml_methods.LogisticRegression import LogisticRegression
+from immuneML.ml_metrics.Metric import Metric
 from immuneML.util.PathBuilder import PathBuilder
 from immuneML.util.RepertoireBuilder import RepertoireBuilder
 from immuneML.workflows.steps.MLMethodAssessment import MLMethodAssessment