From f24678a3188764e5c318bff7a7f194e4aa702f52 Mon Sep 17 00:00:00 2001
From: pavlovicmilena <milenapavlovic775@gmail.com>
Date: Wed, 27 Oct 2021 21:32:04 +0200
Subject: [PATCH] move Metric.py to ml_metrics package & update version

---
 immuneML/dsl/instruction_parsers/TrainMLModelParser.py         | 3 +--
 immuneML/environment/Constants.py                              | 2 +-
 .../hyperparameter_optimization/states/TrainMLModelState.py    | 2 +-
 immuneML/{environment => ml_metrics}/Metric.py                 | 0
 immuneML/presentation/html/HPHTMLBuilder.py                    | 2 +-
 immuneML/reports/ml_reports/TrainingPerformance.py             | 2 +-
 immuneML/workflows/instructions/MLProcess.py                   | 2 +-
 immuneML/workflows/instructions/TrainMLModelInstruction.py     | 2 +-
 immuneML/workflows/steps/MLMethodAssessment.py                 | 2 +-
 immuneML/workflows/steps/MLMethodAssessmentParams.py           | 2 +-
 test/dsl/semantic_model/test_semanticModel.py                  | 2 +-
 test/integration_tests/test_receptorClassification.py          | 2 +-
 test/integration_tests/test_sequenceClassification.py          | 2 +-
 test/reports/analysis_reports/test_CVFeaturePerformance.py     | 2 +-
 test/reports/ml_reports/test_TrainingPerformance.py            | 3 +--
 test/reports/ml_reports/test_mLSettingsPerformance.py          | 2 +-
 test/workflows/instructions/test_HPOptimizationInstruction.py  | 2 +-
 test/workflows/steps/test_MLMethodAssessment.py                | 2 +-
 18 files changed, 17 insertions(+), 19 deletions(-)
 rename immuneML/{environment => ml_metrics}/Metric.py (100%)

diff --git a/immuneML/dsl/instruction_parsers/TrainMLModelParser.py b/immuneML/dsl/instruction_parsers/TrainMLModelParser.py
index 03c310364..459afa29e 100644
--- a/immuneML/dsl/instruction_parsers/TrainMLModelParser.py
+++ b/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
diff --git a/immuneML/environment/Constants.py b/immuneML/environment/Constants.py
index af438ea7e..110f5c3c2 100644
--- a/immuneML/environment/Constants.py
+++ b/immuneML/environment/Constants.py
@@ -1,6 +1,6 @@
 class Constants:
 
-    VERSION = "2.0.5"
+    VERSION = "2.0.6"
 
     # encoding constants
     FEATURE_DELIMITER = "///"
diff --git a/immuneML/hyperparameter_optimization/states/TrainMLModelState.py b/immuneML/hyperparameter_optimization/states/TrainMLModelState.py
index 0136a5ca0..baf5a7ffc 100644
--- a/immuneML/hyperparameter_optimization/states/TrainMLModelState.py
+++ b/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
 
 
diff --git a/immuneML/environment/Metric.py b/immuneML/ml_metrics/Metric.py
similarity index 100%
rename from immuneML/environment/Metric.py
rename to immuneML/ml_metrics/Metric.py
diff --git a/immuneML/presentation/html/HPHTMLBuilder.py b/immuneML/presentation/html/HPHTMLBuilder.py
index bcdeb9332..cf7ff7efa 100644
--- a/immuneML/presentation/html/HPHTMLBuilder.py
+++ b/immuneML/presentation/html/HPHTMLBuilder.py
@@ -7,7 +7,6 @@
 
 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
@@ -15,6 +14,7 @@
 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
diff --git a/immuneML/reports/ml_reports/TrainingPerformance.py b/immuneML/reports/ml_reports/TrainingPerformance.py
index 7d421bcf8..38d32fc2f 100644
--- a/immuneML/reports/ml_reports/TrainingPerformance.py
+++ b/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
diff --git a/immuneML/workflows/instructions/MLProcess.py b/immuneML/workflows/instructions/MLProcess.py
index 2c52dd372..c1d656f0e 100644
--- a/immuneML/workflows/instructions/MLProcess.py
+++ b/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
diff --git a/immuneML/workflows/instructions/TrainMLModelInstruction.py b/immuneML/workflows/instructions/TrainMLModelInstruction.py
index 2a60b93cb..0987099f2 100644
--- a/immuneML/workflows/instructions/TrainMLModelInstruction.py
+++ b/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
diff --git a/immuneML/workflows/steps/MLMethodAssessment.py b/immuneML/workflows/steps/MLMethodAssessment.py
index f81edd070..2c9637882 100644
--- a/immuneML/workflows/steps/MLMethodAssessment.py
+++ b/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
diff --git a/immuneML/workflows/steps/MLMethodAssessmentParams.py b/immuneML/workflows/steps/MLMethodAssessmentParams.py
index 3c20a9066..488b6b896 100644
--- a/immuneML/workflows/steps/MLMethodAssessmentParams.py
+++ b/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
 
 
diff --git a/test/dsl/semantic_model/test_semanticModel.py b/test/dsl/semantic_model/test_semanticModel.py
index f592926cf..907c5ddee 100644
--- a/test/dsl/semantic_model/test_semanticModel.py
+++ b/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
diff --git a/test/integration_tests/test_receptorClassification.py b/test/integration_tests/test_receptorClassification.py
index 1a1757a30..9594b308f 100644
--- a/test/integration_tests/test_receptorClassification.py
+++ b/test/integration_tests/test_receptorClassification.py
@@ -10,7 +10,6 @@
 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
@@ -18,6 +17,7 @@
 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
 
diff --git a/test/integration_tests/test_sequenceClassification.py b/test/integration_tests/test_sequenceClassification.py
index 12c2abe67..5a691efb7 100644
--- a/test/integration_tests/test_sequenceClassification.py
+++ b/test/integration_tests/test_sequenceClassification.py
@@ -10,7 +10,6 @@
 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
@@ -18,6 +17,7 @@
 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
 
diff --git a/test/reports/analysis_reports/test_CVFeaturePerformance.py b/test/reports/analysis_reports/test_CVFeaturePerformance.py
index 07ca73cce..e537c31fd 100644
--- a/test/reports/analysis_reports/test_CVFeaturePerformance.py
+++ b/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
 
diff --git a/test/reports/ml_reports/test_TrainingPerformance.py b/test/reports/ml_reports/test_TrainingPerformance.py
index 3d3023dc1..205d17889 100644
--- a/test/reports/ml_reports/test_TrainingPerformance.py
+++ b/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()
diff --git a/test/reports/ml_reports/test_mLSettingsPerformance.py b/test/reports/ml_reports/test_mLSettingsPerformance.py
index 70b80fe14..25ec1ee9e 100644
--- a/test/reports/ml_reports/test_mLSettingsPerformance.py
+++ b/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
diff --git a/test/workflows/instructions/test_HPOptimizationInstruction.py b/test/workflows/instructions/test_HPOptimizationInstruction.py
index 42b3cf9ea..7c6f220ec 100644
--- a/test/workflows/instructions/test_HPOptimizationInstruction.py
+++ b/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
diff --git a/test/workflows/steps/test_MLMethodAssessment.py b/test/workflows/steps/test_MLMethodAssessment.py
index 6f8e7c173..0d99fe703 100644
--- a/test/workflows/steps/test_MLMethodAssessment.py
+++ b/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