From ceabe7c38feaa86d66e60ec4a3ab935a335427d5 Mon Sep 17 00:00:00 2001 From: anna-charlotte Date: Fri, 17 Jan 2025 15:39:26 +0100 Subject: [PATCH] move files from fdr_analysis to fdrx module --- alphadia/fdrexperimental.py | 1 - alphadia/{fdr_analysis => fdrx}/models/__init__.py | 0 alphadia/{fdr_analysis => fdrx}/models/logistic_regression.py | 0 alphadia/{fdr_analysis => fdrx}/models/two_step_classifier.py | 2 +- alphadia/workflow/manager.py | 2 +- alphadia/workflow/peptidecentric.py | 2 +- 6 files changed, 3 insertions(+), 4 deletions(-) rename alphadia/{fdr_analysis => fdrx}/models/__init__.py (100%) rename alphadia/{fdr_analysis => fdrx}/models/logistic_regression.py (100%) rename alphadia/{fdr_analysis => fdrx}/models/two_step_classifier.py (99%) diff --git a/alphadia/fdrexperimental.py b/alphadia/fdrexperimental.py index 07f22ce3..af9faa01 100644 --- a/alphadia/fdrexperimental.py +++ b/alphadia/fdrexperimental.py @@ -1179,7 +1179,6 @@ def fit(self, x: np.ndarray, y: np.ndarray): x_train_batch = x_train[batch_start:batch_stop] y_train_batch = y_train[batch_start:batch_stop] y_pred = self.network(x_train_batch) - loss_value = loss(y_pred, y_train_batch) self.network.zero_grad() diff --git a/alphadia/fdr_analysis/models/__init__.py b/alphadia/fdrx/models/__init__.py similarity index 100% rename from alphadia/fdr_analysis/models/__init__.py rename to alphadia/fdrx/models/__init__.py diff --git a/alphadia/fdr_analysis/models/logistic_regression.py b/alphadia/fdrx/models/logistic_regression.py similarity index 100% rename from alphadia/fdr_analysis/models/logistic_regression.py rename to alphadia/fdrx/models/logistic_regression.py diff --git a/alphadia/fdr_analysis/models/two_step_classifier.py b/alphadia/fdrx/models/two_step_classifier.py similarity index 99% rename from alphadia/fdr_analysis/models/two_step_classifier.py rename to alphadia/fdrx/models/two_step_classifier.py index 62e8141f..3f0c4290 100644 --- a/alphadia/fdr_analysis/models/two_step_classifier.py +++ b/alphadia/fdrx/models/two_step_classifier.py @@ -285,4 +285,4 @@ def apply_absolute_transformations( f"column '{col}' is not present in df, therefore abs() was not applied." ) - return df \ No newline at end of file + return df diff --git a/alphadia/workflow/manager.py b/alphadia/workflow/manager.py index 78dc5160..07625d13 100644 --- a/alphadia/workflow/manager.py +++ b/alphadia/workflow/manager.py @@ -20,7 +20,7 @@ import alphadia from alphadia import fdr from alphadia.calibration.property import Calibration, calibration_model_provider -from alphadia.fdr_analysis.models import TwoStepClassifier +from alphadia.fdrx.models import TwoStepClassifier from alphadia.workflow import reporting from alphadia.workflow.config import Config diff --git a/alphadia/workflow/peptidecentric.py b/alphadia/workflow/peptidecentric.py index ffcb4eaf..a86e2958 100644 --- a/alphadia/workflow/peptidecentric.py +++ b/alphadia/workflow/peptidecentric.py @@ -15,7 +15,7 @@ # alphadia imports from alphadia import fragcomp, plexscoring, utils -from alphadia.fdr_analysis.models import LogisticRegressionClassifier, TwoStepClassifier +from alphadia.fdrx.models import LogisticRegressionClassifier, TwoStepClassifier from alphadia.peakgroup import search from alphadia.workflow import base, manager, optimization from alphadia.workflow.config import Config