From 118d48e4c8687b2ee413f2f0c387ff18c39d5b96 Mon Sep 17 00:00:00 2001
From: llegregam <legregam@insa-toulouse.fr>
Date: Thu, 13 Jun 2024 15:35:11 +0200
Subject: [PATCH] flake8 linting

---
 physiofit/base/fitter.py        | 8 +++++++-
 physiofit/models/model_3.py     | 6 +++---
 physiofit/tests/test_base.py    | 1 +
 physiofit/tests/test_model_1.py | 8 ++++----
 physiofit/tests/test_model_3.py | 4 ++--
 tox.ini                         | 1 -
 6 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/physiofit/base/fitter.py b/physiofit/base/fitter.py
index 7e6b885..f461e03 100644
--- a/physiofit/base/fitter.py
+++ b/physiofit/base/fitter.py
@@ -413,9 +413,15 @@ def monte_carlo_analysis(self):
             logger.debug(f"New matrix:\n{noisy_matrix}\n")
             logger.debug(f"Sd matrix:\n{self.sd}\n")
             logger.debug(f"time vector:\n{self.model.time_vector}\n")
+            sim_mat = self.model.simulate(
+                opt_res.x,
+                noisy_matrix,
+                self.model.time_vector,
+                self.model.args
+            )
             logger.debug(
                 "simulated matrix:"
-                f"{self.model.simulate(opt_res.x, noisy_matrix, self.model.time_vector, self.model.args)}\n"
+                f"{sim_mat}\n"
             )
             # We optimise the parameters using the noisy matrix as input
 
diff --git a/physiofit/models/model_3.py b/physiofit/models/model_3.py
index b2e9f64..7dac3cf 100644
--- a/physiofit/models/model_3.py
+++ b/physiofit/models/model_3.py
@@ -76,8 +76,8 @@ def simulate(
             m_0 = parameters[i * 2 + 1]
             k = fixed_params[i - 1]
             exp_k_t = np.exp(-k * time_vector)
-            simulated_matrix[:, i] = q * (x_0 / (mu + k)) \
-                                     * (exp_mu_t - exp_k_t) \
-                                     + m_0 * exp_k_t
+            simulated_matrix[:, i] = (q * (x_0 / (mu + k)) * (exp_mu_t
+                                                              - exp_k_t) +
+                                      m_0 * exp_k_t)
 
         return simulated_matrix
diff --git a/physiofit/tests/test_base.py b/physiofit/tests/test_base.py
index 2cb756d..382f2c4 100644
--- a/physiofit/tests/test_base.py
+++ b/physiofit/tests/test_base.py
@@ -59,6 +59,7 @@ def test_wrong_entry_for_model_data(base_test_data):
             "Steady-state batch model",
             "Hello world this is an error"
         )
+        return model
 
 
 def test_optimization_process(base_test_data):
diff --git a/physiofit/tests/test_model_1.py b/physiofit/tests/test_model_1.py
index eef4b7b..e6143b1 100644
--- a/physiofit/tests/test_model_1.py
+++ b/physiofit/tests/test_model_1.py
@@ -93,8 +93,8 @@ def test_model_1_estimation(
         data=model_1_data
     )
     model.get_params()
-    model.args = {"Degradation constants":
-                      {"Glucose": 0, "Acetate": 0, "Glutamine": 1}
+    model.args = {"Degradation constants": {"Glucose": 0, "Acetate": 0,
+                                            "Glutamine": 1}
                   }
     fitter = io.initialize_fitter(
         data=model.data,
@@ -124,8 +124,8 @@ def test_model_1_simulation(
     )
     model.get_params()
     model.parameters.update(parameters)
-    model.args = {"Degradation constants":
-                      {"Glucose": 0, "Acetate": 0, "Glutamine": 1}
+    model.args = {"Degradation constants": {"Glucose": 0, "Acetate": 0,
+                                            "Glutamine": 1}
                   }
     sim_data = model.simulate(
         list(model.parameters.values()),
diff --git a/physiofit/tests/test_model_3.py b/physiofit/tests/test_model_3.py
index 1f67472..1892873 100644
--- a/physiofit/tests/test_model_3.py
+++ b/physiofit/tests/test_model_3.py
@@ -124,8 +124,8 @@ def test_model_3_simulation(
     )
     model.get_params()
     model.parameters.update(parameters)
-    model.args = {"Degradation constants":
-                      {"Glucose": 0, "Acetate": 0, "Glutamine": 1}
+    model.args = {"Degradation constants": {"Glucose": 0, "Acetate": 0,
+                                            "Glutamine": 1}
                   }
     sim_data = model.simulate(
         list(model.parameters.values()),
diff --git a/tox.ini b/tox.ini
index 52138c5..17517ed 100644
--- a/tox.ini
+++ b/tox.ini
@@ -25,4 +25,3 @@ commands = flake8
 deps = flake8
 
 
-