From 3361a92ba7f713d4763e1a2fb7e32906bae55e6e Mon Sep 17 00:00:00 2001
From: alexPatrie <alexanderpatrie@gmail.com>
Date: Tue, 7 May 2024 13:32:33 -0400
Subject: [PATCH] chore: minor refactor

---
 .gitignore                                    |  2 +-
 .../processes/comparator_process.py           | 29 +++++++++----------
 c.sh                                          | 20 -------------
 3 files changed, 15 insertions(+), 36 deletions(-)
 delete mode 100755 c.sh

diff --git a/.gitignore b/.gitignore
index b6c7161f9..9b59054b2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,7 +9,7 @@ dist/
 refresh-env.sh
 smoldyn-2.72-mac/
 build/
-c.sh
+commit.sh
 install.sh
 push-image.sh
 release.sh
diff --git a/biosimulator_processes/processes/comparator_process.py b/biosimulator_processes/processes/comparator_process.py
index 0c8b4d39b..834b5c74c 100644
--- a/biosimulator_processes/processes/comparator_process.py
+++ b/biosimulator_processes/processes/comparator_process.py
@@ -47,21 +47,6 @@ def __init__(self, config=None, core=None):
             self.model_parameter_ids[simulator_name] = simulator_instance.model_parameters_list
             self.reactions[simulator_name] = simulator_instance.reaction_list
 
-
-    def _set_simulator_instances(self) -> Dict:
-        simulator_instances = {}
-        for simulator in self.config['simulators']:
-            module_name = simulator + '_process'
-            class_name = simulator.replace(simulator[0], simulator[0].upper()) + 'Process'
-            import_statement = f'biosimulator_processes.processes.{module_name}'
-            simulator_module = __import__(import_statement, fromlist=[class_name])
-            simulator_instance = getattr(simulator_module, class_name)
-            simulator_instances[simulator] = simulator_instance(config={
-                'model': {
-                    'model_source': self.config['sbml_model_file']}
-            })
-        return simulator_instances
-
     def initial_state(self):
         # TODO: get these values from constructor
         return {
@@ -121,3 +106,17 @@ def update(self, state, interval):
                 results[simulator]['validation_score'] = diff  # TODO: make this more fine-grained with MSE
 
         return results
+
+    def _set_simulator_instances(self) -> Dict:
+        simulator_instances = {}
+        for simulator in self.config['simulators']:
+            module_name = simulator + '_process'
+            class_name = simulator.replace(simulator[0], simulator[0].upper()) + 'Process'
+            import_statement = f'biosimulator_processes.processes.{module_name}'
+            simulator_module = __import__(import_statement, fromlist=[class_name])
+            simulator_instance = getattr(simulator_module, class_name)
+            simulator_instances[simulator] = simulator_instance(config={
+                'model': {
+                    'model_source': self.config['sbml_model_file']}
+            })
+        return simulator_instances
diff --git a/c.sh b/c.sh
deleted file mode 100755
index 11c246019..000000000
--- a/c.sh
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/bin/bash
-
-branch="$1"
-
-if [ "${branch}" == "" ]; then
-  echo "Please specify a branch..."
-  read -r branch
-  if [ "${branch}" == "" ]; then
-    branch="main"
-  fi
-fi
-
-echo "Enter commit message: "
-read -r msg
-
-python3 ./scripts/fix_notebooks.py
-git add --all
-git commit -m "${msg}"
-git push origin "${branch}"
-