From 6020cbd82050cf011f1c8b8017be189b28a85945 Mon Sep 17 00:00:00 2001
From: "Frank T. Bergmann" <frank.thomas.bergmann@gmail.com>
Date: Tue, 13 May 2025 13:36:53 +0200
Subject: [PATCH 1/2]  - add basico to dependencies

 using explicit dependencies, since PEtab select seems incompatible with libroadRunner
---
 pyproject.toml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index c3bd56c..cd02beb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,7 +25,9 @@ dependencies = [
     "python-libsbml",
     "matplotlib",
     "petab",
-    "qtawesome"
+    "qtawesome",
+    "copasi-basico",
+    "copasi-petab-importer"
 ]
 
 [build-system]

From 2681becd14d68a1912f26526a1d736a9d3fb2ed3 Mon Sep 17 00:00:00 2001
From: "Frank T. Bergmann" <frank.thomas.bergmann@gmail.com>
Date: Tue, 13 May 2025 13:37:13 +0200
Subject: [PATCH 2/2]  - add simulate action

---
 .../controllers/mother_controller.py          | 34 +++++++++++++++++++
 src/petab_gui/views/main_view.py              |  1 +
 src/petab_gui/views/task_bar.py               |  1 +
 3 files changed, 36 insertions(+)

diff --git a/src/petab_gui/controllers/mother_controller.py b/src/petab_gui/controllers/mother_controller.py
index 75d8c39..96971e6 100644
--- a/src/petab_gui/controllers/mother_controller.py
+++ b/src/petab_gui/controllers/mother_controller.py
@@ -333,6 +333,12 @@ def setup_actions(self):
         # Recent Files
         actions["recent_files"] = self.recent_files_manager.tool_bar_menu
 
+        # simulate action
+        actions["simulate"] = QAction(
+            qta.icon("mdi6.play"), "Simulate", self.view
+        )
+        actions["simulate"].triggered.connect(self.simulate)
+
         # Filter widget
         filter_widget = QWidget()
         filter_layout = QHBoxLayout()
@@ -919,3 +925,31 @@ def _on_simulation_selection_changed(self, selected, deselected):
             proxy=self.simulation_controller.proxy_model,
             y_axis_col="simulation"
         )
+
+    def simulate(self):
+        """Simulate the model."""
+        # obtain petab problem
+        petab_problem = self.model.current_petab_problem
+
+        # import petabsimualtor
+        from basico.petab import PetabSimulator
+        import basico
+
+        # report current basico / COPASI version 
+        self.logger.log_message(f"Simulate with basico: {basico.__version__}, COPASI: {basico.COPASI.__version__}", color="green")
+
+        import tempfile
+
+        # create temp directory in temp folder: 
+        with tempfile.TemporaryDirectory() as temp_dir:
+            # settings is only current solution statistic for now: 
+            settings = {'method' : {'name': basico.PE.CURRENT_SOLUTION}}
+            # create simulator
+            simulator = PetabSimulator(petab_problem, settings=settings, working_dir=temp_dir)
+
+            # simulate
+            sim_df = simulator.simulate()
+
+        # assign to simulation table
+        self.simulation_controller.overwrite_df(sim_df)
+        self.simulation_controller.model.reset_invalid_cells()
diff --git a/src/petab_gui/views/main_view.py b/src/petab_gui/views/main_view.py
index 8c5da4a..54206e1 100644
--- a/src/petab_gui/views/main_view.py
+++ b/src/petab_gui/views/main_view.py
@@ -180,6 +180,7 @@ def setup_toolbar(self, actions):
         tb.addAction(actions["delete_row"])
         tb.addAction(actions["add_column"])
         tb.addAction(actions["delete_column"])
+        tb.addAction(actions["simulate"])
         tb.addWidget(spacer)
         tb.addWidget(actions["filter_widget"])
 
diff --git a/src/petab_gui/views/task_bar.py b/src/petab_gui/views/task_bar.py
index 8d910b8..1145ed5 100644
--- a/src/petab_gui/views/task_bar.py
+++ b/src/petab_gui/views/task_bar.py
@@ -91,6 +91,7 @@ def __init__(self, parent, actions):
         self.menu.addSeparator()
         # Reset Model
         self.menu.addAction(actions["reset_model"])
+        self.menu.addAction(actions["simulate"])
         self.menu.addSeparator()
         # Settings
         self.menu.addAction(actions["settings"])