From 3a4b9222ceef28290431ca0197d31e35d8165fdd Mon Sep 17 00:00:00 2001
From: Stephen Nneji <steve.nneji@gmail.com>
Date: Tue, 12 May 2026 14:47:50 +0100
Subject: [PATCH 1/2] Add function to run directly from MATLAB API

---
 ratapi/__init__.py     |  3 +-
 ratapi/utils/matlab.py | 67 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 69 insertions(+), 1 deletion(-)
 create mode 100644 ratapi/utils/matlab.py

diff --git a/ratapi/__init__.py b/ratapi/__init__.py
index 98683c7e..8f441f44 100644
--- a/ratapi/__init__.py
+++ b/ratapi/__init__.py
@@ -9,7 +9,7 @@
 from ratapi.outputs import BayesResults, Results
 from ratapi.project import Project
 from ratapi.run import run
-from ratapi.utils import convert, plotting
+from ratapi.utils import convert, matlab, plotting
 
 with suppress(ImportError):  # orsopy is an optional dependency
     from ratapi.utils import orso as orso
@@ -26,4 +26,5 @@
     "run",
     "plotting",
     "convert",
+    "matlab",
 ]
diff --git a/ratapi/utils/matlab.py b/ratapi/utils/matlab.py
new file mode 100644
index 00000000..dad8921b
--- /dev/null
+++ b/ratapi/utils/matlab.py
@@ -0,0 +1,67 @@
+"""Runs RAT from the MATLAB API."""
+
+import os
+import tempfile
+import warnings
+from pathlib import Path
+
+from ..outputs import Results
+from ..project import Project
+from ..wrappers import MatlabWrapper
+
+RUNNER = """function executeRAT()
+project = jsonToProject('{project}');
+controls = jsonToControls('{control}');
+[project, results] = RAT(project, controls);
+
+projectToJson(project, '{project}');
+resultsToJson(results, '{result}');
+end
+"""
+
+
+def run_matlab_directly(project, controls, matlab_rat_path):
+    """Run User provided MATLAB RAT for the given project and controls inputs.
+
+    Parameters
+    ----------
+    project : RAT.Project
+        The project model, which defines the physical system under study.
+    controls : RAT.Controls
+        The controls model, which defines algorithmic properties.
+    matlab_rat_path : str
+        The path to MATLAB RAT folder.
+    """
+    if MatlabWrapper.loader is None:
+        raise ImportError(MatlabWrapper.loader_error_message) from None
+
+    engine = MatlabWrapper.loader.result()
+    cur_dir = os.getcwd()
+
+    with tempfile.TemporaryDirectory() as tmp:
+        project_file = Path(tmp, "project.json")
+        control_file = Path(tmp, "controls.json")
+        result_file = Path(tmp, "results.json")
+        runner_file = Path(tmp, "executeRAT.m")
+
+        with open(runner_file, "w") as f:
+            f.write(RUNNER.format(project=project_file, control=control_file, result=result_file))
+
+        with warnings.catch_warnings():  # Avoid warning about relative paths
+            warnings.simplefilter("ignore")
+            project.save(project_file)
+        controls.save(control_file)
+
+        engine.cd(matlab_rat_path, nargout=0)
+        engine.eval("addPaths", nargout=0)
+        engine.cd(cur_dir, nargout=0)
+
+        engine.addpath(tmp, nargout=0)
+        for file in project.custom_files:
+            engine.addpath(str(file.path), nargout=0)
+
+        engine.executeRAT(nargout=0)
+
+        project = Project.load(project_file)
+        results = Results.load(result_file)
+    return project, results

From f7e3a0c73d3a601638b577c64695ca3ceaeedfe1 Mon Sep 17 00:00:00 2001
From: Stephen Nneji <steve.nneji@gmail.com>
Date: Fri, 15 May 2026 09:26:04 +0100
Subject: [PATCH 2/2] refactor matlab.py

---
 ratapi/utils/matlab.py | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

diff --git a/ratapi/utils/matlab.py b/ratapi/utils/matlab.py
index dad8921b..9784c4a5 100644
--- a/ratapi/utils/matlab.py
+++ b/ratapi/utils/matlab.py
@@ -10,8 +10,17 @@
 from ..wrappers import MatlabWrapper
 
 RUNNER = """function executeRAT()
+
+cur_dir = pwd;
+cd('{rat_path}');
+addPaths;
+cd(cur_dir);
+        
 project = jsonToProject('{project}');
 controls = jsonToControls('{control}');
+for i=1:project.customFile.rowCount
+    addpath(project.customFile.varTable{{i, 5}});
+end
 [project, results] = RAT(project, controls);
 
 projectToJson(project, '{project}');
@@ -36,7 +45,6 @@ def run_matlab_directly(project, controls, matlab_rat_path):
         raise ImportError(MatlabWrapper.loader_error_message) from None
 
     engine = MatlabWrapper.loader.result()
-    cur_dir = os.getcwd()
 
     with tempfile.TemporaryDirectory() as tmp:
         project_file = Path(tmp, "project.json")
@@ -45,22 +53,17 @@ def run_matlab_directly(project, controls, matlab_rat_path):
         runner_file = Path(tmp, "executeRAT.m")
 
         with open(runner_file, "w") as f:
-            f.write(RUNNER.format(project=project_file, control=control_file, result=result_file))
+            f.write(RUNNER.format(project=project_file, control=control_file, result=result_file, 
+                                  rat_path=matlab_rat_path))
 
         with warnings.catch_warnings():  # Avoid warning about relative paths
             warnings.simplefilter("ignore")
             project.save(project_file)
         controls.save(control_file)
-
-        engine.cd(matlab_rat_path, nargout=0)
-        engine.eval("addPaths", nargout=0)
-        engine.cd(cur_dir, nargout=0)
-
+        
         engine.addpath(tmp, nargout=0)
-        for file in project.custom_files:
-            engine.addpath(str(file.path), nargout=0)
-
         engine.executeRAT(nargout=0)
+        engine.rmpath(tmp, nargout=0)
 
         project = Project.load(project_file)
         results = Results.load(result_file)