From c71237dec770a217cfb72ddac2616ce2e6cba9a5 Mon Sep 17 00:00:00 2001
From: Paul Sharp <44529197+DrPaulSharp@users.noreply.github.com>
Date: Mon, 21 Jul 2025 10:21:07 +0100
Subject: [PATCH 1/8] Updates github action for ruff (#173)

---
 .github/workflows/run_ruff.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/run_ruff.yml b/.github/workflows/run_ruff.yml
index 5fc5b79f..64637b07 100644
--- a/.github/workflows/run_ruff.yml
+++ b/.github/workflows/run_ruff.yml
@@ -7,8 +7,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: chartboost/ruff-action@v1
-      - uses: chartboost/ruff-action@v1
-        with:
-          args: 'format --check'
+      - uses: astral-sh/ruff-action@v3
+      - run: ruff format --check
           
\ No newline at end of file

From 45e44ef7831b6513b159e7b11c7bf0168fcc9490 Mon Sep 17 00:00:00 2001
From: StephenNneji <34302892+StephenNneji@users.noreply.github.com>
Date: Wed, 23 Jul 2025 16:04:30 +0100
Subject: [PATCH 2/8] Updates cpp and add Mac ARM to test (#172)

---
 .github/workflows/run_tests.yml | 18 ++++++++++++++----
 cpp/RAT                         |  2 +-
 2 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
index e930df1a..a2de2b66 100644
--- a/.github/workflows/run_tests.yml
+++ b/.github/workflows/run_tests.yml
@@ -19,13 +19,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-13]
+        platform: [windows-latest, ubuntu-latest, macos-13, macos-14]
         version: ["3.10", "3.13"]
     defaults:
       run:
         shell: bash -l {0}
 
-    runs-on: ${{ matrix.os }}
+    runs-on: ${{ matrix.platform}}
 
     steps:
       - uses: actions/checkout@v4      
@@ -35,8 +35,8 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.version }}
-      - name: Install OMP (MacOS) 
-        if: runner.os == 'macOS'
+      - name: Install OMP (MacOS Intel) 
+        if: matrix.platform == 'macos-13'
         run: |
           brew install llvm libomp
           echo "export CC=/usr/local/opt/llvm/bin/clang" >> ~/.bashrc
@@ -45,6 +45,16 @@ jobs:
           echo "export CXXFLAGS=\"$CXXFLAGS -I/usr/local/opt/libomp/include\"" >> ~/.bashrc
           echo "export LDFLAGS=\"$LDFLAGS -Wl,-rpath,/usr/local/opt/libomp/lib -L/usr/local/opt/libomp/lib -lomp\"" >> ~/.bashrc
           source ~/.bashrc
+      - name: Install OMP (MacOS M1) 
+        if: matrix.platform == 'macos-14'
+        run: |
+          brew install llvm libomp
+          echo "export CC=/opt/homebrew/opt/llvm/bin/clang" >> ~/.bashrc
+          echo "export CXX=/opt/homebrew/opt/llvm/bin/clang++" >> ~/.bashrc
+          echo "export CFLAGS=\"$CFLAGS -I/opt/homebrew/opt/libomp/include\"" >> ~/.bashrc
+          echo "export CXXFLAGS=\"$CXXFLAGS -I/opt/homebrew/opt/libomp/include\"" >> ~/.bashrc
+          echo "export LDFLAGS=\"$LDFLAGS -Wl,-rpath,/opt/homebrew/opt/libomp/lib -L/opt/homebrew/opt/libomp/lib -lomp\"" >> ~/.bashrc
+          source ~/.bashrc
       - name: Install OMP (Linux)
         if: runner.os == 'Linux'
         run: |
diff --git a/cpp/RAT b/cpp/RAT
index cf81c8d0..370d46f1 160000
--- a/cpp/RAT
+++ b/cpp/RAT
@@ -1 +1 @@
-Subproject commit cf81c8d00f0d0348cbeb360446362f8381093203
+Subproject commit 370d46f19859eb1ada7b031e6540c7747e328f82

From 50289e3c2a802b813612a4fe1544a5204ec66715 Mon Sep 17 00:00:00 2001
From: StephenNneji <34302892+StephenNneji@users.noreply.github.com>
Date: Tue, 29 Jul 2025 10:02:50 +0100
Subject: [PATCH 3/8] Adds the `shift_value` argument to `plot_ref_sld` (#174)

---
 ratapi/utils/plotting.py | 206 +++------------------------------------
 tests/test_plotting.py   |  18 +---
 2 files changed, 20 insertions(+), 204 deletions(-)

diff --git a/ratapi/utils/plotting.py b/ratapi/utils/plotting.py
index 38d3d777..d4cfa599 100644
--- a/ratapi/utils/plotting.py
+++ b/ratapi/utils/plotting.py
@@ -21,7 +21,7 @@
 from ratapi.rat_core import PlotEventData, makeSLDProfile
 
 
-def _extract_plot_data(event_data: PlotEventData, q4: bool, show_error_bar: bool):
+def _extract_plot_data(event_data: PlotEventData, q4: bool, show_error_bar: bool, shift_value: float):
     """Extract the plot data for the sld, ref, error plot lines.
 
     Parameters
@@ -33,6 +33,8 @@ def _extract_plot_data(event_data: PlotEventData, q4: bool, show_error_bar: bool
         Controls whether Q^4 is plotted on the reflectivity plot
     show_error_bar : bool, default: True
         Controls whether the error bars are shown
+    shift_value : float
+        A value between 1 and 100 that controls the spacing between the reflectivity plots for each of the contrasts
 
     Returns
     -------
@@ -42,9 +44,12 @@ def _extract_plot_data(event_data: PlotEventData, q4: bool, show_error_bar: bool
     """
     results = {"ref": [], "error": [], "sld": [], "sld_resample": []}
 
+    if shift_value < 1 or shift_value > 100:
+        raise ValueError("Parameter `shift_value` must be between 1 and 100")
+
     for i, (r, data, sld) in enumerate(zip(event_data.reflectivity, event_data.shiftedData, event_data.sldProfiles)):
         # Calculate the divisor
-        div = 1 if i == 0 and not q4 else 2 ** (4 * (i + 1))
+        div = 1 if i == 0 and not q4 else 10 ** ((i / 100) * shift_value)
         q4_data = 1 if not q4 or not event_data.dataPresent[i] else data[:, 0] ** 4
         mult = q4_data / div
 
@@ -87,194 +92,6 @@ def _extract_plot_data(event_data: PlotEventData, q4: bool, show_error_bar: bool
     return results
 
 
-class PlotSLDWithBlitting:
-    """Create a SLD plot that uses blitting to get faster draws.
-
-    The blit plot stores the background from an
-    initial draw then updates the foreground (lines and error bars) if the background is not changed.
-
-    Parameters
-    ----------
-    data : PlotEventData
-        The plot event data that contains all the information
-        to generate the ref and sld plots
-    fig : matplotlib.pyplot.figure, optional
-        The figure class that has two subplots
-    linear_x : bool, default: False
-        Controls whether the x-axis on reflectivity plot uses the linear scale
-    q4 : bool, default: False
-        Controls whether Q^4 is plotted on the reflectivity plot
-    show_error_bar : bool, default: True
-        Controls whether the error bars are shown
-    show_grid : bool, default: False
-        Controls whether the grid is shown
-    show_legend : bool, default: True
-        Controls whether the legend is shown
-    """
-
-    def __init__(
-        self,
-        data: PlotEventData,
-        fig: Optional[matplotlib.pyplot.figure] = None,
-        linear_x: bool = False,
-        q4: bool = False,
-        show_error_bar: bool = True,
-        show_grid: bool = False,
-        show_legend: bool = True,
-    ):
-        self.figure = fig
-        self.linear_x = linear_x
-        self.q4 = q4
-        self.show_error_bar = show_error_bar
-        self.show_grid = show_grid
-        self.show_legend = show_legend
-        self.updatePlot(data)
-        self.event_id = self.figure.canvas.mpl_connect("resize_event", self.resizeEvent)
-
-    def __del__(self):
-        self.figure.canvas.mpl_disconnect(self.event_id)
-
-    def resizeEvent(self, _event):
-        """Ensure the background is updated after a resize event."""
-        self.__background_changed = True
-
-    def update(self, data: PlotEventData):
-        """Update the foreground, if background has not changed otherwise it updates full plot.
-
-        Parameters
-        ----------
-        data : PlotEventData
-            The plot event data that contains all the information
-            to generate the ref and sld plots
-        """
-        if self.__background_changed:
-            self.updatePlot(data)
-        else:
-            self.updateForeground(data)
-
-    def __setattr__(self, name, value):
-        super().__setattr__(name, value)
-        if name in ["figure", "linear_x", "q4", "show_error_bar", "show_grid", "show_legend"]:
-            self.__background_changed = True
-
-    def setAnimated(self, is_animated: bool):
-        """Set the animated property of foreground plot elements.
-
-        Parameters
-        ----------
-        is_animated : bool
-            Indicates if the animated property should been set.
-        """
-        for line in self.figure.axes[0].lines:
-            line.set_animated(is_animated)
-        for line in self.figure.axes[1].lines:
-            line.set_animated(is_animated)
-        for container in self.figure.axes[0].containers:
-            container[2][0].set_animated(is_animated)
-
-    def adjustErrorBar(self, error_bar_container, x, y, y_error):
-        """Adjust the error bar data.
-
-        Parameters
-        ----------
-        error_bar_container : Tuple
-            Tuple containing the artist of the errorbar i.e. (data line, cap lines, bar lines)
-        x : np.ndarray
-            The shifted data x axis data
-        y : np.ndarray
-            The shifted data y axis data
-        y_error : np.ndarray
-            The shifted data y axis error data
-        """
-        line, _, (bars_y,) = error_bar_container
-
-        line.set_data(x, y)
-        x_base = x
-        y_base = y
-
-        y_error_top = y_base + y_error
-        y_error_bottom = y_base - y_error
-
-        new_segments_y = [np.array([[x, yt], [x, yb]]) for x, yt, yb in zip(x_base, y_error_top, y_error_bottom)]
-        bars_y.set_segments(new_segments_y)
-
-    def updatePlot(self, data: PlotEventData):
-        """Update the full plot.
-
-        Parameters
-        ----------
-        data : PlotEventData
-            The plot event data that contains all the information
-            to generate the ref and sld plots
-        """
-        if self.figure is not None:
-            self.figure.clf()
-        self.figure = plot_ref_sld_helper(
-            data,
-            self.figure,
-            linear_x=self.linear_x,
-            q4=self.q4,
-            show_error_bar=self.show_error_bar,
-            show_grid=self.show_grid,
-            show_legend=self.show_legend,
-            animated=True,
-        )
-
-        self.bg = self.figure.canvas.copy_from_bbox(self.figure.bbox)
-        for line in self.figure.axes[0].lines:
-            self.figure.axes[0].draw_artist(line)
-        for line in self.figure.axes[1].lines:
-            self.figure.axes[1].draw_artist(line)
-        for container in self.figure.axes[0].containers:
-            self.figure.axes[0].draw_artist(container[2][0])
-        self.figure.canvas.blit(self.figure.bbox)
-        self.setAnimated(False)
-        self.__background_changed = False
-
-    def updateForeground(self, data: PlotEventData):
-        """Update the plot foreground only.
-
-        Parameters
-        ----------
-        data : PlotEventData
-            The plot event data that contains all the information
-            to generate the ref and sld plots
-        """
-        self.setAnimated(True)
-        self.figure.canvas.restore_region(self.bg)
-        plot_data = _extract_plot_data(data, self.q4, self.show_error_bar)
-
-        offset = 2 if self.show_error_bar else 1
-        for i in range(
-            0,
-            len(self.figure.axes[0].lines),
-        ):
-            self.figure.axes[0].lines[i].set_data(plot_data["ref"][i // offset][0], plot_data["ref"][i // offset][1])
-            self.figure.axes[0].draw_artist(self.figure.axes[0].lines[i])
-
-        i = 0
-        for j in range(len(plot_data["sld"])):
-            for sld in plot_data["sld"][j]:
-                self.figure.axes[1].lines[i].set_data(sld[0], sld[1])
-                self.figure.axes[1].draw_artist(self.figure.axes[1].lines[i])
-                i += 1
-
-            if plot_data["sld_resample"]:
-                for resampled in plot_data["sld_resample"][j]:
-                    self.figure.axes[1].lines[i].set_data(resampled[0], resampled[1])
-                    self.figure.axes[1].draw_artist(self.figure.axes[1].lines[i])
-                    i += 1
-
-        for i, container in enumerate(self.figure.axes[0].containers):
-            self.adjustErrorBar(container, plot_data["error"][i][0], plot_data["error"][i][1], plot_data["error"][i][2])
-            self.figure.axes[0].draw_artist(container[2][0])
-            self.figure.axes[0].draw_artist(container[0])
-
-        self.figure.canvas.blit(self.figure.bbox)
-        self.figure.canvas.flush_events()
-        self.setAnimated(False)
-
-
 def plot_ref_sld_helper(
     data: PlotEventData,
     fig: Optional[matplotlib.pyplot.figure] = None,
@@ -285,6 +102,7 @@ def plot_ref_sld_helper(
     show_error_bar: bool = True,
     show_grid: bool = False,
     show_legend: bool = True,
+    shift_value: float = 100,
     animated=False,
 ):
     """Clear the previous plots and updates the ref and SLD plots.
@@ -311,6 +129,8 @@ def plot_ref_sld_helper(
         Controls whether the grid is shown
     show_legend : bool, default: True
         Controls whether the legend is shown
+    shift_value : float, default: 100
+        A value between 1 and 100 that controls the spacing between the reflectivity plots for each of the contrasts
     animated : bool, default: False
         Controls whether the animated property of foreground plot elements should be set.
 
@@ -339,7 +159,7 @@ def plot_ref_sld_helper(
     ref_plot.cla()
     sld_plot.cla()
 
-    plot_data = _extract_plot_data(data, q4, show_error_bar)
+    plot_data = _extract_plot_data(data, q4, show_error_bar, shift_value)
     for i, name in enumerate(data.contrastNames):
         ref_plot.plot(plot_data["ref"][i][0], plot_data["ref"][i][1], label=name, linewidth=1, animated=animated)
         color = ref_plot.get_lines()[-1].get_color()
@@ -427,6 +247,7 @@ def plot_ref_sld(
     show_error_bar: bool = True,
     show_grid: bool = False,
     show_legend: bool = True,
+    shift_value: float = 100,
 ) -> Union[plt.Figure, None]:
     """Plot the reflectivity and SLD profiles.
 
@@ -454,6 +275,8 @@ def plot_ref_sld(
             Controls whether the grid is shown
     show_legend : bool, default: True
             Controls whether the legend is shown
+    shift_value : float, default: 100
+        A value between 1 and 100 that controls the spacing between the reflectivity plots for each of the contrasts
 
     Returns
     -------
@@ -524,6 +347,7 @@ def plot_ref_sld(
         show_error_bar=show_error_bar,
         show_grid=show_grid,
         show_legend=show_legend,
+        shift_value=shift_value,
     )
 
     if return_fig:
diff --git a/tests/test_plotting.py b/tests/test_plotting.py
index 3bb3f69c..c42bfeea 100644
--- a/tests/test_plotting.py
+++ b/tests/test_plotting.py
@@ -481,20 +481,12 @@ def test_bayes_validation(input_project, reflectivity_calculation_results):
 
 @pytest.mark.parametrize("data", [data(), domains_data()])
 def test_extract_plot_data(data) -> None:
-    plot_data = RATplot._extract_plot_data(data, False, True)
+    plot_data = RATplot._extract_plot_data(data, False, True, 50)
     assert len(plot_data["ref"]) == len(data.reflectivity)
     assert len(plot_data["sld"]) == len(data.shiftedData)
 
+    with pytest.raises(ValueError, match=r"Parameter `shift_value` must be between 1 and 100"):
+        RATplot._extract_plot_data(data, False, True, 0)
 
-@patch("ratapi.utils.plotting.plot_ref_sld_helper")
-def test_blit_plot(plot_helper, fig: plt.figure) -> None:
-    plot_helper.return_value = fig
-    event_data = data()
-    new_plot = RATplot.PlotSLDWithBlitting(event_data)
-    assert plot_helper.call_count == 1
-    new_plot.update(event_data)
-    assert plot_helper.call_count == 1  # foreground only is updated so no call to plot helper
-    new_plot.show_grid = False
-    new_plot.figure = plt.subplots(1, 2)[0]
-    new_plot.update(event_data)  # plot properties have changed so update should call plot_helper
-    assert plot_helper.call_count == 2
+    with pytest.raises(ValueError, match=r"Parameter `shift_value` must be between 1 and 100"):
+        RATplot._extract_plot_data(data, False, True, 100.5)

From d6c44cefaa1faddb8691188e16eed9aece42e5dc Mon Sep 17 00:00:00 2001
From: Paul Sharp <44529197+DrPaulSharp@users.noreply.github.com>
Date: Thu, 7 Aug 2025 10:02:15 +0100
Subject: [PATCH 4/8] Removes controls option "calcSLDDuringFit" (#175)

* Removes controls option "calcSLDDuringFit"

* Addresses review comment

* Addresses further review comments
---
 cpp/RAT                                       |  2 +-
 cpp/includes/defines.h                        |  3 --
 cpp/rat.cpp                                   | 36 +++++++++----------
 ratapi/controls.py                            |  4 ---
 .../bayes_benchmark/bayes_benchmark.py        |  2 +-
 .../languages/run_custom_file_languages.py    |  1 -
 ratapi/inputs.py                              |  3 --
 ratapi/utils/enums.py                         |  8 ++---
 setup.py                                      |  6 ++--
 tests/test_controls.py                        | 23 ------------
 tests/test_inputs.py                          |  3 --
 11 files changed, 26 insertions(+), 65 deletions(-)

diff --git a/cpp/RAT b/cpp/RAT
index 370d46f1..16f3ebef 160000
--- a/cpp/RAT
+++ b/cpp/RAT
@@ -1 +1 @@
-Subproject commit 370d46f19859eb1ada7b031e6540c7747e328f82
+Subproject commit 16f3ebef737f4c85ca601046f7a30ffabee4eb47
diff --git a/cpp/includes/defines.h b/cpp/includes/defines.h
index 9e8a5ff1..097ad0eb 100644
--- a/cpp/includes/defines.h
+++ b/cpp/includes/defines.h
@@ -588,8 +588,6 @@ parallel : str
     How the calculation should be parallelised (This uses the Parallel Computing Toolbox). Can be 'single', 'contrasts' or 'points'.
 procedure : str
     Which procedure RAT should execute. Can be 'calculate', 'simplex', 'de', 'ns', or 'dream'.
-calcSldDuringFit : bool
-    Whether SLD will be calculated during fit (for live plotting etc.)
 numSimulationPoints : int
     The number of points used for a reflectivity simulation where no data is present.
 resampleMinAngle : float
@@ -664,7 +662,6 @@ struct Control {
     real_T nMCMC {};
     real_T propScale {};
     real_T nsTolerance {};
-    boolean_T calcSldDuringFit {};
     real_T numSimulationPoints {};
     real_T resampleMinAngle {};
     real_T resampleNPoints {};
diff --git a/cpp/rat.cpp b/cpp/rat.cpp
index ddec2782..31bbe144 100644
--- a/cpp/rat.cpp
+++ b/cpp/rat.cpp
@@ -317,7 +317,6 @@ RAT::Controls createControlsStruct(const Control& control)
     control_struct.nMCMC = control.nMCMC;
     control_struct.propScale = control.propScale;
     control_struct.nsTolerance = control.nsTolerance;
-    control_struct.calcSldDuringFit = control.calcSldDuringFit;
     control_struct.numSimulationPoints = control.numSimulationPoints;
     control_struct.updateFreq = control.updateFreq;
     control_struct.updatePlotFreq = control.updatePlotFreq;
@@ -333,6 +332,7 @@ RAT::Controls createControlsStruct(const Control& control)
     control_struct.resampleNPoints = control.resampleNPoints;
     stringToRatBoundedArray(control.boundHandling, control_struct.boundHandling.data, control_struct.boundHandling.size);
     control_struct.adaptPCR = control.adaptPCR;
+    control_struct.calcSLD = false;
     stringToRatBoundedArray(control.IPCFilePath, control_struct.IPCFilePath.data, control_struct.IPCFilePath.size);
 
     return control_struct;
@@ -910,7 +910,6 @@ PYBIND11_MODULE(rat_core, m) {
         .def_readwrite("nMCMC", &Control::nMCMC)
         .def_readwrite("propScale", &Control::propScale)
         .def_readwrite("nsTolerance", &Control::nsTolerance)
-        .def_readwrite("calcSldDuringFit", &Control::calcSldDuringFit)
         .def_readwrite("numSimulationPoints", &Control::numSimulationPoints)
         .def_readwrite("resampleMinAngle", &Control::resampleMinAngle)
         .def_readwrite("resampleNPoints", &Control::resampleNPoints)
@@ -929,12 +928,12 @@ PYBIND11_MODULE(rat_core, m) {
                 return py::make_tuple(ctrl.parallel, ctrl.procedure, ctrl.display, ctrl.xTolerance, ctrl.funcTolerance, 
                                       ctrl.maxFuncEvals, ctrl.maxIterations, ctrl.populationSize, ctrl.fWeight, ctrl.crossoverProbability, 
                                       ctrl.targetValue, ctrl.numGenerations, ctrl.strategy, ctrl.nLive, ctrl.nMCMC, ctrl.propScale, 
-                                      ctrl.nsTolerance, ctrl.calcSldDuringFit, ctrl.numSimulationPoints, ctrl.resampleMinAngle, ctrl.resampleNPoints,
-                                      ctrl.updateFreq, ctrl.updatePlotFreq, ctrl.nSamples, ctrl.nChains, ctrl.jumpProbability, ctrl.pUnitGamma, 
-                                      ctrl.boundHandling, ctrl.adaptPCR, ctrl.IPCFilePath);
+                                      ctrl.nsTolerance, ctrl.numSimulationPoints, ctrl.resampleMinAngle, ctrl.resampleNPoints,
+                                      ctrl.updateFreq, ctrl.updatePlotFreq, ctrl.nSamples, ctrl.nChains, ctrl.jumpProbability,
+                                      ctrl.pUnitGamma, ctrl.boundHandling, ctrl.adaptPCR, ctrl.IPCFilePath);
             },
             [](py::tuple t) { // __setstate__
-                if (t.size() != 30)
+                if (t.size() != 29)
                     throw std::runtime_error("Encountered invalid state unpickling ProblemDefinition object!");
 
                 /* Create a new C++ instance */
@@ -957,19 +956,18 @@ PYBIND11_MODULE(rat_core, m) {
                 ctrl.nMCMC = t[14].cast<real_T>();
                 ctrl.propScale = t[15].cast<real_T>();
                 ctrl.nsTolerance = t[16].cast<real_T>();
-                ctrl.calcSldDuringFit = t[17].cast<boolean_T>();
-                ctrl.numSimulationPoints = t[18].cast<real_T>();
-                ctrl.resampleMinAngle = t[19].cast<real_T>();
-                ctrl.resampleNPoints = t[20].cast<real_T>();
-                ctrl.updateFreq = t[21].cast<real_T>();
-                ctrl.updatePlotFreq = t[22].cast<real_T>();
-                ctrl.nSamples = t[23].cast<real_T>();
-                ctrl.nChains = t[24].cast<real_T>();
-                ctrl.jumpProbability = t[25].cast<real_T>();
-                ctrl.pUnitGamma = t[26].cast<real_T>();
-                ctrl.boundHandling = t[27].cast<std::string>();
-                ctrl.adaptPCR = t[28].cast<boolean_T>();
-                ctrl.IPCFilePath = t[29].cast<std::string>();
+                ctrl.numSimulationPoints = t[17].cast<real_T>();
+                ctrl.resampleMinAngle = t[18].cast<real_T>();
+                ctrl.resampleNPoints = t[19].cast<real_T>();
+                ctrl.updateFreq = t[20].cast<real_T>();
+                ctrl.updatePlotFreq = t[21].cast<real_T>();
+                ctrl.nSamples = t[22].cast<real_T>();
+                ctrl.nChains = t[23].cast<real_T>();
+                ctrl.jumpProbability = t[24].cast<real_T>();
+                ctrl.pUnitGamma = t[25].cast<real_T>();
+                ctrl.boundHandling = t[26].cast<std::string>();
+                ctrl.adaptPCR = t[27].cast<boolean_T>();
+                ctrl.IPCFilePath = t[28].cast<std::string>();
 
                 return ctrl;
             }));
diff --git a/ratapi/controls.py b/ratapi/controls.py
index 917d78eb..c5408411 100644
--- a/ratapi/controls.py
+++ b/ratapi/controls.py
@@ -23,7 +23,6 @@
 common_fields = [
     "procedure",
     "parallel",
-    "calcSldDuringFit",
     "numSimulationPoints",
     "resampleMinAngle",
     "resampleNPoints",
@@ -58,9 +57,6 @@ class Controls(BaseModel, validate_assignment=True, extra="forbid", use_attribut
     parallel: Parallel = Parallel.Single
     """How the calculation should be parallelised. Can be 'single', 'contrasts' or 'points'."""
 
-    calcSldDuringFit: bool = False
-    """Whether SLD will be calculated during fit (for live plotting etc.)"""
-
     numSimulationPoints: int = Field(500, ge=2)
     """The number of points used for reflectivity simulations where no data is supplied."""
 
diff --git a/ratapi/examples/bayes_benchmark/bayes_benchmark.py b/ratapi/examples/bayes_benchmark/bayes_benchmark.py
index 9840b002..ee6ea96e 100644
--- a/ratapi/examples/bayes_benchmark/bayes_benchmark.py
+++ b/ratapi/examples/bayes_benchmark/bayes_benchmark.py
@@ -250,7 +250,7 @@ def bayes_benchmark_3d(grid_size: int) -> (RAT.outputs.BayesResults, Calculation
     scale_param = problem.scalefactors[0]
     scalefactor = np.linspace(scale_param.min, scale_param.max, grid_size)
 
-    controls = RAT.Controls(procedure="calculate", calcSldDuringFit=True, display="off")
+    controls = RAT.Controls(procedure="calculate", display="off")
 
     def calculate_posterior(roughness_index: int, background_index: int, scalefactor_index: int) -> float:
         """Calculate the posterior for an item in the roughness, background, and scalefactor vectors.
diff --git a/ratapi/examples/languages/run_custom_file_languages.py b/ratapi/examples/languages/run_custom_file_languages.py
index 6e69f80e..2f6025ae 100644
--- a/ratapi/examples/languages/run_custom_file_languages.py
+++ b/ratapi/examples/languages/run_custom_file_languages.py
@@ -11,7 +11,6 @@
 
 project = setup_problem.make_example_problem()
 controls = RAT.Controls()
-controls.calcSldDuringFit = True
 
 # Python
 start = time.time()
diff --git a/ratapi/inputs.py b/ratapi/inputs.py
index 34b695d3..890066f9 100644
--- a/ratapi/inputs.py
+++ b/ratapi/inputs.py
@@ -552,7 +552,6 @@ def make_controls(input_controls: ratapi.Controls) -> Control:
 
     controls.procedure = input_controls.procedure
     controls.parallel = input_controls.parallel
-    controls.calcSldDuringFit = input_controls.calcSldDuringFit
     controls.numSimulationPoints = input_controls.numSimulationPoints
     controls.resampleMinAngle = input_controls.resampleMinAngle
     controls.resampleNPoints = input_controls.resampleNPoints
@@ -583,8 +582,6 @@ def make_controls(input_controls: ratapi.Controls) -> Control:
     controls.pUnitGamma = input_controls.pUnitGamma
     controls.boundHandling = input_controls.boundHandling
     controls.adaptPCR = input_controls.adaptPCR
-    # IPC
-    controls.IPCFilePath = ""
 
     controls.IPCFilePath = input_controls._IPCFilePath
 
diff --git a/ratapi/utils/enums.py b/ratapi/utils/enums.py
index 43272355..24c50cbc 100644
--- a/ratapi/utils/enums.py
+++ b/ratapi/utils/enums.py
@@ -73,22 +73,22 @@ class Strategies(RATEnum):
     """The base vector is random."""
 
     LocalToBest = "local to best"
-    """The base vector is a combination of one randomly-selected local solution 
+    """The base vector is a combination of one randomly-selected local solution
     and the best solution of the previous iteration."""
 
     BestWithJitter = "best jitter"
     """The base vector is the best solution of the previous iteration, with a small random perturbation applied."""
 
     RandomWithPerVectorDither = "vector dither"
-    """The base vector is random, with a random scaling factor applied to each mutant. 
+    """The base vector is random, with a random scaling factor applied to each mutant.
     This scaling factor is different for each mutant."""
 
     RandomWithPerGenerationDither = "generation dither"
-    """The base vector is random, with a random scaling factor applied to each mutant. 
+    """The base vector is random, with a random scaling factor applied to each mutant.
     This scaling factor is the same for every mutant, and randomised every generation."""
 
     RandomEitherOrAlgorithm = "either or"
-    """The base vector is randomly chosen from either a pure random mutation, 
+    """The base vector is randomly chosen from either a pure random mutation,
     or a pure recombination of parent parameter values."""
 
     @classmethod
diff --git a/setup.py b/setup.py
index 30763b21..bda3a43a 100644
--- a/setup.py
+++ b/setup.py
@@ -61,8 +61,8 @@ class BuildExt(build_ext):
     """A custom build extension for adding compiler-specific options."""
 
     c_opts = {
-        "msvc": ["/EHsc"],
-        "unix": ["-fopenmp", "-std=c++11"],
+        "msvc": ["/O2", "/EHsc"],
+        "unix": ["-O2", "-fopenmp", "-std=c++11"],
     }
     l_opts = {
         "msvc": [],
@@ -71,7 +71,7 @@ class BuildExt(build_ext):
 
     if sys.platform == "darwin":
         darwin_opts = ["-stdlib=libc++", "-mmacosx-version-min=10.9"]
-        c_opts["unix"] = [*darwin_opts, "-fopenmp"]
+        c_opts["unix"] = [*darwin_opts, "-fopenmp", "-O2"]
         l_opts["unix"] = [*darwin_opts, "-lomp"]
 
     def build_extensions(self):
diff --git a/tests/test_controls.py b/tests/test_controls.py
index 3e668795..72f0c745 100644
--- a/tests/test_controls.py
+++ b/tests/test_controls.py
@@ -60,7 +60,6 @@ def table_str(self):
             "+---------------------+-----------+\n"
             "|      procedure      | calculate |\n"
             "|       parallel      |   single  |\n"
-            "|   calcSldDuringFit  |   False   |\n"
             "| numSimulationPoints |    500    |\n"
             "|   resampleMinAngle  |    0.9    |\n"
             "|   resampleNPoints   |     50    |\n"
@@ -74,7 +73,6 @@ def table_str(self):
         "control_property, value",
         [
             ("parallel", Parallel.Single),
-            ("calcSldDuringFit", False),
             ("numSimulationPoints", 500),
             ("resampleMinAngle", 0.9),
             ("resampleNPoints", 50),
@@ -90,7 +88,6 @@ def test_calculate_property_values(self, control_property: str, value: Any) -> N
         "control_property, value",
         [
             ("parallel", Parallel.Points),
-            ("calcSldDuringFit", True),
             ("numSimulationPoints", 10),
             ("resampleMinAngle", 0.2),
             ("resampleNPoints", 1),
@@ -186,14 +183,6 @@ def test_calculate_parallel_validation(self, value: Any) -> None:
         with pytest.raises(pydantic.ValidationError, match="Input should be 'single', 'points' or 'contrasts'"):
             self.calculate.parallel = value
 
-    @pytest.mark.parametrize("value", [5.0, 12])
-    def test_calculate_calcSldDuringFit_validation(self, value: Union[int, float]) -> None:
-        """Tests the calcSldDuringFit setter validation in Calculate class."""
-        with pytest.raises(
-            pydantic.ValidationError, match="Input should be a valid boolean, unable to interpret input"
-        ):
-            self.calculate.calcSldDuringFit = value
-
     @pytest.mark.parametrize("value", ["test", "iterate", True, 1, 3.0])
     def test_calculate_display_validation(self, value: Any) -> None:
         """Tests the display setter validation in Calculate class."""
@@ -220,7 +209,6 @@ def table_str(self):
             "+---------------------+---------+\n"
             "|      procedure      | simplex |\n"
             "|       parallel      |  single |\n"
-            "|   calcSldDuringFit  |  False  |\n"
             "| numSimulationPoints |   500   |\n"
             "|   resampleMinAngle  |   0.9   |\n"
             "|   resampleNPoints   |    50   |\n"
@@ -240,7 +228,6 @@ def table_str(self):
         "control_property, value",
         [
             ("parallel", Parallel.Single),
-            ("calcSldDuringFit", False),
             ("numSimulationPoints", 500),
             ("resampleMinAngle", 0.9),
             ("resampleNPoints", 50),
@@ -262,7 +249,6 @@ def test_simplex_property_values(self, control_property: str, value: Any) -> Non
         "control_property, value",
         [
             ("parallel", Parallel.Points),
-            ("calcSldDuringFit", True),
             ("numSimulationPoints", 10),
             ("resampleMinAngle", 0.2),
             ("resampleNPoints", 1),
@@ -380,7 +366,6 @@ def table_str(self):
             "+----------------------+---------------+\n"
             "|      procedure       |       de      |\n"
             "|       parallel       |     single    |\n"
-            "|   calcSldDuringFit   |     False     |\n"
             "| numSimulationPoints  |      500      |\n"
             "|   resampleMinAngle   |      0.9      |\n"
             "|   resampleNPoints    |       50      |\n"
@@ -402,7 +387,6 @@ def table_str(self):
         "control_property, value",
         [
             ("parallel", Parallel.Single),
-            ("calcSldDuringFit", False),
             ("numSimulationPoints", 500),
             ("resampleMinAngle", 0.9),
             ("resampleNPoints", 50),
@@ -424,7 +408,6 @@ def test_de_property_values(self, control_property: str, value: Any) -> None:
         "control_property, value",
         [
             ("parallel", Parallel.Points),
-            ("calcSldDuringFit", True),
             ("numSimulationPoints", 10),
             ("resampleMinAngle", 0.2),
             ("resampleNPoints", 1),
@@ -556,7 +539,6 @@ def table_str(self):
             "+---------------------+--------+\n"
             "|      procedure      |   ns   |\n"
             "|       parallel      | single |\n"
-            "|   calcSldDuringFit  | False  |\n"
             "| numSimulationPoints |  500   |\n"
             "|   resampleMinAngle  |  0.9   |\n"
             "|   resampleNPoints   |   50   |\n"
@@ -574,7 +556,6 @@ def table_str(self):
         "control_property, value",
         [
             ("parallel", Parallel.Single),
-            ("calcSldDuringFit", False),
             ("numSimulationPoints", 500),
             ("resampleMinAngle", 0.9),
             ("resampleNPoints", 50),
@@ -594,7 +575,6 @@ def test_ns_property_values(self, control_property: str, value: Any) -> None:
         "control_property, value",
         [
             ("parallel", Parallel.Points),
-            ("calcSldDuringFit", True),
             ("numSimulationPoints", 10),
             ("resampleMinAngle", 0.2),
             ("resampleNPoints", 1),
@@ -725,7 +705,6 @@ def table_str(self):
             "+---------------------+---------+\n"
             "|      procedure      |  dream  |\n"
             "|       parallel      |  single |\n"
-            "|   calcSldDuringFit  |  False  |\n"
             "| numSimulationPoints |   500   |\n"
             "|   resampleMinAngle  |   0.9   |\n"
             "|   resampleNPoints   |    50   |\n"
@@ -745,7 +724,6 @@ def table_str(self):
         "control_property, value",
         [
             ("parallel", Parallel.Single),
-            ("calcSldDuringFit", False),
             ("numSimulationPoints", 500),
             ("resampleMinAngle", 0.9),
             ("resampleNPoints", 50),
@@ -767,7 +745,6 @@ def test_dream_property_values(self, control_property: str, value: Any) -> None:
         "control_property, value",
         [
             ("parallel", Parallel.Points),
-            ("calcSldDuringFit", True),
             ("numSimulationPoints", 10),
             ("resampleMinAngle", 0.2),
             ("resampleNPoints", 1),
diff --git a/tests/test_inputs.py b/tests/test_inputs.py
index 2c207928..db5b6646 100644
--- a/tests/test_inputs.py
+++ b/tests/test_inputs.py
@@ -359,7 +359,6 @@ def standard_layers_controls():
     controls = Control()
     controls.procedure = Procedures.Calculate
     controls.parallel = Parallel.Single
-    controls.calcSldDuringFit = False
     controls.numSimulationPoints = 500
     controls.resampleMinAngle = 0.9
     controls.resampleNPoints = 50
@@ -398,7 +397,6 @@ def custom_xy_controls():
     controls = Control()
     controls.procedure = Procedures.Calculate
     controls.parallel = Parallel.Single
-    controls.calcSldDuringFit = False
     controls.numSimulationPoints = 500
     controls.resampleMinAngle = 0.9
     controls.resampleNPoints = 50.0
@@ -757,7 +755,6 @@ def check_controls_equal(actual_controls, expected_controls) -> None:
     controls_fields = [
         "procedure",
         "parallel",
-        "calcSldDuringFit",
         "numSimulationPoints",
         "resampleMinAngle",
         "resampleNPoints",

From 9ce6e9fd79970f2f0daa6254827a6b10d049d3a2 Mon Sep 17 00:00:00 2001
From: StephenNneji <34302892+StephenNneji@users.noreply.github.com>
Date: Mon, 18 Aug 2025 13:44:08 +0100
Subject: [PATCH 5/8] Fixes incorrect shift on bayes plots (#176)

---
 ratapi/utils/plotting.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ratapi/utils/plotting.py b/ratapi/utils/plotting.py
index d4cfa599..e61e40ae 100644
--- a/ratapi/utils/plotting.py
+++ b/ratapi/utils/plotting.py
@@ -167,7 +167,7 @@ def plot_ref_sld_helper(
         # Plot confidence intervals if required
         if confidence_intervals is not None:
             # Calculate the divisor
-            div = 1 if i == 0 and not q4 else 2 ** (4 * (i + 1))
+            div = 1 if i == 0 and not q4 else 10 ** ((i / 100) * shift_value)
             ref_min, ref_max = confidence_intervals["reflectivity"][i]
             mult = (1 if not q4 else plot_data["ref"][i][0] ** 4) / div
             ref_plot.fill_between(plot_data["ref"][i][0], ref_min * mult, ref_max * mult, alpha=0.6, color="grey")

From a57541af1fbc7f5f793f7e4b27a929ce1fada6a3 Mon Sep 17 00:00:00 2001
From: StephenNneji <34302892+StephenNneji@users.noreply.github.com>
Date: Mon, 1 Sep 2025 16:22:42 +0100
Subject: [PATCH 6/8] Reverts removal of bliiting  (#177)

---
 ratapi/utils/plotting.py | 205 ++++++++++++++++++++++++++++++++++++++-
 tests/test_orso_utils.py |   3 +
 2 files changed, 207 insertions(+), 1 deletion(-)

diff --git a/ratapi/utils/plotting.py b/ratapi/utils/plotting.py
index e61e40ae..a6f2f557 100644
--- a/ratapi/utils/plotting.py
+++ b/ratapi/utils/plotting.py
@@ -356,6 +356,205 @@ def plot_ref_sld(
     plt.show(block=block)
 
 
+class BlittingSupport:
+    """Create a SLD plot that uses blitting to get faster draws.
+
+    The blit plot stores the background from an
+    initial draw then updates the foreground (lines and error bars) if the background is not changed.
+
+    Parameters
+    ----------
+    data : PlotEventData
+        The plot event data that contains all the information
+        to generate the ref and sld plots
+    fig : matplotlib.pyplot.figure, optional
+        The figure class that has two subplots
+    linear_x : bool, default: False
+        Controls whether the x-axis on reflectivity plot uses the linear scale
+    q4 : bool, default: False
+        Controls whether Q^4 is plotted on the reflectivity plot
+    show_error_bar : bool, default: True
+        Controls whether the error bars are shown
+    show_grid : bool, default: False
+        Controls whether the grid is shown
+    show_legend : bool, default: True
+        Controls whether the legend is shown
+    shift_value : float, default: 100
+        A value between 1 and 100 that controls the spacing between the reflectivity plots for each of the contrasts
+    """
+
+    def __init__(
+        self,
+        data,
+        fig=None,
+        linear_x: bool = False,
+        q4: bool = False,
+        show_error_bar: bool = True,
+        show_grid: bool = False,
+        show_legend: bool = True,
+        shift_value: float = 100,
+    ):
+        self.figure = fig
+        self.linear_x = linear_x
+        self.q4 = q4
+        self.show_error_bar = show_error_bar
+        self.show_grid = show_grid
+        self.show_legend = show_legend
+        self.shift_value = shift_value
+        self.update_plot(data)
+        self.event_id = self.figure.canvas.mpl_connect("resize_event", self.resizeEvent)
+
+    def __del__(self):
+        self.figure.canvas.mpl_disconnect(self.event_id)
+
+    def resizeEvent(self, _event):
+        """Ensure the background is updated after a resize event."""
+        self.__background_changed = True
+
+    def update(self, data):
+        """Update the foreground, if background has not changed otherwise it updates full plot.
+
+        Parameters
+        ----------
+        data : PlotEventData
+            The plot event data that contains all the information
+            to generate the ref and sld plots
+        """
+        if self.__background_changed:
+            self.update_plot(data)
+        else:
+            self.update_foreground(data)
+
+    def __setattr__(self, name, value):
+        old_value = getattr(self, name, None)
+        if value == old_value:
+            return
+
+        super().__setattr__(name, value)
+        if name in ["figure", "linear_x", "q4", "show_error_bar", "show_grid", "show_legend", "shift_value"]:
+            self.__background_changed = True
+
+    def set_animated(self, is_animated: bool):
+        """Set the animated property of foreground plot elements.
+
+        Parameters
+        ----------
+        is_animated : bool
+            Indicates if the animated property should be set.
+        """
+        for line in self.figure.axes[0].lines:
+            line.set_animated(is_animated)
+        for line in self.figure.axes[1].lines:
+            line.set_animated(is_animated)
+        for container in self.figure.axes[0].containers:
+            container[2][0].set_animated(is_animated)
+
+    def adjust_error_bar(self, error_bar_container, x, y, y_error):
+        """Adjust the error bar data.
+
+        Parameters
+        ----------
+        error_bar_container : Tuple
+            Tuple containing the artist of the errorbar i.e. (data line, cap lines, bar lines)
+        x : np.ndarray
+            The shifted data x axis data
+        y : np.ndarray
+            The shifted data y axis data
+        y_error : np.ndarray
+            The shifted data y axis error data
+        """
+        line, _, (bars_y,) = error_bar_container
+
+        line.set_data(x, y)
+        x_base = x
+        y_base = y
+
+        y_error_top = y_base + y_error
+        y_error_bottom = y_base - y_error
+
+        new_segments_y = [np.array([[x, yt], [x, yb]]) for x, yt, yb in zip(x_base, y_error_top, y_error_bottom)]
+        bars_y.set_segments(new_segments_y)
+
+    def update_plot(self, data):
+        """Update the full plot.
+
+        Parameters
+        ----------
+        data : PlotEventData
+            The plot event data that contains all the information
+            to generate the ref and sld plots
+        """
+        if self.figure is not None:
+            self.figure.clf()
+        self.figure = ratapi.plotting.plot_ref_sld_helper(
+            data,
+            self.figure,
+            linear_x=self.linear_x,
+            q4=self.q4,
+            show_error_bar=self.show_error_bar,
+            show_grid=self.show_grid,
+            show_legend=self.show_legend,
+            animated=True,
+        )
+        self.figure.tight_layout(pad=1)
+        self.figure.canvas.draw()
+        self.bg = self.figure.canvas.copy_from_bbox(self.figure.bbox)
+        for line in self.figure.axes[0].lines:
+            self.figure.axes[0].draw_artist(line)
+        for line in self.figure.axes[1].lines:
+            self.figure.axes[1].draw_artist(line)
+        for container in self.figure.axes[0].containers:
+            self.figure.axes[0].draw_artist(container[2][0])
+        self.figure.canvas.blit(self.figure.bbox)
+        self.set_animated(False)
+        self.__background_changed = False
+
+    def update_foreground(self, data):
+        """Update the plot foreground only.
+
+        Parameters
+        ----------
+        data : PlotEventData
+            The plot event data that contains all the information
+            to generate the ref and sld plots
+        """
+        self.set_animated(True)
+        self.figure.canvas.restore_region(self.bg)
+        plot_data = ratapi.plotting._extract_plot_data(data, self.q4, self.show_error_bar, self.shift_value)
+
+        offset = 2 if self.show_error_bar else 1
+        for i in range(
+            0,
+            len(self.figure.axes[0].lines),
+        ):
+            self.figure.axes[0].lines[i].set_data(plot_data["ref"][i // offset][0], plot_data["ref"][i // offset][1])
+            self.figure.axes[0].draw_artist(self.figure.axes[0].lines[i])
+
+        i = 0
+        for j in range(len(plot_data["sld"])):
+            for sld in plot_data["sld"][j]:
+                self.figure.axes[1].lines[i].set_data(sld[0], sld[1])
+                self.figure.axes[1].draw_artist(self.figure.axes[1].lines[i])
+                i += 1
+
+            if plot_data["sld_resample"]:
+                for resampled in plot_data["sld_resample"][j]:
+                    self.figure.axes[1].lines[i].set_data(resampled[0], resampled[1])
+                    self.figure.axes[1].draw_artist(self.figure.axes[1].lines[i])
+                    i += 1
+
+        for i, container in enumerate(self.figure.axes[0].containers):
+            self.adjust_error_bar(
+                container, plot_data["error"][i][0], plot_data["error"][i][1], plot_data["error"][i][2]
+            )
+            self.figure.axes[0].draw_artist(container[2][0])
+            self.figure.axes[0].draw_artist(container[0])
+
+        self.figure.canvas.blit(self.figure.bbox)
+        self.figure.canvas.flush_events()
+        self.set_animated(False)
+
+
 class LivePlot:
     """Create a plot that gets updates from the plot event during a calculation.
 
@@ -369,6 +568,7 @@ class LivePlot:
     def __init__(self, block=False):
         self.block = block
         self.closed = False
+        self.blit_plot = None
 
     def __enter__(self):
         self.figure = plt.subplots(1, 2)[0]
@@ -394,7 +594,10 @@ def plotEvent(self, event):
 
         """
         if not self.closed and self.figure.number in plt.get_fignums():
-            plot_ref_sld_helper(event, self.figure)
+            if self.blit_plot is None:
+                self.blit_plot = BlittingSupport(event, self.figure)
+            else:
+                self.blit_plot.update(event)
 
     def __exit__(self, _exc_type, _exc_val, _traceback):
         ratapi.events.clear(ratapi.events.EventTypes.Plot, self.plotEvent)
diff --git a/tests/test_orso_utils.py b/tests/test_orso_utils.py
index 39137fe9..a8c0791a 100644
--- a/tests/test_orso_utils.py
+++ b/tests/test_orso_utils.py
@@ -36,6 +36,7 @@ def prist():
     ],
 )
 @pytest.mark.parametrize("absorption", [True, False])
+@pytest.mark.skip(reason="orsopy database website (https://slddb.esss.dk/slddb/) is not available")
 def test_orso_model_to_rat(model, absorption):
     """Test that orso_model_to_rat gives the expected parameters, layers and model."""
 
@@ -72,6 +73,7 @@ def test_orso_model_to_rat(model, absorption):
         "prist5_10K_m_025.Rqz.ort",
     ],
 )
+@pytest.mark.skip(reason="orsopy database website (https://slddb.esss.dk/slddb/) is not available")
 def test_load_ort_data(test_data):
     """Test that .ort data is loaded correctly."""
     # manually get the test data for comparison
@@ -104,6 +106,7 @@ def test_load_ort_data(test_data):
         ["prist5_10K_m_025.Rqz.ort", "prist.json"],
     ],
 )
+@pytest.mark.skip(reason="orsopy database website (https://slddb.esss.dk/slddb/) is not available")
 def test_load_ort_project(test_data, expected_data):
     """Test that a project with model data is loaded correctly."""
     ort_data = ORSOProject(Path(TEST_DIR_PATH, test_data))

From cdaa93d10bd36628ff0f47e5721e6e860d1baada Mon Sep 17 00:00:00 2001
From: Paul Sharp <44529197+DrPaulSharp@users.noreply.github.com>
Date: Mon, 1 Sep 2025 17:13:34 +0100
Subject: [PATCH 7/8] Adds "repeat_layers" option to contrasts (#178)

* Adds validator to warn for resample=False for custom XY

* Adds "repeat_layers" option to contrasts

* Reverts changes to test data
---
 cpp/RAT               |  2 +-
 ratapi/inputs.py      |  2 +-
 ratapi/models.py      |  9 +++++++++
 ratapi/project.py     | 31 +++++++++++++++++++++++++++++--
 tests/test_inputs.py  |  2 +-
 tests/test_project.py | 40 ++++++++++++++++++++++++++++++++++++++++
 6 files changed, 81 insertions(+), 5 deletions(-)

diff --git a/cpp/RAT b/cpp/RAT
index 16f3ebef..aae3dc14 160000
--- a/cpp/RAT
+++ b/cpp/RAT
@@ -1 +1 @@
-Subproject commit 16f3ebef737f4c85ca601046f7a30ffabee4eb47
+Subproject commit aae3dc141b6a10c6e10dfb47cd62e07a2a11857d
diff --git a/ratapi/inputs.py b/ratapi/inputs.py
index 890066f9..7d0a8720 100644
--- a/ratapi/inputs.py
+++ b/ratapi/inputs.py
@@ -302,7 +302,7 @@ def make_problem(project: ratapi.Project) -> ProblemDefinition:
     problem.numberOfContrasts = len(project.contrasts)
     problem.geometry = project.geometry
     problem.useImaginary = project.absorption
-    problem.repeatLayers = [1] * len(project.contrasts)
+    problem.repeatLayers = [contrast.repeat_layers for contrast in project.contrasts]
     problem.contrastBackgroundParams = contrast_background_params
     problem.contrastBackgroundTypes = contrast_background_types
     problem.contrastBackgroundActions = [contrast.background_action for contrast in project.contrasts]
diff --git a/ratapi/models.py b/ratapi/models.py
index e882af65..7d0d4f74 100644
--- a/ratapi/models.py
+++ b/ratapi/models.py
@@ -163,6 +163,8 @@ class Contrast(RATModel):
         The name of the instrument resolution for this contrast.
     resample : bool
         Whether adaptive resampling should be used for interface microslicing.
+    repeat_layers : int
+        For standard layers, the number of times the set of layers defined in the model should be repeated.
     model : list[str]
         If this is a standard layers model, this should be a list of layer names
         that make up the slab model for this contrast.
@@ -180,6 +182,7 @@ class Contrast(RATModel):
     scalefactor: str = ""
     resolution: str = ""
     resample: bool = False
+    repeat_layers: int = Field(default=1, gt=0)
     model: list[str] = []
 
     @model_validator(mode="before")
@@ -208,6 +211,7 @@ def __str__(self):
                 self.scalefactor,
                 self.resolution,
                 self.resample,
+                self.repeat_layers,
                 model_entry,
             ]
         )
@@ -238,6 +242,8 @@ class ContrastWithRatio(RATModel):
         The name of the instrument resolution for this contrast.
     resample : bool
         Whether adaptive resampling should be used for interface microslicing.
+    repeat_layers : int
+        For standard layers, the number of times the set of layers defined in the model should be repeated.
     domain_ratio : str
         The name of the domain ratio parameter describing how the first domain should be weighted
         relative to the second.
@@ -258,6 +264,7 @@ class ContrastWithRatio(RATModel):
     scalefactor: str = ""
     resolution: str = ""
     resample: bool = False
+    repeat_layers: int = Field(default=1, gt=0)
     domain_ratio: str = ""
     model: list[str] = []
 
@@ -276,6 +283,8 @@ def __str__(self):
                 self.scalefactor,
                 self.resolution,
                 self.resample,
+                self.repeat_layers,
+                self.domain_ratio,
                 model_entry,
             ]
         )
diff --git a/ratapi/project.py b/ratapi/project.py
index 860f23b7..88555539 100644
--- a/ratapi/project.py
+++ b/ratapi/project.py
@@ -361,8 +361,8 @@ def model_post_init(self, __context: Any) -> None:
         """Set up the Class to protect against disallowed modification.
 
         We initialise the class handle in the ClassLists for empty data fields, set protected parameters, get names of
-        all defined parameters, determine the contents of the "model" field in contrasts,
-        and wrap ClassList routines to control revalidation.
+        all defined parameters, determine the contents of the "model" field in contrasts, and wrap ClassList routines
+        to control revalidation.
         """
         # Ensure all ClassLists have the correct _class_handle defined
         for field in (fields := Project.model_fields):
@@ -454,6 +454,33 @@ def set_layers(self) -> "Project":
             self.layers.data = []
         return self
 
+    @model_validator(mode="after")
+    def set_repeat_layers(self) -> "Project":
+        """If we are not using a standard layers model, warn that the repeat layers setting is not valid."""
+        if self.model != LayerModels.StandardLayers:
+            for contrast in self.contrasts:
+                if "repeat_layers" in contrast.model_fields_set and contrast.repeat_layers != 1:
+                    warnings.warn(
+                        'For a custom layers or custom XY calculation, the "repeat_layers" setting for each '
+                        "contrast is not valid - resetting to 1.",
+                        stacklevel=2,
+                    )
+                contrast.repeat_layers = 1
+        return self
+
+    @model_validator(mode="after")
+    def set_resample(self) -> "Project":
+        """If we are using a custom XY model, warn that the resample setting for each contrast must always be True."""
+        if self.model == LayerModels.CustomXY:
+            for contrast in self.contrasts:
+                if "resample" in contrast.model_fields_set and contrast.resample is False:
+                    warnings.warn(
+                        'For a custom XY calculation, "resample" must be True for each contrast - resetting to True.',
+                        stacklevel=2,
+                    )
+                contrast.resample = True
+        return self
+
     @model_validator(mode="after")
     def set_calculation(self) -> "Project":
         """Apply the calc setting to the project."""
diff --git a/tests/test_inputs.py b/tests/test_inputs.py
index db5b6646..e7a1560e 100644
--- a/tests/test_inputs.py
+++ b/tests/test_inputs.py
@@ -306,7 +306,7 @@ def custom_xy_problem(test_names, test_checks):
     problem.contrastResolutionTypes = ["constant"]
     problem.contrastCustomFiles = [1]
     problem.contrastDomainRatios = [0]
-    problem.resample = [False]
+    problem.resample = [True]
     problem.dataPresent = [0]
     problem.data = [np.empty([0, 6])]
     problem.dataLimits = [[0.0, 0.0]]
diff --git a/tests/test_project.py b/tests/test_project.py
index c2ea92a2..7683dec9 100644
--- a/tests/test_project.py
+++ b/tests/test_project.py
@@ -443,6 +443,46 @@ def test_set_layers(project_parameters: dict) -> None:
     assert project.layers == []
 
 
+@pytest.mark.parametrize(
+    "project_parameters",
+    [
+        (
+            {
+                "model": LayerModels.CustomLayers,
+                "contrasts": [ratapi.models.Contrast(name="Test Contrast", repeat_layers=2)],
+            }
+        ),
+        ({"model": LayerModels.CustomXY, "contrasts": [ratapi.models.Contrast(name="Test Contrast", repeat_layers=2)]}),
+    ],
+)
+def test_set_repeat_layers(project_parameters: dict) -> None:
+    """If we are using a custom layers of custom XY model, the "resample" field of all the contrasts should always
+    be 1."""
+    with pytest.warns(
+        match='For a custom layers or custom XY calculation, the "repeat_layers" setting for each '
+        "contrast is not valid - resetting to 1."
+    ):
+        project = ratapi.Project(**project_parameters)
+    assert all(contrast.repeat_layers == 1 for contrast in project.contrasts)
+
+
+@pytest.mark.parametrize(
+    "project_parameters",
+    [
+        ({"model": LayerModels.CustomXY, "contrasts": [ratapi.models.Contrast(name="Test Contrast")]}),
+    ],
+)
+def test_set_resample(project_parameters: dict) -> None:
+    """If we are using a custom XY model, the "resample" field of all the contrasts should always be True."""
+    project = ratapi.Project(**project_parameters)
+    assert all(contrast.resample for contrast in project.contrasts)
+    with pytest.warns(
+        match='For a custom XY calculation, "resample" must be True for each contrast - resetting to True.'
+    ):
+        project.contrasts.append(name="New Contrast", resample=False)
+    assert all(contrast.resample for contrast in project.contrasts)
+
+
 @pytest.mark.parametrize(
     ["input_calculation", "input_contrast", "new_calculation", "new_contrast_model", "num_domain_ratios"],
     [

From f978f4c7ae3f0ec13ace6b0b7d2cf0cfe0550184 Mon Sep 17 00:00:00 2001
From: StephenNneji <34302892+StephenNneji@users.noreply.github.com>
Date: Tue, 2 Sep 2025 09:00:57 +0100
Subject: [PATCH 8/8] Updates version to 0.0.0.dev8 (#179)

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index bda3a43a..b5871644 100644
--- a/setup.py
+++ b/setup.py
@@ -8,7 +8,7 @@
 from setuptools.command.build_clib import build_clib
 from setuptools.command.build_ext import build_ext
 
-__version__ = "0.0.0.dev7"
+__version__ = "0.0.0.dev8"
 PACKAGE_NAME = "ratapi"
 
 with open("README.md") as f: