From 5e15a6c33d3c4cbe8a74dc8daee350c34f732989 Mon Sep 17 00:00:00 2001
From: Jonathan Haigh <jonathan.haigh@stfc.ac.uk>
Date: Thu, 4 Apr 2024 15:38:31 +0100
Subject: [PATCH 1/2] Switch to using fig.show() from plt.show()

Since upgrading to matplotlib 3.7, plt.show() has sometimes created freezing / hanging behaviour when run from within workbench
---
 .../algorithms/ConvertToReflectometryQ-v1.rst |  2 +-
 .../algorithms/ConvertToReflectometryQ-v2.rst |  2 +-
 docs/source/algorithms/CopySample-v1.rst      |  2 +-
 docs/source/algorithms/HB2AReduce-v1.rst      | 12 ++--
 .../algorithms/LagrangeILLReduction-v1.rst    | 10 +--
 docs/source/algorithms/SetSample-v1.rst       |  2 +-
 .../SingleCrystalDiffuseReduction-v1.rst      |  2 +-
 .../concepts/HowToDefineGeometricShape.rst    |  4 +-
 .../fitfunctions/BivariateGaussian.rst        | 16 ++---
 .../direct/Crystal Field Python Interface.rst |  5 +-
 docs/source/plotting/1DPlotsHelp.rst          | 67 ++-----------------
 docs/source/plotting/3DPlotsHelp.rst          |  6 +-
 docs/source/plotting/ColorfillPlotsHelp.rst   | 30 ++-------
 docs/source/plotting/MeshPlotHelp.rst         |  4 +-
 docs/source/plotting/WaterfallPlotsHelp.rst   |  2 +-
 .../source/release/v5.1.0/mantidworkbench.rst |  3 +-
 docs/source/techniques/CrystalField.rst       | 21 +++---
 .../06_sample_logs.rst                        |  4 +-
 .../getting_started/main_window.rst           | 18 ++---
 .../plotting/01_basic_plot_scripting.rst      | 10 +--
 .../python_in_mantid/solutions/02_pim_sol.rst | 32 ++-------
 .../python_in_mantid/solutions/03_pim_sol.rst |  5 +-
 22 files changed, 83 insertions(+), 176 deletions(-)

diff --git a/docs/source/algorithms/ConvertToReflectometryQ-v1.rst b/docs/source/algorithms/ConvertToReflectometryQ-v1.rst
index 32141ef2b46f..dbebb7f0031e 100644
--- a/docs/source/algorithms/ConvertToReflectometryQ-v1.rst
+++ b/docs/source/algorithms/ConvertToReflectometryQ-v1.rst
@@ -205,7 +205,7 @@ achieved by running the algorithm below.
         axes.set_xlim([-0.0004,0.0004])
         axes.set_ylim([0,0.2])
 
-        plt.show()
+        fig.show()
 
     threadsafe_call(patch_plot, dump_vertexes)
 
diff --git a/docs/source/algorithms/ConvertToReflectometryQ-v2.rst b/docs/source/algorithms/ConvertToReflectometryQ-v2.rst
index 6882f67f61fa..350fb7372901 100644
--- a/docs/source/algorithms/ConvertToReflectometryQ-v2.rst
+++ b/docs/source/algorithms/ConvertToReflectometryQ-v2.rst
@@ -203,7 +203,7 @@ achieved by running the algorithm below.
         axes.set_xlim([-0.0004,0.0004])
         axes.set_ylim([0,0.2])
 
-        plt.show()
+        fig.show()
 
     threadsafe_call(patch_plot, dump_vertexes)
 
diff --git a/docs/source/algorithms/CopySample-v1.rst b/docs/source/algorithms/CopySample-v1.rst
index 5327b1d57276..908b43792157 100644
--- a/docs/source/algorithms/CopySample-v1.rst
+++ b/docs/source/algorithms/CopySample-v1.rst
@@ -130,7 +130,7 @@ After running this example code, the sample shapes can be plotted (see :ref:`Mes
         axes.set_mesh_axes_equal(mesh)
         axes.view_init(elev=20, azim=80)
 
-        plt.show()
+        fig.show()
 
 
 
diff --git a/docs/source/algorithms/HB2AReduce-v1.rst b/docs/source/algorithms/HB2AReduce-v1.rst
index 3269bd9dc739..e90b969ee8a3 100644
--- a/docs/source/algorithms/HB2AReduce-v1.rst
+++ b/docs/source/algorithms/HB2AReduce-v1.rst
@@ -100,7 +100,7 @@ Usage
        ax.plot(ws, specNum=num)
    plt.legend()
    #fig.savefig('HB2AReduce_1.png')
-   plt.show()
+   fig.show()
 
 .. figure:: /images/HB2AReduce_1.png
 
@@ -117,7 +117,7 @@ Usage
    fig, ax = plt.subplots(subplot_kw={'projection':'mantid'})
    ax.plot(ws)
    #fig.savefig('HB2AReduce_2.png')
-   plt.show()
+   fig.show()
 
 .. figure:: /images/HB2AReduce_2.png
 
@@ -134,7 +134,7 @@ Usage
    fig, ax = plt.subplots(subplot_kw={'projection':'mantid'})
    ax.plot(ws)
    #fig.savefig('HB2AReduce_3.png')
-   plt.show()
+   fig.show()
 
 .. figure:: /images/HB2AReduce_3.png
 
@@ -151,7 +151,7 @@ Usage
    fig, ax = plt.subplots(subplot_kw={'projection':'mantid'})
    ax.plot(ws)
    #fig.savefig('HB2AReduce_4.png')
-   plt.show()
+   fig.show()
 
 .. figure:: /images/HB2AReduce_4.png
 
@@ -168,7 +168,7 @@ Usage
    fig, ax = plt.subplots(subplot_kw={'projection':'mantid'})
    ax.plot(ws)
    #fig.savefig('HB2AReduce_5.png')
-   plt.show()
+   fig.show()
 
 .. figure:: /images/HB2AReduce_5.png
 
@@ -191,7 +191,7 @@ single anode *vs* temperature.
    fig, ax = plt.subplots(subplot_kw={'projection':'mantid'})
    ax.plot(ws, specNum=8) # anode8
    #fig.savefig('HB2AReduce_6.png')
-   plt.show()
+   fig.show()
 
 .. figure:: /images/HB2AReduce_6.png
 
diff --git a/docs/source/algorithms/LagrangeILLReduction-v1.rst b/docs/source/algorithms/LagrangeILLReduction-v1.rst
index 84a4af42ae84..97b5bad97c5c 100644
--- a/docs/source/algorithms/LagrangeILLReduction-v1.rst
+++ b/docs/source/algorithms/LagrangeILLReduction-v1.rst
@@ -51,10 +51,12 @@ Usage
     eis = result.readX(0)
     temperatures = run.getLogData('temperature').value
 
-    plt.plot(eis, temperatures)
-    plt.xlabel("Ei (meV)")
-    plt.ylabel("temperature (K)")
-    plt.show()
+    fig, ax = plt.subplots(subplot_kw={'projection': 'mantid'})
+
+    ax.plot(eis, temperatures)
+    ax.set_xlabel("Ei (meV)")
+    ax.set_ylabel("temperature (K)")
+    fig.show()
 
 
 **Multiple monochromators example**
diff --git a/docs/source/algorithms/SetSample-v1.rst b/docs/source/algorithms/SetSample-v1.rst
index ba75f938b3bf..39d273a9452c 100644
--- a/docs/source/algorithms/SetSample-v1.rst
+++ b/docs/source/algorithms/SetSample-v1.rst
@@ -334,7 +334,7 @@ After running this example code to rotate a cuboid by 30° anti-clockwise around
    axes.set_mesh_axes_equal(mesh)
    axes.view_init(elev=20, azim=80)
 
-   plt.show()
+   fig.show()
 
 .. categories::
 
diff --git a/docs/source/algorithms/SingleCrystalDiffuseReduction-v1.rst b/docs/source/algorithms/SingleCrystalDiffuseReduction-v1.rst
index 3ea2fbe65636..795fc6932724 100644
--- a/docs/source/algorithms/SingleCrystalDiffuseReduction-v1.rst
+++ b/docs/source/algorithms/SingleCrystalDiffuseReduction-v1.rst
@@ -240,7 +240,7 @@ Usage
    fig, ax = plt.subplots(subplot_kw={'projection':'mantid'})
    c = ax.pcolormesh(mtd['output'],vmin=0, vmax=1e-5)
    fig.colorbar(c)
-   plt.show()
+   fig.show()
 
 .. figure:: /images/SingleCrystalDiffuseReduction_corelli_multiple_sym_bkg_HH0.png
 
diff --git a/docs/source/concepts/HowToDefineGeometricShape.rst b/docs/source/concepts/HowToDefineGeometricShape.rst
index 690dfd74434f..927058bf9242 100644
--- a/docs/source/concepts/HowToDefineGeometricShape.rst
+++ b/docs/source/concepts/HowToDefineGeometricShape.rst
@@ -332,7 +332,7 @@ Here the dimensions are used to define a 2m x 4m x 0.2m cuboid with its centre a
     axes.text(10.5,11.5,11, "WIDTH", color='b', fontsize=12)
     axes.text(11,9.5,9, "HEIGHT", color='purple', fontsize=12)
 
-    plt.show()
+    fig.show()
 
 In the next example, four points are used to describe a 2m x 0.8m x 0.4m cuboid with the its centre at the origin.
 
@@ -406,7 +406,7 @@ In the next example, four points are used to describe a 2m x 0.8m x 0.4m cuboid
     axes.scatter(0,0,0, color='b')
     axes.text(0,0.1,-0.15, "ORIGIN", color='b', fontsize=12)
 
-    plt.show()
+    fig.show()
 
 
 Hexahedron
diff --git a/docs/source/fitting/fitfunctions/BivariateGaussian.rst b/docs/source/fitting/fitfunctions/BivariateGaussian.rst
index 2a322ee506c2..4497445ac15d 100644
--- a/docs/source/fitting/fitfunctions/BivariateGaussian.rst
+++ b/docs/source/fitting/fitfunctions/BivariateGaussian.rst
@@ -86,16 +86,12 @@ Here is an example of fitting a 2D histogram:
     ZFit = bvg.function2D(pos)
 
     #Plot the results
-    plt.figure(1)
-    plt.clf()
-    plt.subplot(1,2,1)
-    plt.imshow(Z, origin='lower')
-    plt.title('Data')
-    plt.subplot(1,2,2)
-    plt.imshow(ZFit, origin='lower')
-    plt.title('Fit')
-    plt.show()
-
+    fig, axes = plt.subplots(nrows=1, ncols=2, subplot_kw={'projection': 'mantid'})
+    axes[0].imshow(Z, origin='lower')
+    axes[0].set_title('Data')
+    axes[1].imshow(ZFit, origin='lower')
+    axes[1].set_title('Fit')
+    fig.show()
 
 
 .. categories::
diff --git a/docs/source/interfaces/direct/Crystal Field Python Interface.rst b/docs/source/interfaces/direct/Crystal Field Python Interface.rst
index e215904dfe36..e866875a2b3c 100644
--- a/docs/source/interfaces/direct/Crystal Field Python Interface.rst	
+++ b/docs/source/interfaces/direct/Crystal Field Python Interface.rst	
@@ -142,8 +142,9 @@ After the peak shape is defined a spectrum can be calculated::
 The output is a tuple of two 1d numpy arrays (x, y) that can be used with `matplotlib` to plot::
 
   import matplotlib.pyplot as plt
-  plt.plot(*sp)
-  plt.show()
+  fig, ax = plt.subplots(subplot_kw={'projection': 'mantid'})
+  ax.plot(*sp)
+  fig.show()
 
 .. image:: /images/CrystalFieldSpectrum1.png
    :height: 300
diff --git a/docs/source/plotting/1DPlotsHelp.rst b/docs/source/plotting/1DPlotsHelp.rst
index 6ef597edc47e..b758d0594e00 100644
--- a/docs/source/plotting/1DPlotsHelp.rst
+++ b/docs/source/plotting/1DPlotsHelp.rst
@@ -85,14 +85,15 @@ Scripting
 
 Click the generate a script button |GenerateAScript.png| on a 1D Plot:
 
-.. code-block:: python
+.. plot::
+   :include-source:
 
    # import mantid algorithms, numpy and matplotlib
+   from mantid.simpleapi import *
    import matplotlib.pyplot as plt
    from mantid.plots.utility import MantidAxType
-   from mantid.api import AnalysisDataService as ADS
 
-   MAR11060 = ADS.retrieve('MAR11060')
+   MAR11060 = Load('MAR11060')
 
    fig, axes = plt.subplots(edgecolor='#ffffff', num='MAR11060-1', subplot_kw={'projection': 'mantid'})
    axes.plot(MAR11060, color='#1f77b4', label='MAR11060: spec 1', wkspIndex=0)
@@ -105,29 +106,7 @@ Click the generate a script button |GenerateAScript.png| on a 1D Plot:
    axes.set_ylabel('Counts ($\\mu s$)$^{-1}$')
    legend = axes.legend(fontsize=8.0).set_draggable(True).legend
 
-   plt.show()
-
-.. plot::
-
-   # import mantid algorithms, numpy and matplotlib
-   from mantid.simpleapi import *
-   import matplotlib.pyplot as plt
-   from mantid.plots.utility import MantidAxType
-
-   MAR11060 = Load('MAR11060')
-
-   fig, axes = plt.subplots(edgecolor='#ffffff', num='MAR11060-1', subplot_kw={'projection': 'mantid'})
-   axes.plot(MAR11060, color='#1f77b4', label='MAR11060: spec 1', specNum=1)
-   axes.plot(MAR11060, color='#ff7f0e', label='MAR11060: spec 2', specNum=2)
-   axes.plot(MAR11060, color='#2ca02c', label='MAR11060: spec 3', specNum=3)
-   axes.tick_params(axis='x', which='major', **{'gridOn': False, 'tick1On': True, 'tick2On': False, 'label1On': True, 'label2On': False, 'size': 6, 'tickdir': 'out', 'width': 1})
-   axes.tick_params(axis='y', which='major', **{'gridOn': False, 'tick1On': True, 'tick2On': False, 'label1On': True, 'label2On': False, 'size': 6, 'tickdir': 'out', 'width': 1})
-   axes.set_title('MAR11060')
-   axes.set_xlabel('Time-of-flight ($\\mu s$)')
-   axes.set_ylabel('Counts ($\\mu s$)$^{-1}$')
-   legend = axes.legend(fontsize=8.0) # .set_draggable(True).legend # uncomment to set the legend draggable
-
-   plt.show()
+   fig.show()
 
 For more advice: :ref:`02_scripting_plots`
 
@@ -199,40 +178,8 @@ Scripting
 
 An example script for a Tiled Plot:
 
-.. code-block:: python
-
-   # import mantid algorithms, numpy and matplotlib
-   from mantid.simpleapi import *
-   import matplotlib.pyplot as plt
-   from mantid.plots.utility import MantidAxType
-   from mantid.api import AnalysisDataService as ADS
-
-   MAR11060 = ADS.retrieve('MAR11060') #May replace with Load('MAR11060')
-
-   fig, axes = plt.subplots(edgecolor='#ffffff', ncols=2, nrows=2, num='MAR11060-1', subplot_kw={'projection': 'mantid'})
-   axes[0][0].plot(MAR11060, color='#1f77b4', label='MAR11060: spec 1', wkspIndex=0)
-   axes[0][0].set_xlabel('Time-of-flight ($\\mu s$)')
-   axes[0][0].set_ylabel('Counts ($\\mu s$)$^{-1}$')
-   legend = axes[0][0].legend(fontsize=8.0).set_draggable(True).legend
-
-   axes[0][1].plot(MAR11060, color='#1f77b4', label='MAR11060: spec 2', wkspIndex=1)
-   axes[0][1].set_xlabel('Time-of-flight ($\\mu s$)')
-   axes[0][1].set_ylabel('Counts ($\\mu s$)$^{-1}$')
-   legend = axes[0][1].legend(fontsize=8.0).set_draggable(True).legend
-
-   axes[1][0].plot(MAR11060, color='#1f77b4', label='MAR11060: spec 3', wkspIndex=2)
-   axes[1][0].set_xlabel('Time-of-flight ($\\mu s$)')
-   axes[1][0].set_ylabel('Counts ($\\mu s$)$^{-1}$')
-   legend = axes[1][0].legend(fontsize=8.0).set_draggable(True).legend
-
-   axes[1][1].plot(MAR11060, color='#1f77b4', label='MAR11060: spec 4', wkspIndex=3)
-   axes[1][1].set_xlabel('Time-of-flight ($\\mu s$)')
-   axes[1][1].set_ylabel('Counts ($\\mu s$)$^{-1}$')
-   legend = axes[1][1].legend(fontsize=8.0).set_draggable(True).legend
-
-   plt.show()
-
 .. plot::
+   :include-source:
 
    # import mantid algorithms, numpy and matplotlib
    from mantid.simpleapi import *
@@ -262,7 +209,7 @@ An example script for a Tiled Plot:
    axes[1][1].set_ylabel('Counts ($\\mu s$)$^{-1}$')
    legend = axes[1][1].legend(fontsize=8.0) #.set_draggable(True).legend # uncomment to set the legend draggable
 
-   plt.show()
+   fig.show()
 
 For more advice: :ref:`02_scripting_plots`
 
diff --git a/docs/source/plotting/3DPlotsHelp.rst b/docs/source/plotting/3DPlotsHelp.rst
index dbdea3910b77..5b010ceef89c 100644
--- a/docs/source/plotting/3DPlotsHelp.rst
+++ b/docs/source/plotting/3DPlotsHelp.rst
@@ -83,7 +83,8 @@ Basic example of plotting a `Surface <https://matplotlib.org/mpl_toolkits/mplot3
 
     fig, ax = plt.subplots(subplot_kw={'projection':'mantid3d'})
     ax.plot_surface(data, cmap='viridis')
-    plt.show()
+
+    fig.show()
 
 For more advice: :ref:`02_scripting_plots`
 
@@ -150,7 +151,8 @@ Basic example of plotting a `Wireframe <https://matplotlib.org/mpl_toolkits/mplo
 
     fig, ax = plt.subplots(subplot_kw={'projection':'mantid3d'})
     ax.plot_wireframe(data, color='#1f77b4')
-    plt.show()
+
+    fig.show()
 
 For more advice: :ref:`02_scripting_plots`
 
diff --git a/docs/source/plotting/ColorfillPlotsHelp.rst b/docs/source/plotting/ColorfillPlotsHelp.rst
index a7630bd34982..83e71cf2fa9a 100644
--- a/docs/source/plotting/ColorfillPlotsHelp.rst
+++ b/docs/source/plotting/ColorfillPlotsHelp.rst
@@ -68,31 +68,8 @@ Scripting
 
 Click the generate a script button |GenerateAScript.png| on a `Colorfill Plot <https://matplotlib.org/3.2.1/api/_as_gen/matplotlib.pyplot.imshow.html>`_:
 
-.. code-block:: python
-
-   import matplotlib.pyplot as plt
-   import numpy as np
-   from matplotlib.colors import LogNorm
-   from matplotlib.ticker import LogLocator
-   from mantid.api import AnalysisDataService as ADS
-
-   MAR11060 = ADS.retrieve('MAR11060')
-
-   fig, axes = plt.subplots(figsize=[8.0, 7.0], num='MAR11060-1', subplot_kw={'projection': 'mantid'})
-   cfill = axes.imshow(MAR11060, aspect='auto', cmap='viridis', distribution=False, origin='lower')
-   cfill.set_norm(LogNorm(vmin=0.0001, vmax=3792.3352))
-   # If no ticks appear on the color bar remove the subs argument inside the LogLocator below
-   cbar = fig.colorbar(cfill, ax=[axes], ticks=LogLocator(subs=np.arange(1, 10)), pad=0.06)
-   cbar.set_label('Counts ($\\mu s$)$^{-1}$')
-   axes.set_title('MAR11060')
-   axes.set_xlabel('Time-of-flight ($\\mu s$)')
-   axes.set_ylabel('Spectrum')
-   axes.set_xlim([5.0, 19992.0])
-   axes.set_ylim([0.5, 922.5])
-
-   plt.show()
-
 .. plot::
+   :include-source:
 
    # import mantid algorithms, numpy and matplotlib
    from mantid.simpleapi import *
@@ -116,7 +93,7 @@ Click the generate a script button |GenerateAScript.png| on a `Colorfill Plot <h
    axes.set_xlim([5.0, 19992.0])
    axes.set_ylim([0.5, 922.5])
 
-   plt.show()
+   fig.show()
 
 For more advice:
 
@@ -200,7 +177,8 @@ Basic example of plotting a `Contour Plot <https://matplotlib.org/api/_as_gen/ma
    cbar=fig.colorbar(c)
    cbar.set_label('Counts ($\mu s$)$^{-1}$') #add text to colorbar
    fig.tight_layout()
-   plt.show()
+
+   fig.show()
 
 For more advice:
 
diff --git a/docs/source/plotting/MeshPlotHelp.rst b/docs/source/plotting/MeshPlotHelp.rst
index 62d3797b1eb5..e11d7e49bd42 100644
--- a/docs/source/plotting/MeshPlotHelp.rst
+++ b/docs/source/plotting/MeshPlotHelp.rst
@@ -114,7 +114,7 @@ Note Component index 0 is usually the Container.
    sample = ws.getInstrument().getSample().getPos() - source
    arrow(axes, sample, origin=(0,0,-0.04))
    axes.view_init(vertical_axis='y', elev=30, azim=-135)
-   plt.show()
+   fig.show()
 
 
 Plot a cuboid sample shape, rotate it by the goniometer and add lattice vector arrows.
@@ -192,7 +192,7 @@ Plot a cuboid sample shape, rotate it by the goniometer and add lattice vector a
       arrow(axes, reciprocal_lattice[:,i], color = colors[i], linestyle = '--')
 
    axes.view_init(vertical_axis='y', elev=27, azim=50)
-   plt.show()
+   fig.show()
 
 
 **Other Plotting Documentation**
diff --git a/docs/source/plotting/WaterfallPlotsHelp.rst b/docs/source/plotting/WaterfallPlotsHelp.rst
index 1cf5c66fae5f..f56f2f38ff3d 100644
--- a/docs/source/plotting/WaterfallPlotsHelp.rst
+++ b/docs/source/plotting/WaterfallPlotsHelp.rst
@@ -132,7 +132,7 @@ An example script for a Waterfall Plot:
    # Update the offsets
    ax.update_waterfall(x_offset=10, y_offset=30)
 
-   plt.show()
+   fig.show()
 
 For more advice: :ref:`02_scripting_plots`
 
diff --git a/docs/source/release/v5.1.0/mantidworkbench.rst b/docs/source/release/v5.1.0/mantidworkbench.rst
index 7de9c8ac01d0..75ef489eaa5b 100644
--- a/docs/source/release/v5.1.0/mantidworkbench.rst
+++ b/docs/source/release/v5.1.0/mantidworkbench.rst
@@ -92,7 +92,8 @@ Plotting
     ax3d[0].set_title("Surface")
     ax3d[1].set_title("Wireframe")
 
-    #plt.show()# uncomment to show the plots
+    #figC.show()# uncomment to show the plots
+    #fig3d.show()
 
 - The Advanced Plotting menu is now in Workbench. This enables creating surface and contour plots of three or more workspaces, and choosing which log value to plot against.
 
diff --git a/docs/source/techniques/CrystalField.rst b/docs/source/techniques/CrystalField.rst
index 68bec4790c58..2b7f8a3abfe1 100644
--- a/docs/source/techniques/CrystalField.rst
+++ b/docs/source/techniques/CrystalField.rst
@@ -132,16 +132,17 @@ Fitting magnetic susceptibility
    calc_a = mtd['fit_susc_Workspaces'][0]
    calc_b = mtd['fit_susc_Workspaces'][1]
    calc_c = mtd['fit_susc_Workspaces'][2]
-   plt.plot(calc_a.readX(1),calc_a.readY(1),'-k',label='$\chi^a$ Fit')
-   plt.plot(mtd['sus_a'].readX(0),mtd['sus_a'].readY(0),'ok',label='$\chi^a$ Data')
-   plt.plot(calc_b.readX(1),calc_b.readY(1),'-b',label='$\chi^b$ Fit')
-   plt.plot(mtd['sus_b'].readX(0),mtd['sus_b'].readY(0),'ob',label='$\chi^b$ Data')
-   plt.plot(calc_c.readX(1),calc_c.readY(1),'-r',label='$\chi^c$ Fit')
-   plt.plot(mtd['sus_c'].readX(0),mtd['sus_c'].readY(0),'or',label='$\chi^c$ Data')
-   plt.legend(loc='upper left')
-   plt.xlabel('Temperature (K)')
-   plt.ylabel('Inverse Susceptibility (mol/emu)')
-   plt.show()
+   fig, ax = plt.subplots(subplot_kw={'projection': 'mantid'})
+   ax.plot(calc_a.readX(1),calc_a.readY(1),'-k',label='$\chi^a$ Fit')
+   ax.plot(mtd['sus_a'].readX(0),mtd['sus_a'].readY(0),'ok',label='$\chi^a$ Data')
+   ax.plot(calc_b.readX(1),calc_b.readY(1),'-b',label='$\chi^b$ Fit')
+   ax.plot(mtd['sus_b'].readX(0),mtd['sus_b'].readY(0),'ob',label='$\chi^b$ Data')
+   ax.plot(calc_c.readX(1),calc_c.readY(1),'-r',label='$\chi^c$ Fit')
+   ax.plot(mtd['sus_c'].readX(0),mtd['sus_c'].readY(0),'or',label='$\chi^c$ Data')
+   ax.legend(loc='upper left')
+   ax.set_xlabel('Temperature (K)')
+   ax.set_ylabel('Inverse Susceptibility (mol/emu)')
+   fig.show()
 
 
 |FittingMagneticSusceptibility.png|
diff --git a/docs/source/tutorials/mantid_basic_course/connecting_data_to_instruments/06_sample_logs.rst b/docs/source/tutorials/mantid_basic_course/connecting_data_to_instruments/06_sample_logs.rst
index dfd33fa31721..ba06814254d0 100644
--- a/docs/source/tutorials/mantid_basic_course/connecting_data_to_instruments/06_sample_logs.rst
+++ b/docs/source/tutorials/mantid_basic_course/connecting_data_to_instruments/06_sample_logs.rst
@@ -130,8 +130,8 @@ This can be performed directly with :ref:`algm-FilterByTime` or indirectly with
 	axes[2][0].set_xlim(temp_x_limit)
 	axes[2][0].set_ylim(temp_y_limit)
 
-	plt.tight_layout()
-	plt.show()
+	fig.tight_layout()
+	fig.show()
 
 
 Interface
diff --git a/docs/source/tutorials/mantid_basic_course/getting_started/main_window.rst b/docs/source/tutorials/mantid_basic_course/getting_started/main_window.rst
index e82466f145e4..bb10e366ae47 100644
--- a/docs/source/tutorials/mantid_basic_course/getting_started/main_window.rst
+++ b/docs/source/tutorials/mantid_basic_course/getting_started/main_window.rst
@@ -72,14 +72,16 @@ A usual Workspace consists of a number of spectra, each cut into blocks called b
    for i in range(number_of_bins):
        bin_centres[i] = (bin_edges[i+1] + bin_edges[i])/2
 
-   plt.hist(neutrons_detected_at, bins=bin_edges, align='mid', color='b', edgecolor='black',density = False, label='Bins')
-   plt.plot(bin_centres,counts_per_bin,color='red', label = 'Line')
+   fig, ax = plt.subplots(subplot_kw={'projection': 'mantid'})
+
+   ax.hist(neutrons_detected_at, bins=bin_edges, align='mid', color='b', edgecolor='black',density = False, label='Bins')
+   ax.plot(bin_centres,counts_per_bin,color='red', label = 'Line')
 
 
    # Add axis labels
-   plt.xlabel("X data      eg. Time ($\mu s$)")
-   plt.ylabel("Y data      eg. Counts ($\mu s$)$^{-1}$")
-   plt.title("Bins and Line Plots")
-   plt.xticks(bin_edges)
-   plt.legend()
-   plt.show()
\ No newline at end of file
+   ax.set_xlabel("X data      eg. Time ($\mu s$)")
+   ax.set_ylabel("Y data      eg. Counts ($\mu s$)$^{-1}$")
+   ax.set_title("Bins and Line Plots")
+   ax.set_xticks(bin_edges)
+   ax.legend()
+   fig.show()
\ No newline at end of file
diff --git a/docs/source/tutorials/python_in_mantid/plotting/01_basic_plot_scripting.rst b/docs/source/tutorials/python_in_mantid/plotting/01_basic_plot_scripting.rst
index 4aa818925d18..42e41f9aeafe 100644
--- a/docs/source/tutorials/python_in_mantid/plotting/01_basic_plot_scripting.rst
+++ b/docs/source/tutorials/python_in_mantid/plotting/01_basic_plot_scripting.rst
@@ -107,7 +107,7 @@ To overplot on the same window:
     c = axes.imshow(data, origin = 'lower', cmap='viridis', aspect='auto', norm=LogNorm())
     cbar=fig.colorbar(c)
     cbar.set_label('Counts ($\mu s$)$^{-1}$') #add text to colorbar
-    #plt.show()
+    #fig.show()
 
 
 .. plot::
@@ -129,7 +129,7 @@ To overplot on the same window:
     c = ax.pcolormesh(sqw, cmap='plasma', norm=LogNorm())
     cbar=fig.colorbar(c)
     cbar.set_label('Intensity (arb. units)') #add text to colorbar
-    #plt.show()
+    #fig.show()
 
 `Contour lines <https://matplotlib.org/api/_as_gen/matplotlib.axes.Axes.contour.html>`_ can be overlayed on a 2D colorfill:
 
@@ -154,7 +154,7 @@ To overplot on the same window:
 
     cbar=fig.colorbar(c)
     cbar.set_label('Counts ($\mu s$)$^{-1}$') #add text to colorbar
-    #plt.show()
+    #fig.show()
 
 
 3D Surface and Wireframe Plots
@@ -175,7 +175,7 @@ To overplot on the same window:
 
     fig, ax = plt.subplots(subplot_kw={'projection':'mantid3d'})
     ax.plot_surface(data, cmap='viridis')
-    #plt.show()
+    #fig.show()
 
 .. plot::
    :include-source:
@@ -189,7 +189,7 @@ To overplot on the same window:
 
     fig, ax = plt.subplots(subplot_kw={'projection':'mantid3d'})
     ax.plot_wireframe(data, color='green')
-    #plt.show()
+    #fig.show()
 
 
 * See :ref:`here <plotting>` for custom color cycles and colormaps
diff --git a/docs/source/tutorials/python_in_mantid/solutions/02_pim_sol.rst b/docs/source/tutorials/python_in_mantid/solutions/02_pim_sol.rst
index 3ec72383f25a..6ddd4b8c476c 100644
--- a/docs/source/tutorials/python_in_mantid/solutions/02_pim_sol.rst
+++ b/docs/source/tutorials/python_in_mantid/solutions/02_pim_sol.rst
@@ -48,32 +48,8 @@ A - Processing ISIS Data
 B - Plotting ILL Data
 =====================
 
-.. code-block:: python
-
-    # import mantid algorithms, numpy and matplotlib
-    from mantid.simpleapi import *
-    import matplotlib.pyplot as plt
-    import numpy as np
-    from mantid.api import AnalysisDataService as ADS
-
-    _164198 = ADS.retrieve('164198')
-
-    fig, axes = plt.subplots(edgecolor='#ffffff', num='164198-1', subplot_kw={'projection': 'mantid'})
-    axes.plot(_164198, color='#2ca02c', label='164198: spec 100', linewidth=1.0, specNum=100, zorder=2.1)
-    axes.plot(_164198, color='#1f77b4', label='164198: spec 200', linewidth=1.0, specNum=200, zorder=2.1)
-    axes.errorbar(_164198, capsize=1.0, color='#ff7f0e', label='A funky label', linewidth=1.0, specNum=50)
-    axes.plot(_164198, color='#000000', label='164198: spec 300', linewidth=1.0, markeredgecolor='#d62728', markerfacecolor='#d62728', specNum=300, zorder=2.1)
-    axes.set_title('My Beautiful Plot')
-    axes.set_xlabel(r'Time-of-flight ($\mu s$)')
-    axes.set_ylabel('Counts')
-    axes.set_xlim([460.0, 600.0])
-    axes.set_ylim([1.0, 2000.0])
-    axes.set_yscale('log')
-    axes.legend().draggable()
-
-    plt.show()
-
 .. plot::
+    :include-source:
 
     # import mantid algorithms, numpy and matplotlib
     from mantid.simpleapi import *
@@ -88,14 +64,14 @@ B - Plotting ILL Data
     axes.errorbar(_164198, capsize=1.0, color='#ff7f0e', label='A funky label', linewidth=1.0, specNum=50)
     axes.plot(_164198, color='#000000', label='164198: spec 300', linewidth=1.0, markeredgecolor='#d62728', markerfacecolor='#d62728', specNum=300, zorder=2.1)
     axes.set_title('My Beautiful Plot')
-    axes.set_xlabel('Time-of-flight ($\mu s$)')
+    axes.set_xlabel(r'Time-of-flight ($\mu s$)')
     axes.set_ylabel('Counts')
     axes.set_xlim([460.0, 600.0])
     axes.set_ylim([1.0, 2000.0])
     axes.set_yscale('log')
     axes.legend() #.draggable()
 
-    #plt.show()
+    #fig.show()
 
 
 C - Processing and Plotting SNS Data
@@ -134,7 +110,7 @@ C - Processing and Plotting SNS Data
     axes.set_yscale('log')
     axes.legend() #.draggable()
 
-    #plt.show()
+    #fig.show()
 
     # NOTE: This script could be improved further with adding comments,
     # and extracting and logging values for filename and binning params,
diff --git a/docs/source/tutorials/python_in_mantid/solutions/03_pim_sol.rst b/docs/source/tutorials/python_in_mantid/solutions/03_pim_sol.rst
index 3fb1f6ab65f7..da620ec184e9 100644
--- a/docs/source/tutorials/python_in_mantid/solutions/03_pim_sol.rst
+++ b/docs/source/tutorials/python_in_mantid/solutions/03_pim_sol.rst
@@ -42,7 +42,7 @@ A - Direct Matplotlib with SNS Data
 
     # Add a legend with the chosen labels and show the plot
     axes.legend()
-    #plt.show() #uncomment to show the plot
+    #fig.show() #uncomment to show the plot
 
     # Note with the Direct Matplotlib method,
     # there are many more options for formatting the plot
@@ -148,4 +148,5 @@ C - 2D and 3D Plot ILL Data
     ax3d[0].set_title("Surface")
     ax3d[1].set_title("Wireframe")
 
-    #plt.show()# uncomment to show the plots
+    #figC.show()# uncomment to show the plots
+    #fig3d.show()

From 56a3cabfae9be1d8a4a743e90697c377392cf4a2 Mon Sep 17 00:00:00 2001
From: GuiMacielPereira <gui.maciel-pereira@stfc.ac.uk>
Date: Tue, 7 May 2024 14:37:10 +0100
Subject: [PATCH 2/2] Increased noise in data for clearer comparison with fit

- Previous noise was so small that Z and ZFit looked identical
- With increased noise it's clear that one is a smooth fit to the noisy data
---
 docs/source/fitting/fitfunctions/BivariateGaussian.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/fitting/fitfunctions/BivariateGaussian.rst b/docs/source/fitting/fitfunctions/BivariateGaussian.rst
index 4497445ac15d..ba190ccce9e0 100644
--- a/docs/source/fitting/fitfunctions/BivariateGaussian.rst
+++ b/docs/source/fitting/fitfunctions/BivariateGaussian.rst
@@ -53,7 +53,7 @@ Here is an example of fitting a 2D histogram:
     x, y = np.mgrid[-0.5:0.5:.01, -0.5:0.5:.01]
     pos = np.dstack((x, y))
     Z = rv.pdf(pos)
-    Z += 0.1*(np.random.random(x.shape) - 0.5) # Noise
+    Z += 1.5*(np.random.random(x.shape) - 0.5) # Noise
 
     # Here we'll format it so we can fit this as a 1D function:
     ZForFitting = np.empty(Z.shape + (2,))