diff --git a/dev-docs/source/AlgorithmMPISupport.rst b/dev-docs/source/AlgorithmMPISupport.rst
index 74d750cf64dea9777b7e147ad1aceec2809a8892..56b45185385a2584fa187cd30a507df7ac3f6f3c 100644
--- a/dev-docs/source/AlgorithmMPISupport.rst
+++ b/dev-docs/source/AlgorithmMPISupport.rst
@@ -372,7 +372,7 @@ The consequences are as follows:
It should not be logged, written as output, or used for branching execution paths since it is meaningless.
If the total number of spectra in a workspace is required it can be accessed via ``MatrixWorkspace::indexInfo()::globalSize()``.
- User input providing indices or spectrum numbers in one way or another must be translated into local indices by ``IndexInfo``.
- The most common cases are a workspace property that also accepts indices, see `IndexProperty <../concepts/IndexProperty.html>`__.
+ The most common cases are a workspace property that also accepts indices, see :ref:`IndexProperty <IndexProperty>`.
- The distinction between local and global indices must not be exposed to the user.
In particular, the 'global' prefix should be omitted, i.e., for the user interface we keep referring to 'workspace index', even though it is internally not what used to be the workspace index but rather a global index.
Indices provided by a user may never be interpreted as local indices, since a local index has no fixed meaning.
diff --git a/dev-docs/source/GettingStartedWithPyCharm.rst b/dev-docs/source/GettingStartedWithPyCharm.rst
index e9103cd4db6f2854a9c92f91f96365e90d4d14e4..6169cefea8ec0bf1891d458682a6502e4b0a96cb 100644
--- a/dev-docs/source/GettingStartedWithPyCharm.rst
+++ b/dev-docs/source/GettingStartedWithPyCharm.rst
@@ -5,7 +5,7 @@ Getting Started with PyCharm
PyCharm can be installed from `here <https://jetbrains.com/pycharm/download/>`_.
-This tutorial assumes you are familiar with the process of building Mantid (with separate source and build directories inside a root directory), and that you have built a working version. If you are unclear about this see `here <GettingStarted.html>`__
+This tutorial assumes you are familiar with the process of building Mantid (with separate source and build directories inside a root directory), and that you have built a working version. If you are unclear about this see :ref:`here <GettingStarted>`.
.. contents::
:local:
diff --git a/dev-docs/source/MVPTutorial/AddButton.rst b/dev-docs/source/MVPTutorial/AddButton.rst
index f4a07fbdce9ad2d2ab49b912447d29462e058e96..181603d0fccf4bd28a7ab79240a5ba4ba8ab8d87 100644
--- a/dev-docs/source/MVPTutorial/AddButton.rst
+++ b/dev-docs/source/MVPTutorial/AddButton.rst
@@ -1,3 +1,5 @@
+.. _AddButton:
+
===============
Adding a Button
===============
@@ -10,7 +12,7 @@ The View
The below code creates a QWidget containing a single button. When the
button is pressed it will print a message to the terminal screen. It
should be noted that in practice this should be avoided and will be
-discussed in `this section <ReceivingSignalFromView.html>`_.
+discussed in :ref:`this section <ReceivingSignalFromView>`.
First we need to import the relevant packages, this includes PyQt.
@@ -42,10 +44,10 @@ Next we create a layout and add a button to it
# connect button to signal
self.button.clicked.connect(self.btn_click)
- # add button to layout
- grid.addWidget(self.button)
- # set the layout for the view widget
- self.setLayout(grid)
+ # add button to layout
+ grid.addWidget(self.button)
+ # set the layout for the view widget
+ self.setLayout(grid)
The above connect statement means that when the button is pressed, the
function ``btn_click`` is called:
@@ -88,9 +90,9 @@ all been saved in ``view.py``, the ``main.py`` will contain:
def qapp():
if QtGui.QApplication.instance():
_app = QtGui.QApplication.instance()
- else:
+ else:
_app = QtGui.QApplication(sys.argv)
- return _app
+ return _app
app = qapp()
window = demo()
diff --git a/dev-docs/source/MVPTutorial/AddComboBox.rst b/dev-docs/source/MVPTutorial/AddComboBox.rst
index c7162460716359aa17f9c2dfe68f7254b97e3fc9..4789f4959444b9e477b03eee8cc48b912fe72d22 100644
--- a/dev-docs/source/MVPTutorial/AddComboBox.rst
+++ b/dev-docs/source/MVPTutorial/AddComboBox.rst
@@ -1,3 +1,5 @@
+.. _AddComboBox:
+
==============
Add a ComboBox
==============
diff --git a/dev-docs/source/MVPTutorial/AddLineEdit.rst b/dev-docs/source/MVPTutorial/AddLineEdit.rst
index b2c4cbfb978dbacb16ca1bf1b80c9b17705f9d32..d95e920c911b4c100a69c8c6e720c94235fed504 100644
--- a/dev-docs/source/MVPTutorial/AddLineEdit.rst
+++ b/dev-docs/source/MVPTutorial/AddLineEdit.rst
@@ -18,6 +18,6 @@ edit (useful for tables).
Care should be taken before using a line edit as it can give a user
too much freedom. If you know that the input is an integer then a
-`spin box <AddSpinBox.html>`_ is better. If there is a finite list of
-possible options then a `combo box <AddComboBox.html>`_ would be a
+:ref:`spin box <AddSpinBox>` is better. If there is a finite list of
+possible options then a :ref:`combo box <AddComboBox>` would be a
better choice.
diff --git a/dev-docs/source/MVPTutorial/AddSpinBox.rst b/dev-docs/source/MVPTutorial/AddSpinBox.rst
index 86a3abb414f4dc0d0d10f248a4c31e28368465eb..7439e693d5f29eb3810b030e221886aa895cf2fc 100644
--- a/dev-docs/source/MVPTutorial/AddSpinBox.rst
+++ b/dev-docs/source/MVPTutorial/AddSpinBox.rst
@@ -1,3 +1,5 @@
+.. _AddSpinBox:
+
==============
Add a Spin Box
==============
diff --git a/dev-docs/source/MVPTutorial/CompleteGUI.rst b/dev-docs/source/MVPTutorial/CompleteGUI.rst
index c3e4ae7d61667851514f40fba3d81be7ff8145da..2e24bab3602e3f8e737509eac4e065221645f9a0 100644
--- a/dev-docs/source/MVPTutorial/CompleteGUI.rst
+++ b/dev-docs/source/MVPTutorial/CompleteGUI.rst
@@ -146,7 +146,7 @@ Plot Presenter
PlotView
########
-Unchanged from `Matplotlib and MVP <Matplotlib.html>`_.
+Unchanged from :ref:`Matplotlib and MVP <Matplotlib>`.
Presenter
#########
@@ -171,9 +171,9 @@ Presenter
View
####
-Unchanged from `Model Exercise Solution <ModelExerciseSolution.html>`_.
+Unchanged from :ref:`Model Exercise Solution <ModelExerciseSolution>`.
Model
#####
-Unchanged from `Model Exercise Solution <ModelExerciseSolution.html>`_.
+Unchanged from :ref:`Model Exercise Solution <ModelExerciseSolution>`.
diff --git a/dev-docs/source/MVPTutorial/Matplotlib.rst b/dev-docs/source/MVPTutorial/Matplotlib.rst
index 22972a4f8a83c403fd2c561d9e9517c48ae32514..98164e6b31a638e1065e652ad750d5ab0ccd4294 100644
--- a/dev-docs/source/MVPTutorial/Matplotlib.rst
+++ b/dev-docs/source/MVPTutorial/Matplotlib.rst
@@ -1,3 +1,5 @@
+.. _Matplotlib:
+
==================
Matplotlib and MVP
==================
diff --git a/dev-docs/source/MVPTutorial/MockingExercise.rst b/dev-docs/source/MVPTutorial/MockingExercise.rst
index 1770a54c068c818bde111f9bcd4c8da033d74c87..d8af6726d7a8b7cb0f9250655c22161db255f96d 100644
--- a/dev-docs/source/MVPTutorial/MockingExercise.rst
+++ b/dev-docs/source/MVPTutorial/MockingExercise.rst
@@ -8,4 +8,4 @@ mocked and the return values should be present only when necessary (on
this occasion the values do not matter). The ``updatePlot`` function
should be tested to make sure that it calls the correct methods.
-See `here <MockingExerciseSolution.html>`_ for the solution.
+See :ref:`here <MockingExerciseSolution>` for the solution.
diff --git a/dev-docs/source/MVPTutorial/MockingExerciseSolution.rst b/dev-docs/source/MVPTutorial/MockingExerciseSolution.rst
index 14f8be65e83fc8d13e15fc7b36a982a4ef1222e9..19b7050b3edca3cc749136cc48f0f592556cb99e 100644
--- a/dev-docs/source/MVPTutorial/MockingExerciseSolution.rst
+++ b/dev-docs/source/MVPTutorial/MockingExerciseSolution.rst
@@ -1,3 +1,5 @@
+.. _MockingExerciseSolution:
+
=========================
Mocking Exercise Solution
=========================
diff --git a/dev-docs/source/MVPTutorial/ModelExercise.rst b/dev-docs/source/MVPTutorial/ModelExercise.rst
index c3559b53d9ea1a8c77e8b0452b3bfbb2d25f18b3..bb4a390d637428329683eef4470f05c0e9d4a3f4 100644
--- a/dev-docs/source/MVPTutorial/ModelExercise.rst
+++ b/dev-docs/source/MVPTutorial/ModelExercise.rst
@@ -15,4 +15,4 @@ input values
3. In the initialisation of the Presenter get the allowed colours from
the Model and pass them to the View
-See `here <ModelExerciseSolution.html>`_ for the solution.
+See :ref:`here <ModelExerciseSolution>` for the solution.
diff --git a/dev-docs/source/MVPTutorial/ModelExerciseSolution.rst b/dev-docs/source/MVPTutorial/ModelExerciseSolution.rst
index 835bec9e2d275f6f43ac8f0710cab937f7c0dc8c..b360252a41f99ab5142108717e96c9552e23734e 100644
--- a/dev-docs/source/MVPTutorial/ModelExerciseSolution.rst
+++ b/dev-docs/source/MVPTutorial/ModelExerciseSolution.rst
@@ -1,3 +1,5 @@
+.. _ModelExerciseSolution:
+
=======================
Model Exercise Solution
=======================
diff --git a/dev-docs/source/MVPTutorial/MultipleViews.rst b/dev-docs/source/MVPTutorial/MultipleViews.rst
index 115cf9916ace43097508371df0095f1808c9dee2..bd23284e9c1e4b8974f849df55f4d598ab2abf83 100644
--- a/dev-docs/source/MVPTutorial/MultipleViews.rst
+++ b/dev-docs/source/MVPTutorial/MultipleViews.rst
@@ -1,3 +1,5 @@
+.. _MultipleViews:
+
==============
Multiple Views
==============
diff --git a/dev-docs/source/MVPTutorial/PresenterExercise.rst b/dev-docs/source/MVPTutorial/PresenterExercise.rst
index de947f2237034a7af584a484d8a31eda8905d417..657e40b682bc189669b0191d4979dc04ab5ae471 100644
--- a/dev-docs/source/MVPTutorial/PresenterExercise.rst
+++ b/dev-docs/source/MVPTutorial/PresenterExercise.rst
@@ -15,4 +15,4 @@ is pressed the following should be output:
The ``main`` module will also need updating to handle these changes.
-See `here <PresenterExerciseSolution.html>`_ for the solution.
+See :ref:`here <PresenterExerciseSolution>` for the solution.
diff --git a/dev-docs/source/MVPTutorial/PresenterExerciseSolution.rst b/dev-docs/source/MVPTutorial/PresenterExerciseSolution.rst
index a0cb6caedd2c6f08524f767eb5aa2c322c2aef09..d2c556279e8dbebc4af2ececc4bc723da12e4822 100644
--- a/dev-docs/source/MVPTutorial/PresenterExerciseSolution.rst
+++ b/dev-docs/source/MVPTutorial/PresenterExerciseSolution.rst
@@ -1,3 +1,5 @@
+.. _PresenterExerciseSolution:
+
===========================
Presenter Exercise Solution
===========================
@@ -16,7 +18,7 @@ View
plotSignal = QtCore.pyqtSignal()
- def __init__(self, parent=None):
+ def __init__(self, parent=None):
super(view, self).__init__(parent)
grid = QtGui.QVBoxLayout(self)
@@ -52,22 +54,22 @@ View
self.plot.clicked.connect(self.buttonPressed)
- def getColour(self):
+ def getColour(self):
return self.colours.currentText()
- def getGridLines(self):
+ def getGridLines(self):
return self.grid_lines.checkState() == QtCore.Qt.Checked
- def getFreq(self):
+ def getFreq(self):
return float(self.freq.text())
- def getPhase(self):
+ def getPhase(self):
return float(self.phi.text())
- def buttonPressed(self):
+ def buttonPressed(self):
self.plotSignal.emit()
- def setTableRow(self, name, row):
+ def setTableRow(self, name, row):
text = QtGui.QTableWidgetItem(name)
text.setFlags(QtCore.Qt.ItemIsEnabled)
col = 0
@@ -93,18 +95,18 @@ Presenter
class Presenter(object):
# pass the view and model into the presenter
- def __init__(self, view):
+ def __init__(self, view):
self.view = view
- self.view.plotSignal.connect(self.updatePlot)
+ self.view.plotSignal.connect(self.updatePlot)
- # handle signals
- def updatePlot(self):
+ # handle signals
+ def updatePlot(self):
print("The table settings are:")
- print(" colour : " + str(self.view.getColour()))
- print(" Grid lines : " + str(self.view.getGridLines()))
- print(" Frequency : " + str(self.view.getFreq()))
- print(" Phase : " + str(self.view.getPhase()))
+ print(" colour : " + str(self.view.getColour()))
+ print(" Grid lines : " + str(self.view.getGridLines()))
+ print(" Frequency : " + str(self.view.getFreq()))
+ print(" Phase : " + str(self.view.getPhase()))
Main module
###########
@@ -136,12 +138,12 @@ Main module
self.setCentralWidget(my_view)
self.setWindowTitle("view tutorial")
- def qapp():
+ def qapp():
if QtGui.QApplication.instance():
_app = QtGui.QApplication.instance()
- else:
- _app = QtGui.QApplication(sys.argv)
- return _app
+ else:
+ _app = QtGui.QApplication(sys.argv)
+ return _app
app = qapp()
window = demo()
diff --git a/dev-docs/source/MVPTutorial/ReceivingSignalFromView.rst b/dev-docs/source/MVPTutorial/ReceivingSignalFromView.rst
index 5a6beb71c3f33e6b276219c6ac27c7f922488fa6..c4e701e28d6b40d6142bc423772805fc8f0cb2d3 100644
--- a/dev-docs/source/MVPTutorial/ReceivingSignalFromView.rst
+++ b/dev-docs/source/MVPTutorial/ReceivingSignalFromView.rst
@@ -1,8 +1,10 @@
+.. _ReceivingSignalFromView:
+
================================
Receiving a signal from the view
================================
-In the `Add Button <AddButton.html>`_ section we had the response to a button press
+In the :ref:`Add Button <AddButton>` section we had the response to a button press
within the View. In practice this is not a good implementation. If the
response was more complicated then it would be difficult to maintain
the View as it would become extremely long. Furthermore creating the
@@ -23,7 +25,7 @@ pressed. First we will start with the View:
doSomethingSignal = QtCore.pyqtSignal()
- def __init__(self, parent=None):
+ def __init__(self, parent=None):
super(view, self).__init__(parent)
self.button = QtGui.QPushButton('Hi', self)
@@ -44,10 +46,10 @@ pressed. First we will start with the View:
# set the layout for the view widget
self.setLayout(grid)
- #send signals
- def btn_click(self):
+ #send signals
+ def btn_click(self):
print ("hellow from view")
- self.doSomethingSignal.emit()
+ self.doSomethingSignal.emit()
The above code has two new additions. The first is the creation of a
custom signal on line eight. It is also possible to pass objects with
@@ -67,13 +69,13 @@ custom signal from the View to its own function (``handleButton``).
class Presenter(object):
# pass the view and model into the presenter
- def __init__(self, view):
+ def __init__(self, view):
self.view = view
- self.view.doSomethingSignal.connect(self.handleButton)
+ self.view.doSomethingSignal.connect(self.handleButton)
- # handle signals
- def handleButton(self):
+ # handle signals
+ def handleButton(self):
print("hello world, from the presenter")
The main is now:
@@ -105,12 +107,12 @@ The main is now:
self.setCentralWidget(my_view)
self.setWindowTitle("view tutorial")
- def qapp():
+ def qapp():
if QtGui.QApplication.instance():
_app = QtGui.QApplication.instance()
- else:
- _app = QtGui.QApplication(sys.argv)
- return _app
+ else:
+ _app = QtGui.QApplication(sys.argv)
+ return _app
app = qapp()
diff --git a/dev-docs/source/MVPTutorial/ViewExercise1.rst b/dev-docs/source/MVPTutorial/ViewExercise1.rst
index d2311e122f03b45fea871d6b5d3eeab735c6de31..4a26bc22c789e6d038a56b0f7f671d668c91d239 100644
--- a/dev-docs/source/MVPTutorial/ViewExercise1.rst
+++ b/dev-docs/source/MVPTutorial/ViewExercise1.rst
@@ -17,7 +17,7 @@ plot. The table should include options for:
The previous sections are not an exhaustive list of possible widgets.
-The pages `Matplotlib and MVP <Matplotlib.html>`_ and `MultipleView
-<MultipleViews.html>`_ will be useful for the exercise.
+The pages :ref:`Matplotlib and MVP <Matplotlib>` and :ref:`MultipleView
+<MultipleViews>` will be useful for the exercise.
-The solution can be found `here <ViewExercise1Solution.html>`_.
+The solution can be found :ref:`here <ViewExercise1Solution>`.
diff --git a/dev-docs/source/MVPTutorial/ViewExercise1Solution.rst b/dev-docs/source/MVPTutorial/ViewExercise1Solution.rst
index cc17fdfcdf3fe37e224e206f2951e23ae66a822a..c963551162ff1bec73d8bc9e78db38455d4f0c9a 100644
--- a/dev-docs/source/MVPTutorial/ViewExercise1Solution.rst
+++ b/dev-docs/source/MVPTutorial/ViewExercise1Solution.rst
@@ -1,3 +1,5 @@
+.. _ViewExercise1Solution:
+
========================
View Exercise 1 Solution
========================
@@ -30,12 +32,12 @@ main.py
self.setCentralWidget(my_view)
self.setWindowTitle("view tutorial")
- def qapp():
+ def qapp():
if QtGui.QApplication.instance():
_app = QtGui.QApplication.instance()
- else:
- _app = QtGui.QApplication(sys.argv)
- return _app
+ else:
+ _app = QtGui.QApplication(sys.argv)
+ return _app
app = qapp()
window = demo()
diff --git a/dev-docs/source/Standards/AlgorithmDocumentation.rst b/dev-docs/source/Standards/AlgorithmDocumentation.rst
index dc03d48a52c5f9caaebd04855dcdf63a71e309f0..e073f9d8f7297921face86d31e65ebebacb09dbe 100644
--- a/dev-docs/source/Standards/AlgorithmDocumentation.rst
+++ b/dev-docs/source/Standards/AlgorithmDocumentation.rst
@@ -10,7 +10,7 @@ Algorithm Documentation
Summary
=======
-This page deals with the specifics of how to document an algorithm. For a more general guide to the Mantid documentation system see `Documentation Guide For Devs <DocumentationGuideForDevs.html>`__.
+This page deals with the specifics of how to document an algorithm. For a more general guide to the Mantid documentation system see :ref:`Documentation Guide For Devs <DocumentationGuideForDevs>`.
How to Document an Algorithm
============================
@@ -18,7 +18,7 @@ How to Document an Algorithm
Algorithm documentation is stored in two places.
* The code (.cpp / .h / .py) files: For strings that are needed in the GUI for tooltips etc.
-* The .rst file: For all other documentation, including the algorithm description and `usage examples <AlgorithmUsageExamples.html>`__.
+* The .rst file: For all other documentation, including the algorithm description and :ref:`usage examples <AlgorithmUsageExamples>`.
The Code Files
--------------
@@ -69,7 +69,7 @@ For example:
Workflow algorithms
===================
-There should be a flow chart for workflow algorithms. See `here <FlowchartCreation.html>`__ on how to make one.
+There should be a flow chart for workflow algorithms. See :ref:`here <FlowchartCreation>` on how to make one.
Algorithm Directives
====================
@@ -84,7 +84,7 @@ As the **Description** and **Usage** of an algorithm *cannot* be obtained automa
.. summary::
- .. alias::
+ .. relatedalgorithms::
.. properties::
@@ -120,13 +120,16 @@ As the **Description** and **Usage** of an algorithm *cannot* be obtained automa
return "Rebins data with new X bin boundaries. For EventWorkspaces, you can very quickly rebin in-place by keeping the same output name and PreserveEvents=true.";
}
-``.. alias::``
- This directive obtains aliases from the required ``alias`` method in the algorithm, for example, the following method is used in Rebin:
+``.. relatedalgorithms::``
+ This directive obtains a list of related algorithm from the ``seeAlso`` method in the algorithm, for example, the following method is used in Rebin:
.. code-block:: c++
- /// Algorithm's aliases
- const std::string alias() const override { return "rebin"; }
+ /// Algorithm's seeAlso
+ const std::vector<std::string> seeAlso() const override {
+ return {"RebinToWorkspace", "Rebin2D", "Rebunch",
+ "Regroup", "RebinByPulseTimes", "RebinByTimeAtSample"};
+ }
``.. properties::``
As mentioned above, it is *critical* that you include a description for the properties of your algorithm. This directive obtains all of the algorithm's properties (set inside the algorithm's ``init`` method) and outputs in a table format.
@@ -147,7 +150,7 @@ It is possible to add additional categories by passing the directive arguments,
.. categories:: Algorithms, Transforms, Rebin, Example
-``..sourcelink ::``
+``.. sourcelink::``
This directive adds links to the algorithms source code.
Description
@@ -175,7 +178,7 @@ where the first part outside the angle brackets defines the link text and the pa
Usage
=====
-This section *must* be manually entered. The usage is a 'code' example of the algorithm in use. The `testcode` directive must be used to verify the usage code you entered works correctly. See `here <AlgorithmUsageExamples>`__ for more information on how to write usage examples.
+This section *must* be manually entered. The usage is a 'code' example of the algorithm in use. The ``.. testcode::`` directive must be used to verify the usage code you entered works correctly. See :ref:`here <AlgorithmUsageExamples>` for more information on how to write usage examples.
Building the Documentation
==========================
diff --git a/dev-docs/source/Standards/AlgorithmUsageExamples.rst b/dev-docs/source/Standards/AlgorithmUsageExamples.rst
index 3c8ee85ebc3789e7b1a5f89e2d8815f158a3a4d0..f0cdc11c59ee57fe55b07abe133f8515691958c2 100644
--- a/dev-docs/source/Standards/AlgorithmUsageExamples.rst
+++ b/dev-docs/source/Standards/AlgorithmUsageExamples.rst
@@ -18,7 +18,7 @@ From a user's point of view, the main purposes of usage examples are:
* Understanding the algorithm
* Showing hints/comments etc. that help understand Mantid Python scripting in general
-The usage examples are written in `reStructuredText <http://docutils.sourceforge.net/rst.html>`__, which can be converted to HTML and the code in the usage examples can be tested. The image below demonstrates an example of converting reStructuredText to HTML.
+The usage examples are written in `reStructuredText <http://docutils.sourceforge.net/rst.html>`__, which can be converted to HTML and the code in the usage examples can be tested.
Guide
=====
@@ -75,7 +75,7 @@ What is worth keeping in mind is:
* Use comments.
* Use Python ``print`` to output results, which, where possible, helps to understand the algorithm.
-A Jenkins job tests that the usage examples are not broken, i.e. that they continue to provide a working demonstration against the current build. It is vital to stress that the purpose of usage testing is *not to replace unit testing* (or system testing). The purpose of usage testing (better described as demonstration examples), is to provide some happy-path examples, which, where this is possible, can assist the user understanding of the Python code. This is very different from the purposes of testing in general, see `here <UnitTestGoodPractice.html>`__.
+A Jenkins job tests that the usage examples are not broken, i.e. that they continue to provide a working demonstration against the current build. It is vital to stress that the purpose of usage testing is *not to replace unit testing* (or system testing). The purpose of usage testing (better described as demonstration examples), is to provide some happy-path examples, which, where this is possible, can assist the user understanding of the Python code. This is very different from the purposes of testing in general, see :ref:`here <UnitTestGoodPractice>`.
Additional benefits of usage examples:
@@ -181,7 +181,7 @@ For a more simple use of CreateSampleWorkspace see example below (note if no arg
When needing to load a data file
--------------------------------
-Instructions to add a new data file to the repository are available `here <DataFilesForTesting.html>`__. Files from the repository will be bundled up into a .zip file, and this .zip made available for download from the Mantid download page.
+Instructions to add a new data file to the repository are available :ref:`here <DataFilesForTesting>`. Files from the repository will be bundled up into a .zip file, and this .zip made available for download from the Mantid download page.
If you use files you must add the line
@@ -221,4 +221,4 @@ as shown in the example below. This will generate a note to the user explaining
Running the Tests
=================
-See `here <DocumentationGuideForDevs.html>`__ for how to run and test the usage examples locally.
+See :ref:`here <DocumentationGuideForDevs>` for how to run and test the usage examples locally.
diff --git a/dev-docs/source/Standards/DocumentationGuideForDevs.rst b/dev-docs/source/Standards/DocumentationGuideForDevs.rst
index 81dd7ba2e2264540719ab7110866631a9a65269d..e58444b22679d6159e8ef9bd0942ea0d0d82e361 100644
--- a/dev-docs/source/Standards/DocumentationGuideForDevs.rst
+++ b/dev-docs/source/Standards/DocumentationGuideForDevs.rst
@@ -96,12 +96,12 @@ If you wish to place comments in the reST file that will not be rendered anywher
Algorithms
----------
-The algorithm documentation has a slightly more rigid structure and is described in more detail `here <AlgorithmDocumentation.html>`__ and `here <AlgorithmUsageExamples.html>`__.
+The algorithm documentation has a slightly more rigid structure and is described in more detail :ref:`here <AlgorithmDocumentation>` and :ref:`here <AlgorithmUsageExamples>`.
Interfaces
----------
-For documenting custom interfaces, it is recommended that you consult `this <InterfaceDocumentation.html>`__ page, which explains how to document them, and which directives may be used in more detail.
+For documenting custom interfaces, it is recommended that you consult :ref:`this <InterfaceDocumentation>` page, which explains how to document them, and which directives may be used in more detail.
How to define titles, sections etc.
-----------------------------------
@@ -251,6 +251,6 @@ For multi-configuration generators such as Visual Studio or XCode you will need
Building the HTML Development Documentation
===========================================
-The developer documentation is written as `.rst` files in the mantid source folder under ``dev-docs/``, the html files can be built using the `dev-docs-html` target. This will build all the development documentation into the mantid build folder under ``dev-docs/html/``.
+The developer documentation is written as ``.rst`` files in the mantid source folder under ``dev-docs/``, the html files can be built using the `dev-docs-html` target. This will build all the development documentation into the mantid build folder under ``dev-docs/html/``.
-In Visual Studio, this can be found in the "Documentation" folder in the solution explorer for the Mantid solution. Simply right click `dev-docs-html` and select build.
\ No newline at end of file
+In Visual Studio, this can be found in the "Documentation" folder in the solution explorer for the Mantid solution. Simply right click `dev-docs-html` and select build.
diff --git a/dev-docs/source/Standards/InterfaceDocumentation.rst b/dev-docs/source/Standards/InterfaceDocumentation.rst
index 1e49cbb60f01c4148f95f1665f3a1f07918d55f5..eb60abd91477df67125490b83317a9806bccf1f7 100644
--- a/dev-docs/source/Standards/InterfaceDocumentation.rst
+++ b/dev-docs/source/Standards/InterfaceDocumentation.rst
@@ -10,7 +10,7 @@ Interface Documentation
Summary
=======
-This page deals with the specifics of how to document Custom Interfaces. For a more general guide to the Mantid documentation system see `Documentation Guide For Devs <DocumentationGuideForDevs.html>`__.
+This page deals with the specifics of how to document Custom Interfaces. For a more general guide to the Mantid documentation system see :ref:`Documentation Guide For Devs <DocumentationGuideForDevs>`.
The ``interface`` Directive
===========================
diff --git a/dev-docs/source/Testing/ErrorReporter-ProjectRecovery/ProjectRecoveryTesting.rst b/dev-docs/source/Testing/ErrorReporter-ProjectRecovery/ProjectRecoveryTesting.rst
index eeb5f696d01fa76dce22efa94984ec3a597e2cc0..9cd4b57b307f987a28c31c9cbd7be858bd3fcd18 100644
--- a/dev-docs/source/Testing/ErrorReporter-ProjectRecovery/ProjectRecoveryTesting.rst
+++ b/dev-docs/source/Testing/ErrorReporter-ProjectRecovery/ProjectRecoveryTesting.rst
@@ -12,7 +12,7 @@ Project Recovery test
*Preparation*
- Before running these tests, set project recovery to run every 2 seconds. The instructions for this
- are on the `Project Recovery concepts page <http://docs.mantidproject.org/nightly/concepts/ProjectRecovery.html>`_.
+ are on the `Project Recovery concepts page <http://docs.mantidproject.org/nightly/concepts/ProjectRecovery.html>`__.
- Get the ISIS sample dataset from the `Downloads page <http://download.mantidproject.org/>`_.
- `TOPAZ_3132_event.nxs` - availabe in ``/Testing/Data/SystemTest/``, get this by building the `SystemTestData` target. It should be in ``ExternalData/Testing/Data/SystemTest/``
- The files `INTER000*` are in the ISIS sample data