re #9923 updated links and qc, still needs links from algs

Code/Mantid/docs/source/concepts/Algorithm.rst

@@ -8,10 +8,10 @@ What are they?
 
 Algorithms are the verbs of Mantid. They are the actors. If you want to
 manipulate your data in any way it will be done through an algorithm.
-Algorithms operate primarily on data in `workspaces <Workspace>`__. They
-will normally take one or more `workspaces <Workspace>`__ as an input,
+Algorithms operate primarily on data in :ref:`workspaces <Workspace>`. They
+will normally take one or more :ref:`workspaces <Workspace>` as an input,
 perform some processing on them and provide an output as another
-`workspace <Workspace>`__ (although it is possible to have multiple
+:ref:`workspace <Workspace>` (although it is possible to have multiple
 outputs).
 
 Categories, Name and Versions
@@ -27,8 +27,7 @@ A category is a group of algorithms that have some connection in their
 usage. This is primarily used to make the list of algorithms easier to
 work with in graphical user interfaces. Example categories include,
 DataHandling, Diffraction, Muon, Workflow and are currently
-subcategories of
-`Algorithms <http://docs.mantidproject.org/algorithms>`__ category.
+subcategories of Algorithms category.
 
 Name
 ~~~~
@@ -52,7 +51,7 @@ Parameters
 ----------
 
 Each algorithm will have one or more parameters, known within Mantid as
-`properties <properties>`__, that will control how it performs its
+:ref:`properties <properties>`, that will control how it performs its
 processing. These parameters specify both what the inputs and outputs of
 the algorithm will be as well any other options that alter the
 processing.
@@ -66,10 +65,6 @@ Usage
 From MantidScript(Python)
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. raw:: html
-
-   <div style="border:1pt dashed blue; background:#f9f9f9;padding: 1em 0;">
-
 .. code:: python
 
      # where p1,p2 & p3 are values for algorithm "Alg"'s properties
@@ -89,20 +84,13 @@ From MantidScript(Python)
      print alg["Property2"]
      # prints 'p2', etc
 
-.. raw:: html
-
-   </div>
 
 Using the C++ API
 ^^^^^^^^^^^^^^^^^
 
 (for algorithm "Alg" having properties InputWorkspace, OutputWorkspace &
 prop)
 
-.. raw:: html
-
-   <div style="border:1pt dashed blue; background:#f9f9f9;padding: 1em 0;">
-
 .. code:: cpp
 
      // Explicitly setting the parameters and then executing
@@ -117,35 +105,29 @@ prop)
      API::FrameworkManager::Instance().exec("Alg","InWS,OutWS,aValue");
      API::Workspace* ws = API::FrameworkManager::Instance().getWorkspace("OutWS");
 
-.. raw:: html
-
-   </div>
 
 Example Algorithms
 ------------------
 
--  `Plus <http://docs.mantidproject.org/nightly/algorithms/Plus.html>`__
-   - An algorithm for adding data in two `workspaces <Workspace>`__
+-  :ref:`Plus <algm-Plus>`
+   - An algorithm for adding data in two :ref:`workspaces <Workspace>`
    together
--  `Rebin <http://docs.mantidproject.org/nightly/algorithms/Rebin.html>`__
+-  :ref:`Rebin <algm-Rebin>`
    - An algorithm for altering the binning of the data in a
-   `workspace <Workspace>`__.
--  `LoadRaw <http://docs.mantidproject.org/nightly/algorithms/LoadRaw.html>`__
+   :ref:`workspace <Workspace>`.
+-  :ref:`LoadRaw <algm-LoadRaw>`
    - An algorithm for loading the data from a RAW file into a
-   `workspace <Workspace>`__.
--  `GroupDetectors <http://docs.mantidproject.org/nightly/algorithms/GroupDetectors.html>`__
+   :ref:`workspace <Workspace>`.
+-  :ref:`GroupDetectors <algm-GroupDetectors>`
    - An algorithm for grouping two or more detectors into a larger
    'logical' detector.
 
-A full list of algorithms is avilable
-`here <http://docs.mantidproject.org/nightly/algorithms/index.html>`__
-category
 
 Writing your own algorithm
 --------------------------
 
-A primer for this is `here <Writing an Algorithm>`__. Also look at the
-examples in the `UserAlgorithms <UserAlgorithms>`__ directory of your
+A primer for this is `here <http://www.mantidproject.org/Writing_an_Algorithm>`__. Also look at the
+examples in the :ref:`UserAlgorithms <UserAlgorithms>` directory of your
 Mantid installation.
 
 

Code/Mantid/docs/source/concepts/Analysis_Data_Service.rst

@@ -1,33 +1,33 @@
 .. _Analysis Data Service:
 
-Analysis_Data_Service
+Analysis Data Service
 =====================
 
 What is it?
 -----------
 
-The Analysis Data Service is a `Data Service <Data Service>`__ that is
-specialized to hold all of the `workspaces <Workspace>`__ that are
-created by user run `algorithms <Algorithm>`__. Whenever an algorithm is
+The Analysis Data Service is a :ref:`Data Service <Data Service>` that is
+specialized to hold all of the :ref:`workspaces <Workspace>` that are
+created by user run :ref:`algorithms <Algorithm>`. Whenever an algorithm is
 executed it automatically extracts its input workspaces from the
 Analysis Data Service, and inserts its output workspaces upon
 completion.
 
 Extracting a workspace from the Analysis Data Service
 -----------------------------------------------------
 
-The most usual way in user code would be to use the `Framework
-Manager <Framework Manager>`__.
+The most usual way in user code would be to use the :ref:`Framework
+Manager <Framework Manager>`.
 
 ``Workspace* result = FrameworkManager::Instance().getWorkspace("workspaceName")``
 
-Or you could get it directly from the AnalysisDataService (as a `Shared
-Pointer <Shared Pointer>`__)
+Or you could get it directly from the AnalysisDataService (as a :ref:`Shared
+Pointer <Shared Pointer>`)
 
 ``Workspace_sptr result = AnalysisDataService::Instance().retrieve("test_out1");``
 
 If you were writing an algorithm however you would most likely use a
-Workspace `Property <Properties>`__ to access or store your workspaces.
+Workspace :ref:`Property <Properties>` to access or store your workspaces.
 
 
 

Code/Mantid/docs/source/concepts/Create_an_IDF.rst

@@ -0,0 +1,48 @@
+.. _Create_an_IDF:
+
+Create an IDF
+=============
+
+This page will help you get started with making an instrument definition file. For documentation on individual elements of an IDF refer to the :ref:`IDF documentation <InstrumentDefinitionFile>`
+
+Basic Steps
+-----------
+
+The best way to get started is to:
+
+- `Set up an editor for XML that uses schema validation <http://www.mantidproject.org/Using_XML_Schema>`__
+- Read the :ref:`introduction to IDFs <InstrumentDefinitionFile>`
+- Read the annotated existing IDFs
+- Look for similar existing IDFs
+- Use the IDF page for more detailed documentation
+
+Using the Schema
+----------------
+
+To set up your editor with the schema, `Follow These Instructions <http://www.mantidproject.org/Using_XML_Schema>`__.
+The Schema can help with writing the IDF. For example:
+
+- In Visual Studio the schema can be used to auto-insert elements and attributes permitted by the schema.
+- In eclipse the IDF can be created in a design view by selected available elements and attributes without having to type the code yourself.
+The IDF schema (IDFSchema.xsd) is located in your mantid install directory at MantidInstall\instrument\Schema. Note this folder also includes the schema, ParameterFileSchema.xsd, which may be used to assist in writting a :ref:`parameter file <InstrumentParameterFile>`
+
+
+Find a Similar existing IDF
+---------------------------
+
+It may be that an instrument already exists that is similar to the one you wish to add. To see the existing instruments follow the procedure below.
+
+- Install Mantid
+- Open MantidPlot
+- Execute the algorithm LoadEmptyInstrument
+- This open the algorithm window for this algorithm. Click the Browse button and browse to the instrument folder of your Mantid install directory
+- The instrument folder contains all the instruments that Mantid currently support. Select for example SANS2D_Definition.xml. Fill in the output workspace name, and and click 'Run'
+- The created workspace will appear in the Workspaces window. Right click on the workspace and chose 'Show Instrument'
+- A new window appears, which is called the `Instrument view <http://www.mantidproject.org/MantidPlot:_Instrument_View>`__.
+
+In addition below is a list (for now just containing one item) of existing IDFs which have been annotated with the purpose of (hopefully) quickly learn the basis of creating an IDF:
+
+- :ref:`SANS2D: ISIS small angle scattering instrument <SANS2D_Sample_IDF>`
+- :ref:`LET: ISIS direct inelastic instrument<LET_Sample_IDF>`
+
+.. categories:: Concepts

Code/Mantid/docs/source/concepts/Data_Service.rst

@@ -1,6 +1,6 @@
 .. _Data Service:
 
-Data_Service
+Data Service
 ============
 
 What are they?
@@ -17,10 +17,10 @@ deleting it.
 Data Services in Mantid
 -----------------------
 
--  `Analysis Data Service <Analysis Data Service>`__ - A data service
-   holding all of the `workspaces <Workspace>`__ used in this session.
--  `Instrument Data Service <Instrument Data Service>`__ - A data
-   service holding all of the `instruments <Instrument>`__ used in this
+-  :ref:`Analysis Data Service <Analysis Data Service>` - A data service
+   holding all of the :ref:`workspaces <Workspace>` used in this session.
+-  :ref:`Instrument Data Service <Instrument Data Service>` - A data
+   service holding all of the :ref:`instruments <Instrument>` used in this
    session.
 
 

Code/Mantid/docs/source/concepts/Dynamic_Factory.rst

@@ -1,17 +1,17 @@
 .. _Dynamic Factory:
 
-Dynamic_Factory
+Dynamic Factory
 ===============
 
 What is it?
 -----------
 
 A dynamic factory is a software concept that in instrumental in
-implementing the `Plugin <Plugin>`__ technology in Mantid.
+implementing the :ref:`Plugin <Plugin>` technology in Mantid.
 
 A factory in software terms is an class that is responsible for creating
 other objects on demand. In mantid terms the AlgorithmFactory is
-responsible for creating instances of `Algorithms <Algorithm>`__ when
+responsible for creating instances of :ref:`Algorithms <Algorithm>` when
 you need them.
 
 As the factory is dynamic it does not have a set list of objects that it

Code/Mantid/docs/source/concepts/Error_Propagation.rst

@@ -1,6 +1,6 @@
 .. _Error Propagation:
 
-Error_Propagation
+Error Propagation
 =================
 
 The purpose of this document is to explain how Mantid deals with Error

Code/Mantid/docs/source/concepts/EventWorkspace.rst

@@ -6,29 +6,29 @@ EventWorkspace
 Quick Summary For Users
 -----------------------
 
-The EventWorkspace is a type of `MatrixWorkspace <MatrixWorkspace>`__,
+The EventWorkspace is a type of :ref:`MatrixWorkspace <MatrixWorkspace>`,
 where the information about each individual neutron detection event is
 maintained. For you as a user, this means that:
 
--  You can `rebin <rebin>`__ an EventWorkspace over and over and no
+-  You can :ref:`rebin <algm-rebin>` an EventWorkspace over and over and no
    information is ever lost.
 -  The histogram (Y and E values) of an EventWorkspace are only
    calculated when they are requested.
 
    -  You typically get better performance, even for very fine binning.
 
--  You can convert an EventWorkspace to a `Workspace2D <Workspace2D>`__
-   by using the `Rebin <Rebin>`__ algorithm and changing the output
+-  You can convert an EventWorkspace to a :ref:`Workspace2D <Workspace2D>`
+   by using the :ref:`Rebin <algm-Rebin>` algorithm and changing the output
    workspace name.
 -  You cannot modify the histogram Y values (for example, with the
    Divide algorithm) and keep the event data. If you use an algorithm
    that modifies the Y values, the output workspace will be a
-   `Workspace2D <Workspace2D>`__ using the current binning parameters.
+   :ref:`Workspace2D <Workspace2D>` using the current binning parameters.
    If you set the same name on the output as the input of your
    algorithm, then you will overwrite the EventWorkspace and lose that
    event-based information.
 -  Some algorithms are EventWorkspace-aware, meaning that the output of
-   it can be another EventWorkspace. For example, the `Plus <Plus>`__
+   it can be another EventWorkspace. For example, the :ref:`Plus <algm-Plus>`
    algorithm will append the event lists if given two input
    EventWorkspaces.
 -  Since it retains the most information, it is advantageous to keep
@@ -61,7 +61,7 @@ Lists of Events (EventList)
    time of flight or pulse time, as needed.
 
 -  Also contained in the EventList is a std::set of detector ID's. This
-   tracks which `detector <detector>`__\ (s) were hit by the events in
+   tracks which detector(s) were hit by the events in
    the list.
 
 -  The histogram bins (X axis) are also stored in EventList. The Y and E
@@ -70,7 +70,7 @@ Lists of Events (EventList)
 
 The += operator can be used to append two EventList's together. The
 lists of TofEvent's get appended, as is the list of
-`detector <detector>`__ ID's. Don't mess with the udetmap manually if
+detector ID's. Don't mess with the udetmap manually if
 you start appending event lists - just call
 EventWorkpspace->makeSpectraMap to generate the spectra map (map between
 spectrum # and detector IDs) by using the info in each EventList.
@@ -79,7 +79,7 @@ Most Recently Used List (MRUList)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 An EventWorkspace contains a list of the 100 most-recently used
-histograms, a `MRUList <MRUList>`__. This MRU caches the last histogram
+histograms, a MRUList. This MRU caches the last histogram
 data generated for fastest display.
 
 A note about workspace index / spectrum number / detector ID
@@ -95,9 +95,9 @@ Workspace2D compatibility
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 
 EventWorkspace is designed to be able to be read (but not written to)
-like a `Workspace2D <Workspace2D>`__. By default, if an algorithm
+like a :ref:`Workspace2D <Workspace2D>`. By default, if an algorithm
 performs an operation and outputs a new workspace, the
-`WorkspaceFactory <WorkspaceFactory>`__ will create a Workspace2D *copy*
+WorkspaceFactory will create a Workspace2D *copy*
 of your EventWorkspace's histogram representation. If you attempt to
 change an EventWorkspace's Y or E data in place, you will get an error
 message, since that is not possible.

Code/Mantid/docs/source/concepts/Facilities_File.rst

@@ -1,14 +1,14 @@
 .. _Facilities File:
 
-Facilities_File
+Facilities File
 ===============
 
 Summary
 -------
 
 The facilities file, called **facilities.xml**, contains properties of
 facilities and instruments that Mantid is aware of. In order for Mantid
-to function correctly for your facility then the facilites file should
+to function correctly for your facility then the facilities file should
 contain the appropriate definitions as defined below.
 
 File syntax
@@ -17,10 +17,6 @@ File syntax
 Each facility is described using XML with an instrument defined as a sub
 component of a facility. A simple facility definition would be
 
-.. raw:: html
-
-   <div style="border:1pt dashed blue; background:#f9f9f9;padding: 1em 0;">
-
 .. code:: XML
 
     <?xml version="1.0" encoding="UTF-8"?>
@@ -34,10 +30,6 @@ component of a facility. A simple facility definition would be
 
     </facilities>
 
-.. raw:: html
-
-   </div>
-
 which would define a facility called *BrandNew* with an instrument
 called *ABCDEF*. The facilities attributes have the following meanings:
 
@@ -51,10 +43,6 @@ called *ABCDEF*. The facilities attributes have the following meanings:
 An instrument can have further attributes which define properties of the
 that instrument rather than the facility as a whole, e.g.
 
-.. raw:: html
-
-   <div style="border:1pt dashed blue; background:#f9f9f9;padding: 1em 0;">
-
 .. code:: XML
 
     <?xml version="1.0" encoding="UTF-8"?>
@@ -73,10 +61,6 @@ that instrument rather than the facility as a whole, e.g.
 
     </facilities>
 
-.. raw:: html
-
-   </div>
-
 where the attributes are defined as:
 
 -  ``shortName`` gives a shortened version of the instrument name
@@ -99,7 +83,7 @@ Location
 
 The file should be located in the directory pointed to by the
 **instrumentDefinition.directory** key in the
-`.properties <Properties_File>`__ file.
+:ref:`.properties <Properties File>` file.