fix to rtd

Signed-off-by: Alex McCaskey <mccaskeyaj@ornl.gov>

docs/doxygen/Doxyfile.cmake

@@ -315,7 +315,7 @@ EXTENSION_MAPPING      =
 # case of backward compatibilities issues.
 # The default value is: YES.
 
-MARKDOWN_SUPPORT       = YES
+MARKDOWN_SUPPORT       = NO
 
 # When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up
 # to that level are automatically included in the table of contents, even if
@@ -889,7 +889,7 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = ../../quantum/plugins/ibm/accelerator/qiskit-terra/
+#EXCLUDE                = ../../quantum/plugins/ibm/accelerator/qiskit-terra/ ../../xacc/optimizers/nlopt-optimizer/nlopt/ ../../tpls/ ../../quantum/plugins/dwave/embedding/minorminer/
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
@@ -906,6 +906,10 @@ EXCLUDE_SYMLINKS       = NO
 # exclude all test directories for example use the pattern */test/*
 
 EXCLUDE_PATTERNS       = */tests/*
+EXCLUDE_PATTERNS      += */qiskit-terra/*
+EXCLUDE_PATTERNS      += */nlopt/*
+EXCLUDE_PATTERNS      += */tpls/*
+EXCLUDE_PATTERNS      += */minorminer/*
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
@@ -1964,7 +1968,7 @@ MAN_LINKS              = NO
 # captures the structure of the code including all documentation.
 # The default value is: NO.
 
-GENERATE_XML           = YES
+GENERATE_XML           = NO
 
 # The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of

docs/source/basics.rst

@@ -5,20 +5,20 @@ Here we demonstrate leveraging the XACC framework for various
 quantum-classical programming tasks. We provide examples in both
 C++ and Python.
 
-`AcceleratorBuffer` Usage
+``AcceleratorBuffer`` Usage
 -------------------------
-The `AcceleratorBuffer` represents a register of qubits. Programmers allocate
+The ``AcceleratorBuffer`` represents a register of qubits. Programmers allocate
 this register of a certain size, and pass it by reference to all execution tasks.
 These execution tasks are carried out by concrete instances of the `Accelerator`
 interface, and these instances are responsible for persisting information to the
 provided buffer reference. This ensures programmers have access to all execution results
 and metadata upon execution completion.
 
-Programmers can allocate a buffer through the `xacc::qalloc(const int n)` (`xacc.qalloc(int)` in Python) call.
+Programmers can allocate a buffer through the ``xacc::qalloc(const int n)`` (``xacc.qalloc(int)`` in Python) call.
 After execution, measurement results can be queried as well as backend-specific
-execution metadata. Below demonstrate some basic usage of the `AcceleratorBuffer`
+execution metadata. Below demonstrate some basic usage of the ``AcceleratorBuffer``
 
-.. code::
+.. code:: cpp
 
    #include "xacc.hpp"
    ...
@@ -33,7 +33,7 @@ execution metadata. Below demonstrate some basic usage of the `AcceleratorBuffer
 
 in Python
 
-.. code::
+.. code:: python
 
    import xacc
    ...
@@ -54,7 +54,7 @@ is represented in XACC as a `CompositeInstruction`. The creation of `Instruction
 implementation of the `IRProvider`, specifically a 3 instruction circuit with one
 parameterized `Ry` on a variable `theta`.
 
-.. code::
+.. code:: cpp
 
    #include "xacc.hpp"
    ...
@@ -67,7 +67,7 @@ parameterized `Ry` on a variable `theta`.
 
 in Python
 
-.. code::
+.. code::python
 
    import xacc
    ...
@@ -84,7 +84,7 @@ a `Compiler` implementation for the language being used. `Compilers` take kernel
 source strings and produce IR (one or many `CompositeInstruction`s). Here we demonstrate
 the same circuit as above, but using a Quil kernel
 
-.. code::
+.. code:: cpp
 
    #include "xacc.hpp"
    ...
@@ -109,7 +109,7 @@ the same circuit as above, but using a Quil kernel
 
 in Python
 
-.. code::
+.. code:: python
 
    import xacc
    ...
@@ -138,7 +138,7 @@ backend execution.
 Next we demonstrate how one might leverate `IRTransformation` to perform general optimizations
 on IR instances.
 
-.. code::
+.. code:: cpp
 
    #include "xacc.hpp"
    ...
@@ -161,7 +161,7 @@ on IR instances.
 
 in Python
 
-.. code::
+.. code:: python
 
    import xacc
    ...
@@ -193,7 +193,7 @@ The `Observable` concept in XACC dictates measurements to be performed
 on unmeasured an `CompositeInstruction`. XACC provides `pauli` and `fermion`
 `Observable` implementations. Below we demonstrate how one might create these objects.
 
-.. code::
+.. code:: cpp
 
    #include "xacc.hpp"
    #include "xacc_observable.hpp"
@@ -212,7 +212,7 @@ on unmeasured an `CompositeInstruction`. XACC provides `pauli` and `fermion`
 
 in Python
 
-.. code::
+.. code:: python
 
    import xacc
    ...
@@ -235,7 +235,7 @@ Here we demonstrate getting reference to an `Accelerator` and using it to execut
 Note this is a full example, that leverages the `xasm` compiler as well as requisite C++ framework
 initialization and finalization.
 
-.. code::
+.. code:: cpp
 
    #include "xacc.hpp"
    int main(int argc, char **argv) {
@@ -267,7 +267,7 @@ initialization and finalization.
 
 in Python
 
-.. code::
+.. code:: python
 
    import xacc
 
@@ -295,7 +295,7 @@ a thin wrapper for functor-like objects exposing a specific argument structure (
 arg a `vector<double>` representing current iterate's parameters, and another one representing the mutable
 gradient vector). Below is a demonstration of how one might use this utility:
 
-.. code::
+.. code:: cpp
 
    auto optimizer =
       xacc::getOptimizer("nlopt");
@@ -319,7 +319,7 @@ gradient vector). Below is a demonstration of how one might use this utility:
 
 or in Python
 
-.. code::
+.. code:: python
 
    def rosen_with_grad(x):
        g = [-2*(1-x[0]) + 400.*(x[0]**3 - x[1]*x[0]), 200 * (x[1] - x[0]**2)]
@@ -346,7 +346,7 @@ internal compilation database (standard map of CompositeInstruction names to Com
 can get reference to the individual CompositeInstructions via an exposed `getCompiled()` XACC API call. The
 code below demonstrates how one would use `qasm()` and its overall utility.
 
-.. code::
+.. code:: cpp
 
    #include "xacc.hpp"
    ...
@@ -385,7 +385,7 @@ code below demonstrates how one would use `qasm()` and its overall utility.
 
 or in Python
 
-.. code::
+.. code:: python
 
    import xacc
    ...

docs/source/install.rst

@@ -14,7 +14,7 @@ install BLAS and LAPACK as well, which is required to build some optional simula
 We install libunwind-dev which is also optional, but provides verbose stack-trace printing
 upon execution error.
 
-.. code::
+.. code:: bash
 
    $ sudo apt-get update && sudo apt-get install -y software-properties-common
    $ sudo add-apt-repository ppa:ubuntu-toolchain-r/test && sudo apt-get update
@@ -30,7 +30,7 @@ install BLAS and LAPACK as well, which is required to build some optional simula
 We install libunwind-dev which is also optional, but provides verbose stack-trace printing
 upon execution error.
 
-.. code::
+.. code:: bash
 
    $ sudo apt-get update
    $ sudo apt-get -y install gcc g++ git libcurl4-openssl-dev python3 libunwind-dev \
@@ -41,7 +41,7 @@ Centos 7 Prerequisites
 Here we will demonstrate installing from a bare Centos 7 install using GCC 8. We
 install BLAS and LAPACK as well, which is required to build some optional simulators.
 
-.. code::
+.. code:: bash
 
    $ sudo yum install libcurl-devel python3-devel git centos-release-scl make \
           devtoolset-8-gcc devtoolset-8-gcc-c++ blas-devel lapack-devel
@@ -52,7 +52,7 @@ Fedora 30 Prerequisites
 Here we will demonstrate installing from a bare Fedora 30 install using GCC 9. We
 install BLAS and LAPACK as well, which is required to build some optional simulators.
 
-.. code::
+.. code:: bash
 
    $ sudo dnf install python3-devel libcurl-devel git g++ gcc make blas-devel lapack-devel
    $ sudo python3 -m pip install cmake
@@ -64,7 +64,7 @@ standard includes like `wchar.h` and others. See `here <https://stackoverflow.co
 for proper XCode install and configuring to address these types of issues. Here we assume you
 have Homebrew installed.
 
-.. code::
+.. code:: bash
 
    $ brew install python3 openssl curl
 
@@ -72,13 +72,13 @@ Build XACC
 ----------
 The best way to install a recent version of CMake is through Python Pip.
 
-.. code::
+.. code:: bash
 
    $ sudo python3 -m pip install cmake
 
 Now clone and build XACC
 
-.. code::
+.. code:: bash
 
    $ git clone https://github.com/eclipse/xacc
    $ cd xacc && mkdir build && cd build
@@ -92,7 +92,7 @@ Now clone and build XACC
 
 You can run Python examples as well
 
-.. code::
+.. code:: bash
 
    [ you may also want to add this to your .bashrc ]
    $ export PYTHONPATH:$PYTHONPATH:$HOME/.xacc
@@ -100,7 +100,7 @@ You can run Python examples as well
 
 Most users build and install the TNQVM Accelerator
 
-.. code::
+.. code:: bash
 
    $ git clone https://github.com/ornl-qci/tnqvm
    $ cd tnqvm && mkdir build && cd build