Replace Sphinx-specific directives with standard RST links for GitHub

Sphinx :doc:, :ref:, and :code: directives don't render on GitHub's
RST viewer. Convert all 56 instances across 12 doc files to standard
RST hyperlinks (e.g. `Page <Page.rst>`_) and double-backtick inline
code so links work when viewing .rst files directly on GitHub.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: Stephanie Wehner

docs/ConfNodes.rst

@@ -5,7 +5,7 @@ SimulaQron uses two configuration files:
 
 * ``simulaqron_network.json`` — defines nodes, their socket ports, and network topology (described on this page)
 * ``simulaqron_settings.json`` — configures the simulation backend, timeouts, and other settings
-  (see :ref:`settings` in :doc:`GettingStarted`)
+  (see the Settings section in `Getting Started <GettingStarted.rst>`_)
 
 -------------------------------------------
 Running all nodes on a single machine
@@ -221,7 +221,7 @@ SimulaQron can automatically generate certain well-known network topologies:
   :math:`n(n-1)/2` for :math:`n` nodes.
 
 .. note:: Topology generation via the CLI is planned but not yet implemented. For now, specify topologies
-    directly in the ``simulaqron_network.json`` file (see :ref:`network-topologies`).
+    directly in the ``simulaqron_network.json`` file (see `Network topologies`_ below).
 
 Along with setting up the network with the specified topology a .png figure is also generated and stored as
 config/topology.png. This is useful if a random network is used, to easily visualize the network used.
@@ -233,7 +233,7 @@ The network that is then started might look like this:
     :align: center
     :alt: Example network topology
 
-To create a custom topology, see section :ref:`network-topologies`.
+To create a custom topology, see section `Network topologies`_ above.
 
 --------------------------
 Starting multiple networks
@@ -251,5 +251,5 @@ To stop a specific network::
 .. note:: By default the network name is "default". To have multiple networks running at the same time the
     nodes cannot use the same port numbers.
 
-The JSON configuration file can hold more than one network configuration. See :ref:`networkConfig` above for
+The JSON configuration file can hold more than one network configuration. See `Configuring the network`_ above for
 an example with multiple networks.

docs/Examples.rst

@@ -17,38 +17,38 @@ SimulaQron offers three ways to write quantum network programs, from highest-lev
    directly to SimulaQron's virtual quantum nodes.  This is Python-specific and more verbose,
    but gives full control over the simulation backend.
 
-The examples below assume that you have already made your way through :doc:`GettingStarted`:
+The examples below assume that you have already made your way through `Getting Started <GettingStarted.rst>`_:
 you have the virtual node servers up and running.
 
 -----------------
 New SDK examples
 -----------------
 
-* :doc:`new-sdk/Overview` — Key concepts: ``NetQASMConnection``, ``EPRSocket``, ``flush()``, file structure
-* :doc:`new-sdk/Template` — Getting started: single-node and client-server templates
-* :doc:`new-sdk/CorrRNG` — EPR pairs between two nodes, correlated measurement
-* :doc:`new-sdk/Teleport` — Quantum teleportation with classical correction messages
-* :doc:`new-sdk/ExtendGHZ` — Three-party entanglement, multiple EPR sockets
-* :doc:`new-sdk/MidCircuitLogic` — Multiple ``flush()`` calls for mid-circuit classical decisions
+* `Overview <new-sdk/Overview.rst>`_ — Key concepts: ``NetQASMConnection``, ``EPRSocket``, ``flush()``, file structure
+* `Template <new-sdk/Template.rst>`_ — Getting started: single-node and client-server templates
+* `CorrRNG <new-sdk/CorrRNG.rst>`_ — EPR pairs between two nodes, correlated measurement
+* `Teleport <new-sdk/Teleport.rst>`_ — Quantum teleportation with classical correction messages
+* `ExtendGHZ <new-sdk/ExtendGHZ.rst>`_ — Three-party entanglement, multiple EPR sockets
+* `MidCircuitLogic <new-sdk/MidCircuitLogic.rst>`_ — Multiple ``flush()`` calls for mid-circuit classical decisions
 
 ---------------------
 Event-based examples
 ---------------------
 
-* :doc:`event-based/Overview` — Event-based programming model and state machines
-* :doc:`event-based/PingPong` — Classical ping-pong between two nodes
-* :doc:`event-based/PolitePingPong` — State-machine message dispatch pattern
-* :doc:`event-based/QuantumCorrRNG` — Quantum correlated RNG with state machine
-* :doc:`event-based/QuantumCorrRNGVerified` — Correlated RNG with verification protocol
+* `Overview <event-based/Overview.rst>`_ — Event-based programming model and state machines
+* `PingPong <event-based/PingPong.rst>`_ — Classical ping-pong between two nodes
+* `PolitePingPong <event-based/PolitePingPong.rst>`_ — State-machine message dispatch pattern
+* `QuantumCorrRNG <event-based/QuantumCorrRNG.rst>`_ — Quantum correlated RNG with state machine
+* `QuantumCorrRNGVerified <event-based/QuantumCorrRNGVerified.rst>`_ — Correlated RNG with verification protocol
 
 ---------------------
 Native mode examples
 ---------------------
 
-* :doc:`native-mode/Template` — Template for programming in native (Twisted) mode
-* :doc:`native-mode/CorrRng` — Correlated randomness using native mode
-* :doc:`native-mode/Teleport` — Teleportation using native mode
-* :doc:`native-mode/GraphState` — Distributing a graph state across four nodes
+* `Template <native-mode/Template.rst>`_ — Template for programming in native (Twisted) mode
+* `CorrRng <native-mode/CorrRng.rst>`_ — Correlated randomness using native mode
+* `Teleport <native-mode/Teleport.rst>`_ — Teleportation using native mode
+* `GraphState <native-mode/GraphState.rst>`_ — Distributing a graph state across four nodes
 
 .. toctree::
     :hidden:

docs/GettingStarted.rst

@@ -22,7 +22,7 @@ Now, we can install SimulaQron by simply typing::
 
     pip3 install simulaqron
 
-You can then make use of SimulaQron using the command :code:`simulaqron` in the terminal. For more information on how
+You can then make use of SimulaQron using the command ``simulaqron`` in the terminal. For more information on how
 to use this command see below or type::
 
     simulaqron -h
@@ -45,7 +45,7 @@ Before delving into how to write any program yourself, let's first simply run on
 Remember from the Overview that SimulaQron has two parts: the first are the virtual node servers that simulate
 the hardware at each node as well as the quantum communication between them in a transparent manner.
 The second are the applications themselves which can be written in two ways: the direct way is to use the native
-mode using the Python Twisted framework connecting to the virtual node servers (see :doc:`Examples`),
+mode using the Python Twisted framework connecting to the virtual node servers (see `Examples <Examples.rst>`_),
 and the recommended way is to use the NetQASM library that calls the virtual nodes via the NetQASM interface.
 We will here illustrate how to use SimulaQron with the NetQASM library.
 
@@ -59,14 +59,14 @@ the backend of SimulaQron simply type::
 
     simulaqron start
 
-.. warning:: Running :code:`simulaqron start` will be default start up servers on localhost (i.e., your own computer),
+.. warning:: Running ``simulaqron start`` will be default start up servers on localhost (i.e., your own computer),
     using port numbers between 8000 and 9000, to form the simulated quantum internet hardware. SimulaQron does not
     provide any access control to its simulated hardware, so you are responsible to securing access should this be
     relevant for you. You can also run the different simulated nodes on different computers. We do not take any
     responsibility for problems caused by SimulaQron.
 
-For more information on what :code:`./cli/SimulaQron start` does, how to change the nodes and the ports of the network,
-the topology etc, see :doc:`ConfNodes`.
+For more information on what ``./cli/SimulaQron start`` does, how to change the nodes and the ports of the network,
+the topology etc, see `Configuring the Network <ConfNodes.rst>`_.
 
 To stop the backend, simply type::
 
@@ -93,7 +93,7 @@ Evidently, there would be classical means to achieve this trivial task chosen fo
 
 * Both Alice and Bob measure their respective qubits to obtain a classical random number :math:`x \in \{0,1\}`.
 
-The examples can be found in ``examples/new-sdk/`` (see :doc:`Examples` for the full list).
+The examples can be found in ``examples/new-sdk/`` (see `Examples <Examples.rst>`_ for the full list).
 Before seeing how this example works, let us simply run the code::
 
     cd examples/new-sdk/corrRNG
@@ -170,7 +170,7 @@ Similarly the core of bobTest.py is::
     m1_val = int(m1)
     sim_conn.close()
 
-For further examples, see :doc:`Examples` and :doc:`NetQASM` for the full SDK reference.
+For further examples, see `Examples <Examples.rst>`_ and `The NetQASM Interface <NetQASM.rst>`_ for the full SDK reference.
 
 .. _settings:
 
@@ -220,7 +220,7 @@ This command will create a file with the following configuration::
         "t1": 1.0
     }
 
-Section :ref:`settings_fields` provides a description about each one of the configuration options in the file.
+The section `Settings Fields`_ below provides a description about each one of the configuration options in the file.
 
 Alternatively, you can place the ``simulaqron_settings.json`` file in the folder ``~/.simulaqron`` (i.e. a folder
 named ``.simulaqron`` in your home folder). Doing so will make your settings persist across different projects you
@@ -268,7 +268,7 @@ The SimulaQron settings file contains a set of fields to control the configurati
 * ``t1``: T1 parameter to use when applying noise on the emulated qubits. This value is only used when the
   ``noisy_qubit`` option is set to ``true``.
 
-The default value of all these fields can be seen in the :ref:`settings` section.
+The default value of all these fields can be seen in the Settings_ section above.
 
 .. note:: An application can become "stalled" in certain configurations, leaving the application to look "hung". This
     leads to a deadlock of the application. SimulaQron will wait for the configured time before considering the

docs/NetQASM.rst

@@ -2,7 +2,7 @@ The NetQASM interface
 =====================
 
 SimulaQron applications are written using the **NetQASM SDK**. This page describes the core concepts and
-programming model. For complete working examples, see :doc:`Examples`.
+programming model. For complete working examples, see `Examples <Examples.rst>`_.
 
 ------------
 Installation
@@ -91,7 +91,7 @@ You can call ``flush()`` multiple times on the same connection. This enables **m
         other_qubit.X()   # conditional correction
     conn.flush()
 
-See the mid-circuit logic example in :doc:`Examples` for a full demonstration.
+See the mid-circuit logic example in `Examples <Examples.rst>`_ for a full demonstration.
 
 -----------------------
 Minimal example
@@ -173,7 +173,7 @@ receiving classical messages::
         conn.flush()
         conn.close()
 
-See the :doc:`new-sdk/Template` page for how to set up the client and server, and the teleportation example
+See the `Template <new-sdk/Template.rst>`_ page for how to set up the client and server, and the teleportation example
 for a complete two-node program with classical messaging.
 
 -----------------------
@@ -182,9 +182,9 @@ Configuration
 
 Each program needs two configuration files in its directory:
 
-* ``simulaqron_network.json`` — defines the nodes and their socket ports. See :doc:`ConfNodes` for details.
+* ``simulaqron_network.json`` — defines the nodes and their socket ports. See `Configuring the Network <ConfNodes.rst>`_ for details.
 * ``simulaqron_settings.json`` — configures the simulation backend and other settings. See the
-  :ref:`settings` section in :doc:`GettingStarted`.
+  Settings section in `Getting Started <GettingStarted.rst>`_.
 
 The ``stabilizer`` backend is used by default and is recommended unless you need non-Clifford gates (use
 ``qutip`` in that case).
@@ -193,6 +193,6 @@ The ``stabilizer`` backend is used by default and is recommended unless you need
 Further reading
 -----------------------
 
-* :doc:`Examples` — complete working examples from simple to complex
-* :doc:`new-sdk/Overview` — detailed SDK concepts and file structure
+* `Examples <Examples.rst>`_ — complete working examples from simple to complex
+* `New SDK Overview <new-sdk/Overview.rst>`_ — detailed SDK concepts and file structure
 * `NetQASM library documentation <https://netqasm.readthedocs.io/en/latest/>`_

docs/Overview.rst

@@ -15,11 +15,11 @@ In the light of the alternate interface below it may appear inefficient to expor
 the purpose of SimulaQron is precisely to explore and play with higher layer abstractions on top of any hardware, or
 its simulated version, SimulaQron. As such it is best to think of SimulaQron as a piece of simulated hardware with its
 own native interface, which we may first abstract into a higher level command language for programming. Examples of
-how to program SimulaQron in native mode can be found in :doc:`Examples`.
+how to program SimulaQron in native mode can be found in `Examples <Examples.rst>`_.
 
 The second way to run applications is via a higher level interface, the NetQASM interface. If you want your
 applications to later use real quantum hardware more easily instead of SimulaQron, then this is the interface to use.
-Examples of how to program using the NetQASM can be found in :doc:`NetQASM`.
+Examples of how to program using the NetQASM can be found in `The NetQASM Interface <NetQASM.rst>`_.
 
 .. image:: figs/netqasm_architecture.png
     :width: 500px
@@ -170,7 +170,7 @@ Automated tests
 ^^^^^^^^^^^^^^^
 
 There are number of automated tests that test many (but not all) of the features of SimulaQron and the NetQASM interface.
-See :doc:`GettingStarted` for how to run these.
+See `Getting Started <GettingStarted.rst>`_ for how to run these.
 Some of the automated tests use quantum tomography and are thus inherently probabilistic.
 Therefore if you see that one of these fails, you can try to run the test again and see if it is consistent.
 If the tests are to slow on your computer you can also run the short version, which skips the quantum tomography tests.

docs/event-based/Overview.rst

@@ -5,7 +5,7 @@ The event-based examples show how to structure quantum network protocols using
 a **state machine** pattern.  This is the recommended approach for protocols that
 interleave classical negotiation with quantum operations.
 
-Prerequisites: you should understand the :doc:`../new-sdk/Overview` first.
+Prerequisites: you should understand the `New SDK Overview <../new-sdk/Overview.rst>`_ first.
 
 The state machine pattern
 -------------------------
@@ -68,11 +68,11 @@ The examples progress from purely classical to quantum:
 
     * - Example
       - What it teaches
-    * - :doc:`PingPong`
+    * - `PingPong <PingPong.rst>`_
       - Basic event loop with simple if/else message handling
-    * - :doc:`PolitePingPong`
+    * - `PolitePingPong <PolitePingPong.rst>`_
       - Full state machine pattern with dispatch table
-    * - :doc:`QuantumCorrRNG`
+    * - `QuantumCorrRNG <QuantumCorrRNG.rst>`_
       - Adding quantum operations (EPR + measure) to event handlers
-    * - :doc:`QuantumCorrRNGVerified`
+    * - `QuantumCorrRNGVerified <QuantumCorrRNGVerified.rst>`_
       - Multi-state protocol: negotiate, quantum, then classical verification

docs/index.rst

@@ -27,7 +27,7 @@ Quick start
       pip3 install simulaqron
 
 2. **Configure your network** — create a ``simulaqron_network.json`` defining nodes and ports
-   (see :doc:`ConfNodes`)
+   (see `Configuring the Network <ConfNodes.rst>`_)
 
 3. **Write your program** using the NetQASM SDK::
 
@@ -42,17 +42,16 @@ Quick start
       print(int(m))         # read measurement result
       conn.close()
 
-4. **Run examples** — see :doc:`Examples` for complete working programs
+4. **Run examples** — see `Examples <Examples.rst>`_ for complete working programs
 
 Where to go next
 ----------------
 
-* **New to SimulaQron?** Start with :doc:`GettingStarted` for installation and your first example
-* **Want to write programs?** See :doc:`NetQASM` for the NetQASM SDK reference
-* **Looking for examples?** See :doc:`Examples` — new SDK, event-based, and native-mode examples
-* **Configuring networks and settings?** See :doc:`ConfNodes`
-* **Architecture and internals?** See :doc:`Overview`
-* **API reference?** See :ref:`modindex`
+* **New to SimulaQron?** Start with `Getting Started <GettingStarted.rst>`_ for installation and your first example
+* **Want to write programs?** See `The NetQASM Interface <NetQASM.rst>`_ for the NetQASM SDK reference
+* **Looking for examples?** See `Examples <Examples.rst>`_ — new SDK, event-based, and native-mode examples
+* **Configuring networks and settings?** See `Configuring the Network <ConfNodes.rst>`_
+* **Architecture and internals?** See `Overview <Overview.rst>`_
 
 We also have a `paper <http://iopscience.iop.org/article/10.1088/2058-9565/aad56e>`_ describing the design of
 SimulaQron, freely available on `arxiv <https://arxiv.org/abs/1712.08032>`_.
@@ -72,6 +71,6 @@ SimulaQron, freely available on `arxiv <https://arxiv.org/abs/1712.08032>`_.
 Indices and tables
 ==================
 
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+* Index
+* Module Index
+* Search

docs/native-mode/CorrRng.rst

@@ -2,7 +2,7 @@ Generate correlated randomness
 ==============================
 
 .. note:: Native mode is the low-level Twisted interface. For new projects, the NetQASM SDK is recommended.
-   See :doc:`../new-sdk/Overview` and the SDK version of this example at :doc:`../new-sdk/CorrRNG`.
+   See `New SDK Overview <../new-sdk/Overview.rst>`_ and the SDK version of this example at `CorrRNG <../new-sdk/CorrRNG.rst>`_.
 
 Having started the virtual quantum nodes, let us now run a simple test application, which already illustrates some of
 the aspects in realizing protocols. Our objective will be to realize the following protocol which will generate 1

docs/native-mode/GraphState.rst

@@ -2,7 +2,7 @@ Distributing a graph state
 ==========================
 
 .. note:: Native mode is the low-level Twisted interface. For new projects, the NetQASM SDK is recommended.
-   See :doc:`../new-sdk/Overview`.
+   See `New SDK Overview <../new-sdk/Overview.rst>`_.
 
 Here we consider a more complicated example, where we have four parties; Alice, Bob, Charlie and David.
 They will distribute a graph state and transform this with local operations and classical communication to make

docs/native-mode/Teleport.rst

@@ -2,11 +2,11 @@ Teleporting a Qubit
 ===================
 
 .. note:: Native mode is the low-level Twisted interface. For new projects, the NetQASM SDK is recommended.
-   See :doc:`../new-sdk/Overview` and the SDK version of this example at :doc:`../new-sdk/Teleport`.
+   See `New SDK Overview <../new-sdk/Overview.rst>`_ and the SDK version of this example at `Teleport <../new-sdk/Teleport.rst>`_.
 
 Let's now consider a very simple protocol, in which Alice first generates an EPR pair with Bob, and then teleports
 a qubit to Bob. To program it in SimulaQron's native mode, we will use the template described in
-:doc:`Template`.
+`Template <Template.rst>`_.
 
 ------------
 The protocol