TeamGraphix · matulni · Sep 7, 2026 · Sep 14, 2026 · Sep 14, 2026
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -27,7 +27,7 @@
     "sphinx.ext.autosummary",
     "sphinx.ext.autosectionlabel",
     "sphinx.ext.napoleon",
-    "sphinx_gallery.gen_gallery",
+    # "sphinx_gallery.gen_gallery",
 ]
 
 templates_path = ["_templates"]
@@ -85,15 +85,15 @@ def setup(app: Sphinx) -> None:
 
 default_role = "any"
 
-sphinx_gallery_conf = {
-    # path to your example scripts
-    "examples_dirs": ["../../examples"],
-    # path to where to save gallery generated output
-    "gallery_dirs": ["gallery"],
-    "filename_pattern": "/",
-    "thumbnail_size": (800, 550),
-    "parallel": True,
-}
+# sphinx_gallery_conf = {
+#     # path to your example scripts
+#     "examples_dirs": ["../../examples"],
+#     # path to where to save gallery generated output
+#     "gallery_dirs": ["gallery"],
+#     "filename_pattern": "/",
+#     "thumbnail_size": (800, 550),
+#     "parallel": True,
+# }
 
 suppress_warnings = ["config.cache"]
 

diff --git a/docs/source/development/apiref/index.rst b/docs/source/development/apiref/index.rst
@@ -0,0 +1,21 @@
+API Reference
+=============
+*Coming soon...*
+
+Old API Ref (to be updated):
+
+.. toctree::
+    :maxdepth: 2
+
+    source/generator
+    source/data
+    source/modifier
+    source/simulator
+    source/graphsim
+    source/extraction
+    source/clifford
+    source/visualization
+    source/channels
+    source/random_objects
+    source/open_graph
+    source/optimization
diff --git a/docs/source/channels.rst → ...ce/development/apiref/source/channels.rst b/docs/source/channels.rst → ...ce/development/apiref/source/channels.rst
diff --git a/docs/source/clifford.rst → ...ce/development/apiref/source/clifford.rst b/docs/source/clifford.rst → ...ce/development/apiref/source/clifford.rst
diff --git a/docs/source/data.rst → ...source/development/apiref/source/data.rst b/docs/source/data.rst → ...source/development/apiref/source/data.rst
diff --git a/docs/source/extraction.rst → .../development/apiref/source/extraction.rst b/docs/source/extraction.rst → .../development/apiref/source/extraction.rst
diff --git a/docs/source/generator.rst → ...e/development/apiref/source/generator.rst b/docs/source/generator.rst → ...e/development/apiref/source/generator.rst
diff --git a/docs/source/graphsim.rst → ...ce/development/apiref/source/graphsim.rst b/docs/source/graphsim.rst → ...ce/development/apiref/source/graphsim.rst
diff --git a/docs/source/modifier.rst → ...ce/development/apiref/source/modifier.rst b/docs/source/modifier.rst → ...ce/development/apiref/source/modifier.rst
diff --git a/docs/source/open_graph.rst → .../development/apiref/source/open_graph.rst b/docs/source/open_graph.rst → .../development/apiref/source/open_graph.rst
diff --git a/docs/source/optimization.rst → ...evelopment/apiref/source/optimization.rst b/docs/source/optimization.rst → ...evelopment/apiref/source/optimization.rst
diff --git a/docs/source/random_objects.rst → ...elopment/apiref/source/random_objects.rst b/docs/source/random_objects.rst → ...elopment/apiref/source/random_objects.rst
diff --git a/docs/source/simulator.rst → ...e/development/apiref/source/simulator.rst b/docs/source/simulator.rst → ...e/development/apiref/source/simulator.rst
diff --git a/docs/source/visualization.rst → ...velopment/apiref/source/visualization.rst b/docs/source/visualization.rst → ...velopment/apiref/source/visualization.rst
diff --git a/docs/source/development/compatibility.rst b/docs/source/development/compatibility.rst
@@ -0,0 +1,3 @@
+Compatibility
+=============
+*Refer to compatiblity.md*
diff --git a/docs/source/contributing.rst → docs/source/development/contributing.rst b/docs/source/contributing.rst → docs/source/development/contributing.rst
diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst
@@ -0,0 +1,13 @@
+Getting started
+===============
+
+*To be written*
+
+*Simple description of what Graphix does*
+
+
+
+Running your first program
+--------------------------
+
+*Simple circuit transpilation and pattern simulation*
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -1,23 +1,35 @@
 .. graphix documentation master file, created by
    sphinx-quickstart on Sun Nov 20 00:43:54 2022.
 
-Graphix - optimizing and simulating MBQC
-========================================
+Graphix
+=======
+An open-source framework for Measurement-Based Quantum Computation
 
-**Graphix** is an open-source library to generate, optimize and simulate the measurement-based quantum computing (MBQC) command sequence.
+.. toctree::
+   :caption: Documentation
 
+   installation
+   getting_started
+   tutorials/index
+   research_workflows/index
+
 .. toctree::
+   :caption: Development
    :maxdepth: 1
-   :caption: Documentation
+
+   development/contributing
+   development/compatibility
+   development/apiref/index
 
-   tutorial
-   gallery/index
-   references
-   contributing
 
 .. toctree::
-   :maxdepth: 2
-   :caption: Introduction to LC-MBQC
+   :caption: Graphix plugins
 
+   plugins/index
+
+.. toctree::
+   :caption: Old sections
+
+   tutorial
    intro
-   lc-mbqc
+   lc-mbqc
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -0,0 +1,4 @@
+Installation
+============
+
+*To be written*
diff --git a/docs/source/plugins/index.rst b/docs/source/plugins/index.rst
@@ -0,0 +1,3 @@
+Graphix plugins
+===============
+*Coming soon...*
diff --git a/docs/source/references.rst b/docs/source/references.rst
diff --git a/docs/source/research_workflows/index.rst b/docs/source/research_workflows/index.rst
@@ -0,0 +1,3 @@
+Research workflows
+==================
+*Coming soon...*
diff --git a/docs/source/tutorial.rst b/docs/source/tutorial.rst
@@ -4,7 +4,7 @@ Tutorial
 Graphix provides a high-level interface to generate, optimize and classically simulate the measurement-based quantum computing (MBQC).
 
 In this tutorial, we look at how to program MBQC using graphix library.
-We will explain the basics here along with the code, and you can go to :doc:`intro` to learn more about the theoretical background of MBQC and :doc:`references` for module references.
+We will explain the basics here along with the code, and you can go to :doc:`intro` to learn more about the theoretical background of MBQC and references for module references.
 
 Generating measurement patterns
 -------------------------------
@@ -229,7 +229,7 @@ With this, we only need the memory space for three qubits.
 
 This procedure is more effective when the resource state size is large compared to the logical input qubit count;
 for example, the three-qubit `quantum Fourier transform (QFT)
-<https://en.wikipedia.org/wiki/Quantum_Fourier_transform>`_ circuit requires 12 qubits in the resource state after :meth:`~graphix.pattern.Pattern.perform_pauli_measurements()` (see the code in :ref:`QFT example <sphx_glr_gallery_qft_with_tn.py>`); with the proper reordering of the commands, the max_space reduces to 4.
+<https://en.wikipedia.org/wiki/Quantum_Fourier_transform>`_ circuit requires 12 qubits in the resource state after :meth:`~graphix.pattern.Pattern.perform_pauli_measurements()` (see the code in sphx_glr_gallery_qft_with_tn.py); with the proper reordering of the commands, the max_space reduces to 4.
 In fact, for patterns transpiled from gate network, the minimum *space* we can realize is typically :math:`n_w+1` where :math:`n_w` is the width of the circuit.
 
 

diff --git a/docs/source/tutorials/index.rst b/docs/source/tutorials/index.rst
@@ -0,0 +1,21 @@
+Tutorials
+=========
+
+*Overview of MBQC, we can borrow beginning of Sec. 2*
+
+.. toctree::
+    source/graph_mbqc
+    source/measurement_calculus
+    source/transpilation
+    source/flows
+    source/pattern_standardization
+    source/space_minimization
+    source/pauli_removal
+    source/pattern_simulation
+    source/circuit_extraction
+
+.. toctree::
+    :caption: Advanced Tutorials
+
+    source/symbolic
+    source/type_safety
diff --git a/docs/source/tutorials/source/circuit_extraction.rst b/docs/source/tutorials/source/circuit_extraction.rst
@@ -0,0 +1,2 @@
+Circuit extraction
+==================
diff --git a/docs/source/tutorials/source/flows.rst b/docs/source/tutorials/source/flows.rst
@@ -0,0 +1,4 @@
+Flows and determinism
+=====================
+
+*This tutorial should cover sections 2.3 and 3.2 of the paper.*
diff --git a/docs/source/tutorials/source/graph_mbqc.rst b/docs/source/tutorials/source/graph_mbqc.rst
@@ -0,0 +1,6 @@
+Open graphs and correction functions
+====================================
+
+*This tutorial should cover section 2.1 of the paper, a bit less of theory and some more examples*
+
+
diff --git a/docs/source/tutorials/source/measurement_calculus.rst b/docs/source/tutorials/source/measurement_calculus.rst
@@ -0,0 +1,6 @@
+Patterns and the measurement calculus
+=====================================
+
+*This tutorial should cover section 2.2 of the paper without standardization.*
+*Instead of simulating the pattern (box 2.2), we can put a pattern visualization*
+
diff --git a/docs/source/tutorials/source/pattern_simulation.rst b/docs/source/tutorials/source/pattern_simulation.rst
@@ -0,0 +1,5 @@
+Pattern simulation
+===================
+
+*This tutorial could start with a simple pattern simulation example (like in "Getting started"), then cover sections 3.6. No need to put the Figure.*
+*There should be subsections: branch selection, noisy simulation and maybe "Advance usage" : custom noise models.*
diff --git a/docs/source/tutorials/source/pattern_standardization.rst b/docs/source/tutorials/source/pattern_standardization.rst
@@ -0,0 +1,3 @@
+Pattern standardization
+=======================
+*Basic example and maybe some details on `StandardizedPattern` class*
diff --git a/docs/source/tutorials/source/pauli_removal.rst b/docs/source/tutorials/source/pauli_removal.rst
@@ -0,0 +1,2 @@
+Pauli measurement removal
+=========================
diff --git a/docs/source/tutorials/source/space_minimization.rst b/docs/source/tutorials/source/space_minimization.rst
@@ -0,0 +1,3 @@
+Space minimization
+==================
+*Basic example and details on `SpaceMinimizationHeuristic`*
diff --git a/docs/source/tutorials/source/symbolic.rst b/docs/source/tutorials/source/symbolic.rst
@@ -0,0 +1,2 @@
+Symbolic manipulation
+=====================
diff --git a/docs/source/tutorials/source/transpilation.rst b/docs/source/tutorials/source/transpilation.rst
@@ -0,0 +1,3 @@
+From circuits to patterns
+=========================
+*This tutorial should describe the JCZ transpiler and the Circuit API. Fig. 7 is potentially useful*
diff --git a/docs/source/tutorials/source/type_safety.rst b/docs/source/tutorials/source/type_safety.rst
@@ -0,0 +1,3 @@
+Type safety
+===========
+*Description of type hierachies*
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		Pauli measurement removal
		=========================