From b5107262fed6df9a0fb4266c973ff91c1d111d58 Mon Sep 17 00:00:00 2001
From: SS <66886825+EarlMilktea@users.noreply.github.com>
Date: Thu, 10 Oct 2024 18:13:05 +0900
Subject: [PATCH 1/9] :fire: Remove unmaintained benchmarks

---
 benchmarks/graphsim.py      | 135 ----------------------------
 benchmarks/readme.rst       |   4 -
 benchmarks/requirements.txt |   0
 benchmarks/statevec.py      | 169 ------------------------------------
 4 files changed, 308 deletions(-)
 delete mode 100644 benchmarks/graphsim.py
 delete mode 100644 benchmarks/readme.rst
 delete mode 100644 benchmarks/requirements.txt
 delete mode 100644 benchmarks/statevec.py

diff --git a/benchmarks/graphsim.py b/benchmarks/graphsim.py
deleted file mode 100644
index 9f6921e2a..000000000
--- a/benchmarks/graphsim.py
+++ /dev/null
@@ -1,135 +0,0 @@
-"""
-Graph state simulator backends
-=======================================
-
-Here we benchmark our graph state simulator for MBQC with different backends.
-
-Currently, we have two backends: `networkx <https://networkx.org/documentation/stable/index.html>`_
-and `rustworkx <https://qiskit.org/ecosystem/rustworkx/index.html>`_.
-Both Python packages are used to manipulate graphs.
-While networkx is a pure Python package, rustworkx is a Rust package with Python bindings, which is faster than networkx.
-"""
-
-# %%
-# Firstly, let us import relevant modules:
-
-from copy import copy
-from time import perf_counter
-
-import matplotlib.pyplot as plt
-import numpy as np
-
-from graphix import Circuit
-
-# %%
-# Next, define a function to generate random Clifford circuits.
-
-
-def genpair(n_qubits, count, rng):
-    pairs = []
-    for _ in range(count):
-        choice = [j for j in range(n_qubits)]
-        x = rng.choice(choice)
-        choice.pop(x)
-        y = rng.choice(choice)
-        pairs.append((x, y))
-    return pairs
-
-
-def random_clifford_circuit(nqubits, depth, seed=42):
-    rng = np.random.default_rng(seed)
-    circuit = Circuit(nqubits)
-    gate_choice = list(range(5))
-    for _ in range(depth):
-        for j, k in genpair(nqubits, 2, rng):
-            circuit.cnot(j, k)
-        for j in range(nqubits):
-            k = rng.choice(gate_choice)
-            if k == 0:  # H
-                circuit.h(j)
-            elif k == 1:  # S
-                circuit.s(j)
-            elif k == 2:  # X
-                circuit.x(j)
-            elif k == 3:  # Z
-                circuit.z(j)
-            elif k == 4:  # Y
-                circuit.y(j)
-            else:
-                pass
-    return circuit
-
-
-# %%
-# We generate a set of random Clifford circuits with different widths.
-
-DEPTH = 3
-test_cases = [i for i in range(2, 300, 10)]
-graphix_patterns = {}
-
-for i in test_cases:
-    circuit = random_clifford_circuit(i, DEPTH)
-    pattern = circuit.transpile()
-    pattern.standardize()
-    pattern.shift_signals()
-    nodes, edges = pattern.get_graph()
-    graphix_patterns[i] = (circuit, pattern, len(nodes))
-
-
-# %%
-# We then run simulations.
-# First, we run the pattern optimization using networkx.
-networkx_time = []
-networkx_node = []
-
-for width, (_, pattern, num_nodes) in graphix_patterns.items():
-    pattern_copy = copy(pattern)
-    start = perf_counter()
-    pattern_copy.perform_pauli_measurements()
-    end = perf_counter()
-    networkx_node.append(num_nodes)
-    print(f"width: {width}, number of nodes: {num_nodes}, depth: {DEPTH}, time: {end - start}")
-    networkx_time.append(end - start)
-
-
-# %%
-# Next, we run the pattern optimization using rustworkx.
-rustworkx_time = []
-rustworkx_node = []
-
-for width, (_, pattern, num_nodes) in graphix_patterns.items():
-    pattern_copy = copy(pattern)
-    start = perf_counter()
-    pattern_copy.perform_pauli_measurements(use_rustworkx=True)
-    end = perf_counter()
-    rustworkx_node.append(num_nodes)
-    print(f"width: {width}, number of nodes: {num_nodes}, depth: {DEPTH}, time: {end - start}")
-    rustworkx_time.append(end - start)
-
-# %%
-# Lastly, we compare the simulation times.
-assert networkx_node == rustworkx_node
-
-fig = plt.figure()
-ax = fig.add_subplot(111)
-
-ax.scatter(networkx_node, networkx_time, label="networkx", color="blue")
-ax.scatter(rustworkx_node, rustworkx_time, label="rustworkx", color="red")
-ax.set(
-    xlabel="Number of nodes in the graph state",
-    xscale="log",
-    ylabel="Time (s)",
-    yscale="log",
-    title="Time to perform Pauli measurements on the graph state",
-)
-ax.legend()
-fig.show()
-
-# %%
-# Performing pattern optimization using rustworkx is slightly faster than networkx.
-
-import importlib.metadata  # noqa: E402
-
-# print package versions.
-for pkg in ["graphix", "networkx", "rustworkx"]:
-    print(f"{pkg} - {importlib.metadata.version(pkg)}")
diff --git a/benchmarks/readme.rst b/benchmarks/readme.rst
deleted file mode 100644
index 068c3a629..000000000
--- a/benchmarks/readme.rst
+++ /dev/null
@@ -1,4 +0,0 @@
-Graphix benchmarks
-==================
-
-Here are some benchmark of Graphix and related packages.
diff --git a/benchmarks/requirements.txt b/benchmarks/requirements.txt
deleted file mode 100644
index e69de29bb..000000000
diff --git a/benchmarks/statevec.py b/benchmarks/statevec.py
deleted file mode 100644
index 200c04562..000000000
--- a/benchmarks/statevec.py
+++ /dev/null
@@ -1,169 +0,0 @@
-"""
-Statevector simulation of MBQC patterns
-=======================================
-
-Here we benchmark our statevector simulator for MBQC.
-
-The methods and modules we use are the followings:
-    1. :meth:`graphix.pattern.Pattern.simulate_pattern`
-        Pattern simulator with statevector backend.
-    2. :mod:`paddle_quantum.mbqc`
-        Pattern simulation using :mod:`paddle_quantum.mbqc`.
-"""
-
-# %%
-# Firstly, let us import relevant modules:
-
-from time import perf_counter
-
-import matplotlib.pyplot as plt
-import numpy as np
-from paddle import to_tensor
-from paddle_quantum.mbqc.qobject import Circuit as PaddleCircuit
-from paddle_quantum.mbqc.simulator import MBQC as PaddleMBQC  # noqa: N811
-from paddle_quantum.mbqc.transpiler import transpile as paddle_transpile
-
-from graphix import Circuit
-
-rng = np.random.default_rng()
-
-# %%
-# Next, define a circuit to be transpiled into measurement pattern:
-
-
-def simple_random_circuit(nqubit, depth):
-    r"""Generate a test circuit for benchmarking.
-
-    This function generates a circuit with nqubit qubits and depth layers,
-    having layers of CNOT and Rz gates with random placements.
-
-    Parameters
-    ----------
-    nqubit : int
-        number of qubits
-    depth : int
-        number of layers
-
-    Returns
-    -------
-    circuit : graphix.transpiler.Circuit object
-        generated circuit
-    """
-    qubit_index = [i for i in range(nqubit)]
-    circuit = Circuit(nqubit)
-    for _ in range(depth):
-        rng.shuffle(qubit_index)
-        for j in range(len(qubit_index) // 2):
-            circuit.cnot(qubit_index[2 * j], qubit_index[2 * j + 1])
-        for j in range(len(qubit_index)):
-            circuit.rz(qubit_index[j], 2 * np.pi * rng.random())
-    return circuit
-
-
-# %%
-# We define the test cases: shallow (depth=1) random circuits, only changing the number of qubits.
-
-DEPTH = 1
-test_cases = [i for i in range(2, 22)]
-graphix_circuits = {}
-
-pattern_time = []
-circuit_time = []
-
-# %%
-# We then run simulations.
-# First, we run the pattern simulation using `graphix`.
-# For reference, we perform simple statevector simulation of the original gate network.
-# Since transpilation into MBQC involves a significant increase in qubit number,
-# the MBQC simulation is inherently slower as we will see.
-
-for width in test_cases:
-    circuit = simple_random_circuit(width, DEPTH)
-    graphix_circuits[width] = circuit
-    pattern = circuit.transpile()
-    pattern.standardize()
-    pattern.minimize_space()
-    nodes, edges = pattern.get_graph()
-    nqubit = len(nodes)
-    start = perf_counter()
-    pattern.simulate_pattern(max_qubit_num=30)
-    end = perf_counter()
-    print(f"width: {width}, nqubit: {nqubit}, depth: {DEPTH}, time: {end - start}")
-    pattern_time.append(end - start)
-    start = perf_counter()
-    circuit.simulate_statevector()
-    end = perf_counter()
-    circuit_time.append(end - start)
-
-
-# %%
-# Here we benchmark `paddle_quantum`, using the same original gate network and use `paddle_quantum.mbqc` module
-# to transpile into a measurement pattern.
-
-
-def translate_graphix_rc_into_paddle_quantum_circuit(graphix_circuit: Circuit) -> PaddleCircuit:
-    """Translate graphix circuit into paddle_quantum circuit.
-
-    Parameters
-    ----------
-        graphix_circuit : Circuit
-            graphix circuit
-
-    Returns
-    -------
-        paddle_quantum_circuit : PaddleCircuit
-            paddle_quantum circuit
-    """
-    paddle_quantum_circuit = PaddleCircuit(graphix_circuit.width)
-    for instr in graphix_circuit.instruction:
-        if instr.name == "CNOT":
-            paddle_quantum_circuit.cnot(which_qubits=instr[1])
-        elif instr.name == "RZ":
-            paddle_quantum_circuit.rz(which_qubit=instr[1], theta=to_tensor(instr[2], dtype="float64"))
-    return paddle_quantum_circuit
-
-
-test_cases_for_paddle_quantum = [i for i in range(2, 22)]
-paddle_quantum_time = []
-
-for width in test_cases_for_paddle_quantum:
-    graphix_circuit = graphix_circuits[width]
-    paddle_quantum_circuit = translate_graphix_rc_into_paddle_quantum_circuit(graphix_circuit)
-    pat = paddle_transpile(paddle_quantum_circuit)
-    mbqc = PaddleMBQC()
-    mbqc.set_pattern(pat)
-    start = perf_counter()
-    mbqc.run_pattern()
-    end = perf_counter()
-    paddle_quantum_time.append(end - start)
-
-    print(f"width: {width}, depth: {DEPTH}, time: {end - start}")
-
-# %%
-# Lastly, we compare the simulation times.
-
-fig = plt.figure()
-ax = fig.add_subplot(111)
-
-ax.scatter(
-    test_cases, circuit_time, label="direct statevector sim of original gate-based circuit (reference)", marker="x"
-)
-ax.scatter(test_cases, pattern_time, label="graphix pattern simulator")
-ax.scatter(test_cases_for_paddle_quantum, paddle_quantum_time, label="paddle_quantum pattern simulator")
-ax.set(
-    xlabel="Width of the original circuit",
-    ylabel="time (s)",
-    yscale="log",
-    title="Time to simulate random circuits",
-)
-fig.legend(bbox_to_anchor=(0.85, 0.9))
-fig.show()
-
-# %%
-# MBQC simulation is a lot slower than the simulation of original gate network, since the number of qubit involved
-# is significantly larger.
-
-import importlib.metadata  # noqa: E402
-
-# print package versions.
-[print(f"{pkg} - {importlib.metadata.version(pkg)}") for pkg in ["numpy", "graphix", "paddlepaddle", "paddle-quantum"]]

From 767b6f5d17105edb8a2522bc3cba5d1d4955a4ab Mon Sep 17 00:00:00 2001
From: SS <66886825+EarlMilktea@users.noreply.github.com>
Date: Thu, 10 Oct 2024 18:28:02 +0900
Subject: [PATCH 2/9] :fire: Remove doc requirements

---
 docs/requirements.txt | 12 ------------
 1 file changed, 12 deletions(-)
 delete mode 100644 docs/requirements.txt

diff --git a/docs/requirements.txt b/docs/requirements.txt
deleted file mode 100644
index 4f518e626..000000000
--- a/docs/requirements.txt
+++ /dev/null
@@ -1,12 +0,0 @@
-sphinx>=5.0
-sphinx-gallery==0.11.1
-furo
-sphinxawesome-theme==5.1.6
-numpy
-graphix
-matplotlib
-scikit-learn
-seaborn
-ipython
-
--r ../benchmarks/requirements.txt

From bda094395ca4373efdc5b4db4d82a66252307c1a Mon Sep 17 00:00:00 2001
From: SS <66886825+EarlMilktea@users.noreply.github.com>
Date: Thu, 10 Oct 2024 18:28:26 +0900
Subject: [PATCH 3/9] :technologist: Update requirements

---
 pyproject.toml         | 1 +
 requirements-dev.txt   | 8 --------
 requirements-doc.txt   | 8 ++++++++
 requirements-extra.txt | 4 ++++
 requirements.txt       | 1 -
 5 files changed, 13 insertions(+), 9 deletions(-)
 create mode 100644 requirements-doc.txt

diff --git a/pyproject.toml b/pyproject.toml
index 40eeb707e..382b618b5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -39,6 +39,7 @@ dependencies = { file = ["requirements.txt"] }
 
 [tool.setuptools.dynamic.optional-dependencies]
 dev = { file = ["requirements-dev.txt"] }
+doc = { file = ["requirements-doc.txt"] }
 extra = { file = ["requirements-extra.txt"] }
 
 [tool.ruff]
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 5a18f48f1..98684c73c 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -13,11 +13,3 @@ pytest
 pytest-cov
 pytest-mock
 tox
-
-# Optional dependencies
-qiskit>=1.0
-qiskit-aer
-rustworkx
-
-# Optional dependency. Pinned due to version changes often being incompatible
-pyzx==0.8.0
diff --git a/requirements-doc.txt b/requirements-doc.txt
new file mode 100644
index 000000000..17c5c3a11
--- /dev/null
+++ b/requirements-doc.txt
@@ -0,0 +1,8 @@
+furo
+ipython
+matplotlib
+scikit-learn
+seaborn
+sphinxawesome-theme
+sphinx-gallery
+sphinx>=5.0
diff --git a/requirements-extra.txt b/requirements-extra.txt
index a87155897..c691ea6cc 100644
--- a/requirements-extra.txt
+++ b/requirements-extra.txt
@@ -1,2 +1,6 @@
 graphix-ibmq
 graphix-perceval
+pyzx==0.8.0
+qiskit-aer
+qiskit>=1.0
+rustworkx
diff --git a/requirements.txt b/requirements.txt
index e84c035be..b1e63b312 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,3 @@
-autoray>=0.6.0
 eval_type_backport
 galois>=0.3.0
 matplotlib

From 2f3213f2816c208315079fd11ab5dc9bc5cbb665 Mon Sep 17 00:00:00 2001
From: SS <66886825+EarlMilktea@users.noreply.github.com>
Date: Thu, 10 Oct 2024 18:28:42 +0900
Subject: [PATCH 4/9] :green_heart: Update CIs

---
 .github/workflows/cov.yml       | 2 +-
 .github/workflows/doc.yml       | 4 ++--
 .github/workflows/typecheck.yml | 2 +-
 tox.ini                         | 5 ++---
 4 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/cov.yml b/.github/workflows/cov.yml
index b86b59309..b5a66777e 100644
--- a/.github/workflows/cov.yml
+++ b/.github/workflows/cov.yml
@@ -22,7 +22,7 @@ jobs:
         run: python -m pip install --upgrade pip
 
       - name: Install graphix with dev deps.
-        run: pip install .[dev]
+        run: pip install .[dev,extra]
 
       - name: Run pytest
         run: pytest --cov=./graphix --cov-report=xml
diff --git a/.github/workflows/doc.yml b/.github/workflows/doc.yml
index 9547c58b8..b5f4e7d26 100644
--- a/.github/workflows/doc.yml
+++ b/.github/workflows/doc.yml
@@ -31,7 +31,7 @@ jobs:
         run: python -m pip install --upgrade pip
 
       - name: Install requirements
-        run: pip install -r requirements.txt -r requirements-dev.txt -r docs/requirements.txt
+        run: pip install .[dev,doc]
 
       - name: Make docs
-        run: make -C docs html SPHINXOPTS="--fail-on-warning"
+        run: sphinx-build -M html docs/source docs/build
diff --git a/.github/workflows/typecheck.yml b/.github/workflows/typecheck.yml
index c105a9045..92736df27 100644
--- a/.github/workflows/typecheck.yml
+++ b/.github/workflows/typecheck.yml
@@ -25,7 +25,7 @@ jobs:
 
       - run: |
           python -m pip install --upgrade pip
-          pip install -e .[dev]
+          pip install -e .[dev,extra]
 
       - run: mypy
 
diff --git a/tox.ini b/tox.ini
index fb0869ba9..b69a47a8d 100644
--- a/tox.ini
+++ b/tox.ini
@@ -14,6 +14,7 @@ description = Run the unit tests
 deps =
     -r {toxinidir}/requirements.txt
     -r {toxinidir}/requirements-dev.txt
+    -r {toxinidir}/requirements-extra.txt
 commands =
     pytest {toxinidir}
 
@@ -21,8 +22,6 @@ commands =
 description = Run the unit tests with minimum dependencies
 deps =
     -r {toxinidir}/requirements.txt
-    pytest
-    pytest-mock
-    psutil
+    -r {toxinidir}/requirements-dev.txt
 commands =
     pytest {toxinidir}

From b4a5c77268db07feb4705b320349e7bdf9d2cfd3 Mon Sep 17 00:00:00 2001
From: SS <66886825+EarlMilktea@users.noreply.github.com>
Date: Thu, 10 Oct 2024 18:31:23 +0900
Subject: [PATCH 5/9] :poop: Comment out dead deps.

---
 requirements-extra.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/requirements-extra.txt b/requirements-extra.txt
index c691ea6cc..3304cd229 100644
--- a/requirements-extra.txt
+++ b/requirements-extra.txt
@@ -1,5 +1,5 @@
-graphix-ibmq
-graphix-perceval
+# graphix-ibmq
+# graphix-perceval
 pyzx==0.8.0
 qiskit-aer
 qiskit>=1.0

From 2bf4e569ddd3111cd13dc01d5414c5a954c80af0 Mon Sep 17 00:00:00 2001
From: SS <66886825+EarlMilktea@users.noreply.github.com>
Date: Thu, 10 Oct 2024 18:38:07 +0900
Subject: [PATCH 6/9] :construction_worker: Fail on error

---
 .github/workflows/doc.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/doc.yml b/.github/workflows/doc.yml
index b5f4e7d26..0e66dc704 100644
--- a/.github/workflows/doc.yml
+++ b/.github/workflows/doc.yml
@@ -34,4 +34,4 @@ jobs:
         run: pip install .[dev,doc]
 
       - name: Make docs
-        run: sphinx-build -M html docs/source docs/build
+        run: sphinx-build -M html docs/source docs/build --fail-on-warning

From 25e31df596cd66223eec94923aadecf75eab8b64 Mon Sep 17 00:00:00 2001
From: SS <66886825+EarlMilktea@users.noreply.github.com>
Date: Thu, 10 Oct 2024 18:43:05 +0900
Subject: [PATCH 7/9] :wrench: Update rtd config

---
 .readthedocs.yaml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index e4481b896..eb1aa776a 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -6,15 +6,17 @@
 version: 2
 
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.12"
 
 sphinx:
   configuration: docs/source/conf.py
 
 python:
   install:
-    - requirements: docs/requirements.txt
+    - requirements: requirements.txt
+    - requirements: requirements-extra.txt
+    - requirements: requirements-doc.txt
     - method: pip
       path: .

From fdfa77527f884f72f6ef6ad7c28d89b11e36fd18 Mon Sep 17 00:00:00 2001
From: SS <66886825+EarlMilktea@users.noreply.github.com>
Date: Thu, 10 Oct 2024 18:46:06 +0900
Subject: [PATCH 8/9] :bug: Fix CI fail

---
 docs/source/conf.py  | 1 -
 requirements-doc.txt | 1 -
 2 files changed, 2 deletions(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 7e49705eb..0b8d0f19b 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -23,7 +23,6 @@
     "sphinx.ext.autosectionlabel",
     "sphinx.ext.napoleon",
     "sphinx_gallery.gen_gallery",
-    "sphinxawesome_theme.highlighting",
 ]
 
 templates_path = ["_templates"]
diff --git a/requirements-doc.txt b/requirements-doc.txt
index 17c5c3a11..394a2341c 100644
--- a/requirements-doc.txt
+++ b/requirements-doc.txt
@@ -3,6 +3,5 @@ ipython
 matplotlib
 scikit-learn
 seaborn
-sphinxawesome-theme
 sphinx-gallery
 sphinx>=5.0

From c5a3a5432194fafadc47e202f6386fc76b59cb1c Mon Sep 17 00:00:00 2001
From: SS <66886825+EarlMilktea@users.noreply.github.com>
Date: Thu, 17 Oct 2024 15:55:56 +0900
Subject: [PATCH 9/9] :construction_worker: Update noxfile

---
 noxfile.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/noxfile.py b/noxfile.py
index 508ba024f..6f32db51f 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -17,5 +17,5 @@ def tests_minimal(session: Session) -> None:
 @nox.session(python=["3.8", "3.9", "3.10", "3.11", "3.12"])
 def tests(session: Session) -> None:
     """Run the test suite with full dependencies."""
-    session.install("-e", ".[dev]")
+    session.install("-e", ".[extra]")
     session.run("pytest")