Merge pull request #20 from QSAR-UBC/glassnotes/add-pre-commit-hooks

Add pre-commit hooks and update formatting / linting to use ruff

.github/workflows/python-package.yml

@@ -5,40 +5,36 @@ name: Python package
 
 on:
   push:
-    branches: [ "main" ]
+    branches: ["main"]
   pull_request:
-    branches: [ "main", "rc-0.*" ]
+    branches: ["main", "rc-0.*"]
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
         python-version: ["3.9", "3.10", "3.11"]
 
     steps:
-    - uses: actions/checkout@v4
-      with:
-        repository: ${{ github.event.pull_request.head.repo.full_name }}
-        ref: ${{ github.event.pull_request.head.ref }}
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-        cache: 'pip'
-    - name: Install dependencies
-      run: |
-        python -m pip install -U pip poetry
-        poetry --version
-        poetry install
-    - name: Check formatting with black
-      run: |
-        poetry run black -l 100 ionizer/*.py tests/*.py
-    - name: Lint with pylint
-      run: |
-        poetry run pylint ionizer/*.py tests/*.py
-    - name: Test with pytest
-      run: |
-        poetry run pytest tests/test_*.py
+      - uses: actions/checkout@v4
+        with:
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+          ref: ${{ github.event.pull_request.head.ref }}
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - name: Install dependencies
+        run: |
+          python -m pip install -U pip poetry
+          poetry --version
+          poetry install
+      - name: Check linting and formatting with ruff
+        run: |
+          poetry run ruff check ionizer/*.py tests/*.py
+      - name: Test with pytest
+        run: |
+          poetry run pytest tests/test_*.py

.pre-commit-config.yaml

@@ -0,0 +1,83 @@
+# To run all pre-commit checks, use:
+#
+#     pre-commit run -a
+#
+# To install pre-commit hooks that run every time you commit:
+#
+#     pre-commit install
+#
+# This file was constructed based on an example file provided by our friends
+# at TUM Chair for Design Automation - thanks!
+
+ci:
+  autoupdate_commit_msg: "update pre-commit hooks"
+  autofix_commit_msg: "pre-commit fixes"
+
+repos:
+  # Standard hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.6.0"
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+
+  # Handling unwanted unicode characters
+  - repo: https://github.com/sirosen/texthooks
+    rev: "0.6.6"
+    hooks:
+      - id: fix-ligatures
+      - id: fix-smartquotes
+
+  # Check for common mistakes
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+
+  # Check for spelling
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.3.0"
+    hooks:
+      - id: codespell
+
+  # Format configuration files with prettier
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v4.0.0-alpha.8"
+    hooks:
+      - id: prettier
+        types_or: [yaml, markdown, html, css, javascript, json]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.9
+    hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
+        types_or: [python, pyi, jupyter]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+
+  # Also run Black on examples in the documentation
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: 1.16.0
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==24.*]
+
+  # Catch common capitalization mistakes
+  - repo: local
+    hooks:
+      - id: disallow-caps
+        name: Disallow improper capitalization
+        language: pygrep
+        entry: PyBind|Numpy|Github|PyTest|Pennylane
+        exclude: .pre-commit-config.yaml

README.md

@@ -9,9 +9,10 @@ of code!
 ```python
 from ionizer.transforms import ionize
 
+
 @qml.qnode(dev)
 @ionize
-def circuit(x): 
+def circuit(x):
     qml.Hadamard(wires=0)
     qml.CNOT(wires=[0, 1])
     qml.RX(x, wires=1)
@@ -21,14 +22,14 @@ def circuit(x):
 ```pycon
 >>> qml.draw(circuit)(0.3)
 0: ──GPI2(0.00)─╭MS──GPI2(-1.57)─────────────────────────┤  <Z>
-1: ──GPI2(3.14)─╰MS──GPI2(1.57)───GPI(-1.42)──GPI2(1.57)─┤     
+1: ──GPI2(3.14)─╰MS──GPI2(1.57)───GPI(-1.42)──GPI2(1.57)─┤
 ```
 
-
 ## Installation
 
 Requirements:
- * PennyLane >= 0.33
+
+- PennyLane >= 0.33
 
 The Ionizer is not currently available via a package manager. To install, clone the repository and run
 
@@ -52,30 +53,31 @@ transforms](https://arxiv.org/abs/2202.13414), similar to PennyLane's [existing
 compilation
 tools](https://docs.pennylane.ai/en/stable/introduction/compiling_circuits.html). To
 compile and execute the circuit using trapped ion gates, the
-``@ionize`` decorator  performs the following steps:
+`@ionize` decorator performs the following steps:
 
- * Decomposes all operations into Paulis/Pauli rotations, Hadamard, and CNOT 
- * Merges all single-qubit rotations
- * Converts everything except RZ to GPI/GPI2/MS gates (`@ionizer.transforms.convert_to_gpi`)
- * Virtually applies all RZ gates (`@ionizer.transforms.virtualize_rz_gates`)
- * Repeatedly applies gate fusion and commutation through MS gates which performs simplification based on some circuit identities (`@ionizer.transforms.single_qubit_fusion_gpi` and `@ionizer.transforms.commute_through_ms_gates`)
+- Decomposes all operations into Paulis/Pauli rotations, Hadamard, and CNOT
+- Merges all single-qubit rotations
+- Converts everything except RZ to GPI/GPI2/MS gates (`@ionizer.transforms.convert_to_gpi`)
+- Virtually applies all RZ gates (`@ionizer.transforms.virtualize_rz_gates`)
+- Repeatedly applies gate fusion and commutation through MS gates which performs simplification based on some circuit identities (`@ionizer.transforms.single_qubit_fusion_gpi` and `@ionizer.transforms.commute_through_ms_gates`)
 
 ```python
 from ionizer.transforms import ionize
 
+
 @qml.qnode(dev)
 @ionize
 def circuit_ionized(params):
     for idx in range(5):
         qml.Hadamard(wires=idx)
-        
+
     for idx in range(4):
         qml.RY(params[idx], wires=idx)
-        qml.CNOT(wires=[idx+1, idx])
-        
+        qml.CNOT(wires=[idx + 1, idx])
+
     for wire in dev.wires:
         qml.PauliX(wires=wire)
-        
+
     return qml.expval(qml.PauliX(0))
 ```
 
@@ -97,7 +99,7 @@ tensor(0.99500417, requires_grad=True)
 
 ```
 
-Note that while this comes packaged together as the ``@ionize`` transform, the
+Note that while this comes packaged together as the `@ionize` transform, the
 individual transforms can also be accessed and used independently.
 
 There is currently not direct support for other frameworks. However, if you would like to do this with a Qiskit circuit, it can be accomplished as follows through the [`pennylane-qiskit`](https://github.com/PennyLaneAI/pennylane-qiskit) package.
@@ -108,32 +110,32 @@ qiskit_circuit = QuantumCircuit(...)
 # Turns a Qiskit circuit into a PennyLane quantum function
 qfunc = qml.from_qiskit(qiskit_circuit)
 
+
 @qml.qnode(dev)
 @ionize
 def pennylane_circuit():
     qfunc()
     return qml.expval(qml.PauliX(0))
 ```
 
-
 ## Notes
 
 This package is a work in progress. While it has been verified to work on some
 fairly large circuits, we still need to work on:
- * finding circuit identities involving the 2-qubit gate
- * improving the documentation and usage instructions
- * ensuring differentiability of variational parameters
- * writing more tests (compile at your own risk!)
 
+- finding circuit identities involving the 2-qubit gate
+- improving the documentation and usage instructions
+- ensuring differentiability of variational parameters
+- writing more tests (compile at your own risk!)
 
 ## Resources
 
- * [IonQ documentation](https://ionq.com/docs/getting-started-with-native-gates)
- * [Basic circuit compilation techniques for an ion-trap quantum machine](https://arxiv.org/abs/1603.07678)
-   
- ## Citing
+- [IonQ documentation](https://ionq.com/docs/getting-started-with-native-gates)
+- [Basic circuit compilation techniques for an ion-trap quantum machine](https://arxiv.org/abs/1603.07678)
+
+## Citing
 
- If you use the Ionizer as part of your workflow, we would appreciate if you cite it using the BibTeX below.
+If you use the Ionizer as part of your workflow, we would appreciate if you cite it using the BibTeX below.
 
 ```
 @software{di_matteo_2024_10761367,

ionizer/decompositions.py

@@ -17,6 +17,7 @@
 """
 Custom decompositions of operations into the {GPI, GPI2, MS} native gate set.
 """
+
 from pennylane import math
 import numpy as np
 
@@ -136,7 +137,11 @@ def gpi_ry(phi, wires):
         List[Operation]: The sequence of GPI/GPI2 rotations that implements
         the gate up to a global phase.
     """
-    return [GPI2(np.pi, wires=wires), GPI(phi / 2, wires=wires), GPI2(np.pi, wires=wires)]
+    return [
+        GPI2(np.pi, wires=wires),
+        GPI(phi / 2, wires=wires),
+        GPI2(np.pi, wires=wires),
+    ]
 
 
 def gpi_rz(phi, wires):

ionizer/identity_hunter.py

@@ -36,8 +36,11 @@ def _test_inclusion_in_identity_db(db_subset, single_gates, candidate_angles, ca
     """
     # Loop over GPI/GPI2 for all the special angles
     for id_gate, gate_angle_list in single_gates.items():
-        # Get their explicit reference angles and matrix reprensentations
-        angles, matrices = [x[0] for x in gate_angle_list], [x[1] for x in gate_angle_list]
+        # Get their explicit reference angles and matrix representations
+        angles, matrices = (
+            [x[0] for x in gate_angle_list],
+            [x[1] for x in gate_angle_list],
+        )
 
         # Test each reference against the candidate to see if any are equivalent
         for ref_angle, ref_matrix in zip(angles, matrices):

ionizer/ops.py

@@ -17,6 +17,7 @@
 """
 Native gates for IonQ hardware as PennyLane operations.
 """
+
 import numpy as np
 
 import pennylane as qml
@@ -114,7 +115,10 @@ def compute_matrix(phi):  # pylint: disable=arguments-differ
         """
         exponent = -1j * phi
         return qml.math.stack(
-            [[1, -1j * qml.math.exp(exponent)], [-1j * qml.math.exp(qml.math.conj(exponent)), 1]]
+            [
+                [1, -1j * qml.math.exp(exponent)],
+                [-1j * qml.math.exp(qml.math.conj(exponent)), 1],
+            ]
         ) / np.sqrt(2)
 
     def adjoint(self):

ionizer/transforms.py

@@ -21,6 +21,7 @@
 expansions and simplifications of the tape. The transforms it uses during this
 process can also be called individually.
 """
+
 from typing import Sequence, Callable
 from functools import partial
 
@@ -211,7 +212,10 @@ def virtualize_rz_gates(tape: QuantumTape) -> (Sequence[QuantumTape], Callable):
                 # this way we can commute it through.
                 if apply_accumulated_phase_gate:
                     new_operations.append(
-                        GPI(-rescale_angles(accumulated_rz_phase) / 2, wires=current_gate.wires)
+                        GPI(
+                            -rescale_angles(accumulated_rz_phase) / 2,
+                            wires=current_gate.wires,
+                        )
                     )
                     new_operations.append(GPI(0.0, wires=current_gate.wires))
 

ionizer/utils.py

@@ -17,6 +17,7 @@
 """
 Utility functions.
 """
+
 import numpy as np
 from pennylane import math