Add pre-commit hooks (QCHackers#291)

Fixes QCHackers#288 by introducing `pre-commit` that should run on each commit
AND on CI.

.github/ISSUE_TEMPLATE/question.md

@@ -3,7 +3,7 @@ name: Asking a question
 about: I have a question to ask that is neither a feature request nor a bug report.
 title: "[Question]: "
 labels: "question"
-assignees: 
+assignees:
   - nelimee
 ---
 

.github/workflows/ci.yml

@@ -9,14 +9,30 @@ on:
       - main
 
 jobs:
+  pre-commit-ci:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+          cache: "pip"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements.txt -r requirements-dev.txt
+      - name: Run pre-commit hooks
+        run: pre-commit run --all-files
+
   build-and-test-python:
     runs-on: ubuntu-latest
+    needs: pre-commit-ci
     strategy:
       matrix:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v4
-
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
@@ -25,24 +41,26 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements.txt -r requirements-dev.txt
+          python -m pip install -r requirements.txt -r requirements-dev.txt
       - name: Analyze code with pylint
         run: |
-          pip install pylint
+          python -m pip install pylint
           pylint $(git ls-files '*.py')
         continue-on-error: true
       - name: Build
         run: pip install .
       - name: Test and coverage
         run: |
-          pip install pytest pytest-cov
+          python -m pip install pytest pytest-cov
           pytest --cov=src/tqec $(git ls-files '*_test.py')
       - name: Mypy type checking
         run: |
-          pip install mypy
+          python -m pip install mypy
           mypy src/tqec/
+
   build-and-test-nodejs:
     runs-on: ubuntu-latest
+    needs: pre-commit-ci
     defaults:
       run:
         working-directory: frontend

.pre-commit-config.yaml

@@ -0,0 +1,34 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.17.0
+    hooks:
+      - id: pyupgrade
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.5.6
+    hooks:
+      # Run the linter.
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+        args: [--fix]
+      # Run the formatter.
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.23.6
+    hooks:
+      - id: typos
+  - repo: https://github.com/gitleaks/gitleaks
+    rev: v8.18.4
+    hooks:
+      - id: gitleaks
+  - repo: https://github.com/PyCQA/docformatter
+    rev: v1.7.5
+    hooks:
+      - id: docformatter

README.md

@@ -5,7 +5,7 @@
 
 Design automation software tools for Topological Quantum Error Correction
 
-Live endpoint: https://tqec.app
+Live endpoint: [https://tqec.app](https://tqec.app)
 
 ## Installation
 
@@ -40,12 +40,12 @@ The next step is to install the package and its dependencies using
 python -m pip install "."
 ```
 
-If you want to run the
-[`logical_qubit_memory_experiment.ipynb`](https://github.com/QCHackers/tqec/blob/main/notebooks/logical_qubit_memory_experiment.ipynb)
-notebook, you will also have to install a few other packages:
+If you want to help developing the `tqec` Python package, you should install the development
+environment by using instead
 
 ```sh
 python -m pip install ".[dev]"
+pre-commit install
 ```
 
 If no errors happen, the package is installed! You can try to launch a jupyter

_typos.toml

@@ -0,0 +1,5 @@
+[default]
+extend-ignore-identifiers-re = [
+    # Corrected to "and" but always mean "ancilla".
+    "anc_.*",
+]

docs/detectors.rst

@@ -1,53 +1,53 @@
 Automatic detector computation
 ==============================
 
-The ``tqec`` package implements a method to automatically compute detectors from a 
+The ``tqec`` package implements a method to automatically compute detectors from a
 given quantum circuit representing a quantum error corrected computation.
 
-An accompanying notebook showcasing the different steps to find detectors is located 
+An accompanying notebook showcasing the different steps to find detectors is located
 `here <media/detectors/detector_computation_illustration.ipynb>`_.
 
-Difference from the main ``tqec`` package 
+Difference from the main ``tqec`` package
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 The implementation to automatically find detectors in a given quantum circuit representing
-a quantum error corrected computation is currently kept as isolated from the ``tqec`` package 
-as possible and will very likely be outsourced into its own independent package in the future. 
+a quantum error corrected computation is currently kept as isolated from the ``tqec`` package
+as possible and will very likely be outsourced into its own independent package in the future.
 The implementation can be found in ``tqec.circuit.detectors`` and a few restrictions applies
 specifically to the code in this sub-module:
 
 - it should be self-contained, or in other words it should not call code from the main
   ``tqec`` package, with the exception of code within ``tqec.circuit.detectors``,
-- it should avoid uneeded dependencies. For that reason, the code in ``tqec.circuit.detectors``
-  does not use ``cirq`` as its intermediary representation but directly operates on 
+- it should avoid unneeded dependencies. For that reason, the code in ``tqec.circuit.detectors``
+  does not use ``cirq`` as its intermediary representation but directly operates on
   ``stim`` data-structures.
 
 Concepts used through the sub-module
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-A few core concepts are re-used through the whole sub-module. This section aims at 
+A few core concepts are re-used through the whole sub-module. This section aims at
 presenting these core concepts in an accessible manner.
 
-Terms that are conventionally used in quantum computing, such as "circuit", will not 
-be defined here. 
+Terms that are conventionally used in quantum computing, such as "circuit", will not
+be defined here.
 
 .. _moments-section:
 
 Moments
 ^^^^^^^
 
-The concept of "moment" is central to the sub-module. A "moment" is a portion of a 
+The concept of "moment" is central to the sub-module. A "moment" is a portion of a
 quantum circuit that is located between two ``TICK`` instructions. Conventionally,
 moments may end with a ``TICK`` instruction, but do not start with one.
 
-This definition is close, but not equivalent, to the definition used by ``cirq``. One of 
-the main difference is that ``cirq`` defines a moment as a sub-circuit of depth 1: no 
-instruction in the moment overlaps with another instruction in the same moment. 
-In the definition given above, there is no notion of depth, and even though ``TICK`` 
-instruction are generally used in ``stim`` such as the moment definition above 
+This definition is close, but not equivalent, to the definition used by ``cirq``. One of
+the main difference is that ``cirq`` defines a moment as a sub-circuit of depth 1: no
+instruction in the moment overlaps with another instruction in the same moment.
+In the definition given above, there is no notion of depth, and even though ``TICK``
+instruction are generally used in ``stim`` such as the moment definition above
 is equivalent to the definition used by ``cirq``, this is not required.
 
-For example, the circuit 
+For example, the circuit
 
 .. code-block::
 
@@ -72,20 +72,20 @@ Fragments
 
 Fragments are a collection of moments that check the following order:
 
-1. zero or more moments exclusively composed of `reset`, annotation or 
+1. zero or more moments exclusively composed of `reset`, annotation or
    noisy-gate instructions,
-2. zero or more moments composed of "computation" instructions (anything 
+2. zero or more moments composed of "computation" instructions (anything
    that is not a measurement, a reset, a noisy gate or an annotation),
-3. one or more moments exclusively composed of `measurement`, annotation 
+3. one or more moments exclusively composed of `measurement`, annotation
    or noisy-gate instructions.
 
 The circuit provided in :ref:`moments-section` contains 4 moments that form
 a fragment.
 
-Note that the circuit 
+Note that the circuit
 
 .. code-block::
-    
+
     M 1 3
     DETECTOR(1, 0) rec[-2]
     DETECTOR(3, 0) rec[-1]
@@ -94,9 +94,9 @@ Note that the circuit
     DETECTOR(3, 1) rec[-1] rec[-2] rec[-4]
     OBSERVABLE_INCLUDE(0) rec[-1]
 
-also form a fragment! 
+also form a fragment!
 
-Flows 
+Flows
 ^^^^^
 
 Stabilizers can propagate through a fragment, but can also be created or destroyed by it.
@@ -115,53 +115,53 @@ Let's use the following quantum circuit to illustrate:
 
 You can also `check it interactively using crumble <https://algassert.com/crumble#circuit=Q(0,0)0;Q(1,0)1;Q(2,0)2;Q(3,0)3;Q(4,0)4;R_1_3;TICK;CX_0_1_2_3;TICK;CX_2_1_4_3;TICK;M_1_3;DT(1,0,0)rec[-2];DT(3,0,0)rec[-1]_rec[-2];DT(3,0,1)rec[-1]/>`_.
 
-This quantum circuit can "propagate" a stabilizer, for example if a ``Z`` stabilizer 
+This quantum circuit can "propagate" a stabilizer, for example if a ``Z`` stabilizer
 on qubit ``2`` is given as input, a ``Z`` stabilizer on qubit ``2`` is propagated
 through:
 
 .. image:: media/detectors/stabilizer-propagation.png
 
-The quantum circuit also "creates" propagation of stabilizers with its resets, as 
+The quantum circuit also "creates" propagation of stabilizers with its resets, as
 shown in the illustration below:
 
 .. image:: media/detectors/stabilizer-creation.png
 
-Here, the fragment is creating a ``Z0Z2`` stabilizer: the ``Z`` Pauli string 
-comes out of the final moment of the fragment on qubits ``0`` and ``2``. 
+Here, the fragment is creating a ``Z0Z2`` stabilizer: the ``Z`` Pauli string
+comes out of the final moment of the fragment on qubits ``0`` and ``2``.
 
-Quantum circuit can also "destroy" some incomming stabilizers with its measurements 
+Quantum circuit can also "destroy" some incoming stabilizers with its measurements
 as shown below:
 
 .. image:: media/detectors/stabilizer-destruction.png
 
 Here, the fragment is destroying an incoming ``Z0Z2`` stabilizer.
 
-These three kinds of stabilizer propagation are "flows". A "flow" is describing the 
+These three kinds of stabilizer propagation are "flows". A "flow" is describing the
 way a stabilizer propagates through a fragment.
 
 Collapsing operations
 ^^^^^^^^^^^^^^^^^^^^^
 
-Collapsing operations are operations that are involved in the collapsing 
-(i.e., "destruction") or "creation" of flows. 
+Collapsing operations are operations that are involved in the collapsing
+(i.e., "destruction") or "creation" of flows.
 
 Measurements and resets are the only collapsing operations.
 
-Note that, by construction, collapsing operations can only be encountered at the 
+Note that, by construction, collapsing operations can only be encountered at the
 boundaries (beginning/end) of a fragment.
 
-Boundary stabilizers 
+Boundary stabilizers
 ^^^^^^^^^^^^^^^^^^^^
 
-An important data-structure used in the package is ``BoundaryStabilizer``. This 
-data-structure represents the state of a flow at the boundaries of a fragment. 
+An important data-structure used in the package is ``BoundaryStabilizer``. This
+data-structure represents the state of a flow at the boundaries of a fragment.
 It stores:
 
 1. a Pauli string, representing the state of a flow that propagated from one boundary,
    just before encountering the collapsing operations of the other boundary,
 2. a list of Pauli strings, each representing one of the collapsing operations that
    will be encountered by the propagated Pauli string,
-3. a list of measurements that are involved (either as sources for a destruction flow 
+3. a list of measurements that are involved (either as sources for a destruction flow
    or as sinks for a creation flow) in the flow propagation and that will be used later
    to know which measurements to include in the detectors.
 
@@ -173,18 +173,18 @@ can be represented by a ``BoundaryStabilizer`` instance with the following attri
 
 1. ``Z0Z1Z2`` for the stabilizer, as before encountering the measurement, the propagated
    stabilizer is ``Z0Z1Z2``.
-2. ``[Z1, Z3]`` as collapsing operations, as the measurements present in the above circuit 
+2. ``[Z1, Z3]`` as collapsing operations, as the measurements present in the above circuit
    are performed in the ``Z`` basis, and on qubits ``1`` and ``3``.
-3. a data-structure that will represent the measurement performed on qubit ``1``, as the 
+3. a data-structure that will represent the measurement performed on qubit ``1``, as the
    only measurement that is taking part in the stabilizer propagation is this one.
 
 As another example, the following flow:
 
 .. image:: media/detectors/stabilizer-destruction.png
 
-can be represented by a ``BoundaryStabilizer`` instance that has exactly the same attributes 
+can be represented by a ``BoundaryStabilizer`` instance that has exactly the same attributes
 as the one described above.
 
-To distinguish between these two ``BoundaryStabilizer`` (one representing a creation flow, 
+To distinguish between these two ``BoundaryStabilizer`` (one representing a creation flow,
 the other representing a destruction flow), they will be stored in a data-structure that
 will differentiate creation and destruction flows: ``FragmentFlow`` (or ``FragmentLoopFlow``).

docs/index.rst

@@ -10,12 +10,12 @@ TQEC
 .. toctree::
    :maxdepth: 2
    :hidden:
-   
+
    Introduction <self>
    Automatic detector computation <detectors>
 
 .. toctree::
    :maxdepth: 2
    :caption: Notebooks:
-   
-   Automatic detector computation <media/detectors/detector_computation_illustration>
+
+   Automatic detector computation <media/detectors/detector_computation_illustration>

docs/media/detectors/detector_computation_illustration.ipynb

@@ -324,7 +324,7 @@
             "\n",
             "In such cases, there is an intermediary step `1.5` that consist in try to merge several anti-commuting flows together to form new commuting flows.\n",
             "\n",
-            "Comming back to the code, detectors can be listed by calling `match_detectors_from_flows_shallow`:"
+            "Coming back to the code, detectors can be listed by calling `match_detectors_from_flows_shallow`:"
          ]
       },
       {

frontend/.gcloudignore

@@ -14,4 +14,4 @@
 .gitignore
 
 # Node.js dependencies:
-node_modules/
+node_modules/

frontend/src/plaquettes/Footprint.js

@@ -140,10 +140,10 @@ export default class Footprint {
 
   /**
    * Update the visibility and event listeners
-   * @function updateVisiblityAndEventListeners
+   * @function updateVisibilityAndEventListeners
    * @returns {void}
    */
-  updateVisiblityAndEventListeners() {
+  updateVisibilityAndEventListeners() {
     this.isDragging = true;
     this.container.name = 'footprint';
     // Create the buttons