chore(deps): Bump cda-tum/mqt-workflows from 1.3 to 1.4 in the github…

…-actions group (#69)

Bumps the github-actions group with 1 update:
[cda-tum/mqt-workflows](https://github.com/cda-tum/mqt-workflows).

Updates `cda-tum/mqt-workflows` from 1.3 to 1.4
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/cda-tum/mqt-workflows/releases">cda-tum/mqt-workflows's
releases</a>.</em></p>
<blockquote>
<h2>MQT Reusable Workflows 1.4.0 Release</h2>
<h2>👀 What Changed</h2>
<p>This release refactors the way tests on Python are distributed and
run. Instead of running separate sessions for each Python version, this
PR changes the workflows to run all sessions in a single workflow run
per operating system.
This should allow for maximum caching reuse across builds and reduce the
number of CI runners that need to be waited for.
It also reduces the number of macOS runners requested per CI run, which
is now fixed to 2 for the python tests regardless of the number of
supported Python versions.</p>
<p>While, previously, only the <code>ubuntu-latest</code> runner would
run tests on all Python versions, this PR changes the workflows so that
also macOS and Windows runners test all the versions.
This should not cause a noticable runtime increase given the excessive
caching opportunities, both via <code>ccache</code> and
<code>uv</code>.</p>
<blockquote>
<p>[!IMPORTANT]<br />
This change will require consuming workflows to adapt their
configuration!</p>
<p>The <code>skip-testing-latest-python</code> workflow input has been
removed and the Python versions being tested are solely defined by the
nox sessions configuration.
Consequently, if a package should not be tested under Python 3.13 yet
for example, <code>&quot;3.13&quot;</code> should be removed from the
<code>PYTHON_ALL_VERSIONS</code> array in the
<code>noxfile.py</code>.</p>
</blockquote>
<p>In addition, this release switches to the official
<code>setup-uv</code> action and employs <code>uv</code> in a couple
more places (see <a
href="https://redirect.github.com/cda-tum/mqt-workflows/issues/31">#31</a>
for further details).</p>
<h2>🚀 Features and Enhancements</h2>
<ul>
<li>♻️ unify Python testing <a
href="https://github.com/burgholzer"><code>@​burgholzer</code></a> (<a
href="https://redirect.github.com/cda-tum/mqt-workflows/issues/32">#32</a>)</li>
<li>⚡ use official <code>setup-uv</code> action and more of
<code>uv</code> <a
href="https://github.com/burgholzer"><code>@​burgholzer</code></a> (<a
href="https://redirect.github.com/cda-tum/mqt-workflows/issues/31">#31</a>)</li>
<li>🚸 no longer need to explicitly provide <code>GITHUB_TOKEN</code> to
<code>setup-z3</code> <a
href="https://github.com/burgholzer"><code>@​burgholzer</code></a> (<a
href="https://redirect.github.com/cda-tum/mqt-workflows/issues/30">#30</a>)</li>
</ul>
<h2>🤖 CI</h2>
<ul>
<li>♻️ unify Python testing <a
href="https://github.com/burgholzer"><code>@​burgholzer</code></a> (<a
href="https://redirect.github.com/cda-tum/mqt-workflows/issues/32">#32</a>)</li>
<li>⚡ use official <code>setup-uv</code> action and more of
<code>uv</code> <a
href="https://github.com/burgholzer"><code>@​burgholzer</code></a> (<a
href="https://redirect.github.com/cda-tum/mqt-workflows/issues/31">#31</a>)</li>
</ul>
<h2>⬆️ Dependencies</h2>
<!-- raw HTML omitted -->
<ul>
<li>Bump pypa/cibuildwheel from 2.20 to 2.21 in the github-actions group
<a href="https://github.com/dependabot"><code>@​dependabot</code></a>
(<a
href="https://redirect.github.com/cda-tum/mqt-workflows/issues/33">#33</a>)</li>
<li>♻️ unify Python testing <a
href="https://github.com/burgholzer"><code>@​burgholzer</code></a> (<a
href="https://redirect.github.com/cda-tum/mqt-workflows/issues/32">#32</a>)</li>
<li>⚡ use official <code>setup-uv</code> action and more of
<code>uv</code> <a
href="https://github.com/burgholzer"><code>@​burgholzer</code></a> (<a
href="https://redirect.github.com/cda-tum/mqt-workflows/issues/31">#31</a>)</li>
<li>🚸 no longer need to explicitly provide <code>GITHUB_TOKEN</code> to
<code>setup-z3</code> <a
href="https://github.com/burgholzer"><code>@​burgholzer</code></a> (<a
href="https://redirect.github.com/cda-tum/mqt-workflows/issues/30">#30</a>)</li>
<li>Bump peter-evans/create-pull-request from 6 to 7 in the
github-actions group <a
href="https://github.com/dependabot"><code>@​dependabot</code></a> (<a
href="https://redirect.github.com/cda-tum/mqt-workflows/issues/29">#29</a>)</li>
<li>⬆️🪝 update pre-commit hooks <a
href="https://github.com/pre-commit-ci"><code>@​pre-commit-ci</code></a>
(<a
href="https://redirect.github.com/cda-tum/mqt-workflows/issues/28">#28</a>)</li>
<li>⬆️🪝 update pre-commit hooks <a
href="https://github.com/pre-commit-ci"><code>@​pre-commit-ci</code></a>
(<a
href="https://redirect.github.com/cda-tum/mqt-workflows/issues/27">#27</a>)</li>
</ul>
<!-- raw HTML omitted -->
<p><strong>Full Changelog</strong>: <a
href="https://github.com/cda-tum/mqt-workflows/compare/v1.3.2...v1.4.0">https://github.com/cda-tum/mqt-workflows/compare/v1.3.2...v1.4.0</a></p>
<h2>MQT Reusable Workflows 1.3.2 Release</h2>
<h2>👀 What Changed</h2>
<p>A small bugfix release for the MQT Core Update workflow.</p>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/cda-tum/mqt-workflows/commit/7bc94c4133e6849d3e6503b717ff470fb752b5a4"><code>7bc94c4</code></a>
Bump pypa/cibuildwheel from 2.20 to 2.21 in the github-actions group (<a
href="https://redirect.github.com/cda-tum/mqt-workflows/issues/33">#33</a>)</li>
<li><a
href="https://github.com/cda-tum/mqt-workflows/commit/c256b51441fdf2e8bb11d1f2e66edf3028897f12"><code>c256b51</code></a>
♻️ unify Python testing (<a
href="https://redirect.github.com/cda-tum/mqt-workflows/issues/32">#32</a>)</li>
<li><a
href="https://github.com/cda-tum/mqt-workflows/commit/0b6eabc6083793121777d2e18ff5e99e0878a329"><code>0b6eabc</code></a>
⚡ use official <code>setup-uv</code> action and more of <code>uv</code>
(<a
href="https://redirect.github.com/cda-tum/mqt-workflows/issues/31">#31</a>)</li>
<li><a
href="https://github.com/cda-tum/mqt-workflows/commit/fdc30c7975f9cb39ffe964703d5084e3171052de"><code>fdc30c7</code></a>
🚸 no longer need to explicitly provide <code>GITHUB_TOKEN</code> to
<code>setup-z3</code> (<a
href="https://redirect.github.com/cda-tum/mqt-workflows/issues/30">#30</a>)</li>
<li><a
href="https://github.com/cda-tum/mqt-workflows/commit/dba77f053b165199edd988cf09241a92d72063f8"><code>dba77f0</code></a>
Bump peter-evans/create-pull-request from 6 to 7 in the github-actions
group ...</li>
<li><a
href="https://github.com/cda-tum/mqt-workflows/commit/8dea125a6d32c96930430a76362ba3e8316886a5"><code>8dea125</code></a>
⬆️🪝 update pre-commit hooks (<a
href="https://redirect.github.com/cda-tum/mqt-workflows/issues/28">#28</a>)</li>
<li><a
href="https://github.com/cda-tum/mqt-workflows/commit/38b81a0148818efff3d8eac03c7c802986aaafbd"><code>38b81a0</code></a>
⬆️🪝 update pre-commit hooks (<a
href="https://redirect.github.com/cda-tum/mqt-workflows/issues/27">#27</a>)</li>
<li>See full diff in <a
href="https://github.com/cda-tum/mqt-workflows/compare/v1.3...v1.4">compare
view</a></li>
</ul>
</details>
<br />


[![Dependabot compatibility
score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=cda-tum/mqt-workflows&package-manager=github_actions&previous-version=1.3&new-version=1.4)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)

Dependabot will resolve any conflicts with this PR as long as you don't
alter it yourself. You can also trigger a rebase manually by commenting
`@dependabot rebase`.

[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)

---

<details>
<summary>Dependabot commands and options</summary>
<br />

You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits
that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
- `@dependabot squash and merge` will squash and merge this PR after
your CI passes on it
- `@dependabot cancel merge` will cancel a previously requested merge
and block automerging
- `@dependabot reopen` will reopen this PR if it is closed
- `@dependabot close` will close this PR and stop Dependabot recreating
it. You can achieve the same result by closing it manually
- `@dependabot show <dependency name> ignore conditions` will show all
of the ignore conditions of the specified dependency
- `@dependabot ignore <dependency name> major version` will close this
group update PR and stop Dependabot creating any more for the specific
dependency's major version (unless you unignore this specific
dependency's major version or upgrade to it yourself)
- `@dependabot ignore <dependency name> minor version` will close this
group update PR and stop Dependabot creating any more for the specific
dependency's minor version (unless you unignore this specific
dependency's minor version or upgrade to it yourself)
- `@dependabot ignore <dependency name>` will close this group update PR
and stop Dependabot creating any more for the specific dependency
(unless you unignore this specific dependency or upgrade to it yourself)
- `@dependabot unignore <dependency name>` will remove all of the ignore
conditions of the specified dependency
- `@dependabot unignore <dependency name> <ignore condition>` will
remove the ignore condition of the specified dependency and ignore
conditions


</details>

.github/release-drafter.yml

@@ -6,28 +6,30 @@ categories:
       - "feature"
       - "enhancement"
       - "usability"
+      - "refactor"
   - title: "🐛 Bug Fixes"
     labels:
       - "bug"
       - "fix"
   - title: "📄 Documentation"
     labels:
       - "documentation"
-  - title: "🤖 CI"
-    labels:
-      - "continuous integration"
   - title: "📦 Packaging"
     labels:
       - "packaging"
   - title: "🧹 Code Quality"
     labels:
       - "code quality"
+  - title: "🤖 CI"
+    labels:
+      - "continuous integration"
   - title: "⬆️ Dependencies"
     collapse-after: 5
     labels:
       - "dependencies"
       - "submodules"
       - "github_actions"
+      - "pre-commit"
 change-template: "- $TITLE @$AUTHOR (#$NUMBER)"
 change-title-escapes: '\<*_&'
 version-resolver:
@@ -41,10 +43,6 @@ version-resolver:
     labels:
       - "patch"
   default: patch
-autolabeler:
-  - label: "dependencies"
-    title:
-      - "/update pre-commit hooks/i"
 
 template: |
   ## 👀 What Changed

.github/workflows/cd.yml

@@ -10,7 +10,7 @@ on:
 jobs:
   python-packaging:
     name: 🐍 Packaging
-    uses: cda-tum/mqt-workflows/.github/workflows/reusable-python-packaging.yml@v1.3
+    uses: cda-tum/mqt-workflows/.github/workflows/reusable-python-packaging.yml@v1.4
     with:
       pure-python: true
 

.github/workflows/ci.yml

@@ -14,21 +14,19 @@ concurrency:
 jobs:
   change-detection:
     name: 🔍 Change
-    uses: cda-tum/mqt-workflows/.github/workflows/reusable-change-detection.yml@v1.3
+    uses: cda-tum/mqt-workflows/.github/workflows/reusable-change-detection.yml@v1.4
 
   python-tests:
     name: 🐍 Test
     needs: change-detection
     if: fromJSON(needs.change-detection.outputs.run-python-tests)
-    uses: cda-tum/mqt-workflows/.github/workflows/[email protected]
-    with:
-      skip-testing-latest-python: true
+    uses: cda-tum/mqt-workflows/.github/workflows/[email protected]
 
   code-ql:
     name: 📝 CodeQL
     needs: change-detection
     if: fromJSON(needs.change-detection.outputs.run-code-ql)
-    uses: cda-tum/mqt-workflows/.github/workflows/reusable-code-ql-python.yml@v1.3
+    uses: cda-tum/mqt-workflows/.github/workflows/reusable-code-ql-python.yml@v1.4
 
   required-checks-pass: # This job does nothing and is only used for branch protection
     name: 🚦 Check

.pre-commit-config.yaml

@@ -44,11 +44,10 @@ repos:
       - id: rst-inline-touching-normal
 
   # Check for spelling
-  - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.26.0
     hooks:
-      - id: codespell
-        args: ["-L", "wille,linz", "--skip", "*.ipynb"]
+      - id: typos
 
   # Format configuration files with prettier
   - repo: https://github.com/rbubley/mirrors-prettier
@@ -62,9 +61,7 @@ repos:
     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
@@ -83,12 +80,11 @@ repos:
     rev: v1.11.2
     hooks:
       - id: mypy
-        files: ^(src|tests|setup.py)
+        files: ^(src|tests|noxfile.py)
         args: []
         additional_dependencies:
           - importlib_resources
           - types-setuptools
-          - python_tsp
           - networkx
           - pytest
           - sympy
@@ -97,6 +93,7 @@ repos:
           - tsplib95
           - types-Pillow
           - referencing
+          - nox
 
   # Catch common capitalization mistakes
   - repo: local

.python_version

@@ -0,0 +1 @@
+3.12

docs/conf.py

@@ -55,7 +55,6 @@
     "sphinx.ext.githubpages",
     "sphinxcontrib.bibtex",
     "sphinx_copybutton",
-    "hoverxref.extension",
     "nbsphinx",
     "sphinxext.opengraph",
     "sphinx_autodoc_typehints",
@@ -84,20 +83,6 @@
 
 autosectionlabel_prefix_document = True
 
-hoverxref_auto_ref = True
-hoverxref_domains = ["cite", "py"]
-hoverxref_roles = []
-hoverxref_mathjax = True
-hoverxref_role_types = {
-    "ref": "tooltip",
-    "p": "tooltip",
-    "labelpar": "tooltip",
-    "class": "tooltip",
-    "meth": "tooltip",
-    "func": "tooltip",
-    "attr": "tooltip",
-    "property": "tooltip",
-}
 exclude_patterns = ["_build", "build", "**.ipynb_checkpoints", "Thumbs.db", ".DS_Store", ".env"]
 
 

notebooks/tsp.ipynb

@@ -48,7 +48,7 @@
    "source": [
     "### Parameters\n",
     "\n",
-    "We begin by setting up our paramters for the QUBOGenerator. The `PathFindingQUBOGenerator` supports the following parameters:\n",
+    "We begin by setting up our parameters for the QUBOGenerator. The `PathFindingQUBOGenerator` supports the following parameters:\n",
     "\n",
     "- `encoding_type`: One of `ONE_HOT`, `DOMAIN_WALL`, or `BINARY`. the encoding for the binary variables in  the QUBO formulation.\n",
     "- `n_paths`: The number of paths to be searched.\n",
@@ -379,7 +379,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "_Find the shortest paths $\\pi_1$ and $\\pi_2$ from $s_p$ to $t_p$ respectively that don't interesect_"
+    "_Find the shortest paths $\\pi_1$ and $\\pi_2$ from $s_p$ to $t_p$ respectively that don't intersect_"
    ]
   },
   {

noxfile.py

@@ -4,6 +4,7 @@
 
 import argparse
 import os
+import shutil
 from typing import TYPE_CHECKING
 
 import nox
@@ -16,7 +17,7 @@
 
 nox.options.sessions = ["lint", "tests"]
 
-PYTHON_ALL_VERSIONS = ["3.9", "3.10", "3.11", "3.12", "3.13"]
+PYTHON_ALL_VERSIONS = ["3.9", "3.10", "3.11", "3.12"]
 
 BUILD_REQUIREMENTS = [
     "setuptools_scm>=8.1",
@@ -30,12 +31,11 @@
 
 @nox.session(reuse_venv=True)
 def lint(session: nox.Session) -> None:
-    """Lint the Python part of the codebase using pre-commit.
+    """Run the linter."""
+    if shutil.which("pre-commit") is None:
+        session.install("pre-commit")
 
-    Simply execute `nox -rs lint` to run all configured hooks.
-    """
-    session.install("pre-commit")
-    session.run("pre-commit", "run", "--all-files", *session.posargs)
+    session.run("pre-commit", "run", "--all-files", *session.posargs, external=True)
 
 
 def _run_tests(

pyproject.toml

@@ -16,20 +16,20 @@ authors = [
 ]
 keywords = ["MQT", "quantum-computing", "qubo", "shortest-path", "design-automation"]
 license = { file = "LICENSE" }
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 dynamic = ["version"]
 
 dependencies = [
     "importlib_resources>=5.0; python_version < '3.10'",
     "qiskit>=1.0.0",
     "joblib>=1.3.2",
-    "numpy>=1.26.4,<3.0; python_version > '3.11'", # some of our dependencies are not yet compatible with numpy 2.0
-    "numpy>=1.17.0,<2.0; python_version <= '3.11'", # some of our dependencies are not yet compatible with numpy 2.0
+    "numpy>=1.26; python_version >= '3.12'",
+    "numpy>=1.24; python_version >= '3.11'",
+    "numpy>=1.22",
     "sympy>=1.13.1",
     "matplotlib>=3.9.0; python_version > '3.11'",
     "matplotlib>=3.7.0; python_version <= '3.11'",
     "networkx>=2.8.8",
-    "python_tsp>=0.4.0",
     "docplex>=2.25.236",
     "qiskit_optimization>=0.6.0",
     "tsplib95>=0.7.1",
@@ -61,20 +61,16 @@ classifiers = [
 ]
 
 [project.optional-dependencies]
-test = ["pytest>=7"]
+test = ["pytest>=7.2"]
 coverage = ["mqt.qubomaker[test]", "pytest-cov>=4"]
 docs = [
-    "furo>=2023.08.17",
-    "sphinx>=7,<9",
-    "setuptools-scm>=8",
+    "furo>=2023.9.10",
+    "setuptools-scm>=8.1",
     "sphinxcontrib-bibtex>=2.4.2",
-    "sphinx-copybutton",
-    "sphinx-hoverxref",
-    "pybtex>=0.24",
-    "ipython",
+    "sphinx-copybutton>=0.5",
     "ipykernel",
     "nbsphinx",
-    "sphinxext-opengraph",
+    "sphinxext-opengraph>=0.9",
     "sphinx-autodoc-typehints",
     "qiskit[visualization]",
 ]
@@ -92,15 +88,14 @@ Discussions = "https://github.com/cda-tum/mqt-qubomaker/discussions"
 "mqt.qubomaker.pathfinder" = ["resources/*", "resources/constraints/*"]
 
 [tool.pytest.ini_options]
-minversion = "7.0"
+minversion = "7.2"
 testpaths = ["tests"]
 addopts = ["-ra", "--strict-markers", "--strict-config", "--showlocals"]
 log_cli_level = "INFO"
 xfail_strict = true
 filterwarnings = [
     "error",
     "ignore:.*invalid escape sequence.*::.*docplex.*",
-    "ignore:.*Qiskit with Python 3.8.*:DeprecationWarning:",
 ]
 
 [tool.coverage]
@@ -115,20 +110,19 @@ report.exclude_also = [
 [tool.mypy]
 mypy_path = "$MYPY_CONFIG_FILE_DIR/src,$MYPY_CONFIG_FILE_DIR/stubs"
 files = ["src", "tests"]
-python_version = "3.8"
+python_version = "3.9"
 strict = true
 enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
 warn_unreachable = true
 explicit_package_bases = true
 pretty = true
 
 [[tool.mypy.overrides]]
-module = ["types-Pillow", "jsonschema", "tsplib95.*", "ipywidgets.*", "IPython.*", "qiskit.*", "qiskit_algorithms.*", "matplotlib.*", "python_tsp.*", "networkx.*", "mqt.ddsim.*", "joblib.*", "qiskit_optimization.*", "docplex.*", "typing_extensions.*"]
+module = ["types-Pillow", "jsonschema", "tsplib95.*", "ipywidgets.*", "IPython.*", "qiskit.*", "qiskit_algorithms.*", "matplotlib.*", "networkx.*", "mqt.ddsim.*", "joblib.*", "qiskit_optimization.*", "docplex.*", "typing_extensions.*", "numpy.*"]
 ignore_missing_imports = true
 
 [tool.ruff]
 line-length = 120
-extend-include = ["*.ipynb"]
 preview = true
 unsafe-fixes = true
 
@@ -197,3 +191,14 @@ isort.required-imports = ["from __future__ import annotations"]
 
 [tool.ruff.lint.pydocstyle]
 convention = "google"
+
+
+[tool.typos]
+default.extend-ignore-re = [
+    '"id": ".*",',
+    "(?Rm)^.*(#|//)\\s*spellchecker:disable-line$",  # ignore line
+    "(?s)(#|//)\\s*spellchecker:off.*?\\n\\s*(#|//)\\s*spellchecker:on", # ignore block
+    "NDArray",
+]
+[tool.typos.default.extend-words]
+wille = "wille"

src/mqt/qubomaker/__init__.py

@@ -1,6 +1,6 @@
 """A package for generating QUBO formulations automatically from a set of constraints QUBOs for different problem classes.
 
-It allows users to create a `QUBOGenerator` object, and graudally add penalty terms and constraints to it.
+It allows users to create a `QUBOGenerator` object, and gradually add penalty terms and constraints to it.
 When done, the object can be used to construct a QUBO formulation of the project on multiple granularity levels.
 
 ## Available Subpackages

src/mqt/qubomaker/graph.py

@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Tuple, Union
+from typing import TYPE_CHECKING, Union, cast
 
 import networkx as nx
 import numpy as np
@@ -12,7 +12,7 @@
 if TYPE_CHECKING:
     from io import TextIOWrapper
 
-    Edge = Union[Tuple[int, int], Tuple[int, int, int], Tuple[int, int, float]]
+    Edge = Union[tuple[int, int], tuple[int, int, int], tuple[int, int, float]]
 
 
 class Graph:
@@ -162,7 +162,7 @@ def __eq__(self, value: object) -> bool:
         """
         if not isinstance(value, Graph):
             return False
-        return np.array_equal(self.adjacency_matrix, value.adjacency_matrix)
+        return cast(bool, np.array_equal(self.adjacency_matrix, value.adjacency_matrix))
 
     def __hash__(self) -> int:
         """Returns the hash of the graph.