Merge branch 'main' into new_structure

Signed-off-by: Shaobo-Zhou <109073755+Shaobo-Zhou@users.noreply.github.com>

Author: Shaobo-Zhou

.pre-commit-config.yaml

@@ -19,9 +19,12 @@ repos:
     rev: v6.0.0
     hooks:
       - id: check-added-large-files
+        args: ["--maxkb=2048"]
       - id: check-case-conflict
-      - id: check-docstring-first
+      - id: check-vcs-permalinks
       - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-json
       - id: check-toml
       - id: check-yaml
       - id: debug-statements
@@ -55,12 +58,17 @@ repos:
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
 
+  # Ensure uv lock file is up-to-date
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    rev: 0.9.13
+    hooks:
+      - id: uv-lock
+
   # Python linting and formatting using ruff
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.6
+    rev: v0.14.7
     hooks:
       - id: ruff-check
-        args: ["--fix", "--show-fixes"]
       - id: ruff-format
 
   # Also run Black on examples in the documentation
@@ -72,20 +80,20 @@ repos:
 
   # Check for license headers
   - repo: https://github.com/emzeat/mz-lictools
-    rev: v2.8.0
+    rev: v2.9.0
     hooks:
       - id: license-tools
 
   # Format configuration files with prettier
   - repo: https://github.com/rbubley/mirrors-prettier
-    rev: v3.6.2
+    rev: v3.7.3
     hooks:
       - id: prettier
         types_or: [yaml, markdown, html, css, scss, javascript, json]
 
   # Check static types with mypy
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.18.2
+    rev: v1.19.0
     hooks:
       - id: mypy
         files: ^(src/mqt|test/python)
@@ -104,7 +112,7 @@ repos:
 
   # Check for spelling
   - repo: https://github.com/crate-ci/typos
-    rev: v1.39.2
+    rev: v1.40.0
     hooks:
       - id: typos
 

noxfile.py

@@ -54,10 +54,10 @@ def preserve_lockfile() -> Generator[None]:
 @nox.session(reuse_venv=True, default=True)
 def lint(session: nox.Session) -> None:
     """Run the linter."""
-    if shutil.which("pre-commit") is None:
-        session.install("pre-commit")
+    if shutil.which("prek") is None:
+        session.install("prek")
 
-    session.run("pre-commit", "run", "--all-files", *session.posargs, external=True)
+    session.run("prek", "run", "--all-files", *session.posargs, external=True)
 
 
 def _run_tests(

pyproject.toml

@@ -55,42 +55,42 @@ dependencies = [
 classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Developers",
-    "Operating System :: Microsoft :: Windows",
+    "Intended Audience :: Science/Research",
+    "Natural Language :: English",
     "Operating System :: MacOS",
+    "Operating System :: Microsoft :: Windows",
     "Operating System :: POSIX :: Linux",
+    "Programming Language :: Python",
     "Programming Language :: Python :: 3 :: Only",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
-    "Programming Language :: Python :: 3.14",
-    "Intended Audience :: Science/Research",
-    "Natural Language :: English",
     "Topic :: Scientific/Engineering :: Electronic Design Automation (EDA)",
+    "Typing :: Typed",
 ]
 
 [dependency-groups]
 test = [
-    "pytest>=8.4.1",
-    "pytest-cov>=6.2.1",
+    "pytest>=9.0.1",
+    "pytest-cov>=7.0.0",
 ]
 docs = [
-    "furo>=2024.8.6",
-    "myst-nb>=1.2.0",
-    "setuptools-scm>=8.3.1",
-    "sphinx-design>=0.6.1",
+    "furo>=2025.09.25",
+    "myst-nb>=1.3.0",
+    "setuptools-scm>=9.2.2",
+    "sphinx>=8.1.3",
+    "sphinx>=8.2.3; python_version >= '3.11'",
     "sphinx-autoapi>=3.6.0",
     "sphinx-copybutton>=0.5.2",
+    "sphinx-design>=0.6.1",
     "sphinxcontrib-bibtex>=2.6.5",
     "sphinxcontrib-svg2pdfconverter>=1.3.0",
-    "sphinxext-opengraph>=0.10.0",
-    "sphinx>=7.4.7",
-    "sphinx>=8.1.3; python_version >= '3.10'",
-    "sphinx>=8.2.3; python_version >= '3.11'",
+    "sphinxext-opengraph>=0.13.0",
 ]
 dev = [
-  {include-group = "test"},
-  {include-group = "docs"},
+    {include-group = "test"},
+    "nox>=2025.11.12",
 ]
 
 [project.urls]
@@ -109,17 +109,15 @@ source = "vcs"
 version-file = "src/mqt/predictor/_version.py"
 
 
-[tool.pytest.ini_options]
-minversion = "7.2"
-testpaths = ["tests/"]
+[tool.pytest]
+minversion = "9.0"
+testpaths = ["tests"]
+strict = true
 addopts = [
     "-ra",
-    "--strict-markers",
-    "--strict-config",
     "--showlocals",
 ]
 log_level = "INFO"
-xfail_strict = true
 filterwarnings = [
     'error',
     'ignore:.*pytorch.*:UserWarning:',
@@ -135,6 +133,7 @@ filterwarnings = [
 
 ]
 
+
 [tool.coverage]
 run.source = ["mqt.predictor"]
 report.exclude_also = [
@@ -146,11 +145,11 @@ report.exclude_also = [
 run.disable_warnings = [
     "no-sysmon",
 ]
-
 show_missing = true
 skip_empty = true
 precision = 1
 
+
 [tool.mypy]
 mypy_path = "$MYPY_CONFIG_FILE_DIR/src"
 files = ["src", "tests"]
@@ -173,19 +172,25 @@ implicit_reexport = true
 module = ["qiskit.*", "joblib.*", "sklearn.*", "matplotlib.*", "gymnasium.*", "mqt.bench.*", "sb3_contrib.*", "bqskit.*", "qiskit_ibm_runtime.*", "networkx.*", "stable_baselines3.*","qiskit_ibm_transpiler.*"]
 ignore_missing_imports = true
 
+
 [tool.ruff]
 line-length = 120
-extend-include = ["*.ipynb"]
+namespace-packages = ["mqt"]
 preview = true
+fix = true
 unsafe-fixes = true
+show-fixes = true
+
+[tool.ruff.format]
+docstring-code-format = true
 
 [tool.ruff.lint]
 extend-select = [
     "A",           # flake8-builtins
     "ANN",         # flake8-annotations
     "ARG",         # flake8-unused-arguments
     "ASYNC",       # flake8-async
-    "B",  "B904",  # flake8-bugbear
+    "B",           # flake8-bugbear
     "C4",          # flake8-comprehensions
     "D",           # pydocstyle
     "EM",          # flake8-errmsg
@@ -220,9 +225,8 @@ extend-select = [
     "YTT",         # flake8-2020
 ]
 ignore = [
-    "ISC001",  # Conflicts with formatter
     "E501",    # Line too long (Black is enough)
-    "PLR",     # Design related pylint codes
+    "PLR",     # Design-related pylint codes
     "S101",    # Use of assert detected
 ]
 flake8-unused-arguments.ignore-variadic-names = true
@@ -249,12 +253,14 @@ default.extend-ignore-re = [
   "(?Rm)^.*(#|//)\\s*spellchecker:disable-line$",  # ignore line
   "(?s)(#|//)\\s*spellchecker:off.*?\\n\\s*(#|//)\\s*spellchecker:on" # ignore block
 ]
+
 [tool.typos.default.extend-words]
 wille = "wille"
 anc = "anc"
 aer = "aer"
 fom = "fom"
 
+
 [tool.repo-review]
 ignore = ["GH200"]