🚨 update pre-commit, lockfile, and adjust for Qiskit 1.3 (#341)

## Description

This PR combines a couple of updates for the project configuration that
are long overdue.

## Checklist:

<!---
This checklist serves as a reminder of a couple of things that ensure
your pull request will be merged swiftly.
-->

- [x] The pull request only contains commits that are related to it.
- [x] I have added appropriate tests and documentation.
- [x] I have made sure that all CI jobs on GitHub pass.
- [x] The pull request introduces no new warnings and follows the
project's style guidelines.

---------

Signed-off-by: burgholzer <[email protected]>

.github/workflows/cd.yml

@@ -17,7 +17,7 @@ jobs:
   # whether the workflow is triggered from a PR, a push to main, or a release, respectively.
   python-packaging:
     name: 🐍 Packaging
-    uses: cda-tum/mqt-workflows/.github/workflows/reusable-python-packaging.yml@v1.4
+    uses: cda-tum/mqt-workflows/.github/workflows/reusable-python-packaging.yml@v1.5
     with:
       # Do not include local version information on pushes to main to facilitate TestPyPI uploads.
       no-local-version: ${{ github.ref == 'refs/heads/main' && github.event_name == 'push' }}
@@ -60,7 +60,7 @@ jobs:
           path: dist
           merge-multiple: true
       - name: Generate artifact attestation for sdist and wheel(s)
-        uses: actions/attest-build-provenance@v1.4.4
+        uses: actions/attest-build-provenance@v2
         with:
           subject-path: "dist/*"
       - uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/ci.yml

@@ -14,37 +14,37 @@ concurrency:
 jobs:
   change-detection:
     name: 🔍 Change
-    uses: cda-tum/mqt-workflows/.github/workflows/reusable-change-detection.yml@v1.4
+    uses: cda-tum/mqt-workflows/.github/workflows/reusable-change-detection.yml@v1.5
 
   cpp-tests:
     name: 🇨‌ Test
     needs: change-detection
     if: fromJSON(needs.change-detection.outputs.run-cpp-tests)
-    uses: cda-tum/mqt-workflows/.github/workflows/reusable-cpp-ci.yml@v1.4
+    uses: cda-tum/mqt-workflows/.github/workflows/reusable-cpp-ci.yml@v1.5
 
   cpp-linter:
     name: 🇨‌ Lint
     needs: change-detection
     if: fromJSON(needs.change-detection.outputs.run-cpp-linter)
-    uses: cda-tum/mqt-workflows/.github/workflows/reusable-cpp-linter.yml@v1.4
+    uses: cda-tum/mqt-workflows/.github/workflows/reusable-cpp-linter.yml@v1.5
 
   python-tests:
     name: 🐍 Test
     needs: change-detection
     if: fromJSON(needs.change-detection.outputs.run-python-tests)
-    uses: cda-tum/mqt-workflows/.github/workflows/reusable-python-ci.yml@v1.4
+    uses: cda-tum/mqt-workflows/.github/workflows/reusable-python-ci.yml@v1.5
 
   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.yml@v1.4
+    uses: cda-tum/mqt-workflows/.github/workflows/reusable-code-ql.yml@v1.5
 
   cd:
     name: 🚀 CD
     needs: change-detection
     if: fromJSON(needs.change-detection.outputs.run-cd)
-    uses: cda-tum/mqt-workflows/.github/workflows/reusable-python-packaging.yml@v1.4
+    uses: cda-tum/mqt-workflows/.github/workflows/reusable-python-packaging.yml@v1.5
 
   required-checks-pass: # This job does nothing and is only used for branch protection
     name: 🚦 Check

.github/workflows/update-mqt-core.yml

@@ -21,6 +21,6 @@ concurrency:
 jobs:
   update-mqt-core:
     name: ⬆️ Update MQT Core
-    uses: cda-tum/mqt-workflows/.github/workflows/reusable-mqt-core-update.yml@v1.4
+    uses: cda-tum/mqt-workflows/.github/workflows/reusable-mqt-core-update.yml@v1.5
     with:
       update-to-head: ${{ github.event.inputs.update-to-head == 'true' }}

.pre-commit-config.yaml

@@ -59,7 +59,7 @@ repos:
 
   #  Python linting and formatting using ruff
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.3
+    rev: v0.8.2
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes"]
@@ -87,13 +87,13 @@ repos:
 
   # Check for spelling
   - repo: https://github.com/crate-ci/typos
-    rev: v1.28.2
+    rev: typos-dict-v0.11.37
     hooks:
       - id: typos
 
   # Clang-format the C++ part of the code base automatically
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v19.1.4
+    rev: v19.1.5
     hooks:
       - id: clang-format
         types_or: [c++, c, cuda]
@@ -140,6 +140,6 @@ repos:
 
   # Check the pyproject.toml file
   - repo: https://github.com/henryiii/validate-pyproject-schema-store
-    rev: 2024.11.11
+    rev: 2024.11.25
     hooks:
       - id: validate-pyproject

noxfile.py

@@ -61,13 +61,13 @@ def _run_tests(
     if shutil.which("ninja") is None:
         session.install("ninja")
 
-    _extras = ["test", *extras]
+    extras_ = ["test", *extras]
     if "--cov" in posargs:
-        _extras.append("coverage")
+        extras_.append("coverage")
         posargs.append("--cov-config=pyproject.toml")
 
     session.install(*BUILD_REQUIREMENTS, *install_args, env=env)
-    install_arg = f"-ve.[{','.join(_extras)}]"
+    install_arg = f"-ve.[{','.join(extras_)}]"
     session.install("--no-build-isolation", install_arg, *install_args, env=env)
     session.run("pytest", *run_args, *posargs, env=env)
 

pyproject.toml

@@ -57,7 +57,7 @@ dependencies = [
     "numba>=0.57; python_version <= '3.11'",
     "pymatching>=2.2.1",
     "qsample>=0.0.2",
-    "urllib3>=1.26.20,<2.0", # Required by qsample
+    "urllib3>=1.26.20", # Required by qsample (to be removed)
     "fastcore>=1.7.10" # Required by qsample (to be removed)
 ]
 dynamic = ["version"]
@@ -157,14 +157,20 @@ addopts = ["-ra", "--strict-markers", "--strict-config", "--showlocals"]
 log_cli_level = "INFO"
 xfail_strict = true
 filterwarnings = [
-    "error",
-    "ignore:.*pkg_resources.*:DeprecationWarning:",
-    "ignore:.*The retworkx package is deprecated*:DeprecationWarning:pymatching",
-    'ignore:.*qiskit.providers.provider.Provider.*:DeprecationWarning:',
-    'ignore::DeprecationWarning:.*(simpleeval).*',
-    'ignore::RuntimeWarning:.*(qsample).*',
-    'ignore:.*invalid escape sequence.*::.*qsample.*',
-    'ignore:.*invalid escape sequence.*::.*latextools.*',
+  "error",
+  "ignore:.*pkg_resources.*:DeprecationWarning:",
+  "ignore:.*The retworkx package is deprecated*:DeprecationWarning:pymatching",
+  'ignore:.*qiskit.providers.provider.Provider.*:DeprecationWarning:',
+  'ignore::DeprecationWarning:.*(simpleeval).*',
+  'ignore::RuntimeWarning:.*(qsample).*',
+  'ignore:.*invalid escape sequence.*::.*qsample.*',
+  'ignore:.*invalid escape sequence.*::.*latextools.*',
+  # Qiskit 1.3 deprecations
+  'ignore:.*``qiskit.dagcircuit.dagcircuit.DAGCircuit.*`` is deprecated as of qiskit 1.3.0.*:DeprecationWarning:',
+  'ignore:.*``qiskit.circuit.instruction.Instruction.condition`` is deprecated as of qiskit 1.3.0.*:DeprecationWarning:',
+  'ignore:.*Conditioned gates in qasm2 will be loaded as an IfElseOp starting in Qiskit 2.0.*:FutureWarning:',
+  'ignore:.*``qiskit.circuit.singleton.*`` is deprecated as of qiskit 1.3.0.*:DeprecationWarning:',
+  'ignore:.*``qiskit.circuit.instruction.Instruction.c_if.*`` is deprecated as of qiskit 1.3.0.*:DeprecationWarning:',
 ]
 
 [tool.coverage]
@@ -243,20 +249,17 @@ extend-select = [
     "SLOT",        # flake8-slots
     "SIM",         # flake8-simplify
     "T20",         # flake8-print
-    "TCH",         # flake8-type-checking
+    "TC",          # flake8-type-checking
     "TID251",      # flake8-tidy-imports.banned-api
     "TRY",         # tryceratops
     "UP",          # pyupgrade
     "YTT",         # flake8-2020
 ]
 ignore = [
-    "ANN101",  # Missing type annotation for `self` in method
-    "ANN102",  # Missing type annotation for `cls` in classmethod
     "ISC001",  # Conflicts with formatter
     "PLR09",   # Too many <...>
     "PLR2004", # Magic value used in comparison
     "PLC0415", # Import should be at top of file
-    "PT004",   # Incorrect, just usefixtures instead.
     "S101",    # Use of assert detected
 ]
 isort.required-imports = ["from __future__ import annotations"]
@@ -304,7 +307,7 @@ archs = "auto64"
 test-command = "python -c \"from mqt import qecc\""
 test-skip = ["cp313*"] # skip testing on Python 3.13 until our dependencies are ready
 build-frontend = "build[uv]"
-free-threaded-support = true
+enable = ["cpython-freethreading"]
 manylinux-x86_64-image = "manylinux_2_28"
 manylinux-aarch64-image = "manylinux_2_28"
 manylinux-ppc64le-image = "manylinux_2_28"

src/mqt/qecc/analog_information_decoding/utils/data_utils.py

@@ -258,19 +258,19 @@ def merge_datasets(datasets: list[dict[str, Any]]) -> dict[str, Any]:
     return merged_data
 
 
-def _merge_datasets_x(_datasets: list[dict[str, Any]]) -> dict[str, Any]:
+def _merge_datasets_x(datasets_: list[dict[str, Any]]) -> dict[str, Any]:
     """Merges a list of dictionaries into a single dictionary.
 
     The values for the fields "nr_runs", "x_success_cnt" and "z_success_cnt" are extracted from each dictionary and added together.
 
     Args:
-        datasets (List[Dict[str, Any]]): A list of dictionaries to be merged.
+        datasets_ (List[Dict[str, Any]]): A list of dictionaries to be merged.
 
     Returns:
         Dict[str, Any]: A dictionary containing the merged data.
     """
     # remove datasets that do not contain x_success_cnt
-    datasets = [data for data in _datasets if "x_success_cnt" in data]
+    datasets = [data for data in datasets_ if "x_success_cnt" in data]
 
     if not datasets:
         return {}
@@ -305,19 +305,19 @@ def _merge_datasets_x(_datasets: list[dict[str, Any]]) -> dict[str, Any]:
     return merged_data
 
 
-def _merge_datasets_z(_datasets: list[dict[str, Any]]) -> dict[str, Any]:
+def _merge_datasets_z(datasets_: list[dict[str, Any]]) -> dict[str, Any]:
     """Merges a list of dictionaries into a single dictionary. The values for the fields "nr_runs".
 
     "x_success_cnt" and "z_success_cnt" are extracted from each dictionary and added together.
 
     Args:
-        datasets (List[Dict[str, Any]]): A list of dictionaries to be merged.
+        datasets_ (List[Dict[str, Any]]): A list of dictionaries to be merged.
 
     Returns:
         Dict[str, Any]: A dictionary containing the merged data.
     """
     # remove datasets that do not contain z_success_cnt
-    datasets = [data for data in _datasets if "z_success_cnt" in data]
+    datasets = [data for data in datasets_ if "z_success_cnt" in data]
 
     if not datasets:
         return {}

src/mqt/qecc/cc_decoder/plots.py

@@ -48,7 +48,7 @@ def threshold_fit(
     """Compute standard fit function for the threshold."""
     p, ell = variables
     expr = (p - pth) * (ell ** (1 / mu))
-    return cast(float, b0 + b1 * expr + b2 * (expr**2))
+    return cast("float", b0 + b1 * expr + b2 * (expr**2))
 
 
 def calculate_threshold(

src/mqt/qecc/circuit_synthesis/encoding.py

@@ -36,7 +36,7 @@ def heuristic_encoding_circuit(
     Returns:
         The synthesized encoding circuit and the qubits that are used to encode the logical qubits.
     """
-    logging.info("Starting encoding circuit synthesis.")
+    logger.info("Starting encoding circuit synthesis.")
 
     checks, logicals, use_x_checks = _get_matrix_with_fewest_checks(code)
     n_checks = checks.shape[0]
@@ -93,7 +93,7 @@ def gate_optimal_encoding_circuit(
     Returns:
         The synthesized encoding circuit and the qubits that are used to encode the logical qubits.
     """
-    logging.info("Starting optimal encoding circuit synthesis.")
+    logger.info("Starting optimal encoding circuit synthesis.")
     checks, logicals, use_x_checks = _get_matrix_with_fewest_checks(code)
     assert checks is not None
     n_checks = checks.shape[0]
@@ -141,7 +141,7 @@ def depth_optimal_encoding_circuit(
     Returns:
         The synthesized encoding circuit and the qubits that are used to encode the logical qubits.
     """
-    logging.info("Starting optimal encoding circuit synthesis.")
+    logger.info("Starting optimal encoding circuit synthesis.")
     checks, logicals, use_x_checks = _get_matrix_with_fewest_checks(code)
     assert checks is not None
     n_checks = checks.shape[0]

src/mqt/qecc/circuit_synthesis/simulation.py

@@ -19,6 +19,8 @@
 
     from ..codes import CSSCode
 
+logger = logging.getLogger(__name__)
+
 
 class NoisyNDFTStatePrepSimulator:
     """Class for simulating noisy state preparation circuit using a depolarizing noise model."""
@@ -245,8 +247,7 @@ def logical_error_rate(
         while i <= int(np.ceil(shots / batch)) or at_least_min_errors:
             num_logical_errors_batch, discarded_batch = self._simulate_batch(batch)
 
-            logging.log(
-                logging.INFO,
+            logger.info(
                 f"Batch {i}: {num_logical_errors_batch} logical errors and {discarded_batch} discarded shots. {batch - discarded_batch} shots used.",
             )
             p_l_batch = num_logical_errors_batch / (batch - discarded_batch) if discarded_batch != batch else 0.0