Bump setuptools from 81.0.0 to 82.0.1

[dependabot]

Bumps setuptools from 81.0.0 to 82.0.1.

Changelog

Sourced from setuptools's changelog.

v82.0.1

Bugfixes

• Fix the loading of launcher manifest.xml file. (#5047)
• Replaced deprecated json.__version__ with fixture in tests. (#5186)

Improved Documentation

• Add advice about how to improve predictability when installing sdists. (#5168)

Misc

• #4941, #5157, #5169, #5175

v82.0.0

Deprecations and Removals

• pkg_resources has been removed from Setuptools. Most common uses of pkg_resources have been superseded by the importlib.resources <https://docs.python.org/3/library/importlib.resources.html>_ and importlib.metadata <https://docs.python.org/3/library/importlib.metadata.html>_ projects. Projects and environments relying on pkg_resources for namespace packages or other behavior should depend on older versions of setuptools. (#3085)

Commits

• 5a13876 Bump version: 82.0.0 → 82.0.1
• 51ab8f1 Avoid using (deprecated) 'json.version' in tests (#5194)
• f9c37b2 Docs/CI: Fix intersphinx references (#5195)
• 8173db2 Docs: Fix intersphinx references
• 09bafbc Fix past tense on newsfragment
• 461ea56 Add news fragment
• c4ffe53 Avoid using (deprecated) 'json.version' in tests
• 749258b Cleanup pkg_resources dependencies and configuration (#5175)
• 2019c16 Parse ext-module.define-macros from pyproject.toml as list of tuples (#5169)
• b809c86 Sync setuptools schema with validate-pyproject (#5157)
• Additional commits viewable in compare view

[github-actions]

❌MegaLinter analysis: Error

Descriptor	Linter	Files	Fixed	Errors	Warnings	Elapsed time
✅ COPYPASTE	jscpd	yes		no	no	13.85s
✅ JSON	prettier	2	0	0	0	0.41s
✅ JSON	v8r	2		0	0	2.38s
✅ MARKDOWN	markdownlint	2	0	0	0	0.68s
✅ MARKDOWN	markdown-table-formatter	2	0	0	0	0.21s
✅ PYTHON	bandit	349		0	0	5.39s
✅ PYTHON	black	349	10	0	0	8.64s
✅ PYTHON	flake8	349		0	0	2.94s
✅ PYTHON	isort	349	11	0	0	0.7s
✅ PYTHON	mypy	349		0	0	4.83s
❌ PYTHON	pylint	349		5	0	108.19s
✅ PYTHON	ruff	349	11	0	0	0.07s
✅ REPOSITORY	checkov	yes		no	no	23.4s
✅ REPOSITORY	gitleaks	yes		no	no	6.97s
✅ REPOSITORY	git_diff	yes		no	no	0.14s
✅ REPOSITORY	secretlint	yes		no	no	6.91s
✅ REPOSITORY	syft	yes		no	no	4.15s
✅ REPOSITORY	trivy-sbom	yes		no	no	2.25s
✅ REPOSITORY	trufflehog	yes		no	no	18.93s
✅ YAML	prettier	4	0	0	0	0.46s
✅ YAML	v8r	4		0	0	4.77s
✅ YAML	yamllint	4		0	0	0.46s

Detailed Issues

❌ PYTHON / pylint - 5 errors

************* Module update_init_helper
update_init_helper.py:1:0: R0801: Similar lines in 2 files
==pyrecest.utils.nonrigid_point_set_registration:[211:221]
==pyrecest.utils.point_set_registration:[241:251]
    costs = asarray(cost_matrix)
    if costs.ndim != 2:
        raise ValueError("cost_matrix must be two-dimensional.")
    if costs.shape[0] == 0:
        return zeros((0,), dtype=int64)
    if costs.shape[1] == 0:
        return zeros((costs.shape[0],), dtype=int64) - 1

    finite_mask = isfinite(costs)
    finite_costs = costs[finite_mask] (duplicate-code)
update_init_helper.py:1:0: R0801: Similar lines in 2 files
==pyrecest.utils.nonrigid_point_set_registration:[124:135]
==pyrecest.utils.point_set_registration:[107:118]
    assignment: Any
    matched_reference_indices: Any
    matched_moving_indices: Any
    transformed_reference_points: Any
    matched_costs: Any
    rmse: float
    n_iterations: int
    converged: bool


def _as_point_array(points): (duplicate-code)
update_init_helper.py:1:0: R0801: Similar lines in 2 files
==pyrecest.utils.nonrigid_point_set_registration:[319:329]
==pyrecest.utils.point_set_registration:[390:400]
    association_cost = _default_cost if cost_function is None else cost_function

    for iteration in range(1, max_iterations + 1):
        transformed_reference = transform.apply(reference)
        current_costs = asarray(association_cost(transformed_reference, moving))
        if current_costs.shape != (reference.shape[0], moving.shape[0]):
            raise ValueError(
                "cost_function must return an array of shape (n_reference, n_moving)."
            )
 (duplicate-code)
update_init_helper.py:1:0: R0801: Similar lines in 2 files
==pyrecest.utils.nonrigid_point_set_registration:[146:154]
==pyrecest.utils.point_set_registration:[129:137]
    source = _as_point_array(source_points)
    target = _as_point_array(target_points)
    if source.shape != target.shape:
        raise ValueError("source_points and target_points must have the same shape.")
    return source, target


def _normalize_weights(weights, n_points): (duplicate-code)
update_init_helper.py:1:0: R0801: Similar lines in 2 files
==pyrecest.utils.nonrigid_point_set_registration:[230:236]
==pyrecest.utils.point_set_registration:[262:268]
    row_indices, col_indices = linear_sum_assignment(padded_costs)
    assignment = zeros((costs.shape[0],), dtype=int64) - 1

    for row_index, col_index in zip(row_indices, col_indices):
        if row_index >= costs.shape[0] or col_index >= costs.shape[1]:
            continue (duplicate-code)

------------------------------------
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[github-actions]

Test Results

    12 files  ±0     12 suites  ±0   4h 33m 15s ⏱️ + 2m 6s
   997 tests ±0    997 ✅ ±0      0 💤 ±0  0 ❌ ±0 
12 248 runs  ±0  9 460 ✅ ±0  2 788 💤 ±0  0 ❌ ±0 

Results for commit 6d08494. ± Comparison against base commit 4e875a1.

♻️ This comment has been updated with latest results.

[FlorianPfaff]

@dependabot rebase