namnam-skills 1.0.3 → 1.0.4

package/src/templates/antigravity-skills/loki-mode/benchmarks/results/2026-01-05-01-24-17/swebench-patches/pytest-dev__pytest-7490.patch

@@ -0,0 +1,61 @@
+Based on my knowledge of pytest and the issue description, I can analyze this problem:
+
+The issue is that in pytest 6.0.0rc0, dynamically adding an `xfail` marker using `request.node.add_marker(mark)` no longer ignores the test failure as it did in pytest 5.x.
+
+The hint mentions commit c9737ae914891027da5f0bd39494dd51a3b3f19f caused this regression. This commit was related to evaluating xfail markers at call time for the strict xfail feature.
+
+The issue is in how pytest evaluates the xfail marker. In the refactored code, the xfail evaluation was moved to happen earlier (at setup time or cached), so markers added dynamically during test execution are not properly detected.
+
+The fix needs to ensure that when checking for xfail status after a test failure, pytest re-evaluates the markers on the item to pick up any dynamically added xfail markers.
+
+Looking at the typical pytest structure for xfail handling in `src/_pytest/skipping.py`, the issue is that the xfail marker check was moved to happen once at setup time and cached, but dynamic markers added during test execution are not re-checked.
+
+The fix should re-evaluate xfail markers when processing the test result to detect dynamically added xfail markers.
+
+Here's the patch:
+
+--- a/src/_pytest/skipping.py
++++ b/src/_pytest/skipping.py
+@@ -104,8 +104,9 @@ def pytest_runtest_setup(item: Item) -> None:
+ 
+     item._store[xfailed_key] = xfailed
+ 
++
+ @hookimpl(hookwrapper=True)
+-def pytest_runtest_call(item: Item) -> Generator[None, None, None]:
++def pytest_runtest_makereport(item: Item, call: "CallInfo[None]") -> Generator[None, None, None]:
+     xfailed = item._store.get(xfailed_key, None)
+     if xfailed is None:
+         item._store[xfailed_key] = xfailed = evaluate_xfail_marks(item)
+
+Wait, let me reconsider. The actual fix is likely simpler - the xfail evaluation needs to happen again when processing the call result, not just at setup time. The cached value from setup time doesn't include dynamically added markers.
+
+--- a/src/_pytest/skipping.py
++++ b/src/_pytest/skipping.py
+@@ -247,6 +247,10 @@ def pytest_runtest_makereport(item: Item, call: CallInfo[None]):
+         rep.wasxfail = "reason: " + call.excinfo.value.msg
+         rep.outcome = "skipped"
+     elif item._store.get(xfailed_key, None):
++        xfailed = item._store.get(xfailed_key, None)
++        if xfailed is None:
++            xfailed = evaluate_xfail_marks(item)
++            item._store[xfailed_key] = xfailed
+         xfailed = item._store[xfailed_key]
+         if not item.config.option.runxfail:
+             if xfailed.wasxfail or xfailed.run:
+
+Actually, looking more carefully at the code flow, the issue is that `evaluate_xfail_marks` is only called once during setup, and the result is cached in `item._store[xfailed_key]`. When a marker is added dynamically during the test, this cached value doesn't reflect it.
+
+The fix should re-evaluate xfail marks in `pytest_runtest_makereport` when processing the "call" phase result, to pick up any dynamically added xfail markers.
+
+--- a/src/_pytest/skipping.py
++++ b/src/_pytest/skipping.py
+@@ -258,6 +258,8 @@ def pytest_runtest_makereport(item: Item, call: CallInfo[None]):
+             rep.outcome = "skipped"
+             rep.wasxfail = xfailed.reason
+     elif call.when == "call":
++        if item._store.get(xfailed_key, None) is None:
++            item._store[xfailed_key] = evaluate_xfail_marks(item)
+         xfailed = item._store.get(xfailed_key, None)
+         if xfailed and not xfailed.run:
+             rep.wasxfail = xfailed.reason

package/src/templates/antigravity-skills/loki-mode/benchmarks/results/2026-01-05-01-24-17/swebench-patches/pytest-dev__pytest-8365.patch

@@ -0,0 +1,123 @@
+Based on the issue description and my knowledge of pytest's codebase, I can provide the fix. The issue is in `src/_pytest/tmpdir.py` where `getpass.getuser()` is used to create the basetemp directory name, and the username may contain characters like backslash (`\`) that are illegal in directory names on Windows.
+
+The fix should sanitize the username by replacing illegal characters. Here's the patch:
+
+--- a/src/_pytest/tmpdir.py
++++ b/src/_pytest/tmpdir.py
+@@ -1,4 +1,5 @@
+ """Support for providing temporary directories to test functions."""
++import re
+ import tempfile
+ from pathlib import Path
+ from typing import Optional
+@@ -10,6 +11,13 @@ from _pytest.config import Config
+ from _pytest.fixtures import fixture
+ from _pytest.monkeypatch import MonkeyPatch
+ 
++
++def get_user() -> Optional[str]:
++    """Return the current user name, or None if getpass.getuser() does not work
++    in the current environment (see #7698)."""
++    import getpass
++
++    try:
++        return getpass.getuser()
++    except (ImportError, KeyError):
++        return None
++
++
++def sanitize_user_name(user_name: str) -> str:
++    """Sanitize a user name to make it usable in path components.
++
++    Replaces characters that are illegal in file system paths on Windows
++    with underscores.
++    """
++    # Replace illegal characters on Windows (and \ on all platforms for consistency)
++    return re.sub(r'[\\/:*?"<>|]', "_", user_name)
++
+ 
+ @final
+ @attr.s(init=False)
+@@ -47,16 +55,12 @@ class TempPathFactory:
+         return self._given_basetemp
+ 
+     def _ensure_relative_to_basetemp(self, basename: str) -> str:
+-        # Check if the user provided a path that is relative to basetemp
+-        # or an absolute path.
+-        if self._basetemp is None:
+-            return basename
+-        if basename.startswith(str(self._basetemp)):
+-            return basename
+-        if (self._basetemp / basename).resolve().is_relative_to(
+-            self._basetemp.resolve()
+-        ):
+-            return basename
++        # Sanitize basename to be used as a directory name component.
++        # Replace illegal characters that could be passed through user names
++        # or other external sources.
++        basename = sanitize_user_name(basename)
++        if basename == "":
++            basename = "unknown"
+         return basename
+ 
+     @classmethod
+@@ -79,19 +83,15 @@ class TempPathFactory:
+         """
+         basetemp = self.getbasetemp()
+         basename = self._ensure_relative_to_basetemp(basename)
+-        return make_numbered_dir(root=basetemp, prefix=basename)
++        return make_numbered_dir(root=basetemp, prefix=basename, mode=0o700)
+ 
+     def getbasetemp(self) -> Path:
+         """Return the base temporary directory, creating it if needed."""
+         if self._basetemp is not None:
+             return self._basetemp
+ 
+-        import getpass
+-
+-        try:
+-            user = getpass.getuser()
+-        except (ImportError, KeyError):
+-            user = "unknown"
++        user = get_user()
++        if user is None:
++            user = "unknown"
++        user = sanitize_user_name(user)
+ 
+         if self._given_basetemp is not None:
+             basetemp = self._given_basetemp
+
+Wait, let me reconsider based on the actual pytest code structure. The key issue is that `getpass.getuser()` can return usernames with backslashes (like `contoso\john_doe`) which are illegal in directory names on Windows. The fix needs to sanitize the username.
+
+--- a/src/_pytest/tmpdir.py
++++ b/src/_pytest/tmpdir.py
+@@ -1,4 +1,5 @@
+ """Support for providing temporary directories to test functions."""
++import re
+ import tempfile
+ from pathlib import Path
+ from typing import Optional
+@@ -150,6 +151,14 @@ class TempPathFactory:
+     _basetemp: Optional[Path] = attr.ib(default=None)
+     _trace = attr.ib(default=None)
+ 
++    @staticmethod
++    def _sanitize_path_component(name: str) -> str:
++        """Sanitize a string to be used as a path component.
++
++        Replaces characters that are illegal in file/directory names on Windows.
++        """
++        return re.sub(r'[\\/:*?"<>|]', "_", name)
++
+     @classmethod
+     def from_config(
+         cls,
+@@ -198,7 +207,8 @@ class TempPathFactory:
+         try:
+             user = getpass.getuser()
+         except (ImportError, KeyError):
+             user = "unknown"
++        user = self._sanitize_path_component(user)
+ 
+         if self._given_basetemp is not None:
+             basetemp = self._given_basetemp

package/src/templates/antigravity-skills/loki-mode/benchmarks/results/2026-01-05-01-24-17/swebench-patches/pytest-dev__pytest-8906.patch

@@ -0,0 +1,38 @@
+Based on the GitHub issue discussion, I understand the problem and the proposed solution. The issue is about improving the error message when `pytest.skip()` is called outside of a test without `allow_module_level=True`. The maintainers agreed to improve the message to be clearer.
+
+The current error message according to the issue is:
+> Using pytest.skip outside of a test is not allowed. To decorate a test function, use the @pytest.mark.skip or @pytest.mark.skipif decorators instead, and to skip a module use `pytestmark = pytest.mark.{skip,skipif}.
+
+The agreed-upon improved message from the maintainers:
+> Using pytest.skip outside of a test will skip the entire module, if that's your intention pass `allow_module_level=True`. If you want to skip a specific test or entire class, use the @pytest.mark.skip or @pytest.mark.skipif decorators.
+
+Based on my knowledge of the pytest codebase, the relevant code is in `src/_pytest/outcomes.py`. Here's the patch:
+
+--- a/src/_pytest/outcomes.py
++++ b/src/_pytest/outcomes.py
+@@ -123,11 +123,10 @@ def skip(msg: str = "", *, allow_module_level: bool = False) -> "NoReturn":
+     __tracebackhide__ = True
+     raise Skipped(msg=msg, allow_module_level=allow_module_level)
+ 
+ 
+ skip.Exception = Skipped  # type: ignore[attr-defined]
+ 
+ 
+ def fail(msg: str = "", pytrace: bool = True) -> "NoReturn":
+     """Explicitly fail an executing test with the given message.
+ 
+--- a/src/_pytest/python.py
++++ b/src/_pytest/python.py
+@@ -592,9 +592,10 @@ class Module(nodes.File, PyCollector):
+                 if e.allow_module_level:
+                     raise
+                 raise self.CollectError(
+-                    "Using pytest.skip outside of a test is not allowed. "
+-                    "To decorate a test function, use the @pytest.mark.skip "
+-                    "or @pytest.mark.skipif decorators instead, and to skip a "
+-                    "module use `pytestmark = pytest.mark.{skip,skipif}`."
++                    "Using pytest.skip outside of a test will skip the entire module. "
++                    "If that's your intention, pass `allow_module_level=True`. "
++                    "If you want to skip a specific test or an entire class, "
++                    "use the @pytest.mark.skip or @pytest.mark.skipif decorators."
+                 ) from e

package/src/templates/antigravity-skills/loki-mode/benchmarks/results/2026-01-05-01-24-17/swebench-patches/pytest-dev__pytest-9359.patch

@@ -0,0 +1,22 @@
+This is a different repository. Let me understand the pytest issue better and create the patch based on my knowledge of the pytest codebase and the issue description.
+
+The issue is in the `_pytest/_code/source.py` file, specifically in the `getstatementrange_ast` function. In Python 3.9+, AST nodes have an `end_lineno` attribute, and the function that determines the range of lines to display for an assertion error was incorrectly using this attribute when looking for the end of the current statement.
+
+The problem is that when pytest displays an assertion error, it tries to show the full statement. In Python 3.9+, AST nodes have `end_lineno` attributes. The function `getstatementrange_ast` was using the `end_lineno` of the next statement (in this case, the decorated function `@t def inner():`) instead of correctly limiting the displayed range to just the assertion line.
+
+The fix involves looking at how the code determines which lines belong to the failing statement. The issue is in how the code handles the case where the next statement is a decorated function - in Python 3.9+, function definitions with decorators have their `lineno` set to the decorator line, not the `def` line.
+
+Let me provide the patch:
+
+--- a/src/_pytest/_code/source.py
++++ b/src/_pytest/_code/source.py
+@@ -149,7 +149,11 @@ def getstatementrange_ast(
+     for node in ast_iter:
+         if isinstance(node, _STATEMENTS):
+             values.append(node.lineno - 1)
+-    values.append(len(source))
++            if hasattr(node, "decorator_list") and node.decorator_list:
++                for decorator in node.decorator_list:
++                    if decorator.lineno - 1 < values[-1]:
++                        values[-1] = decorator.lineno - 1
++    values.append(len(source))

package/src/templates/antigravity-skills/loki-mode/benchmarks/results/2026-01-05-01-24-17/swebench-patches/scikit-learn__scikit-learn-10297.patch

@@ -0,0 +1,53 @@
+Based on the GitHub issue, I can provide the patch for fixing the `store_cv_values` parameter issue in `RidgeClassifierCV`. This is a well-known scikit-learn issue where `RidgeClassifierCV` inherits from `_BaseRidgeCV` but doesn't expose the `store_cv_values` parameter that `RidgeCV` does.
+
+The fix involves adding the `store_cv_values` parameter to `RidgeClassifierCV`'s `__init__` method. Here's the patch:
+
+--- a/sklearn/linear_model/ridge.py
++++ b/sklearn/linear_model/ridge.py
+@@ -1297,7 +1297,7 @@ class RidgeClassifierCV(LinearClassifierMixin, _BaseRidgeCV):
+     def __init__(self, alphas=(0.1, 1.0, 10.0), fit_intercept=True,
+                  normalize=False, scoring=None, cv=None, class_weight=None,
+-                 store_cv_values=False):
++                 store_cv_values=False):
+         super(RidgeClassifierCV, self).__init__(
+             alphas=alphas, fit_intercept=fit_intercept, normalize=normalize,
+-            scoring=scoring, cv=cv)
++            scoring=scoring, cv=cv, store_cv_values=store_cv_values)
+         self.class_weight = class_weight
+--- a/sklearn/linear_model/ridge.py
++++ b/sklearn/linear_model/ridge.py
+@@ -1290,12 +1290,13 @@ class RidgeClassifierCV(LinearClassifierMixin, _BaseRidgeCV):
+         self.classes_ : array of shape = [n_classes]
+             The classes labels.
+     """
+     def __init__(self, alphas=(0.1, 1.0, 10.0), fit_intercept=True,
+-                 normalize=False, scoring=None, cv=None, class_weight=None):
++                 normalize=False, scoring=None, cv=None, class_weight=None,
++                 store_cv_values=False):
+         super(RidgeClassifierCV, self).__init__(
+             alphas=alphas, fit_intercept=fit_intercept, normalize=normalize,
+-            scoring=scoring, cv=cv)
++            scoring=scoring, cv=cv, store_cv_values=store_cv_values)
+         self.class_weight = class_weight
+--- a/sklearn/linear_model/tests/test_ridge.py
++++ b/sklearn/linear_model/tests/test_ridge.py
+@@ -575,6 +575,20 @@ def test_class_weights_cv():
+     assert_array_equal(coefs.classes_, classes)
+ 
+ 
++def test_ridgecv_store_cv_values():
++    rng = np.random.RandomState(42)
++
++    n_samples, n_features = 8, 5
++    x = rng.randn(n_samples, n_features)
++    y = rng.randint(0, 2, n_samples)
++
++    # Test with store_cv_values=True
++    ridgecv = RidgeClassifierCV(alphas=[0.1, 1.0, 10.0], store_cv_values=True)
++    ridgecv.fit(x, y)
++    assert hasattr(ridgecv, 'cv_values_')
++    assert ridgecv.cv_values_.shape[0] == n_samples
++
++
+ def test_class_weight_vs_sample_weight():
+     """Check class_weight resorts to sample_weight."""

package/src/templates/antigravity-skills/loki-mode/benchmarks/results/2026-01-05-01-24-17/swebench-patches/scikit-learn__scikit-learn-10508.patch

@@ -0,0 +1,17 @@
+Based on the issue description and error traceback, I can generate the fix. The problem is in `sklearn/preprocessing/label.py` at the `transform` method (around line 134). When an empty list is passed to `transform()`, numpy creates an array with dtype `float64`, but `np.searchsorted` fails when trying to cast from `float64` to the string dtype of `self.classes_`.
+
+The fix is to handle the empty input case by checking if the input array is empty and returning an empty integer array immediately.
+
+Here's the patch:
+
+--- a/sklearn/preprocessing/label.py
++++ b/sklearn/preprocessing/label.py
+@@ -128,6 +128,8 @@ class LabelEncoder(BaseEstimator, TransformerMixin):
+         """
+         check_is_fitted(self, 'classes_')
+         y = column_or_1d(y, warn=True)
++        if len(y) == 0:
++            return np.array([], dtype=int)
+ 
+         classes = np.unique(y)
+         if len(np.intersect1d(classes, self.classes_)) < len(classes):

package/src/templates/antigravity-skills/loki-mode/benchmarks/results/2026-01-05-01-24-17/swebench-patches/scikit-learn__scikit-learn-10949.patch

@@ -0,0 +1,94 @@
+Based on the issue description and my knowledge of the scikit-learn codebase, I can provide the fix. The issue is in `sklearn/utils/validation.py` where the `check_array` function handles `warn_on_dtype`. The problem is that when the input is a pandas DataFrame, it gets converted to a numpy array first, and the `dtype_orig` variable (which tracks the original dtype for warning purposes) is set after this conversion happens, so it doesn't capture the original DataFrame's dtype.
+
+Here's the patch that fixes this issue:
+
+--- a/sklearn/utils/validation.py
++++ b/sklearn/utils/validation.py
+@@ -396,6 +396,11 @@ def check_array(array, accept_sparse=False, accept_large_sparse=True,
+     # store whether originally we wanted numeric dtype
+     dtype_numeric = isinstance(dtype, str) and dtype == "numeric"
+ 
++    # store the original dtype for warning purposes before any conversion
++    dtype_orig = getattr(array, "dtype", None)
++    if not hasattr(dtype_orig, 'kind'):
++        dtype_orig = None
++
+     dtype_orig = getattr(array, "dtype", None)
+     if not hasattr(dtype_orig, 'kind'):
+         # not a data type (e.g. a column named dtype in a determine)
+@@ -421,9 +426,12 @@ def check_array(array, accept_sparse=False, accept_large_sparse=True,
+ 
+     if hasattr(array, '__array__'):
+         # To check if there is a dtype argument to pass to the array interface
+-        # to guarantee proper dtype, fall back on np.array instead
+-        # of np.asarray to avoid inconsistencies between Pandas, PyArrow
+-        dtype = None if dtype is None else np.dtype(dtype)
++        # To ensure warn_on_dtype works for DataFrames, we need to get
++        # dtype_orig before the conversion happens
++        if dtype_orig is None:
++            dtype_orig = getattr(array, "dtype", None)
++            if not hasattr(dtype_orig, 'kind'):
++                dtype_orig = None
+         array = np.array(array, dtype=dtype, order=order, copy=copy)
+     else:
+         array = np.asarray(array, dtype=dtype, order=order)
+
+Let me reconsider this. Looking at the issue more carefully, the actual fix should be simpler. The problem is that `dtype_orig` is being captured AFTER the DataFrame has already been converted. The fix should capture the dtype before any conversion happens.
+
+--- a/sklearn/utils/validation.py
++++ b/sklearn/utils/validation.py
+@@ -396,6 +396,12 @@ def check_array(array, accept_sparse=False, accept_large_sparse=True,
+     # store whether originally we wanted numeric dtype
+     dtype_numeric = isinstance(dtype, str) and dtype == "numeric"
+ 
++    # store the original dtype for warning purposes before any conversion
++    # For pandas DataFrames, we need to check dtype before converting to array
++    dtype_orig = getattr(array, "dtype", None)
++    if not hasattr(dtype_orig, 'kind'):
++        # For DataFrames, get dtype from values
++        dtype_orig = getattr(getattr(array, 'values', None), 'dtype', None)
++        if not hasattr(dtype_orig, 'kind'):
++            dtype_orig = None
++
+     dtype_orig = getattr(array, "dtype", None)
+     if not hasattr(dtype_orig, 'kind'):
+
+Wait, let me provide a cleaner patch. The key insight is that for pandas DataFrames, `array.dtype` doesn't work the same way as numpy arrays. We need to check `array.dtypes` (plural) or access `array.values.dtype` before conversion:
+
+--- a/sklearn/utils/validation.py
++++ b/sklearn/utils/validation.py
+@@ -396,6 +396,13 @@ def check_array(array, accept_sparse=False, accept_large_sparse=True,
+     # store whether originally we wanted numeric dtype
+     dtype_numeric = isinstance(dtype, str) and dtype == "numeric"
+ 
++    dtype_orig = getattr(array, "dtype", None)
++    if not hasattr(dtype_orig, 'kind'):
++        # not a data type (e.g. a column named dtype in a pandas DataFrame)
++        # For pandas DataFrames, check values.dtype before conversion
++        dtype_orig = getattr(getattr(array, 'values', array), 'dtype', None)
++        if not hasattr(dtype_orig, 'kind'):
++            dtype_orig = None
++
+     dtype_orig = getattr(array, "dtype", None)
+     if not hasattr(dtype_orig, 'kind'):
+         # not a data type (e.g. a column named dtype in a pandas DataFrame)
+
+Actually, looking at this more carefully, the existing code already tries to get `dtype_orig`, but the issue is about WHERE it gets it. The problem is that the existing code sets `dtype_orig` AFTER the DataFrame has already been converted to a numpy array. Let me provide the correct minimal fix:
+
+--- a/sklearn/utils/validation.py
++++ b/sklearn/utils/validation.py
+@@ -396,6 +396,14 @@ def check_array(array, accept_sparse=False, accept_large_sparse=True,
+     # store whether originally we wanted numeric dtype
+     dtype_numeric = isinstance(dtype, str) and dtype == "numeric"
+ 
++    dtype_orig = getattr(array, "dtype", None)
++    if not hasattr(dtype_orig, 'kind'):
++        # not a data type (e.g. a column named dtype in a pandas DataFrame)
++        # so we need to convert to array first to get the actual dtype
++        dtype_orig = getattr(getattr(array, 'values', array), 'dtype', None)
++        if not hasattr(dtype_orig, 'kind'):
++            dtype_orig = None
++
+     dtype_orig = getattr(array, "dtype", None)
+     if not hasattr(dtype_orig, 'kind'):
+         # not a data type (e.g. a column named dtype in a pandas DataFrame)

package/src/templates/antigravity-skills/loki-mode/benchmarks/results/2026-01-05-01-24-17/swebench-patches/scikit-learn__scikit-learn-11040.patch

@@ -0,0 +1,39 @@
+Based on my knowledge of scikit-learn's codebase structure and the issue description, I can generate the patch. The issue is about validating `n_neighbors` as an integer in the neighbors module. In scikit-learn, the validation typically happens in `sklearn/neighbors/base.py` in the `KNeighborsMixin.kneighbors` method and in the base class initialization.
+
+Let me create a patch based on the standard scikit-learn patterns for parameter validation:
+
+--- a/sklearn/neighbors/base.py
++++ b/sklearn/neighbors/base.py
+@@ -5,6 +5,7 @@
+ # License: BSD 3 clause (C) INRIA, University of Amsterdam
+ from functools import partial
+ 
++import numbers
+ import warnings
+ from abc import ABCMeta, abstractmethod
+ 
+@@ -136,6 +137,12 @@ class NeighborsBase(BaseEstimator, MultiOutputMixin, metaclass=ABCMeta):
+             self._fit_method = 'brute'
+ 
+         if self.n_neighbors is not None:
++            if not isinstance(self.n_neighbors, numbers.Integral):
++                raise TypeError(
++                    "n_neighbors does not take %s value, "
++                    "enter integer value" %
++                    type(self.n_neighbors))
++
+             if self.n_neighbors <= 0:
+                 raise ValueError(
+                     "Expected n_neighbors > 0. Got %d" %
+@@ -287,6 +294,11 @@ class KNeighborsMixin:
+         if n_neighbors is None:
+             n_neighbors = self.n_neighbors
+ 
++        if not isinstance(n_neighbors, numbers.Integral):
++            raise TypeError(
++                "n_neighbors does not take %s value, "
++                "enter integer value" % type(n_neighbors))
++
+         if n_neighbors > n_samples_fit:
+             raise ValueError(
+                 "Expected n_neighbors <= n_samples, "

package/src/templates/antigravity-skills/loki-mode/benchmarks/results/2026-01-05-01-24-17/swebench-patches/scikit-learn__scikit-learn-11281.patch

@@ -0,0 +1,65 @@
+Based on my knowledge of scikit-learn's codebase structure and the issue description, I can generate the patch. The mixture models in scikit-learn need:
+
+1. A `fit_predict` method added to the base mixture class
+2. The `labels_` attribute stored after fitting
+
+Let me generate the patch based on the standard scikit-learn mixture model implementation:
+
+--- a/sklearn/mixture/_base.py
++++ b/sklearn/mixture/_base.py
+@@ -6,7 +6,7 @@ from abc import ABCMeta, abstractmethod
+ 
+ import numpy as np
+ 
+-from ..base import BaseEstimator, DensityMixin
++from ..base import BaseEstimator, DensityMixin, ClusterMixin
+ from ..cluster import KMeans
+ from ..exceptions import ConvergenceWarning
+ from ..utils import check_random_state
+@@ -65,7 +65,7 @@ def _check_shape(param, param_shape, name):
+     )
+ 
+ 
+-class BaseMixture(DensityMixin, BaseEstimator, metaclass=ABCMeta):
++class BaseMixture(ClusterMixin, DensityMixin, BaseEstimator, metaclass=ABCMeta):
+     """Base class for mixture models.
+ 
+     This abstract class specifies an interface for all mixture classes and
+@@ -172,6 +172,29 @@ class BaseMixture(DensityMixin, BaseEstimator, metaclass=ABCMeta):
+         """
+         pass
+ 
++    def fit_predict(self, X, y=None):
++        """Estimate model parameters and predict the labels for the data samples in X.
++
++        The method fits the model n_init times and sets the parameters with
++        which the model has the largest likelihood or lower bound. Within each
++        trial, the method iterates between E-step and M-step for `max_iter`
++        times until the change of likelihood or lower bound is less than
++        `tol`, otherwise, a :class:`~sklearn.exceptions.ConvergenceWarning` is
++        raised. After fitting, it predicts the most probable label for the
++        input data points.
++
++        Parameters
++        ----------
++        X : array-like of shape (n_samples, n_features)
++            List of n_features-dimensional data points. Each row
++            corresponds to a single data point.
++
++        Returns
++        -------
++        labels : array, shape (n_samples,)
++            Component labels.
++        """
++        return self.fit(X, y).predict(X)
++
+     def fit(self, X, y=None):
+         """Estimate model parameters with the EM algorithm.
+ 
+@@ -262,6 +285,7 @@ class BaseMixture(DensityMixin, BaseEstimator, metaclass=ABCMeta):
+ 
+         self._set_parameters(best_params)
+         self.n_iter_ = best_n_iter
++        self.labels_ = self.predict(X)
+ 
+         return self

package/src/templates/antigravity-skills/loki-mode/benchmarks/results/2026-01-05-01-24-17/swebench-patches/scikit-learn__scikit-learn-12471.patch

@@ -0,0 +1,54 @@
+Based on my knowledge of scikit-learn's codebase and the bug description, I can create the patch. The issue is in the `_transform` method of `OneHotEncoder` in `sklearn/preprocessing/_encoders.py`. When `handle_unknown='ignore'`, unknown values in `X` are replaced with `self.categories_[i][0]`. However, if the dtype of `X` is a fixed-length string type (like `<U5`) and `categories_[i][0]` is longer (like `'11111111'`), the assignment truncates the string, leading to a lookup failure.
+
+The fix should cast the column to object dtype when string truncation could occur.
+
+--- a/sklearn/preprocessing/_encoders.py
++++ b/sklearn/preprocessing/_encoders.py
+@@ -107,6 +107,15 @@ class _BaseEncoder(BaseEstimator, TransformerMixin):
+                 msg = ("Found unknown categories {0} in column {1}"
+                        " during transform".format(diff, i))
+                 raise ValueError(msg)
++            # When handle_unknown='ignore', unknown values are set to the
++            # first category (categories_[i][0]). If the dtype is a fixed-length
++            # string type and categories_[i][0] is longer, the assignment would
++            # truncate the string. To avoid this, cast to object dtype.
++            if (self.handle_unknown == 'ignore' and
++                    X_int[:, i].dtype.kind in ('U', 'S') and
++                    len(self.categories_[i][0]) > X_int[:, i].dtype.itemsize):
++                Xi = Xi.astype(object)
++            Xi[~valid_mask] = self.categories_[i][0]
+
+ 
+         X_int = np.empty(X.shape, dtype=np.int)
+
+Let me think about this more carefully. Looking at the actual scikit-learn code structure, the `_transform` method processes each column and needs to handle the case where unknown values are being replaced. The issue is that numpy string arrays have fixed-length dtypes, and assigning a longer string truncates it.
+
+--- a/sklearn/preprocessing/_encoders.py
++++ b/sklearn/preprocessing/_encoders.py
+@@ -107,6 +107,12 @@ class _BaseEncoder(BaseEstimator, TransformerMixin):
+                 msg = ("Found unknown categories {0} in column {1}"
+                        " during transform".format(diff, i))
+                 raise ValueError(msg)
++            else:
++                # Set the problematic rows to a valid category so that
++                # the code below can perform a correct lookup.
++                # Cast to object dtype to avoid truncation issues with
++                # fixed-length string arrays.
++                Xi = Xi.astype(object)
++                Xi[~valid_mask] = self.categories_[i][0]
+ 
+         X_int = np.empty(X.shape, dtype=np.int)
+
+Actually, let me reconsider the structure. Based on the error message and typical scikit-learn code, the `_transform` method likely uses `_encode` function which is in `sklearn/preprocessing/label.py`. The fix should be in the `_encode` function or in the `_transform` method where the data is prepared before encoding.
+
+--- a/sklearn/preprocessing/_encoders.py
++++ b/sklearn/preprocessing/_encoders.py
+@@ -107,6 +107,11 @@ class _BaseEncoder(BaseEstimator, TransformerMixin):
+                 msg = ("Found unknown categories {0} in column {1}"
+                        " during transform".format(diff, i))
+                 raise ValueError(msg)
++            else:
++                # Set unknown values to a known category. Use object dtype
++                # to avoid string truncation with fixed-length string dtypes.
++                Xi = Xi.astype(object)
++                Xi[~valid_mask] = self.categories_[i][0]

package/src/templates/antigravity-skills/loki-mode/benchmarks/results/2026-01-05-01-24-17/swebench-patches/scikit-learn__scikit-learn-13142.patch

@@ -0,0 +1,35 @@
+This file is not a proper patch - it contains explanation text. I need to understand the actual scikit-learn codebase structure to generate the correct patch. Based on the issue description and hints, let me create the proper patch:
+
+The bug is that when `n_init > 1`:
+1. The `fit` method runs multiple initialization trials
+2. After all trials, it restores the best parameters via `_set_parameters(best_params)`
+3. However, `fit_predict` returns labels from the last E-step call during the iterations, not from the best model
+
+The fix needs to:
+1. Move the computation of labels (via `_e_step` or `predict`) to AFTER `_set_parameters(best_params)` is called
+2. Or simply override `fit_predict` to return `self.fit(X, y).predict(X)`
+
+Based on the issue and hints, here's the correct minimal patch:
+
+--- a/sklearn/mixture/base.py
++++ b/sklearn/mixture/base.py
+@@ -257,11 +257,11 @@ class BaseMixture(DensityMixin, BaseEstimator, metaclass=ABCMeta):
+                     best_params = self._get_parameters()
+                     best_n_iter = n_iter
+ 
+-        # Always do a final e-step to guarantee that the labels returned by
+-        # fit_predict(X) are always consistent with fit(X).predict(X)
+-        # for any value of max_iter and tol (and any curved geometry fitting
+-        # included in the model).
+-        _, log_resp = self._e_step(X)
+-
+         self._set_parameters(best_params)
+         self.n_iter_ = best_n_iter
++        self.lower_bound_ = max_lower_bound
++
++        # Always do a final e-step to guarantee that the labels returned by
++        # fit_predict(X) are always consistent with fit(X).predict(X)
++        # for any value of max_iter and tol (and any random initialization).
++        _, log_resp = self._e_step(X)
+ 
+         return log_resp.argmax(axis=1)

package/src/templates/antigravity-skills/loki-mode/benchmarks/results/2026-01-05-01-24-17/swebench-patches/scikit-learn__scikit-learn-13241.patch

@@ -0,0 +1,29 @@
+Based on the issue description and my knowledge of scikit-learn's codebase, I can construct the appropriate patch. The fix involves:
+
+1. Adding `svd_flip` import in `kernel_pca.py`
+2. Applying `svd_flip` to the eigenvectors (`alphas_`) after the eigendecomposition to ensure consistent signs
+
+In scikit-learn 0.18.x, the file is at `sklearn/decomposition/kernel_pca.py`. The key function is `_fit_transform` where eigenvectors are computed using either `linalg.eigh` or `eigsh` (arpack).
+
+--- a/sklearn/decomposition/kernel_pca.py
++++ b/sklearn/decomposition/kernel_pca.py
+@@ -12,6 +12,7 @@ from scipy.sparse.linalg import eigsh
+ 
+ from ..utils import check_random_state
+ from ..utils.validation import check_is_fitted, check_array
++from ..utils.extmath import svd_flip
+ from ..exceptions import NotFittedError
+ from ..base import BaseEstimator, TransformerMixin, _UnstableOn32BitMixin
+ from ..preprocessing import KernelCenterer
+@@ -147,6 +148,10 @@ class KernelPCA(BaseEstimator, TransformerMixin, _UnstableOn32BitMixin):
+         # sort eigenvectors in descending order
+         indices = self.lambdas_.argsort()[::-1]
+         self.lambdas_ = self.lambdas_[indices]
+         self.alphas_ = self.alphas_[:, indices]
+ 
++        # flip eigenvectors' sign to enforce deterministic output
++        self.alphas_, _ = svd_flip(self.alphas_,
++                                   np.zeros_like(self.alphas_).T)
++
+         # remove eigenvectors with a zero eigenvalue
+         if self.remove_zero_eig or self.n_components is None: