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6 tests fail #853
Description
================================================================================================================== FAILURES ==================================================================================================================
______________________________________________________________________________________________________ test_jive_docstring_examples_run ______________________________________________________________________________________________________
def test_jive_docstring_examples_run():
with_examples, failures = run_docstring_examples(IVJIVE, "IVJIVE")
> assert not failures, "".join(failures)
E AssertionError: Trying:
E import numpy as np
E Expecting nothing
E ok
E Trying:
E from linearmodels.iv import IVJIVE
E Expecting nothing
E ok
E Trying:
E rng = np.random.default_rng(0)
E Expecting nothing
E ok
E Trying:
E n = 500
E Expecting nothing
E ok
E Trying:
E z = rng.standard_normal((n, 3))
E Expecting nothing
E ok
E Trying:
E x = z[:, 0] + rng.standard_normal(n)
E Expecting nothing
E ok
E Trying:
E exog = np.ones((n, 1))
E Expecting nothing
E ok
E Trying:
E y = x + rng.standard_normal(n)
E Expecting nothing
E ok
E Trying:
E mod = IVJIVE(y, exog, x[:, None], z)
E Expecting nothing
E ok
E Trying:
E res = mod.fit()
E Expecting nothing
E ok
E Trying:
E from linearmodels.datasets import wage
E Expecting nothing
E ok
E Trying:
E from linearmodels.iv import IVJIVE
E Expecting nothing
E ok
E Trying:
E data = wage.load()
E Expecting nothing
E ok
E Trying:
E formula = "np.log(wage) ~ 1 + exper + I(exper ** 2) + brthord + [educ ~ sibs]"
E Expecting nothing
E ok
E Trying:
E mod = IVJIVE.from_formula(formula, data)
E Expecting nothing
E ok
E
E assert not ['Trying:\n import numpy as np\nExpecting nothing\n', 'ok\n', 'Trying:\n from linearmodels.iv import IVJIVE\nExpecting nothing\n', 'ok\n', 'Trying:\n rng = np.random.default_rng(0)\nExpecting nothing\n', 'ok\n', ...]
linearmodels/tests/iv/test_new_feature_hardening.py:102: AssertionError
____________________________________________________________________________ test_system_gmm_explicit_bandwidth_works_with_the_observations_that_raise[bartlett] _____________________________________________________________________________
kernel = 'bartlett'
@pytest.mark.parametrize("kernel", CANONICAL)
def test_system_gmm_explicit_bandwidth_works_with_the_observations_that_raise(kernel):
nobs = fewest_observations(kernel) - 1
equations = system_equations(nobs, True)
explicit = IVSystemGMM(
equations, weight_type="kernel", kernel=kernel, bandwidth=1
> ).fit()
^^^^^
linearmodels/tests/test_kernel_bandwidth_few_observations.py:951:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
linearmodels/system/model.py:2514: in fit
vinv = inv(v)
^^^^^^
/usr/local/lib/python3.12/site-packages/numpy/linalg/_linalg.py:647: in inv
ainv = _umath_linalg.inv(a, signature=signature)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
err = 'invalid value', flag = 8
def _raise_linalgerror_singular(err, flag):
> raise LinAlgError("Singular matrix")
E numpy.linalg.LinAlgError: Singular matrix
/usr/local/lib/python3.12/site-packages/numpy/linalg/_linalg.py:144: LinAlgError
_____________________________________________________________________________ test_system_gmm_explicit_bandwidth_works_with_the_observations_that_raise[parzen] ______________________________________________________________________________
kernel = 'parzen'
@pytest.mark.parametrize("kernel", CANONICAL)
def test_system_gmm_explicit_bandwidth_works_with_the_observations_that_raise(kernel):
nobs = fewest_observations(kernel) - 1
equations = system_equations(nobs, True)
explicit = IVSystemGMM(
equations, weight_type="kernel", kernel=kernel, bandwidth=1
).fit()
assert explicit.weight_config["bandwidth"] == 1
restored = IVSystemGMM(
equations, weight_type="kernel", kernel=kernel, optimal_bw=False
> ).fit()
^^^^^
linearmodels/tests/test_kernel_bandwidth_few_observations.py:955:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
linearmodels/system/model.py:2501: in fit
beta = self._blocked_gmm(
linearmodels/system/model.py:2587: in _blocked_gmm
wi = np.linalg.inv(w)
^^^^^^^^^^^^^^^^
/usr/local/lib/python3.12/site-packages/numpy/linalg/_linalg.py:647: in inv
ainv = _umath_linalg.inv(a, signature=signature)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
err = 'invalid value', flag = 8
def _raise_linalgerror_singular(err, flag):
> raise LinAlgError("Singular matrix")
E numpy.linalg.LinAlgError: Singular matrix
/usr/local/lib/python3.12/site-packages/numpy/linalg/_linalg.py:144: LinAlgError
___________________________________________________________________________________________ test_system_gmm_with_the_fewest_observations[bartlett] ___________________________________________________________________________________________
kernel = 'bartlett'
@pytest.mark.parametrize("kernel", CANONICAL)
def test_system_gmm_with_the_fewest_observations(kernel):
nobs = fewest_observations(kernel)
equations = system_equations(nobs, True)
res = IVSystemGMM(
equations, weight_type="kernel", kernel=kernel, optimal_bw=True
> ).fit(cov_type="kernel", kernel=kernel)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
linearmodels/tests/test_kernel_bandwidth_few_observations.py:965:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
linearmodels/system/model.py:2501: in fit
beta = self._blocked_gmm(
linearmodels/system/model.py:2587: in _blocked_gmm
wi = np.linalg.inv(w)
^^^^^^^^^^^^^^^^
/usr/local/lib/python3.12/site-packages/numpy/linalg/_linalg.py:647: in inv
ainv = _umath_linalg.inv(a, signature=signature)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
err = 'invalid value', flag = 8
def _raise_linalgerror_singular(err, flag):
> raise LinAlgError("Singular matrix")
E numpy.linalg.LinAlgError: Singular matrix
/usr/local/lib/python3.12/site-packages/numpy/linalg/_linalg.py:144: LinAlgError
________________________________________________________________________________________________________________ test_runner _________________________________________________________________________________________________________________
'gpu' not found in `markers` configuration option
------------------------------------------------------------------------------------------------------------ Captured stdout call ------------------------------------------------------------------------------------------------------------
tests/shared/test_typed_getters.py
/usr/ports/math/py-linearmodels/work-py312/linearmodels-7.1/linearmodels
/usr/ports/math/py-linearmodels/work-py312/linearmodels-7.1/linearmodels/tests/shared/test_typed_getters.py
running: pytest /usr/ports/math/py-linearmodels/work-py312/linearmodels-7.1/linearmodels/tests/shared/test_typed_getters.py --tb=auto
______________________________________________________________________________________________________________ test_extra_args _______________________________________________________________________________________________________________
'gpu' not found in `markers` configuration option
------------------------------------------------------------------------------------------------------------ Captured stdout call ------------------------------------------------------------------------------------------------------------
tests/shared/test_typed_getters.py
/usr/ports/math/py-linearmodels/work-py312/linearmodels-7.1/linearmodels
/usr/ports/math/py-linearmodels/work-py312/linearmodels-7.1/linearmodels/tests/shared/test_typed_getters.py
running: pytest /usr/ports/math/py-linearmodels/work-py312/linearmodels-7.1/linearmodels/tests/shared/test_typed_getters.py --tb=short
============================================================================================================== warnings summary ==============================================================================================================
linearmodels/tests/test_tester.py::test_runner
linearmodels/tests/test_tester.py::test_extra_args
/usr/local/lib/python3.12/site-packages/dash/testing/plugin.py:104: PytestRemovedIn10Warning: The hookimpl pytest_addhooks uses old-style configuration options (marks or attributes).
Please use the pytest.hookimpl(tryfirst=True) decorator instead
to configure the hooks.
See https://docs.pytest.org/en/latest/deprecations.html#configuring-hook-specs-impls-using-markers
@pytest.mark.tryfirst
linearmodels/tests/test_tester.py::test_runner
linearmodels/tests/test_tester.py::test_extra_args
/usr/local/lib/python3.12/site-packages/aiomisc/pytest.py:541: PytestRemovedIn10Warning: The hookimpl pytest_pyfunc_call uses old-style configuration options (marks or attributes).
Please use the pytest.hookimpl(tryfirst=True) decorator instead
to configure the hooks.
See https://docs.pytest.org/en/latest/deprecations.html#configuring-hook-specs-impls-using-markers
@pytest.mark.tryfirst
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:45: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
dynamic: list[str] | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:57: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
supported_platform: list[str] | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:72: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
description_content_type: str | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:89: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
download_url: str | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:105: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
maintainer: str | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:111: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
maintainer_email: str | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:126: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
classifier: list[str] | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:133: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
requires_dist: list[str] | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:140: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
requires_python: str | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:148: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
requires_external: list[str] | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:157: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
project_url: list[str] | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:163: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
provides_extra: list[str] | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:172: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
provides_dist: list[str] | None = Field(None, min_ver="1.2")
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:173: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
obsoletes_dist: list[str] | None = Field(None, min_ver="1.2")
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/contributions/_contributions.py:46: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'hide_docs'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
keybindings: list[KeyBindingContribution] | None = Field(None, hide_docs=True)
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/schema.py:101: PydanticDeprecatedSince20: `allow_mutation` is deprecated and will be removed. use `frozen` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
name: Annotated[str, BeforeValidator(_validators.package_name)] = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/schema.py:197: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'hide_docs'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
package_metadata: PackageMetadata | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/schema.py:206: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'hide_docs'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
npe1_shim: bool = Field(
-- Docs: https:================================================================================================================== FAILURES ==================================================================================================================
______________________________________________________________________________________________________ test_jive_docstring_examples_run ______________________________________________________________________________________________________
def test_jive_docstring_examples_run():
with_examples, failures = run_docstring_examples(IVJIVE, "IVJIVE")
> assert not failures, "".join(failures)
E AssertionError: Trying:
E import numpy as np
E Expecting nothing
E ok
E Trying:
E from linearmodels.iv import IVJIVE
E Expecting nothing
E ok
E Trying:
E rng = np.random.default_rng(0)
E Expecting nothing
E ok
E Trying:
E n = 500
E Expecting nothing
E ok
E Trying:
E z = rng.standard_normal((n, 3))
E Expecting nothing
E ok
E Trying:
E x = z[:, 0] + rng.standard_normal(n)
E Expecting nothing
E ok
E Trying:
E exog = np.ones((n, 1))
E Expecting nothing
E ok
E Trying:
E y = x + rng.standard_normal(n)
E Expecting nothing
E ok
E Trying:
E mod = IVJIVE(y, exog, x[:, None], z)
E Expecting nothing
E ok
E Trying:
E res = mod.fit()
E Expecting nothing
E ok
E Trying:
E from linearmodels.datasets import wage
E Expecting nothing
E ok
E Trying:
E from linearmodels.iv import IVJIVE
E Expecting nothing
E ok
E Trying:
E data = wage.load()
E Expecting nothing
E ok
E Trying:
E formula = "np.log(wage) ~ 1 + exper + I(exper ** 2) + brthord + [educ ~ sibs]"
E Expecting nothing
E ok
E Trying:
E mod = IVJIVE.from_formula(formula, data)
E Expecting nothing
E ok
E
E assert not ['Trying:\n import numpy as np\nExpecting nothing\n', 'ok\n', 'Trying:\n from linearmodels.iv import IVJIVE\nExpecting nothing\n', 'ok\n', 'Trying:\n rng = np.random.default_rng(0)\nExpecting nothing\n', 'ok\n', ...]
linearmodels/tests/iv/test_new_feature_hardening.py:102: AssertionError
____________________________________________________________________________ test_system_gmm_explicit_bandwidth_works_with_the_observations_that_raise[bartlett] _____________________________________________________________________________
kernel = 'bartlett'
@pytest.mark.parametrize("kernel", CANONICAL)
def test_system_gmm_explicit_bandwidth_works_with_the_observations_that_raise(kernel):
nobs = fewest_observations(kernel) - 1
equations = system_equations(nobs, True)
explicit = IVSystemGMM(
equations, weight_type="kernel", kernel=kernel, bandwidth=1
> ).fit()
^^^^^
linearmodels/tests/test_kernel_bandwidth_few_observations.py:951:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
linearmodels/system/model.py:2514: in fit
vinv = inv(v)
^^^^^^
/usr/local/lib/python3.12/site-packages/numpy/linalg/_linalg.py:647: in inv
ainv = _umath_linalg.inv(a, signature=signature)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
err = 'invalid value', flag = 8
def _raise_linalgerror_singular(err, flag):
> raise LinAlgError("Singular matrix")
E numpy.linalg.LinAlgError: Singular matrix
/usr/local/lib/python3.12/site-packages/numpy/linalg/_linalg.py:144: LinAlgError
_____________________________________________________________________________ test_system_gmm_explicit_bandwidth_works_with_the_observations_that_raise[parzen] ______________________________________________________________________________
kernel = 'parzen'
@pytest.mark.parametrize("kernel", CANONICAL)
def test_system_gmm_explicit_bandwidth_works_with_the_observations_that_raise(kernel):
nobs = fewest_observations(kernel) - 1
equations = system_equations(nobs, True)
explicit = IVSystemGMM(
equations, weight_type="kernel", kernel=kernel, bandwidth=1
).fit()
assert explicit.weight_config["bandwidth"] == 1
restored = IVSystemGMM(
equations, weight_type="kernel", kernel=kernel, optimal_bw=False
> ).fit()
^^^^^
linearmodels/tests/test_kernel_bandwidth_few_observations.py:955:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
linearmodels/system/model.py:2501: in fit
beta = self._blocked_gmm(
linearmodels/system/model.py:2587: in _blocked_gmm
wi = np.linalg.inv(w)
^^^^^^^^^^^^^^^^
/usr/local/lib/python3.12/site-packages/numpy/linalg/_linalg.py:647: in inv
ainv = _umath_linalg.inv(a, signature=signature)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
err = 'invalid value', flag = 8
def _raise_linalgerror_singular(err, flag):
> raise LinAlgError("Singular matrix")
E numpy.linalg.LinAlgError: Singular matrix
/usr/local/lib/python3.12/site-packages/numpy/linalg/_linalg.py:144: LinAlgError
___________________________________________________________________________________________ test_system_gmm_with_the_fewest_observations[bartlett] ___________________________________________________________________________________________
kernel = 'bartlett'
@pytest.mark.parametrize("kernel", CANONICAL)
def test_system_gmm_with_the_fewest_observations(kernel):
nobs = fewest_observations(kernel)
equations = system_equations(nobs, True)
res = IVSystemGMM(
equations, weight_type="kernel", kernel=kernel, optimal_bw=True
> ).fit(cov_type="kernel", kernel=kernel)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
linearmodels/tests/test_kernel_bandwidth_few_observations.py:965:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
linearmodels/system/model.py:2501: in fit
beta = self._blocked_gmm(
linearmodels/system/model.py:2587: in _blocked_gmm
wi = np.linalg.inv(w)
^^^^^^^^^^^^^^^^
/usr/local/lib/python3.12/site-packages/numpy/linalg/_linalg.py:647: in inv
ainv = _umath_linalg.inv(a, signature=signature)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
err = 'invalid value', flag = 8
def _raise_linalgerror_singular(err, flag):
> raise LinAlgError("Singular matrix")
E numpy.linalg.LinAlgError: Singular matrix
/usr/local/lib/python3.12/site-packages/numpy/linalg/_linalg.py:144: LinAlgError
________________________________________________________________________________________________________________ test_runner _________________________________________________________________________________________________________________
'gpu' not found in `markers` configuration option
------------------------------------------------------------------------------------------------------------ Captured stdout call ------------------------------------------------------------------------------------------------------------
tests/shared/test_typed_getters.py
/usr/ports/math/py-linearmodels/work-py312/linearmodels-7.1/linearmodels
/usr/ports/math/py-linearmodels/work-py312/linearmodels-7.1/linearmodels/tests/shared/test_typed_getters.py
running: pytest /usr/ports/math/py-linearmodels/work-py312/linearmodels-7.1/linearmodels/tests/shared/test_typed_getters.py --tb=auto
______________________________________________________________________________________________________________ test_extra_args _______________________________________________________________________________________________________________
'gpu' not found in `markers` configuration option
------------------------------------------------------------------------------------------------------------ Captured stdout call ------------------------------------------------------------------------------------------------------------
tests/shared/test_typed_getters.py
/usr/ports/math/py-linearmodels/work-py312/linearmodels-7.1/linearmodels
/usr/ports/math/py-linearmodels/work-py312/linearmodels-7.1/linearmodels/tests/shared/test_typed_getters.py
running: pytest /usr/ports/math/py-linearmodels/work-py312/linearmodels-7.1/linearmodels/tests/shared/test_typed_getters.py --tb=short
============================================================================================================== warnings summary ==============================================================================================================
linearmodels/tests/test_tester.py::test_runner
linearmodels/tests/test_tester.py::test_extra_args
/usr/local/lib/python3.12/site-packages/dash/testing/plugin.py:104: PytestRemovedIn10Warning: The hookimpl pytest_addhooks uses old-style configuration options (marks or attributes).
Please use the pytest.hookimpl(tryfirst=True) decorator instead
to configure the hooks.
See https://docs.pytest.org/en/latest/deprecations.html#configuring-hook-specs-impls-using-markers
@pytest.mark.tryfirst
linearmodels/tests/test_tester.py::test_runner
linearmodels/tests/test_tester.py::test_extra_args
/usr/local/lib/python3.12/site-packages/aiomisc/pytest.py:541: PytestRemovedIn10Warning: The hookimpl pytest_pyfunc_call uses old-style configuration options (marks or attributes).
Please use the pytest.hookimpl(tryfirst=True) decorator instead
to configure the hooks.
See https://docs.pytest.org/en/latest/deprecations.html#configuring-hook-specs-impls-using-markers
@pytest.mark.tryfirst
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:45: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
dynamic: list[str] | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:57: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
supported_platform: list[str] | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:72: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
description_content_type: str | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:89: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
download_url: str | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:105: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
maintainer: str | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:111: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
maintainer_email: str | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:126: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
classifier: list[str] | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:133: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
requires_dist: list[str] | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:140: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
requires_python: str | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:148: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
requires_external: list[str] | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:157: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
project_url: list[str] | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:163: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
provides_extra: list[str] | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:172: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
provides_dist: list[str] | None = Field(None, min_ver="1.2")
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/_package_metadata.py:173: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'min_ver'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
obsoletes_dist: list[str] | None = Field(None, min_ver="1.2")
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/contributions/_contributions.py:46: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'hide_docs'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
keybindings: list[KeyBindingContribution] | None = Field(None, hide_docs=True)
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/schema.py:101: PydanticDeprecatedSince20: `allow_mutation` is deprecated and will be removed. use `frozen` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
name: Annotated[str, BeforeValidator(_validators.package_name)] = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/schema.py:197: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'hide_docs'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
package_metadata: PackageMetadata | None = Field(
linearmodels/tests/test_tester.py::test_runner
/usr/local/lib/python3.12/site-packages/npe2/manifest/schema.py:206: PydanticDeprecatedSince20: Using extra keyword arguments on `Field` is deprecated and will be removed. Use `json_schema_extra` instead. (Extra keys: 'hide_docs'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.13/migration/
npe1_shim: bool = Field(
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
========================================================================================================== short test summary info ===========================================================================================================
SKIPPED [310] linearmodels/conftest.py:42: skipping due to --skip-slow
SKIPPED [288] linearmodels/tests/iv/test_against_stata.py:194: Comparison result not available
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:167: Weighted GMM differs slightly
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:174: Weighted GMM differs slightly
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:181: Weighted GMM differs slightly
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:186: Weighted GMM differs slightly
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:191: Weighted GMM differs slightly
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:198: Weighted GMM differs slightly
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:204: Weighted GMM differs slightly
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:210: Weighted GMM differs slightly
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:217: Weighted GMM differs slightly
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:228: Weighted GMM differs slightly
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:235: Weighted GMM differs slightly
SKIPPED [4] linearmodels/tests/panel/test_formula.py:305: Cannot test with numpy arrays
SKIPPED [12] linearmodels/tests/panel/test_results.py:366: Cannot test with missing values
SKIPPED [45] linearmodels/tests/panel/test_simulated_against_stata.py:145: Result not available for testing
============================================================================= 6 failed, 22966 passed, 2771 skipped, 47 xfailed, 22 warnings in 450.45s (0:07:30) =============================================================================
*** Error code 1
//docs.pytest.org/en/stable/how-to/capture-warnings.html
========================================================================================================== short test summary info ===========================================================================================================
SKIPPED [310] linearmodels/conftest.py:42: skipping due to --skip-slow
SKIPPED [288] linearmodels/tests/iv/test_against_stata.py:194: Comparison result not available
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:167: Weighted GMM differs slightly
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:174: Weighted GMM differs slightly
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:181: Weighted GMM differs slightly
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:186: Weighted GMM differs slightly
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:191: Weighted GMM differs slightly
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:198: Weighted GMM differs slightly
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:204: Weighted GMM differs slightly
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:210: Weighted GMM differs slightly
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:217: Weighted GMM differs slightly
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:228: Weighted GMM differs slightly
SKIPPED [192] linearmodels/tests/iv/test_against_stata.py:235: Weighted GMM differs slightly
SKIPPED [4] linearmodels/tests/panel/test_formula.py:305: Cannot test with numpy arrays
SKIPPED [12] linearmodels/tests/panel/test_results.py:366: Cannot test with missing values
SKIPPED [45] linearmodels/tests/panel/test_simulated_against_stata.py:145: Result not available for testing
============================================================================= 6 failed, 22966 passed, 2771 skipped, 47 xfailed, 22 warnings in 450.45s (0:07:30) =============================================================================
*** Error code 1
Version: 7.1
Activity
bashtage commentedon Oct 22, 2026
These probably fall into those that are near-singular but depending on the compiler, compiler flags, blas used, and perhaps OS specifics, can be pushed over. They probably should be made more robust. What is the compiler? Clang? Am I right this is on FreeBSD?
yurivict commentedon Oct 22, 2026
Yes: FreeBSD, Clang-21
bashtage commentedon Oct 22, 2026
These tests were knife-edge singular but passed on other platforms by luck. These tests were changed in #854, so they are less problematic. I have also added some additional instructions in the README for running tests.
yurivict commentedon Oct 22, 2026
Do other platforms do FP operations differently?
How is this possible since hardware is the same and FP operations are performed by the CPU?
Where does the "luck" come from?
bashtage commentedon Oct 22, 2026
No, but the instructions used to implement a math op and the order of the instructions may differ accross compilers and system libraries (if used). Suppose we have a math op that we know is analytically 0. We could end up with a number like 1e-16, or even 1e-13 depending on the operation and the input data. If you have an exact 0, 1/0 is an error. If you have 1e-13, 1/1e-13 is not an error.
Basically the tests were too close to 0, and occasionally gave exactly 0, hence the singular errors. These will be fixed soon so that they are all far enough from 0 that they should not raise on any platforms.
bashtage commentedon Oct 22, 2026
In terms of linearmodels 7.1 passing on FreeBSD, you could either disable these tests or pull in the relevant patch from #854. All fixes are test only fixes, not changing the actual code that is run.
bashtage commentedon Oct 22, 2026
I'm going to close as fixed. If you have other problems after this, please let me know.