Update pre-commit-config and add deps to pyproject by Kitchi · Pull Request #223 · casangi/astroviper

Kitchi · 2026-04-08T15:03:52Z

Update the pre-commit config YAML file to include nbstripout. It also removes an old poetry config that was failing, and added a fix for the AWS credential check failing if it didn't find any valid credentials.

Add nbstripout and pre-commit to the pyproject [all] dependency list.

Update the pre-commit config YAML file to include nbstripout. It also removes an old poetry config that was failing, and added a fix for the AWS credential check failing if it didn't find any valid credentials. Add nbstripout and pre-commit to the pyproject [all] dependency list.

Copilot

Pull request overview

This PR updates the repository’s development tooling configuration by refining pre-commit hooks (including adding nbstripout) and ensuring the relevant tooling dependencies are included in the pyproject.toml optional [all] extras.

Changes:

Add pre-commit and nbstripout to the all optional dependency set in pyproject.toml.
Update .pre-commit-config.yaml by removing Poetry hooks, adding nbstripout, adjusting detect-aws-credentials behavior, and bumping/adjusting some hook configurations (e.g., pyupgrade, isort).

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
`pyproject.toml`	Adds `pre-commit` and `nbstripout` to the `[project.optional-dependencies].all` extras list.
`.pre-commit-config.yaml`	Removes Poetry hooks, adds `nbstripout`, and updates hook args/versions (including AWS credentials hook behavior).

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.pre-commit-config.yaml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

codecov · 2026-04-08T15:11:21Z

❌ 13 Tests Failed:

Tests completed	Failed	Passed	Skipped
528	13	515	0

View the top 3 failed test(s) by shortest run time

tests/unit/core/imaging/imaging_utils/test_standard_image_grid_preparation.py::TestStandardImGridPrep::test_remove_padding

Stack Traces | 0.008s run time

self = <test_standard_image_grid_preparation.TestStandardImGridPrep testMethod=test_remove_padding>

    def test_remove_padding(self):
        a = self.make_image_xds()
        ra_o, dec_o = (
>           a.right_ascension[99, 99].data,
            ^^^^^^^^^^^^^^^^^
            a.declination[99, 99].data,
        )

.../imaging/imaging_utils/test_standard_image_grid_preparation.py:70: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <xarray.Dataset> Size: 163kB
Dimensions:            (time: 1, frequency: 1, polarization: 1, l: 200, m: 200,
         ...{}}
    coordinate_system_info:  {'reference_direction': {'attrs': {'frame': 'fk5...
    type:                    image
name = 'right_ascension'

    def __getattr__(self, name: str) -> Any:
        if name not in {"__dict__", "__setstate__"}:
            # this avoids an infinite loop when pickle looks for the
            # __setstate__ attribute before the xarray object is initialized
            for source in self._attr_sources:
                with suppress(KeyError):
                    return source[name]
>       raise AttributeError(
            f"{type(self).__name__!r} object has no attribute {name!r}"
        )
E       AttributeError: 'Dataset' object has no attribute 'right_ascension'

.../hostedtoolcache/Python/3.11.15.../x64/lib/python3.11.../xarray/core/common.py:306: AttributeError

tests/unit/core/imaging/test_imager.py::TestEndToEnd::test_stokes_i_only

Stack Traces | 0.125s run time

self = <xarray.Dataset> Size: 323kB
Dimensions:            (time: 1, frequency: 1, polarization: 1, l: 200, m: 200,
         ...{}}
    coordinate_system_info:  {'reference_direction': {'attrs': {'frame': 'fk5...
    type:                    image
name = 'right_ascension'

    def _construct_dataarray(self, name: Hashable) -> DataArray:
        """Construct a DataArray by indexing this dataset"""
        from xarray.core.dataarray import DataArray
    
        try:
>           variable = self._variables[name]
                       ^^^^^^^^^^^^^^^^^^^^^
E           KeyError: 'right_ascension'

.../hostedtoolcache/Python/3.11.15.........................../x64/lib/python3.11.../xarray/core/dataset.py:1237: KeyError

During handling of the above exception, another exception occurred:

self = <xarray.Dataset> Size: 323kB
Dimensions:            (time: 1, frequency: 1, polarization: 1, l: 200, m: 200,
         ...{}}
    coordinate_system_info:  {'reference_direction': {'attrs': {'frame': 'fk5...
    type:                    image
key = 'right_ascension'

    def __getitem__(
        self, key: Mapping[Any, Any] | Hashable | Iterable[Hashable]
    ) -> Self | DataArray:
        """Access variables or coordinates of this dataset as a
        :py:class:`~xarray.DataArray` or a subset of variables or a indexed dataset.
    
        Indexing with a list of names will return a new ``Dataset`` object.
        """
        from xarray.core.formatting import shorten_list_repr
    
        if utils.is_dict_like(key):
            return self.isel(**key)
        if utils.hashable(key):
            try:
>               return self._construct_dataarray(key)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.../hostedtoolcache/Python/3.11.15.........................../x64/lib/python3.11.../xarray/core/dataset.py:1344: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
.../hostedtoolcache/Python/3.11.15.........................../x64/lib/python3.11.../xarray/core/dataset.py:1239: in _construct_dataarray
    _, name, variable = _get_virtual_variable(self._variables, name, self.sizes)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

variables = {'RESIDUAL': <xarray.Variable (time: 1, frequency: 1, polarization: 1, l: 200, m: 200)> Size: 320kB
array([[[[[-0.7090...-04, -2.032622e-04])
Attributes:
    note:     l is the angle measured from the reference direction to the eas..., ...}
key = 'right_ascension'
dim_sizes = Frozen({'time': 1, 'frequency': 1, 'polarization': 1, 'l': 200, 'm': 200, 'beam_params_label': 3})

    def _get_virtual_variable(
        variables, key: Hashable, dim_sizes: Mapping | None = None
    ) -> tuple[Hashable, Hashable, Variable]:
        """Get a virtual variable (e.g., 'time.year') from a dict of xarray.Variable
        objects (if possible)
    
        """
        from xarray.core.dataarray import DataArray
    
        if dim_sizes is None:
            dim_sizes = {}
    
        if key in dim_sizes:
            data = pd.Index(range(dim_sizes[key]), name=key)
            variable = IndexVariable((key,), data)
            return key, key, variable
    
        if not isinstance(key, str):
            raise KeyError(key)
    
        split_key = key.split(".", 1)
        if len(split_key) != 2:
>           raise KeyError(key)
E           KeyError: 'right_ascension'

.../hostedtoolcache/Python/3.11.15.........................../x64/lib/python3.11.../xarray/core/dataset_utils.py:79: KeyError

The above exception was the direct cause of the following exception:

self = <tests.unit.core.imaging.test_imager.TestEndToEnd object at 0x7f63706cdcd0>
ms4_copy = ([array([ 93, 122, 111, 104]), array([ 82,  82,  77, 118]), array([1., 1., 1., 1.])], 200, np.float64(2.05315385437059...   WIND_SPEED           (station_name, time_weather) float64 4kB ...
        Attributes:
            type:     weather)
default_params = {'cell_size': (np.float64(-2.053153854370599e-06), np.float64(2.053153854370599e-06)), 'corr_type': 'linear', 'image_size': (200, 200)}

    def test_stokes_i_only(self, ms4_copy, default_params):
        _, npix, _, ms4 = ms4_copy
        params = {**default_params, "stokes": ["I"], "niter": 100, "nmajor": 1}
>       model, residual, _, _ = run_imaging_loop(ms4, params)
                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.../core/imaging/test_imager.py:294: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
.../hostedtoolcache/Python/3.11.15.........................../x64/lib/python3.11.../core/imaging/imager.py:301: in run_imaging_loop
    return_dict, new_model_xds, residual_xds = deconvolve(
.../hostedtoolcache/Python/3.11.15.........................../x64/lib/python3.11.../core/imaging/deconvolution.py:198: in deconvolve
    phase_center = get_phase_center(dirty_image_xds)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.../hostedtoolcache/Python/3.11.15.........................../x64/lib/python3.11.../core/imaging/deconvolution.py:34: in get_phase_center
    ra_shape = dirty_image_xds.coords["right_ascension"].shape
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.../hostedtoolcache/Python/3.11.15.........................../x64/lib/python3.11.../xarray/core/coordinates.py:927: in __getitem__
    return self._data[key]
           ^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <xarray.Dataset> Size: 323kB
Dimensions:            (time: 1, frequency: 1, polarization: 1, l: 200, m: 200,
         ...{}}
    coordinate_system_info:  {'reference_direction': {'attrs': {'frame': 'fk5...
    type:                    image
key = 'right_ascension'

    def __getitem__(
        self, key: Mapping[Any, Any] | Hashable | Iterable[Hashable]
    ) -> Self | DataArray:
        """Access variables or coordinates of this dataset as a
        :py:class:`~xarray.DataArray` or a subset of variables or a indexed dataset.
    
        Indexing with a list of names will return a new ``Dataset`` object.
        """
        from xarray.core.formatting import shorten_list_repr
    
        if utils.is_dict_like(key):
            return self.isel(**key)
        if utils.hashable(key):
            try:
                return self._construct_dataarray(key)
            except KeyError as e:
                message = f"No variable named {key!r}."
    
                best_guess = utils.did_you_mean(key, self.variables.keys())
                if best_guess:
                    message += f" {best_guess}"
                else:
                    message += f" Variables on the dataset include {shorten_list_repr(list(self.variables.keys()), max_items=10)}"
    
                # If someone attempts `ds['foo' , 'bar']` instead of `ds[['foo', 'bar']]`
                if isinstance(key, tuple):
                    message += f"\nHint: use a list to select multiple variables, for example `ds[{list(key)}]`"
>               raise KeyError(message) from e
E               KeyError: "No variable named 'right_ascension'. Variables on the dataset include ['time', 'frequency', 'velocity', 'polarization', 'l', 'm', 'beam_params_label', 'RESIDUAL']"

.../hostedtoolcache/Python/3.11.15.........................../x64/lib/python3.11.../xarray/core/dataset.py:1357: KeyError

tests/unit/core/imaging/test_imager.py::TestEndToEnd::test_shapes

Stack Traces | 0.126s run time

self = <xarray.Dataset> Size: 643kB
Dimensions:            (time: 1, frequency: 1, polarization: 2, l: 200, m: 200,
         ...{}}
    coordinate_system_info:  {'reference_direction': {'attrs': {'frame': 'fk5...
    type:                    image
name = 'right_ascension'

    def _construct_dataarray(self, name: Hashable) -> DataArray:
        """Construct a DataArray by indexing this dataset"""
        from xarray.core.dataarray import DataArray
    
        try:
>           variable = self._variables[name]
                       ^^^^^^^^^^^^^^^^^^^^^
E           KeyError: 'right_ascension'

.../hostedtoolcache/Python/3.11.15.........................../x64/lib/python3.11.../xarray/core/dataset.py:1237: KeyError

During handling of the above exception, another exception occurred:

self = <xarray.Dataset> Size: 643kB
Dimensions:            (time: 1, frequency: 1, polarization: 2, l: 200, m: 200,
         ...{}}
    coordinate_system_info:  {'reference_direction': {'attrs': {'frame': 'fk5...
    type:                    image
key = 'right_ascension'

    def __getitem__(
        self, key: Mapping[Any, Any] | Hashable | Iterable[Hashable]
    ) -> Self | DataArray:
        """Access variables or coordinates of this dataset as a
        :py:class:`~xarray.DataArray` or a subset of variables or a indexed dataset.
    
        Indexing with a list of names will return a new ``Dataset`` object.
        """
        from xarray.core.formatting import shorten_list_repr
    
        if utils.is_dict_like(key):
            return self.isel(**key)
        if utils.hashable(key):
            try:
>               return self._construct_dataarray(key)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.../hostedtoolcache/Python/3.11.15.........................../x64/lib/python3.11.../xarray/core/dataset.py:1344: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
.../hostedtoolcache/Python/3.11.15.........................../x64/lib/python3.11.../xarray/core/dataset.py:1239: in _construct_dataarray
    _, name, variable = _get_virtual_variable(self._variables, name, self.sizes)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

variables = {'RESIDUAL': <xarray.Variable (time: 1, frequency: 1, polarization: 2, l: 200, m: 200)> Size: 640kB
array([[[[[-7.0908...-04, -2.032622e-04])
Attributes:
    note:     l is the angle measured from the reference direction to the eas..., ...}
key = 'right_ascension'
dim_sizes = Frozen({'time': 1, 'frequency': 1, 'polarization': 2, 'l': 200, 'm': 200, 'beam_params_label': 3})

    def _get_virtual_variable(
        variables, key: Hashable, dim_sizes: Mapping | None = None
    ) -> tuple[Hashable, Hashable, Variable]:
        """Get a virtual variable (e.g., 'time.year') from a dict of xarray.Variable
        objects (if possible)
    
        """
        from xarray.core.dataarray import DataArray
    
        if dim_sizes is None:
            dim_sizes = {}
    
        if key in dim_sizes:
            data = pd.Index(range(dim_sizes[key]), name=key)
            variable = IndexVariable((key,), data)
            return key, key, variable
    
        if not isinstance(key, str):
            raise KeyError(key)
    
        split_key = key.split(".", 1)
        if len(split_key) != 2:
>           raise KeyError(key)
E           KeyError: 'right_ascension'

.../hostedtoolcache/Python/3.11.15.........................../x64/lib/python3.11.../xarray/core/dataset_utils.py:79: KeyError

The above exception was the direct cause of the following exception:

self = <tests.unit.core.imaging.test_imager.TestEndToEnd object at 0x7f63706ce0d0>
ms4_copy = ([array([ 93, 122, 111, 104]), array([ 82,  82,  77, 118]), array([1., 1., 1., 1.])], 200, np.float64(2.05315385437059...   WIND_SPEED           (station_name, time_weather) float64 4kB ...
        Attributes:
            type:     weather)
default_params = {'cell_size': (np.float64(-2.053153854370599e-06), np.float64(2.053153854370599e-06)), 'corr_type': 'linear', 'image_size': (200, 200)}

    def test_shapes(self, ms4_copy, default_params):
        _, npix, _, ms4 = ms4_copy
        params = {**default_params, "niter": 100, "nmajor": 1}
>       model, residual, _, _ = run_imaging_loop(ms4, params)
                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.../core/imaging/test_imager.py:339: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
.../hostedtoolcache/Python/3.11.15.........................../x64/lib/python3.11.../core/imaging/imager.py:301: in run_imaging_loop
    return_dict, new_model_xds, residual_xds = deconvolve(
.../hostedtoolcache/Python/3.11.15.........................../x64/lib/python3.11.../core/imaging/deconvolution.py:198: in deconvolve
    phase_center = get_phase_center(dirty_image_xds)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.../hostedtoolcache/Python/3.11.15.........................../x64/lib/python3.11.../core/imaging/deconvolution.py:34: in get_phase_center
    ra_shape = dirty_image_xds.coords["right_ascension"].shape
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.../hostedtoolcache/Python/3.11.15.........................../x64/lib/python3.11.../xarray/core/coordinates.py:927: in __getitem__
    return self._data[key]
           ^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <xarray.Dataset> Size: 643kB
Dimensions:            (time: 1, frequency: 1, polarization: 2, l: 200, m: 200,
         ...{}}
    coordinate_system_info:  {'reference_direction': {'attrs': {'frame': 'fk5...
    type:                    image
key = 'right_ascension'

    def __getitem__(
        self, key: Mapping[Any, Any] | Hashable | Iterable[Hashable]
    ) -> Self | DataArray:
        """Access variables or coordinates of this dataset as a
        :py:class:`~xarray.DataArray` or a subset of variables or a indexed dataset.
    
        Indexing with a list of names will return a new ``Dataset`` object.
        """
        from xarray.core.formatting import shorten_list_repr
    
        if utils.is_dict_like(key):
            return self.isel(**key)
        if utils.hashable(key):
            try:
                return self._construct_dataarray(key)
            except KeyError as e:
                message = f"No variable named {key!r}."
    
                best_guess = utils.did_you_mean(key, self.variables.keys())
                if best_guess:
                    message += f" {best_guess}"
                else:
                    message += f" Variables on the dataset include {shorten_list_repr(list(self.variables.keys()), max_items=10)}"
    
                # If someone attempts `ds['foo' , 'bar']` instead of `ds[['foo', 'bar']]`
                if isinstance(key, tuple):
                    message += f"\nHint: use a list to select multiple variables, for example `ds[{list(key)}]`"
>               raise KeyError(message) from e
E               KeyError: "No variable named 'right_ascension'. Variables on the dataset include ['time', 'frequency', 'velocity', 'polarization', 'l', 'm', 'beam_params_label', 'RESIDUAL']"

.../hostedtoolcache/Python/3.11.15.........................../x64/lib/python3.11.../xarray/core/dataset.py:1357: KeyError

tests/unit/core/imaging/test_imager.py::TestEndToEnd::test_auto_stokes_2corr_linear