DEPR: deprecation cycle (4.0 -> 4.1)

doc/source/cookbook/complex_plots.rst

@@ -46,10 +46,7 @@ or during image creation with the ``buff_size`` argument to any
 of the four preceding classes.
 
 2. ``figure_size``, which can be altered with either
-:meth:`~yt.visualization.plot_container.PlotContainer.set_figure_size`
-or with :meth:`~yt.visualization.plot_container.PlotWindow.set_window_size`
-(the latter simply calls
-:meth:`~yt.visualization.plot_container.PlotContainer.set_figure_size`),
+:meth:`~yt.visualization.plot_container.PlotContainer.set_figure_size`,
 or can be set during image creation with the ``window_size`` argument.
 This sets the size of the final image (including the visualization and,
 if applicable, the axes and colorbar as well) in inches.

doc/source/reference/api/api.rst

@@ -637,7 +637,6 @@ particularly with complicated layouts.
    ~yt.visualization.eps_writer.single_plot
    ~yt.visualization.eps_writer.multiplot
    ~yt.visualization.eps_writer.multiplot_yt
-   ~yt.visualization.eps_writer.return_cmap
    ~yt.visualization.eps_writer.return_colormap
 
 .. _derived-quantities-api:
@@ -663,7 +662,6 @@ See :ref:`derived-quantities`.
    ~yt.data_objects.derived_quantities.TotalMass
    ~yt.data_objects.derived_quantities.TotalQuantity
    ~yt.data_objects.derived_quantities.WeightedAverageQuantity
-   ~yt.data_objects.derived_quantities.WeightedVariance
 
 .. _callback-api:
 
@@ -675,7 +673,6 @@ See also :ref:`callbacks`.
 
 .. autosummary::
 
-   ~yt.visualization.plot_window.PWViewerMPL.annotate_clear
    ~yt.visualization.plot_window.PWViewerMPL.clear_annotations
    ~yt.visualization.plot_modifications.ArrowCallback
    ~yt.visualization.plot_modifications.CellEdgesCallback
@@ -709,7 +706,6 @@ See also :ref:`colormaps`.
 
 .. autosummary::
 
-   ~yt.visualization.color_maps.add_cmap
    ~yt.visualization.color_maps.add_colormap
    ~yt.visualization.color_maps.make_colormap
    ~yt.visualization.color_maps.show_colormaps

yt/__init__.py

@@ -77,7 +77,6 @@
 import yt.visualization.volume_rendering.api as volume_rendering
 from yt.frontends.stream.api import hexahedral_connectivity
 from yt.frontends.ytdata.api import save_as_dataset
-from yt.loaders import simulation  # deprecated alias for load_simulation
 from yt.loaders import (
     load,
     load_amr_grids,
@@ -142,17 +141,3 @@
 
 #    TransferFunctionHelper, MultiVariateTransferFunction
 #    off_axis_projection
-
-
-def _check_deprecated_parameters():
-    from yt._maintenance.deprecation import issue_deprecation_warning
-    from yt.config import ytcfg
-
-    if ytcfg.get("yt", "load_field_plugins"):
-        issue_deprecation_warning(
-            "Found deprecated parameter 'load_field_plugins' in yt's configuration file.",
-            removal="4.1.0",
-        )
-
-
-_check_deprecated_parameters()

yt/config.py

@@ -4,7 +4,6 @@
 import toml
 from more_itertools import always_iterable
 
-from yt._maintenance.deprecation import issue_deprecation_warning
 from yt.utilities.configuration_tree import ConfigLeaf, ConfigNode
 
 ytcfg_defaults = {}
@@ -77,17 +76,8 @@ def config_dir():
     return conf_dir
 
 
-def old_config_file():
-    return os.path.join(config_dir(), "ytrc")
-
-
-def old_config_dir():
-    return os.path.join(os.path.expanduser("~"), ".yt")
-
-
 # For backward compatibility, do not use these vars internally in yt
 CONFIG_DIR = config_dir()
-_OLD_CONFIG_FILE = old_config_file()
 
 
 class YTConfig:
@@ -199,26 +189,6 @@ def _repr_json_(self):
 _global_config_file = YTConfig.get_global_config_file()
 _local_config_file = YTConfig.get_local_config_file()
 
-if os.path.exists(old_config_file()):
-    if os.path.exists(_global_config_file):
-        issue_deprecation_warning(
-            f"The configuration file {old_config_file()} is deprecated in "
-            f"favor of {_global_config_file}. Currently, both are present. "
-            "Please manually remove the deprecated one to silence "
-            "this warning.",
-            since="4.0.0",
-            removal="4.1.0",
-        )
-    else:
-        issue_deprecation_warning(
-            f"The configuration file {_OLD_CONFIG_FILE} is deprecated. "
-            f"Please migrate your config to {_global_config_file} by running: "
-            "'yt config migrate'",
-            since="4.0.0",
-            removal="4.1.0",
-        )
-
-
 if not os.path.exists(_global_config_file):
     cfg = {"yt": {}}
     try:

yt/data_objects/derived_quantities.py

@@ -1,6 +1,5 @@
 import numpy as np
 
-from yt._maintenance.deprecation import issue_deprecation_warning
 from yt.funcs import camelcase_to_underscore, iter_fields
 from yt.units.yt_array import array_like_field
 from yt.utilities.exceptions import YTParticleTypeNotFound
@@ -459,18 +458,6 @@ def reduce_intermediate(self, values):
         return rvals
 
 
-class WeightedVariance(WeightedStandardDeviation):
-    def __call__(self, fields, weight):
-        issue_deprecation_warning(
-            "'weighted_variance' incorrectly returns the "
-            "standard deviation and has been deprecated. "
-            "Use 'weighted_standard_deviation' instead.",
-            since="4.0.0",
-            removal="4.1.0",
-        )
-        return super().__call__(fields, weight)
-
-
 class AngularMomentumVector(DerivedQuantity):
     r"""
     Calculates the angular momentum vector, using gas (grid-based) and/or particles.

yt/data_objects/index_subobjects/octree_subset.py

@@ -5,7 +5,6 @@
 
 import yt.geometry.particle_deposit as particle_deposit
 import yt.geometry.particle_smooth as particle_smooth
-from yt._maintenance.deprecation import issue_deprecation_warning
 from yt.data_objects.selection_objects.data_selection_objects import (
     YTSelectionContainer,
 )
@@ -526,15 +525,6 @@ def select_particles(self, selector, x, y, z):
         return mask
 
     def get_vertex_centered_data(self, fields):
-        _old_api = isinstance(fields, (str, tuple))
-        if _old_api:
-            message = (
-                "get_vertex_centered_data() requires list of fields, rather than "
-                "a single field as an argument."
-            )
-            issue_deprecation_warning(message, since="4.0.0", removal="4.1.0")
-            fields = [fields]
-
         # Make sure the field list has only unique entries
         fields = list(set(fields))
         new_fields = {}
@@ -550,8 +540,6 @@ def get_vertex_centered_data(self, fields):
             np.add(new_fields[field], cg[field][:-1, :-1, :-1], new_fields[field])
             np.multiply(new_fields[field], 0.125, new_fields[field])
 
-        if _old_api:
-            return new_fields[fields[0]]
         return new_fields
 
 

yt/data_objects/static_output.py

@@ -274,25 +274,6 @@ def periodicity(self):
             return (True, True, True)
         return self._periodicity
 
-    @periodicity.setter
-    def periodicity(self, val):
-        # remove this setter to break backward compatibility
-        issue_deprecation_warning(
-            "Dataset.periodicity should not be overridden manually. "
-            "In the future, this will become an error. "
-            "Use `Dataset.force_periodicity` instead.",
-            since="4.0.0",
-            removal="4.1.0",
-        )
-        err_msg = f"Expected a 3-element boolean tuple, received `{val}`."
-        if not is_sequence(val):
-            raise TypeError(err_msg)
-        if len(val) != 3:
-            raise ValueError(err_msg)
-        if any(not isinstance(p, (bool, np.bool_)) for p in val):
-            raise TypeError(err_msg)
-        self._periodicity = tuple(bool(p) for p in val)
-
     def force_periodicity(self, val=True):
         """
         Override box periodicity to (True, True, True).
@@ -1703,51 +1684,7 @@ def _deposit_field(field, data):
         )
         return ("deposit", field_name)
 
-    def add_smoothed_particle_field(
-        self, smooth_field, method="volume_weighted", nneighbors=64, kernel_name="cubic"
-    ):
-        """Add a new smoothed particle field
-
-        WARNING: This method is deprecated since yt-4.0.
-
-        Creates a new smoothed field based on the particle *smooth_field*.
-
-        Parameters
-        ----------
-
-        smooth_field : tuple
-           The field name tuple of the particle field the smoothed field will
-           be created from.  This must be a field name tuple so yt can
-           appropriately infer the correct particle type.
-        method : string, default 'volume_weighted'
-           The particle smoothing method to use. Can only be 'volume_weighted'
-           for now.
-        nneighbors : int, default 64
-            The number of neighbors to examine during the process.
-        kernel_name : string, default `cubic`
-            This is the name of the smoothing kernel to use. Current supported
-            kernel names include `cubic`, `quartic`, `quintic`, `wendland2`,
-            `wendland4`, and `wendland6`.
-
-        Returns
-        -------
-
-        The field name tuple for the newly created field.
-        """
-        issue_deprecation_warning(
-            "This method is deprecated. "
-            "Since yt-4.0, it's no longer necessary to add a field specifically for "
-            "smoothing, because the global octree is removed. The old behavior of "
-            "interpolating onto a grid structure can be recovered through data objects "
-            "like ds.arbitrary_grid, ds.covering_grid, and most closely ds.octree. The "
-            "visualization machinery now treats SPH fields properly by smoothing onto "
-            "pixel locations. See this page to learn more: "
-            "https://yt-project.org/doc/yt4differences.html",
-            since="4.0.0",
-            removal="4.1.0",
-        )
-
-    def add_gradient_fields(self, fields=None, input_field=None):
+    def add_gradient_fields(self, fields=None):
         """Add gradient fields.
 
         Creates four new grid-based fields that represent the components of the gradient
@@ -1792,18 +1729,6 @@ def add_gradient_fields(self, fields=None, input_field=None):
         For instance, with cylindrical data, one gets 'density_gradient_<r,theta,z>'
 
         """
-        if input_field is not None:
-            issue_deprecation_warning(
-                "keyword argument 'input_field' is deprecated in favor of 'fields' "
-                "and will be removed in a future version of yt.",
-                since="4.0.0",
-                removal="4.1.0",
-            )
-            if fields is not None:
-                raise TypeError(
-                    "Can not use both 'fields' and 'input_field' keyword arguments"
-                )
-            fields = input_field
         if fields is None:
             raise TypeError("Missing required positional argument: fields")
 

yt/data_objects/time_series.py

@@ -8,7 +8,6 @@
 import numpy as np
 from more_itertools import always_iterable
 
-from yt._maintenance.deprecation import issue_deprecation_warning
 from yt.config import ytcfg
 from yt.data_objects.analyzer_objects import AnalysisTask, create_quantity_proxy
 from yt.data_objects.particle_trajectories import ParticleTrajectories
@@ -353,58 +352,6 @@ def eval(self, tasks, obj=None):
                 store.result.append(rv)
         return [v for k, v in sorted(return_values.items())]
 
-    @classmethod
-    def from_filenames(cls, filenames, parallel=True, setup_function=None, **kwargs):
-        r"""Create a time series from either a filename pattern or a list of
-        filenames.
-
-        This method provides an easy way to create a
-        :class:`~yt.data_objects.time_series.DatasetSeries`, given a set of
-        filenames or a pattern that matches them.  Additionally, it can set the
-        parallelism strategy.
-
-        Parameters
-        ----------
-        filenames : list or pattern
-            This can either be a list of filenames (such as ["DD0001/DD0001",
-            "DD0002/DD0002"]) or a pattern to match, such as
-            "DD*/DD*.index").  If it's the former, they will be loaded in
-            order.  The latter will be identified with the glob module and then
-            sorted.
-        parallel : True, False or int
-            This parameter governs the behavior when .piter() is called on the
-            resultant DatasetSeries object.  If this is set to False, the time
-            series will not iterate in parallel when .piter() is called.  If
-            this is set to either True or an integer, it will be iterated with
-            1 or that integer number of processors assigned to each parameter
-            file provided to the loop.
-        setup_function : callable, accepts a ds
-            This function will be called whenever a dataset is loaded.
-
-        Examples
-        --------
-
-        >>> def print_time(ds):
-        ...     print(ds.current_time)
-        ...
-        >>> ts = DatasetSeries.from_filenames(
-        ...     "GasSloshingLowRes/sloshing_low_res_hdf5_plt_cnt_0[0-6][0-9]0",
-        ...     setup_function=print_time,
-        ... )
-        ...
-        >>> for ds in ts:
-        ...     SlicePlot(ds, "x", ("gas", "density")).save()
-
-        """
-        issue_deprecation_warning(
-            "DatasetSeries.from_filenames() is deprecated and will be removed "
-            "in a future version of yt. Use DatasetSeries() directly.",
-            since="4.0.0",
-            removal="4.1.0",
-        )
-        obj = cls(filenames, parallel=parallel, setup_function=setup_function, **kwargs)
-        return obj
-
     @classmethod
     def from_output_log(cls, output_log, line_prefix="DATASET WRITTEN", parallel=True):
         filenames = []

yt/fields/field_info_container.py

@@ -5,7 +5,6 @@
 import numpy as np
 from unyt.exceptions import UnitConversionError
 
-from yt._maintenance.deprecation import issue_deprecation_warning
 from yt.fields.field_exceptions import NeedsConfiguration
 from yt.funcs import mylog, only_on_root
 from yt.geometry.geometry_handler import is_curvilinear
@@ -267,7 +266,7 @@ def setup_fluid_aliases(self, ftype="gas"):
                 self.alias((ftype, alias), field)
 
     @staticmethod
-    def _sanitize_sampling_type(sampling_type, particle_type=None):
+    def _sanitize_sampling_type(sampling_type):
         """Detect conflicts between deprecated and new parameters to specify the
         sampling type in a new field.
 
@@ -277,9 +276,6 @@ def _sanitize_sampling_type(sampling_type, particle_type=None):
         ----------
         sampling_type : str
             One of "cell", "particle" or "local" (case insensitive)
-        particle_type : str
-            This is a deprecated argument of the add_field method,
-            which was replaced by sampling_type.
 
         Raises
         ------
@@ -300,20 +296,6 @@ def _sanitize_sampling_type(sampling_type, particle_type=None):
                 sampling_type,
                 ", ".join(acceptable_samplings),
             )
-
-        if particle_type:
-            issue_deprecation_warning(
-                "'particle_type' keyword argument is deprecated in favour "
-                "of the positional argument 'sampling_type'.",
-                since="4.0.0",
-                removal="4.1.0",
-            )
-            if sampling_type != "particle":
-                raise RuntimeError(
-                    "Conflicting values for parameters "
-                    "'sampling_type' and 'particle_type'."
-                )
-
         return sampling_type
 
     def add_field(self, name, function, sampling_type, **kwargs):