doc: fix a bunch of broken references in the docs

doc/source/analyzing/astropy_integrations.rst

@@ -15,8 +15,7 @@ similar to that in yt. For this reason, we have implemented "round-trip"
 conversions between :class:`~yt.units.yt_array.YTArray` objects
 and AstroPy's :class:`~astropy.units.Quantity` objects. These are implemented
 in the :meth:`~yt.units.yt_array.YTArray.from_astropy` and
-:meth:`~yt.units.yt_array.YTArray.to_astropy` methods. See
-:ref:`fields_and_unit_conversion` for more information.
+:meth:`~yt.units.yt_array.YTArray.to_astropy` methods.
 
 FITS Image File Reading and Writing
 -----------------------------------
@@ -48,7 +47,7 @@ specifically a
 `QTable <http://docs.astropy.org/en/stable/table/mixin_columns.html#quantity-and-qtable>`_.
 ``QTable`` is unit-aware, and can be manipulated in a number of ways
 and written to disk in several formats, including ASCII text or FITS
-files. For more details, see :ref:`fields-astropy-export`.
+files.
 
 Similarly, 1D profile objects can also be exported to AstroPy
 ``QTable``, optionally writing all of the profile bins or only the ones

doc/source/analyzing/domain_analysis/index.rst

@@ -62,9 +62,7 @@ not kept up to date as yt evolved. Tools in here are looking for
 a new owner and a new home. If you find something in here that
 you'd like to bring back to life, either by adding it to
 :ref:`yt-astro` or as part of your own package, you are welcome
-to it! If you'd like any help, let us know! See
-:ref:`yt_attic:attic_modules` for a list of inventory of the
-attic.
+to it! If you'd like any help, let us know!
 
 Extensions
 ----------

doc/source/analyzing/units.rst

@@ -160,6 +160,9 @@ about the dataset's code unit system and can convert data into it. Unit objects
 from ``unyt`` or ``yt.units`` will not know about any particular dataset's unit
 system.
 
+
+.. cosmological-units::
+
 Comoving units for Cosmological Simulations
 -------------------------------------------
 

doc/source/developing/creating_frontend.rst

@@ -39,7 +39,6 @@ To get started
 
 * make a new directory in ``yt/frontends`` with the name of your code and add the name
 into ``yt/frontends/api.py:_frontends`` (in alphabetical order).
-
 * copy the contents of the ``yt/frontends/_skeleton`` directory, and replace every
 occurence of ``Skeleton`` with your frontend's name (preserving case). This adds a lot of
 boilerplate for the required classes and methods that are needed.

doc/source/index.rst

@@ -188,6 +188,7 @@ Table of Contents
    intro/index
    installing
    yt Quickstart <quickstart/index>
+   yt4differences
    yt3differences
    cookbook/index
    visualizing/index

doc/source/reference/api/api.rst

@@ -103,7 +103,7 @@ geometric.
    ~yt.data_objects.selection_objects.object_collection.YTDataCollection
    ~yt.data_objects.selection_objects.spheroids.YTSphere
    ~yt.data_objects.selection_objects.spheroids.YTEllipsoid
-   ~yt.data_objects.selection_objects.cur_region.YTCutRegion
+   ~yt.data_objects.selection_objects.cut_region.YTCutRegion
    ~yt.data_objects.index_subobjects.grid_patch.AMRGridPatch
    ~yt.data_objects.index_subobjects.octree_subset.OctreeSubset
    ~yt.data_objects.index_subobjects.particle_container.ParticleContainer
@@ -157,27 +157,16 @@ These objects generate an "index" into multiresolution data.
 Units
 -----
 
-These classes and functions enable yt's symbolic unit handling system.
+yt's symbolic unit handling system is now based on the external library unyt. In
+complement, Dataset objects support the following methods to build arrays and
+scalars with physical dimensions.
 
 .. autosummary::
 
    yt.data_objects.static_output.Dataset.arr
    yt.data_objects.static_output.Dataset.quan
-   ~yt.units.unit_object.define_unit
-   ~yt.units.unit_object.Unit
-   ~yt.units.unit_registry.UnitRegistry
-   ~yt.units.unit_systems.UnitSystem
-   ~yt.units.yt_array.YTArray
-   ~yt.units.yt_array.YTQuantity
-   ~yt.units.yt_array.uconcatenate
-   ~yt.units.yt_array.uintersect1d
-   ~yt.units.yt_array.uunion1d
-   ~yt.units.yt_array.unorm
-   ~yt.units.yt_array.udot
-   ~yt.units.yt_array.uvstack
-   ~yt.units.yt_array.uhstack
-   ~yt.units.yt_array.ustack
-   ~yt.units.yt_array.display_ytarray
+
+
 
 Frontends
 ---------
@@ -531,11 +520,11 @@ Field Functions
 
    ~yt.fields.field_info_container.FieldInfoContainer.add_field
    ~yt.data_objects.static_output.Dataset.add_field
-   ~yt.data_objects.static_outputs.add_deposited_particle_field
-   ~yt.data_objects.static_outputs.add_mesh_sampling_particle_field
-   ~yt.data_objects.static_outputs.add_smoothed_particle_field
-   ~yt.data_objects.static_outputs.add_gradient_fields
-   ~yt.frontends.stream.data_structures.add_SPH_fields
+   ~yt.data_objects.static_output.Dataset.add_deposited_particle_field
+   ~yt.data_objects.static_output.Dataset.add_mesh_sampling_particle_field
+   ~yt.data_objects.static_output.Dataset.add_smoothed_particle_field
+   ~yt.data_objects.static_output.Dataset.add_gradient_fields
+   ~yt.frontends.stream.data_structures.StreamParticleDataset.add_SPH_fields
 
 Particle Filters
 ----------------
@@ -797,7 +786,7 @@ Miscellaneous Types
 
 .. autosummary::
 
-   ~yt.config.YTConfigParser
+   ~yt.config.YTConfig
    ~yt.utilities.parameter_file_storage.ParameterFileStore
    ~yt.utilities.parallel_tools.parallel_analysis_interface.ObjectIterator
    ~yt.utilities.parallel_tools.parallel_analysis_interface.ParallelAnalysisInterface
@@ -819,7 +808,6 @@ Cosmology Calculator
    ~yt.utilities.cosmology.Cosmology.angular_scale
    ~yt.utilities.cosmology.Cosmology.luminosity_distance
    ~yt.utilities.cosmology.Cosmology.lookback_time
-   ~yt.utilities.cosmology.Cosmology.hubble_time
    ~yt.utilities.cosmology.Cosmology.critical_density
    ~yt.utilities.cosmology.Cosmology.hubble_parameter
    ~yt.utilities.cosmology.Cosmology.expansion_factor
@@ -858,17 +846,13 @@ These are for the pytest infrastructure:
 
 .. autosummary::
 
-    ~conftest.tempdir
-    ~conftest.answer_file
     ~conftest.hashing
     ~yt.utilities.answer_testing.answer_tests.grid_hierarchy
     ~yt.utilities.answer_testing.answer_tests.parentage_relationships
     ~yt.utilities.answer_testing.answer_tests.grid_values
     ~yt.utilities.answer_testing.answer_tests.projection_values
     ~yt.utilities.answer_testing.answer_tests.field_values
     ~yt.utilities.answer_testing.answer_tests.pixelized_projection_values
-    ~yt.utilities.answer_testing.answer_tests.simulated_halo_mass_function
-    ~yt.utilities.answer_testing.answer_tests.analytic_halo_mass_function
     ~yt.utilities.answer_testing.answer_tests.small_patch_amr
     ~yt.utilities.answer_testing.answer_tests.big_patch_amr
     ~yt.utilities.answer_testing.answer_tests.generic_array
@@ -878,6 +862,5 @@ These are for the pytest infrastructure:
     ~yt.utilities.answer_testing.answer_tests.phase_plot_attribute
     ~yt.utilities.answer_testing.answer_tests.generic_image
     ~yt.utilities.answer_testing.answer_tests.axial_pixelization
-    ~yt.utilities.answer_testing.answer_tests.light_cone_projection
     ~yt.utilities.answer_testing.answer_tests.extract_connected_sets
     ~yt.utilities.answer_testing.answer_tests.VR_image_comparison

doc/source/reference/changelog.rst

@@ -39,8 +39,8 @@ Major Changes and New Features
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 
-- New frontend support for the code AMRVAC. Many thanks to Clement Robert
-  and Niels Claes who were major contributors to this initiative. Relevant PRs include:
+- New frontend support for the code AMRVAC. Many thanks to Clément Robert
+and Niels Claes who were major contributors to this initiative. Relevant PRs include:
     - Initial PR to support AMRVAC native data files
       `PR 2321 <https://github.com/yt-project/yt/pull/2321>`__.
     - added support for dust fields and derived fields

doc/source/reference/configuration.rst

@@ -14,7 +14,9 @@ The Configuration
 
 The configuration is stored in simple text files (in the `toml <https://github.com/toml-lang/toml>`_ format).
 The files allow to set internal yt variables to custom default values to be used in future sessions.
-The configuration can either be stored :ref:`globally<Global Configuration>` or :ref:`locally<Local Configuration>`.
+The configuration can either be stored :ref:`globally<global-conf>` or :ref:`locally<local-conf>`.
+
+.. global-conf::
 
 Global Configuration
 ^^^^^^^^^^^^^^^^^^^^
@@ -45,6 +47,8 @@ options from the configuration file, e.g.:
    $ yt config rm yt maximum_stored_datasets
 
 
+.. local-conf::
+
 Local Configuration
 ^^^^^^^^^^^^^^^^^^^
 

doc/source/reference/demeshening.rst

@@ -9,7 +9,7 @@ an octree (the structure of which was determined by particle number density),
 in yt-4.0 this system was overhauled to utilize a `bitmap
 index<https://en.wikipedia.org/wiki/Bitmap_index>`_ based on a space-filling
 curve, using a `enhanced word-aligned
-hybrid<https://github.com/lemire/ewahboolarray>` boolean array as their
+hybrid<https://github.com/lemire/ewahboolarray>`_ boolean array as their
 backend.
 
 .. note::

doc/source/visualizing/plots.rst

@@ -553,10 +553,10 @@ Two workaround methods are available for plotting non-SPH particles with off-axi
 projections.
 
 1. :ref:`smooth-non-sph` - this method involves extracting particle data to be
-   reloaded with :ref:`~yt.loaders.load_particles` and using the
-   :ref:`~yt.frontends.stream.data_structures.add_SPH_fields` function to
-   create smoothing lengths. This works well for relatively small datasets,
-   but is not parallelized and may take too long for larger data.
+   reloaded with :meth:`~yt.loaders.load_particles` and using the
+   :meth:`~yt.frontends.stream.data_structures.StreamParticleDataset.add_SPH_fields`
+   function to create smoothing lengths. This works well for relatively small
+   datasets, but is not parallelized and may take too long for larger data.
 
 2. Plot from a saved
    :class:`~yt.data_objects.construction_data_containers.YTCoveringGrid`,

doc/source/yt4differences.rst

@@ -72,7 +72,7 @@ The list below is arranged in order of most to least important changes.
   field was actually a field for kinetic energy density, and so it has been
   renamed to ``"gas", "kinetic_energy_density"``. The old name still exists
   as an alias as of yt v4.0.0, but it will be removed in yt v4.1.0. See
-  :ref:`deprecated_field_names` below for more information.
+  next item below for more information.
   Other examples include ``"gas", "specific_thermal_energy"`` for thermal
   energy per unit mass, and ``("gas", "momentum_density_x")`` for the x-axis
   component of momentum density. See :ref:`efields` for more information.

yt/loaders.py

@@ -1308,16 +1308,16 @@ def flatten(l):
 def load_sample(
     fn: Optional[str] = None, *, progressbar: bool = True, timeout=None, **kwargs
 ):
-    """
+    r"""
     Load sample data with yt.
 
-    This is a simple wrapper around `yt.load` to include fetching
+    This is a simple wrapper around :func:`~yt.loaders.load` to include fetching
     data with pooch from remote source.
 
     The data registry table can be retrieved and visualized using
-    `yt.sample_data.api.get_data_registry_table()`.
+    :func:`~yt.sample_data.api.get_data_registry_table`.
     The `filename` column contains usable keys that can be passed
-    as the first positional argument to `load_sample`.
+    as the first positional argument to load_sample.
     Some data samples contain series of datasets. It may be required to
     supply the relative path to a specific dataset.
 
@@ -1338,7 +1338,7 @@ def load_sample(
     Notes
     -----
     - This function is experimental as of yt 4.0.0, do not rely on its exact behaviour.
-    - Any additional keyword argument is passed down to `yt.load`.
+    - Any additional keyword argument is passed down to :func:`~yt.loaders.load`.
     - In case of collision with predefined keyword arguments as set in
     the data registry, the ones passed to this function take priority.
     - Datasets with slashes '/' in their names can safely be used even on Windows.