[yt-svn] commit/yt: 16 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Fri May 19 14:07:18 PDT 2017
16 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/7ffd0f86849f/
Changeset: 7ffd0f86849f
User: xarthisius
Date: 2017-05-17 16:13:45+00:00
Summary: The label must precede a section header
Affected #: 2 files
diff -r 85556c2cc9ece324e2111b7d997e6661da3d7a47 -r 7ffd0f86849fa9733301ef34caf7918eaaea98c4 doc/source/analyzing/analysis_modules/star_analysis.rst
--- a/doc/source/analyzing/analysis_modules/star_analysis.rst
+++ b/doc/source/analyzing/analysis_modules/star_analysis.rst
@@ -1,11 +1,11 @@
-.. _star_analysis:
-
.. note::
This module has been deprecated as it is unmaintained. The code has been
moved to the `yt attic <https://github.com/yt-project/yt_attic>`__.
If you'd like to take it over, please do!
+.. _star_analysis:
+
Star Particle Analysis
======================
.. sectionauthor:: Stephen Skory <sskory at physics.ucsd.edu>
diff -r 85556c2cc9ece324e2111b7d997e6661da3d7a47 -r 7ffd0f86849fa9733301ef34caf7918eaaea98c4 doc/source/analyzing/analysis_modules/two_point_functions.rst
--- a/doc/source/analyzing/analysis_modules/two_point_functions.rst
+++ b/doc/source/analyzing/analysis_modules/two_point_functions.rst
@@ -1,11 +1,11 @@
-.. _two_point_functions:
-
.. note::
This module has been deprecated as it is unmaintained. The code has been
moved to the `yt attic <https://github.com/yt-project/yt_attic>`__.
If you'd like to take it over, please do!
+.. _two_point_functions:
+
Two Point Functions
===================
.. sectionauthor:: Stephen Skory <sskory at physics.ucsd.edu>
https://bitbucket.org/yt_analysis/yt/commits/c64ef5bb4884/
Changeset: c64ef5bb4884
User: xarthisius
Date: 2017-05-17 16:17:34+00:00
Summary: Only one line per argument is allowed
Affected #: 1 file
diff -r 7ffd0f86849fa9733301ef34caf7918eaaea98c4 -r c64ef5bb488493193a043e4ab9ea1f87e3892bec yt/analysis_modules/halo_analysis/enzofof_merger_tree.py
--- a/yt/analysis_modules/halo_analysis/enzofof_merger_tree.py
+++ b/yt/analysis_modules/halo_analysis/enzofof_merger_tree.py
@@ -713,8 +713,8 @@
The filename to which you saved the hdf5 data from save_halo_evolution
halo_id : int
The halo in 'filename' that you want to follow
- x_quantity, y_quantity : str, optional
- The quantity that you want to plot as the x_coord (or y_coords).
+ x_quantity : str, optional
+ The quantity that you want to plot as the x_coord.
Valid options are:
* cycle
@@ -732,8 +732,12 @@
* COM_vy
* COM_vz
- x_log, y_log : bool, optional
- Do you want the x(y)-axis to be in log or linear?
+ y_quantity : str, optional
+ The quantity that you want to plot as the y_coord.
+ x_log : bool, optional
+ Do you want the x-axis to be in log or linear?
+ y_log : bool, optional
+ Do you want the y-axis to be in log or linear?
FOF_directory : str, optional
Directory where FOF files (and hdf file) are located
https://bitbucket.org/yt_analysis/yt/commits/056e03402c6e/
Changeset: 056e03402c6e
User: xarthisius
Date: 2017-05-17 16:19:18+00:00
Summary: Reference a proper Dataset class
Affected #: 1 file
diff -r c64ef5bb488493193a043e4ab9ea1f87e3892bec -r 056e03402c6e2f1e2711df261156fa71628f7638 yt/analysis_modules/halo_finding/rockstar/rockstar.py
--- a/yt/analysis_modules/halo_finding/rockstar/rockstar.py
+++ b/yt/analysis_modules/halo_finding/rockstar/rockstar.py
@@ -114,29 +114,29 @@
Parameters
----------
- ts: DatasetSeries, Dataset
+ ts : DatasetSeries, ~yt.data_objects.static_output.Dataset
This is the data source containing the DM particles. Because
halo IDs may change from one snapshot to the next, the only
way to keep a consistent halo ID across time is to feed
Rockstar a set of snapshots, ie, via DatasetSeries.
- num_readers: int
+ num_readers : int
The number of reader can be increased from the default
of 1 in the event that a single snapshot is split among
many files. This can help in cases where performance is
IO-limited. Default is 1. If run inline, it is
equal to the number of MPI threads.
- num_writers: int
+ num_writers : int
The number of writers determines the number of processing threads
as well as the number of threads writing output data.
The default is set to comm.size-num_readers-1. If run inline,
the default is equal to the number of MPI threads.
- outbase: str
+ outbase : str
This is where the out*list files that Rockstar makes should be
placed. Default is 'rockstar_halos'.
- particle_type: str
+ particle_type : str
This is the "particle type" that can be found in the data. This can be
a filtered particle or an inherent type.
- force_res: float
+ force_res : float
This parameter specifies the force resolution that Rockstar uses
in units of Mpc/h.
If no value is provided, this parameter is automatically set to
https://bitbucket.org/yt_analysis/yt/commits/ac415b405dd3/
Changeset: ac415b405dd3
User: xarthisius
Date: 2017-05-17 16:23:05+00:00
Summary: Drop type definition of 'fields' as it's not easy to express
Affected #: 1 file
diff -r 056e03402c6e2f1e2711df261156fa71628f7638 -r ac415b405dd32f566d2e42a1f008c260fbed2159 yt/data_objects/derived_quantities.py
--- a/yt/data_objects/derived_quantities.py
+++ b/yt/data_objects/derived_quantities.py
@@ -156,8 +156,8 @@
Parameters
----------
- fields : field or list of fields
- The field to be summed.
+ fields
+ The field or list of fields to be summed.
Examples
--------
@@ -487,8 +487,9 @@
Parameters
----------
- fields : field or list of fields
- The field over which the extrema are to be calculated.
+ fields
+ The field or list of fields over which the extrema are to be
+ calculated.
non_zero : bool
If True, only positive values are considered in the calculation.
Default: False
https://bitbucket.org/yt_analysis/yt/commits/ad64d8552c80/
Changeset: ad64d8552c80
User: xarthisius
Date: 2017-05-17 16:28:46+00:00
Summary: Reference a proper Dataset class
Affected #: 1 file
diff -r ac415b405dd32f566d2e42a1f008c260fbed2159 -r ad64d8552c80e7161c941a79a4345d5af158a297 yt/data_objects/selection_data_containers.py
--- a/yt/data_objects/selection_data_containers.py
+++ b/yt/data_objects/selection_data_containers.py
@@ -49,7 +49,7 @@
periodic its position will be corrected to lie inside
the range [DLE,DRE) to ensure one and only one cell may
match that point
- ds: Dataset, optional
+ ds: ~yt.data_objects.static_output.Dataset, optional
An optional dataset to use rather than self.ds
field_parameters : dictionary
A dictionary of field parameters than can be accessed by derived
@@ -95,7 +95,7 @@
that this is in the plane coordinates: so if you are casting along
x, this will be (y, z). If you are casting along y, this will be
(z, x). If you are casting along z, this will be (x, y).
- ds: Dataset, optional
+ ds: ~yt.data_objects.static_output.Dataset, optional
An optional dataset to use rather than self.ds
field_parameters : dictionary
A dictionary of field parameters than can be accessed by derived
@@ -162,7 +162,7 @@
The place where the ray starts.
end_point : array-like set of 3 floats
The place where the ray ends.
- ds: Dataset, optional
+ ds: ~yt.data_objects.static_output.Dataset, optional
An optional dataset to use rather than self.ds
field_parameters : dictionary
A dictionary of field parameters than can be accessed by derived
@@ -248,7 +248,7 @@
center : array_like, optional
The 'center' supplied to fields that use it. Note that this does
not have to have `coord` as one value. optional.
- ds: Dataset, optional
+ ds: ~yt.data_objects.static_output.Dataset, optional
An optional dataset to use rather than self.ds
field_parameters : dictionary
A dictionary of field parameters than can be accessed by derived
@@ -355,7 +355,7 @@
north_vector: array_like, optional
An optional vector to describe the north-facing direction in the resulting
plane.
- ds: Dataset, optional
+ ds: ~yt.data_objects.static_output.Dataset, optional
An optional dataset to use rather than self.ds
field_parameters : dictionary
A dictionary of field parameters than can be accessed by derived
@@ -556,7 +556,7 @@
bottom planes
fields : array of fields, optional
any fields to be pre-loaded in the cylinder object
- ds: Dataset, optional
+ ds: ~yt.data_objects.static_output.Dataset, optional
An optional dataset to use rather than self.ds
field_parameters : dictionary
A dictionary of field parameters than can be accessed by derived
https://bitbucket.org/yt_analysis/yt/commits/f8fda7759502/
Changeset: f8fda7759502
User: xarthisius
Date: 2017-05-17 16:54:32+00:00
Summary: Fix all occurrences of Dataset
Affected #: 17 files
diff -r ad64d8552c80e7161c941a79a4345d5af158a297 -r f8fda775950276563f8b2e59d62e73975956e72e yt/analysis_modules/cosmological_observation/light_ray/light_ray.py
--- a/yt/analysis_modules/cosmological_observation/light_ray/light_ray.py
+++ b/yt/analysis_modules/cosmological_observation/light_ray/light_ray.py
@@ -53,7 +53,7 @@
Parameters
----------
- parameter_filename : string or :class:`yt.data_objects.static_output.Dataset`
+ parameter_filename : string or :class:`~yt.data_objects.static_output.Dataset`
For simple rays, one may pass either a loaded dataset object or
the filename of a dataset.
For compound rays, one must pass the filename of the simulation
diff -r ad64d8552c80e7161c941a79a4345d5af158a297 -r f8fda775950276563f8b2e59d62e73975956e72e yt/convenience.py
--- a/yt/convenience.py
+++ b/yt/convenience.py
@@ -32,9 +32,9 @@
"""
This function attempts to determine the base data type of a filename or
other set of arguments by calling
- :meth:`yt.data_objects.api.Dataset._is_valid` until it finds a
+ :meth:`yt.data_objects.static_output.Dataset._is_valid` until it finds a
match, at which point it returns an instance of the appropriate
- :class:`yt.data_objects.api.Dataset` subclass.
+ :class:`yt.data_objects.static_output.Dataset` subclass.
"""
candidates = []
args = [os.path.expanduser(arg) if isinstance(arg, string_types)
diff -r ad64d8552c80e7161c941a79a4345d5af158a297 -r f8fda775950276563f8b2e59d62e73975956e72e yt/data_objects/data_containers.py
--- a/yt/data_objects/data_containers.py
+++ b/yt/data_objects/data_containers.py
@@ -132,7 +132,7 @@
def __init__(self, ds, field_parameters):
"""
Typically this is never called directly, but only due to inheritance.
- It associates a :class:`~yt.data_objects.api.Dataset` with the class,
+ It associates a :class:`~yt.data_objects.static_output.Dataset` with the class,
sets its initial set of fields, and the remainder of the arguments
are passed as field_parameters.
"""
diff -r ad64d8552c80e7161c941a79a4345d5af158a297 -r f8fda775950276563f8b2e59d62e73975956e72e yt/data_objects/particle_trajectories.py
--- a/yt/data_objects/particle_trajectories.py
+++ b/yt/data_objects/particle_trajectories.py
@@ -29,7 +29,7 @@
Parameters
----------
- outputs : `yt.data_objects.time_series.DatasetSeries`
+ outputs : ~yt.data_objects.time_series.DatasetSeries
DatasetSeries object from which to draw the particles.
indices : array_like
An integer array of particle indices whose trajectories we
diff -r ad64d8552c80e7161c941a79a4345d5af158a297 -r f8fda775950276563f8b2e59d62e73975956e72e yt/data_objects/static_output.py
--- a/yt/data_objects/static_output.py
+++ b/yt/data_objects/static_output.py
@@ -1399,7 +1399,7 @@
----------
symbol : string
The symbol for the new unit.
- value : (value, unit) tuple or YTQuantity
+ value : tuple or ~yt.units.yt_array.YTQuantity
The definition of the new unit in terms of some other units. For example,
one would define a new "mph" unit with (1.0, "mile/hr")
tex_repr : string, optional
@@ -1407,7 +1407,7 @@
be generated automatically based on the symbol string.
offset : float, optional
The default offset for the unit. If not set, an offset of 0 is assumed.
- prefixable : boolean, optional
+ prefixable : bool, optional
Whether or not the new unit can use SI prefixes. Default: False
Examples
diff -r ad64d8552c80e7161c941a79a4345d5af158a297 -r f8fda775950276563f8b2e59d62e73975956e72e yt/fields/xray_emission_fields.py
--- a/yt/fields/xray_emission_fields.py
+++ b/yt/fields/xray_emission_fields.py
@@ -159,7 +159,7 @@
The maximum energy in keV for the energy band.
redshift : float, optional
The cosmological redshift of the source of the field. Default: 0.0.
- metallicity : field or float, optional
+ metallicity : str or tuple of str or float, optional
Either the name of a metallicity field or a single floating-point
number specifying a spatially constant metallicity. Must be in
solar units. If set to None, no metals will be assumed. Default:
diff -r ad64d8552c80e7161c941a79a4345d5af158a297 -r f8fda775950276563f8b2e59d62e73975956e72e yt/frontends/fits/misc.py
--- a/yt/frontends/fits/misc.py
+++ b/yt/frontends/fits/misc.py
@@ -49,7 +49,7 @@
Parameters
----------
- ds : `~yt.data_objects.static_output.Dataset`
+ ds : ~yt.data_objects.static_output.Dataset
The FITS events file dataset to add the counts fields to.
ebounds : list of tuples
A list of tuples, one for each field, with (emin, emax) as the
diff -r ad64d8552c80e7161c941a79a4345d5af158a297 -r f8fda775950276563f8b2e59d62e73975956e72e yt/frontends/stream/data_structures.py
--- a/yt/frontends/stream/data_structures.py
+++ b/yt/frontends/stream/data_structures.py
@@ -908,7 +908,7 @@
Parameters
----------
- base_ds : `~yt.data_objects.static_output.Dataset`
+ base_ds : ~yt.data_objects.static_output.Dataset
This is any static output. It can also be a stream static output, for
instance as returned by load_uniform_data.
refinement_critera : list of :class:`~yt.utilities.flagging_methods.FlaggingMethod`
diff -r ad64d8552c80e7161c941a79a4345d5af158a297 -r f8fda775950276563f8b2e59d62e73975956e72e yt/units/yt_array.py
--- a/yt/units/yt_array.py
+++ b/yt/units/yt_array.py
@@ -228,16 +228,16 @@
Parameters
----------
- input_array : Iterable
+ input_array : iterable
A tuple, list, or array to attach units to
input_units : String unit specification, unit symbol object, or astropy units
The units of the array. Powers must be specified using python
syntax (cm**3, not cm^3).
- registry : A UnitRegistry object
+ registry : ~yt.units.unit_registry.UnitRegistry
The registry to create units from. If input_units is already associated
with a unit registry and this is specified, this will be used instead of
the registry associated with the unit object.
- dtype : string or NumPy dtype object
+ dtype : data-type
The dtype of the array data. Defaults to the dtype of the input data,
or, if none is found, uses np.float64
bypass_validation : boolean
diff -r ad64d8552c80e7161c941a79a4345d5af158a297 -r f8fda775950276563f8b2e59d62e73975956e72e yt/utilities/grid_data_format/writer.py
--- a/yt/utilities/grid_data_format/writer.py
+++ b/yt/utilities/grid_data_format/writer.py
@@ -40,8 +40,8 @@
The yt data to write out.
gdf_path : string
The path of the file to output.
- fields : field or list of fields
- The fields(s) to write out. If None, defaults to
+ fields
+ The field or list of fields to write out. If None, defaults to
ds.field_list.
data_author : string, optional
The name of the author who wrote the data. Default: None.
diff -r ad64d8552c80e7161c941a79a4345d5af158a297 -r f8fda775950276563f8b2e59d62e73975956e72e yt/visualization/fits_image.py
--- a/yt/visualization/fits_image.py
+++ b/yt/visualization/fits_image.py
@@ -529,7 +529,7 @@
Parameters
----------
- ds : :class:`yt.data_objects.api.Dataset`
+ ds : :class:`~yt.data_objects.static_output.Dataset`
The dataset object.
axis : character or integer
The axis of the slice. One of "x","y","z", or 0,1,2.
@@ -584,7 +584,7 @@
Parameters
----------
- ds : :class:`yt.data_objects.api.Dataset`
+ ds : :class:`~yt.data_objects.static_output.Dataset`
The dataset object.
axis : character or integer
The axis along which to project. One of "x","y","z", or 0,1,2.
@@ -641,7 +641,7 @@
Parameters
----------
- ds : :class:`yt.data_objects.api.Dataset`
+ ds : :class:`~yt.data_objects.static_output.Dataset`
The dataset object.
normal : a sequence of floats
The vector normal to the projection plane.
@@ -700,7 +700,7 @@
Parameters
----------
- ds : :class:`yt.data_objects.api.Dataset`
+ ds : :class:`~yt.data_objects.static_output.Dataset`
This is the dataset object corresponding to the
simulation output to be plotted.
normal : a sequence of floats
diff -r ad64d8552c80e7161c941a79a4345d5af158a297 -r f8fda775950276563f8b2e59d62e73975956e72e yt/visualization/particle_plots.py
--- a/yt/visualization/particle_plots.py
+++ b/yt/visualization/particle_plots.py
@@ -363,7 +363,7 @@
Parameters
----------
- ds : :class:`yt.data_objects.api.Dataset`
+ ds : :class:`yt.data_objects.static_output.Dataset`
This is the dataset object corresponding to the
simulation output to be plotted.
x_field : string
diff -r ad64d8552c80e7161c941a79a4345d5af158a297 -r f8fda775950276563f8b2e59d62e73975956e72e yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -1536,7 +1536,7 @@
Parameters
----------
- ds : :class:`yt.data_objects.api.Dataset`
+ ds : :class:`yt.data_objects.static_output.Dataset`
This is the dataset object corresponding to the
simulation output to be plotted.
normal : a sequence of floats
@@ -1672,7 +1672,7 @@
Parameters
----------
- ds : :class:`yt.data_objects.api.Dataset`
+ ds : :class:`yt.data_objects.static_output.Dataset`
This is the dataset object corresponding to the
simulation output to be plotted.
normal : a sequence of floats
@@ -1855,7 +1855,7 @@
Parameters
----------
- ds : :class:`yt.data_objects.api.Dataset`
+ ds : :class:`yt.data_objects.static_output.Dataset`
This is the dataset object corresponding to the
simulation output to be plotted.
normal : int or one of 'x', 'y', 'z', or sequence of floats
diff -r ad64d8552c80e7161c941a79a4345d5af158a297 -r f8fda775950276563f8b2e59d62e73975956e72e yt/visualization/streamlines.py
--- a/yt/visualization/streamlines.py
+++ b/yt/visualization/streamlines.py
@@ -37,17 +37,17 @@
Parameters
----------
- ds : `~yt.data_objects.Dataset`
+ ds : ~yt.data_objects.static_output.Dataset
This is the dataset to streamline
pos : array_like
An array of initial starting positions of the streamlines.
- xfield: field, optional
+ xfield : str or tuple of str, optional
The x component of the vector field to be streamlined.
Default:'velocity_x'
- yfield: field, optional
+ yfield : str or tuple of str, optional
The y component of the vector field to be streamlined.
Default:'velocity_y'
- zfield: field, optional
+ zfield : str or tuple of str, optional
The z component of the vector field to be streamlined.
Default:'velocity_z'
volume : `yt.extensions.volume_rendering.AMRKDTree`, optional
diff -r ad64d8552c80e7161c941a79a4345d5af158a297 -r f8fda775950276563f8b2e59d62e73975956e72e yt/visualization/volume_rendering/off_axis_projection.py
--- a/yt/visualization/volume_rendering/off_axis_projection.py
+++ b/yt/visualization/volume_rendering/off_axis_projection.py
@@ -38,7 +38,7 @@
Parameters
----------
- data_source : `~yt.data_objects.static_output.Dataset` or `~yt.data_objects.data_containers.YTSelectionDataContainer`
+ data_source : ~yt.data_objects.static_output.Dataset or ~yt.data_objects.data_containers.YTSelectionDataContainer
This is the dataset or data object to volume render.
center : array_like
The current 'center' of the view port -- the focal point for the
diff -r ad64d8552c80e7161c941a79a4345d5af158a297 -r f8fda775950276563f8b2e59d62e73975956e72e yt/visualization/volume_rendering/old_camera.py
--- a/yt/visualization/volume_rendering/old_camera.py
+++ b/yt/visualization/volume_rendering/old_camera.py
@@ -100,7 +100,7 @@
the volume rendering mechanism.
sub_samples : int, optional
The number of samples to take inside every cell per ray.
- ds : `~yt.data_objects.api.Dataset`
+ ds : ~yt.data_objects.static_output.Dataset
For now, this is a require parameter! But in the future it will become
optional. This is the dataset to volume render.
use_kd: bool, optional
@@ -1190,7 +1190,7 @@
the volume rendering mechanism.
sub_samples : int, optional
The number of samples to take inside every cell per ray.
- ds : `~yt.data_objects.api.Dataset`
+ ds : ~yt.data_objects.static_output.Dataset
For now, this is a require parameter! But in the future it will become
optional. This is the dataset to volume render.
use_kd: bool, optional
@@ -2155,7 +2155,7 @@
Parameters
----------
- ds : `~yt.data_objects.api.Dataset`
+ ds : ~yt.data_objects.static_output.Dataset
This is the dataset to volume render.
center : array_like
The current 'center' of the view port -- the focal point for the
diff -r ad64d8552c80e7161c941a79a4345d5af158a297 -r f8fda775950276563f8b2e59d62e73975956e72e yt/visualization/volume_rendering/scene.py
--- a/yt/visualization/volume_rendering/scene.py
+++ b/yt/visualization/volume_rendering/scene.py
@@ -640,7 +640,7 @@
Parameters
----------
- ds : :class:`yt.data_objects.api.Dataset`
+ ds : :class:`yt.data_objects.static_output.Dataset`
This is the dataset object corresponding to the
simulation being rendered. Used to get the domain bounds.
https://bitbucket.org/yt_analysis/yt/commits/e27c71739f3f/
Changeset: e27c71739f3f
User: xarthisius
Date: 2017-05-17 16:56:27+00:00
Summary: Only one line per argument is allowed
Affected #: 1 file
diff -r f8fda775950276563f8b2e59d62e73975956e72e -r e27c71739f3f740f47a482587be09894fc9c4db2 yt/visualization/volume_rendering/old_camera.py
--- a/yt/visualization/volume_rendering/old_camera.py
+++ b/yt/visualization/volume_rendering/old_camera.py
@@ -258,9 +258,12 @@
Default : 0.3
cmap : string, optional
Colormap to be used mapping grid levels to colors.
- min_level, max_level : int, optional
- Optional parameters to specify the min and max level grid boxes
- to overplot on the image.
+ min_level : int, optional
+ Optional parameter to specify the min level grid boxes
+ to overplot on the image.
+ max_level : int, optional
+ Optional parameters to specify the max level grid boxes
+ to overplot on the image.
Returns
-------
https://bitbucket.org/yt_analysis/yt/commits/22833916bd59/
Changeset: 22833916bd59
User: xarthisius
Date: 2017-05-17 17:52:57+00:00
Summary: Fix docstrings of params with a shape definition
Affected #: 3 files
diff -r e27c71739f3f740f47a482587be09894fc9c4db2 -r 22833916bd591be6cd517821508a797bb621a9c5 yt/utilities/sdf.py
--- a/yt/utilities/sdf.py
+++ b/yt/utilities/sdf.py
@@ -1164,7 +1164,7 @@
"""Get floating point bounding box for a given midx cell
Returns:
- bbox: array-like, shape (3,2)
+ bbox: array-like of shape (3,2)
"""
cell_iarr = np.array(cell_iarr, dtype="int64")
@@ -1294,7 +1294,7 @@
"""
Returns:
- bbox: array-like, shape (3,2)
+ bbox: array-like of shape (3,2)
"""
bbox = self.get_cell_bbox(level, cell_iarr)
diff -r e27c71739f3f740f47a482587be09894fc9c4db2 -r 22833916bd591be6cd517821508a797bb621a9c5 yt/visualization/volume_rendering/render_source.py
--- a/yt/visualization/volume_rendering/render_source.py
+++ b/yt/visualization/volume_rendering/render_source.py
@@ -735,7 +735,7 @@
Parameters
----------
- color: array of ints, shape (4), optional
+ color: array_like of shape (4,), optional
The RGBA value to use to draw the mesh lines.
Default is black.
alpha : float, optional
@@ -801,16 +801,16 @@
Parameters
----------
- positions: array, shape (N, 3)
+ positions: array_like of shape (N, 3)
The positions of points to be added to the scene. If specified with no
units, the positions will be assumed to be in code units.
- colors : array, shape (N, 4), optional
+ colors : array_like of shape (N, 4), optional
The colors of the points, including an alpha channel, in floating
point running from 0..1.
color_stride : int, optional
The stride with which to access the colors when putting them on the
scene.
- radii : array, shape (N), optional
+ radii : array_like of shape (N), optional
The radii of the points in the final image, in pixels (int)
Examples
@@ -922,12 +922,12 @@
Parameters
----------
- positions: array, shape (N, 2, 3)
+ positions: array_like of shape (N, 2, 3)
The positions of the starting and stopping points for each line.
For example,positions[0][0] and positions[0][1] would give the (x, y, z)
coordinates of the beginning and end points of the first line,
respectively. If specified with no units, assumed to be in code units.
- colors : array, shape (N, 4), optional
+ colors : array_like of shape (N, 4), optional
The colors of the points, including an alpha channel, in floating
point running from 0..1. The four channels correspond to r, g, b, and
alpha values. Note that they correspond to the line segment succeeding
@@ -1049,11 +1049,11 @@
Parameters
----------
- left_edge: array-like, shape (3,), float
+ left_edge: array-like of shape (3,), float
The left edge coordinates of the box.
- right_edge : array-like, shape (3,), float
+ right_edge : array-like of shape (3,), float
The right edge coordinates of the box.
- color : array-like, shape (4,), float, optional
+ color : array-like of shape (4,), float, optional
The colors (including alpha) to use for the lines.
Examples
@@ -1212,7 +1212,7 @@
Parameters
----------
- colors: array-like, shape (3,4), optional
+ colors: array-like of shape (3,4), optional
The x, y, z RGBA values to use to draw the vectors.
alpha : float, optional
The opacity of the vectors.
diff -r e27c71739f3f740f47a482587be09894fc9c4db2 -r 22833916bd591be6cd517821508a797bb621a9c5 yt/visualization/volume_rendering/scene.py
--- a/yt/visualization/volume_rendering/scene.py
+++ b/yt/visualization/volume_rendering/scene.py
@@ -711,7 +711,7 @@
Parameters
----------
- colors: array of ints, shape (4), optional
+ colors: array_like of shape (4,), optional
The RGBA value to use to draw the mesh lines.
Default is black.
alpha : float, optional
@@ -732,7 +732,7 @@
Parameters
----------
- colors: array-like, shape (3,4), optional
+ colors: array-like of shape (3,4), optional
The x, y, z RGBA values to use to draw the axes.
alpha : float, optional
The opacity of the vectors.
https://bitbucket.org/yt_analysis/yt/commits/08cb755dff7d/
Changeset: 08cb755dff7d
User: xarthisius
Date: 2017-05-17 17:55:44+00:00
Summary: Move type details into the long description
Affected #: 1 file
diff -r 22833916bd591be6cd517821508a797bb621a9c5 -r 08cb755dff7d119417cbb7ee3cee298e45b9c5a9 yt/visualization/volume_rendering/transfer_functions.py
--- a/yt/visualization/volume_rendering/transfer_functions.py
+++ b/yt/visualization/volume_rendering/transfer_functions.py
@@ -654,10 +654,10 @@
colormap : string, optional
An acceptable colormap. See either yt.visualization.color_maps or
http://www.scipy.org/Cookbook/Matplotlib/Show_colormaps .
- col_bounds: array_like [min, max], optional
- Limits the values over which the colormap spans to these
- values. Useful for sampling an entire colormap over a
- range smaller than the transfer function bounds.
+ col_bounds: array_like, optional
+ Limits ([min, max]) the values over which the colormap spans to
+ these values. Useful for sampling an entire colormap over a range
+ smaller than the transfer function bounds.
See Also
--------
@@ -769,10 +769,10 @@
colormap : string, optional
An acceptable colormap. See either yt.visualization.color_maps or
http://www.scipy.org/Cookbook/Matplotlib/Show_colormaps .
- col_bounds: array_like [min, max], optional
- Limits the values over which the colormap spans to these
- values. Useful for sampling an entire colormap over a
- range smaller than the transfer function bounds.
+ col_bounds: array_like, optional
+ Limits ([min, max]) the values over which the colormap spans to
+ these values. Useful for sampling an entire colormap over a range
+ smaller than the transfer function bounds.
See Also
--------
https://bitbucket.org/yt_analysis/yt/commits/d67a1f297fa7/
Changeset: d67a1f297fa7
User: xarthisius
Date: 2017-05-17 20:53:10+00:00
Summary: Fix GagdetFOFHaloContainer docstring
Affected #: 1 file
diff -r 08cb755dff7d119417cbb7ee3cee298e45b9c5a9 -r d67a1f297fa7e05516e0612fbb46d2fff2290a6a yt/frontends/gadget_fof/data_structures.py
--- a/yt/frontends/gadget_fof/data_structures.py
+++ b/yt/frontends/gadget_fof/data_structures.py
@@ -462,8 +462,8 @@
class GagdetFOFHaloContainer(YTSelectionContainer):
"""
Create a data container to get member particles and individual
- values from halos and subhalos. Halo mass, position, and
- velocity are set as attributes. Halo IDs are accessible
+ values from halos and subhalos. Halo mass, position, and
+ velocity are set as attributes. Halo IDs are accessible
through the field, "member_ids". Other fields that are one
value per halo are accessible as normal. The field list for
halo objects can be seen in `ds.halos_field_list`.
@@ -473,13 +473,13 @@
ptype : string
The type of halo, either "Group" for the main halo or
"Subhalo" for subhalos.
- particle_identifier : int or tuple of (int, int)
+ particle_identifier : int or tuple of ints
The halo or subhalo id. If requesting a subhalo, the id
can also be given as a tuple of the main halo id and
subgroup id, such as (1, 4) for subgroup 4 of halo 1.
- Halo Container Attributes
- -------------------------
+ Attributes
+ ----------
particle_identifier : int
The id of the halo or subhalo.
group_identifier : int
@@ -496,14 +496,13 @@
velocity : array of floats
Halo velocity.
- Relevant Fields
- ---------------
- particle_number :
- number of particles
- subhalo_number :
- number of subhalos
- group_identifier :
- id of parent group for subhalos
+ Note
+ ----
+ Relevant Fields:
+
+ * particle_number - number of particles
+ * subhalo_number - number of subhalos
+ * group_identifier - id of parent group for subhalos
Examples
--------
https://bitbucket.org/yt_analysis/yt/commits/361c7941895c/
Changeset: 361c7941895c
User: xarthisius
Date: 2017-05-17 20:53:43+00:00
Summary: More docstring fixes
Affected #: 2 files
diff -r d67a1f297fa7e05516e0612fbb46d2fff2290a6a -r 361c7941895cd0229c2aaa82bdac5201c29c7875 yt/units/unit_object.py
--- a/yt/units/unit_object.py
+++ b/yt/units/unit_object.py
@@ -729,7 +729,7 @@
----------
symbol : string
The symbol for the new unit.
- value : (value, unit) tuple or YTQuantity
+ value : tuple or ~yt.units.yt_array.YTQuantity
The definition of the new unit in terms of some other units. For example,
one would define a new "mph" unit with (1.0, "mile/hr")
tex_repr : string, optional
diff -r d67a1f297fa7e05516e0612fbb46d2fff2290a6a -r 361c7941895cd0229c2aaa82bdac5201c29c7875 yt/units/yt_array.py
--- a/yt/units/yt_array.py
+++ b/yt/units/yt_array.py
@@ -1307,7 +1307,7 @@
The registry to create units from. If input_units is already associated
with a unit registry and this is specified, this will be used instead of
the registry associated with the unit object.
- dtype : string or NumPy dtype object
+ dtype : data-type
The dtype of the array data.
Examples
https://bitbucket.org/yt_analysis/yt/commits/234008cf410c/
Changeset: 234008cf410c
User: xarthisius
Date: 2017-05-17 21:06:29+00:00
Summary: Do not crossref 'iterable'
Affected #: 4 files
diff -r 361c7941895cd0229c2aaa82bdac5201c29c7875 -r 234008cf410c0b0a4be1c6732021d9a37f3f934b yt/extern/tqdm/_tqdm.py
--- a/yt/extern/tqdm/_tqdm.py
+++ b/yt/extern/tqdm/_tqdm.py
@@ -217,7 +217,7 @@
"""
Parameters
----------
- iterable : iterable, optional
+ iterable : !iterable, optional
Iterable to decorate with a progressbar.
Leave blank [default: None] to manually manage the updates.
desc : str, optional
diff -r 361c7941895cd0229c2aaa82bdac5201c29c7875 -r 234008cf410c0b0a4be1c6732021d9a37f3f934b yt/units/yt_array.py
--- a/yt/units/yt_array.py
+++ b/yt/units/yt_array.py
@@ -228,7 +228,7 @@
Parameters
----------
- input_array : iterable
+ input_array : !iterable
A tuple, list, or array to attach units to
input_units : String unit specification, unit symbol object, or astropy units
The units of the array. Powers must be specified using python
diff -r 361c7941895cd0229c2aaa82bdac5201c29c7875 -r 234008cf410c0b0a4be1c6732021d9a37f3f934b yt/visualization/volume_rendering/camera.py
--- a/yt/visualization/volume_rendering/camera.py
+++ b/yt/visualization/volume_rendering/camera.py
@@ -163,7 +163,7 @@
Parameters
----------
- position : number, YTQuantity, iterable, or 3 element YTArray
+ position : number, YTQuantity, !iterable, or 3 element YTArray
If a scalar, assumes that the position is the same in all three
coordinates. If an iterable, must contain only scalars or
(length, unit) tuples.
@@ -192,7 +192,7 @@
Parameters
----------
- width : number, YTQuantity, iterable, or 3 element YTArray
+ width : number, YTQuantity, !iterable, or 3 element YTArray
The width of the volume rendering in the horizontal, vertical, and
depth directions. If a scalar, assumes that the width is the same in
all three directions. If an iterable, must contain only scalars or
@@ -220,7 +220,7 @@
Parameters
----------
- focus : number, YTQuantity, iterable, or 3 element YTArray
+ focus : number, YTQuantity, !iterable, or 3 element YTArray
The width of the volume rendering in the horizontal, vertical, and
depth directions. If a scalar, assumes that the width is the same in
all three directions. If an iterable, must contain only scalars or
@@ -357,7 +357,7 @@
Parameters
----------
- width : number, YTQuantity, iterable, or 3 element YTArray
+ width : number, YTQuantity, !iterable, or 3 element YTArray
The width of the volume rendering in the horizontal, vertical, and
depth directions. If a scalar, assumes that the width is the same in
all three directions. If an iterable, must contain only scalars or
@@ -376,7 +376,7 @@
Parameters
----------
- width : number, YTQuantity, iterable, or 3 element YTArray
+ width : number, YTQuantity, !iterable, or 3 element YTArray
If a scalar, assumes that the position is the same in all three
coordinates. If an iterable, must contain only scalars or
(length, unit) tuples.
@@ -400,7 +400,7 @@
Parameters
----------
- focus : number, YTQuantity, iterable, or 3 element YTArray
+ focus : number, YTQuantity, !iterable, or 3 element YTArray
If a scalar, assumes that the focus is the same is all three
coordinates. If an iterable, must contain only scalars or
(length, unit) tuples.
diff -r 361c7941895cd0229c2aaa82bdac5201c29c7875 -r 234008cf410c0b0a4be1c6732021d9a37f3f934b yt/visualization/volume_rendering/interactive_vr.py
--- a/yt/visualization/volume_rendering/interactive_vr.py
+++ b/yt/visualization/volume_rendering/interactive_vr.py
@@ -86,11 +86,11 @@
Parameters
----------
- position : iterable, or 3 element array in code_length
+ position : !iterable, or 3 element array in code_length
The initial position of the camera.
- focus : iterable, or 3 element array in code_length
+ focus : !iterable, or 3 element array in code_length
A point in space that the camera is looking at.
- up : iterable, or 3 element array in code_length
+ up : !iterable, or 3 element array in code_length
The 'up' direction for the camera.
fov : float, optional
An angle defining field of view in degrees.
https://bitbucket.org/yt_analysis/yt/commits/518b0c6aea91/
Changeset: 518b0c6aea91
User: xarthisius
Date: 2017-05-17 21:08:52+00:00
Summary: Do not crossref 'value'
Affected #: 1 file
diff -r 234008cf410c0b0a4be1c6732021d9a37f3f934b -r 518b0c6aea91e60b5ace7a19dbc787c124c62447 yt/visualization/volume_rendering/transfer_functions.py
--- a/yt/visualization/volume_rendering/transfer_functions.py
+++ b/yt/visualization/volume_rendering/transfer_functions.py
@@ -702,7 +702,7 @@
colormap : string, optional
An acceptable colormap. See either yt.visualization.color_maps or
http://www.scipy.org/Cookbook/Matplotlib/Show_colormaps .
- scale_func: function(value, minval, maxval), optional
+ scale_func: function(!value, !minval, !maxval), optional
A user-defined function that can be used to scale the alpha channel
as a function of the TransferFunction field values. Function maps
value to somewhere between minval and maxval.
https://bitbucket.org/yt_analysis/yt/commits/9ecdffab1ac7/
Changeset: 9ecdffab1ac7
User: xarthisius
Date: 2017-05-18 16:21:33+00:00
Summary: Expand exclude for api docs
Affected #: 1 file
diff -r 518b0c6aea91e60b5ace7a19dbc787c124c62447 -r 9ecdffab1ac78b6bd2acf26efbf6eeab6078a84e doc/Makefile
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -49,7 +49,8 @@
ifneq ($(READTHEDOCS),True)
SPHINX_APIDOC_OPTIONS=members,undoc-members,inherited-members,show-inheritance sphinx-apidoc \
-o source/reference/api/ \
- -e ../yt ../yt/extern/* $(shell find ../yt -name "*tests*" -type d) ../yt/utilities/voropp*
+ -e ../yt ../yt/extern* $(shell find ../yt -name "*tests*" -type d) ../yt/utilities/voropp* \
+ ../yt/analysis_modules/halo_finding/{fof,hop}
endif
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
https://bitbucket.org/yt_analysis/yt/commits/849fdfae58c1/
Changeset: 849fdfae58c1
User: xarthisius
Date: 2017-05-18 17:12:00+00:00
Summary: Use full :py: syntax to prevent reference creation
Affected #: 5 files
diff -r 9ecdffab1ac78b6bd2acf26efbf6eeab6078a84e -r 849fdfae58c1b5b5f634a8332441b1398b4e60c5 yt/extern/tqdm/_tqdm.py
--- a/yt/extern/tqdm/_tqdm.py
+++ b/yt/extern/tqdm/_tqdm.py
@@ -217,7 +217,7 @@
"""
Parameters
----------
- iterable : !iterable, optional
+ iterable : :obj:`!iterable`, optional
Iterable to decorate with a progressbar.
Leave blank [default: None] to manually manage the updates.
desc : str, optional
diff -r 9ecdffab1ac78b6bd2acf26efbf6eeab6078a84e -r 849fdfae58c1b5b5f634a8332441b1398b4e60c5 yt/units/yt_array.py
--- a/yt/units/yt_array.py
+++ b/yt/units/yt_array.py
@@ -228,7 +228,7 @@
Parameters
----------
- input_array : !iterable
+ input_array : :obj:`!iterable`
A tuple, list, or array to attach units to
input_units : String unit specification, unit symbol object, or astropy units
The units of the array. Powers must be specified using python
diff -r 9ecdffab1ac78b6bd2acf26efbf6eeab6078a84e -r 849fdfae58c1b5b5f634a8332441b1398b4e60c5 yt/visualization/volume_rendering/camera.py
--- a/yt/visualization/volume_rendering/camera.py
+++ b/yt/visualization/volume_rendering/camera.py
@@ -163,7 +163,7 @@
Parameters
----------
- position : number, YTQuantity, !iterable, or 3 element YTArray
+ position : number, YTQuantity, :obj:`!iterable`, or 3 element YTArray
If a scalar, assumes that the position is the same in all three
coordinates. If an iterable, must contain only scalars or
(length, unit) tuples.
@@ -192,7 +192,7 @@
Parameters
----------
- width : number, YTQuantity, !iterable, or 3 element YTArray
+ width : number, YTQuantity, :obj:`!iterable`, or 3 element YTArray
The width of the volume rendering in the horizontal, vertical, and
depth directions. If a scalar, assumes that the width is the same in
all three directions. If an iterable, must contain only scalars or
@@ -220,7 +220,7 @@
Parameters
----------
- focus : number, YTQuantity, !iterable, or 3 element YTArray
+ focus : number, YTQuantity, :obj:`!iterable`, or 3 element YTArray
The width of the volume rendering in the horizontal, vertical, and
depth directions. If a scalar, assumes that the width is the same in
all three directions. If an iterable, must contain only scalars or
@@ -357,7 +357,7 @@
Parameters
----------
- width : number, YTQuantity, !iterable, or 3 element YTArray
+ width : number, YTQuantity, :obj:`!iterable`, or 3 element YTArray
The width of the volume rendering in the horizontal, vertical, and
depth directions. If a scalar, assumes that the width is the same in
all three directions. If an iterable, must contain only scalars or
@@ -376,7 +376,7 @@
Parameters
----------
- width : number, YTQuantity, !iterable, or 3 element YTArray
+ width : number, YTQuantity, :obj:`!iterable`, or 3 element YTArray
If a scalar, assumes that the position is the same in all three
coordinates. If an iterable, must contain only scalars or
(length, unit) tuples.
@@ -400,7 +400,7 @@
Parameters
----------
- focus : number, YTQuantity, !iterable, or 3 element YTArray
+ focus : number, YTQuantity, :obj:`!iterable`, or 3 element YTArray
If a scalar, assumes that the focus is the same is all three
coordinates. If an iterable, must contain only scalars or
(length, unit) tuples.
diff -r 9ecdffab1ac78b6bd2acf26efbf6eeab6078a84e -r 849fdfae58c1b5b5f634a8332441b1398b4e60c5 yt/visualization/volume_rendering/interactive_vr.py
--- a/yt/visualization/volume_rendering/interactive_vr.py
+++ b/yt/visualization/volume_rendering/interactive_vr.py
@@ -86,11 +86,11 @@
Parameters
----------
- position : !iterable, or 3 element array in code_length
+ position : :obj:`!iterable`, or 3 element array in code_length
The initial position of the camera.
- focus : !iterable, or 3 element array in code_length
+ focus : :obj:`!iterable`, or 3 element array in code_length
A point in space that the camera is looking at.
- up : !iterable, or 3 element array in code_length
+ up : :obj:`!iterable`, or 3 element array in code_length
The 'up' direction for the camera.
fov : float, optional
An angle defining field of view in degrees.
diff -r 9ecdffab1ac78b6bd2acf26efbf6eeab6078a84e -r 849fdfae58c1b5b5f634a8332441b1398b4e60c5 yt/visualization/volume_rendering/transfer_functions.py
--- a/yt/visualization/volume_rendering/transfer_functions.py
+++ b/yt/visualization/volume_rendering/transfer_functions.py
@@ -702,7 +702,7 @@
colormap : string, optional
An acceptable colormap. See either yt.visualization.color_maps or
http://www.scipy.org/Cookbook/Matplotlib/Show_colormaps .
- scale_func: function(!value, !minval, !maxval), optional
+ scale_func: function(:obj:`!value`, :obj:`!minval`, :obj:`!maxval`), optional
A user-defined function that can be used to scale the alpha channel
as a function of the TransferFunction field values. Function maps
value to somewhere between minval and maxval.
https://bitbucket.org/yt_analysis/yt/commits/4409c8396c9a/
Changeset: 4409c8396c9a
User: ngoldbaum
Date: 2017-05-19 21:06:57+00:00
Summary: Merge pull request #1398 from Xarthisius/doc_fix
Documetation fixes
Affected #: 32 files
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a doc/Makefile
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -49,7 +49,8 @@
ifneq ($(READTHEDOCS),True)
SPHINX_APIDOC_OPTIONS=members,undoc-members,inherited-members,show-inheritance sphinx-apidoc \
-o source/reference/api/ \
- -e ../yt ../yt/extern/* $(shell find ../yt -name "*tests*" -type d) ../yt/utilities/voropp*
+ -e ../yt ../yt/extern* $(shell find ../yt -name "*tests*" -type d) ../yt/utilities/voropp* \
+ ../yt/analysis_modules/halo_finding/{fof,hop}
endif
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a doc/source/analyzing/analysis_modules/star_analysis.rst
--- a/doc/source/analyzing/analysis_modules/star_analysis.rst
+++ b/doc/source/analyzing/analysis_modules/star_analysis.rst
@@ -1,11 +1,11 @@
-.. _star_analysis:
-
.. note::
This module has been deprecated as it is unmaintained. The code has been
moved to the `yt attic <https://github.com/yt-project/yt_attic>`__.
If you'd like to take it over, please do!
+.. _star_analysis:
+
Star Particle Analysis
======================
.. sectionauthor:: Stephen Skory <sskory at physics.ucsd.edu>
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a doc/source/analyzing/analysis_modules/two_point_functions.rst
--- a/doc/source/analyzing/analysis_modules/two_point_functions.rst
+++ b/doc/source/analyzing/analysis_modules/two_point_functions.rst
@@ -1,11 +1,11 @@
-.. _two_point_functions:
-
.. note::
This module has been deprecated as it is unmaintained. The code has been
moved to the `yt attic <https://github.com/yt-project/yt_attic>`__.
If you'd like to take it over, please do!
+.. _two_point_functions:
+
Two Point Functions
===================
.. sectionauthor:: Stephen Skory <sskory at physics.ucsd.edu>
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/analysis_modules/cosmological_observation/light_ray/light_ray.py
--- a/yt/analysis_modules/cosmological_observation/light_ray/light_ray.py
+++ b/yt/analysis_modules/cosmological_observation/light_ray/light_ray.py
@@ -53,7 +53,7 @@
Parameters
----------
- parameter_filename : string or :class:`yt.data_objects.static_output.Dataset`
+ parameter_filename : string or :class:`~yt.data_objects.static_output.Dataset`
For simple rays, one may pass either a loaded dataset object or
the filename of a dataset.
For compound rays, one must pass the filename of the simulation
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/analysis_modules/halo_analysis/enzofof_merger_tree.py
--- a/yt/analysis_modules/halo_analysis/enzofof_merger_tree.py
+++ b/yt/analysis_modules/halo_analysis/enzofof_merger_tree.py
@@ -713,8 +713,8 @@
The filename to which you saved the hdf5 data from save_halo_evolution
halo_id : int
The halo in 'filename' that you want to follow
- x_quantity, y_quantity : str, optional
- The quantity that you want to plot as the x_coord (or y_coords).
+ x_quantity : str, optional
+ The quantity that you want to plot as the x_coord.
Valid options are:
* cycle
@@ -732,8 +732,12 @@
* COM_vy
* COM_vz
- x_log, y_log : bool, optional
- Do you want the x(y)-axis to be in log or linear?
+ y_quantity : str, optional
+ The quantity that you want to plot as the y_coord.
+ x_log : bool, optional
+ Do you want the x-axis to be in log or linear?
+ y_log : bool, optional
+ Do you want the y-axis to be in log or linear?
FOF_directory : str, optional
Directory where FOF files (and hdf file) are located
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/analysis_modules/halo_finding/rockstar/rockstar.py
--- a/yt/analysis_modules/halo_finding/rockstar/rockstar.py
+++ b/yt/analysis_modules/halo_finding/rockstar/rockstar.py
@@ -114,29 +114,29 @@
Parameters
----------
- ts: DatasetSeries, Dataset
+ ts : DatasetSeries, ~yt.data_objects.static_output.Dataset
This is the data source containing the DM particles. Because
halo IDs may change from one snapshot to the next, the only
way to keep a consistent halo ID across time is to feed
Rockstar a set of snapshots, ie, via DatasetSeries.
- num_readers: int
+ num_readers : int
The number of reader can be increased from the default
of 1 in the event that a single snapshot is split among
many files. This can help in cases where performance is
IO-limited. Default is 1. If run inline, it is
equal to the number of MPI threads.
- num_writers: int
+ num_writers : int
The number of writers determines the number of processing threads
as well as the number of threads writing output data.
The default is set to comm.size-num_readers-1. If run inline,
the default is equal to the number of MPI threads.
- outbase: str
+ outbase : str
This is where the out*list files that Rockstar makes should be
placed. Default is 'rockstar_halos'.
- particle_type: str
+ particle_type : str
This is the "particle type" that can be found in the data. This can be
a filtered particle or an inherent type.
- force_res: float
+ force_res : float
This parameter specifies the force resolution that Rockstar uses
in units of Mpc/h.
If no value is provided, this parameter is automatically set to
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/convenience.py
--- a/yt/convenience.py
+++ b/yt/convenience.py
@@ -32,9 +32,9 @@
"""
This function attempts to determine the base data type of a filename or
other set of arguments by calling
- :meth:`yt.data_objects.api.Dataset._is_valid` until it finds a
+ :meth:`yt.data_objects.static_output.Dataset._is_valid` until it finds a
match, at which point it returns an instance of the appropriate
- :class:`yt.data_objects.api.Dataset` subclass.
+ :class:`yt.data_objects.static_output.Dataset` subclass.
"""
candidates = []
args = [os.path.expanduser(arg) if isinstance(arg, string_types)
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/data_objects/data_containers.py
--- a/yt/data_objects/data_containers.py
+++ b/yt/data_objects/data_containers.py
@@ -132,7 +132,7 @@
def __init__(self, ds, field_parameters):
"""
Typically this is never called directly, but only due to inheritance.
- It associates a :class:`~yt.data_objects.api.Dataset` with the class,
+ It associates a :class:`~yt.data_objects.static_output.Dataset` with the class,
sets its initial set of fields, and the remainder of the arguments
are passed as field_parameters.
"""
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/data_objects/derived_quantities.py
--- a/yt/data_objects/derived_quantities.py
+++ b/yt/data_objects/derived_quantities.py
@@ -156,8 +156,8 @@
Parameters
----------
- fields : field or list of fields
- The field to be summed.
+ fields
+ The field or list of fields to be summed.
Examples
--------
@@ -487,8 +487,9 @@
Parameters
----------
- fields : field or list of fields
- The field over which the extrema are to be calculated.
+ fields
+ The field or list of fields over which the extrema are to be
+ calculated.
non_zero : bool
If True, only positive values are considered in the calculation.
Default: False
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/data_objects/particle_trajectories.py
--- a/yt/data_objects/particle_trajectories.py
+++ b/yt/data_objects/particle_trajectories.py
@@ -29,7 +29,7 @@
Parameters
----------
- outputs : `yt.data_objects.time_series.DatasetSeries`
+ outputs : ~yt.data_objects.time_series.DatasetSeries
DatasetSeries object from which to draw the particles.
indices : array_like
An integer array of particle indices whose trajectories we
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/data_objects/selection_data_containers.py
--- a/yt/data_objects/selection_data_containers.py
+++ b/yt/data_objects/selection_data_containers.py
@@ -49,7 +49,7 @@
periodic its position will be corrected to lie inside
the range [DLE,DRE) to ensure one and only one cell may
match that point
- ds: Dataset, optional
+ ds: ~yt.data_objects.static_output.Dataset, optional
An optional dataset to use rather than self.ds
field_parameters : dictionary
A dictionary of field parameters than can be accessed by derived
@@ -95,7 +95,7 @@
that this is in the plane coordinates: so if you are casting along
x, this will be (y, z). If you are casting along y, this will be
(z, x). If you are casting along z, this will be (x, y).
- ds: Dataset, optional
+ ds: ~yt.data_objects.static_output.Dataset, optional
An optional dataset to use rather than self.ds
field_parameters : dictionary
A dictionary of field parameters than can be accessed by derived
@@ -162,7 +162,7 @@
The place where the ray starts.
end_point : array-like set of 3 floats
The place where the ray ends.
- ds: Dataset, optional
+ ds: ~yt.data_objects.static_output.Dataset, optional
An optional dataset to use rather than self.ds
field_parameters : dictionary
A dictionary of field parameters than can be accessed by derived
@@ -248,7 +248,7 @@
center : array_like, optional
The 'center' supplied to fields that use it. Note that this does
not have to have `coord` as one value. optional.
- ds: Dataset, optional
+ ds: ~yt.data_objects.static_output.Dataset, optional
An optional dataset to use rather than self.ds
field_parameters : dictionary
A dictionary of field parameters than can be accessed by derived
@@ -355,7 +355,7 @@
north_vector: array_like, optional
An optional vector to describe the north-facing direction in the resulting
plane.
- ds: Dataset, optional
+ ds: ~yt.data_objects.static_output.Dataset, optional
An optional dataset to use rather than self.ds
field_parameters : dictionary
A dictionary of field parameters than can be accessed by derived
@@ -556,7 +556,7 @@
bottom planes
fields : array of fields, optional
any fields to be pre-loaded in the cylinder object
- ds: Dataset, optional
+ ds: ~yt.data_objects.static_output.Dataset, optional
An optional dataset to use rather than self.ds
field_parameters : dictionary
A dictionary of field parameters than can be accessed by derived
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/data_objects/static_output.py
--- a/yt/data_objects/static_output.py
+++ b/yt/data_objects/static_output.py
@@ -1399,7 +1399,7 @@
----------
symbol : string
The symbol for the new unit.
- value : (value, unit) tuple or YTQuantity
+ value : tuple or ~yt.units.yt_array.YTQuantity
The definition of the new unit in terms of some other units. For example,
one would define a new "mph" unit with (1.0, "mile/hr")
tex_repr : string, optional
@@ -1407,7 +1407,7 @@
be generated automatically based on the symbol string.
offset : float, optional
The default offset for the unit. If not set, an offset of 0 is assumed.
- prefixable : boolean, optional
+ prefixable : bool, optional
Whether or not the new unit can use SI prefixes. Default: False
Examples
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/extern/tqdm/_tqdm.py
--- a/yt/extern/tqdm/_tqdm.py
+++ b/yt/extern/tqdm/_tqdm.py
@@ -217,7 +217,7 @@
"""
Parameters
----------
- iterable : iterable, optional
+ iterable : :obj:`!iterable`, optional
Iterable to decorate with a progressbar.
Leave blank [default: None] to manually manage the updates.
desc : str, optional
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/fields/xray_emission_fields.py
--- a/yt/fields/xray_emission_fields.py
+++ b/yt/fields/xray_emission_fields.py
@@ -159,7 +159,7 @@
The maximum energy in keV for the energy band.
redshift : float, optional
The cosmological redshift of the source of the field. Default: 0.0.
- metallicity : field or float, optional
+ metallicity : str or tuple of str or float, optional
Either the name of a metallicity field or a single floating-point
number specifying a spatially constant metallicity. Must be in
solar units. If set to None, no metals will be assumed. Default:
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/frontends/fits/misc.py
--- a/yt/frontends/fits/misc.py
+++ b/yt/frontends/fits/misc.py
@@ -49,7 +49,7 @@
Parameters
----------
- ds : `~yt.data_objects.static_output.Dataset`
+ ds : ~yt.data_objects.static_output.Dataset
The FITS events file dataset to add the counts fields to.
ebounds : list of tuples
A list of tuples, one for each field, with (emin, emax) as the
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/frontends/gadget_fof/data_structures.py
--- a/yt/frontends/gadget_fof/data_structures.py
+++ b/yt/frontends/gadget_fof/data_structures.py
@@ -462,8 +462,8 @@
class GagdetFOFHaloContainer(YTSelectionContainer):
"""
Create a data container to get member particles and individual
- values from halos and subhalos. Halo mass, position, and
- velocity are set as attributes. Halo IDs are accessible
+ values from halos and subhalos. Halo mass, position, and
+ velocity are set as attributes. Halo IDs are accessible
through the field, "member_ids". Other fields that are one
value per halo are accessible as normal. The field list for
halo objects can be seen in `ds.halos_field_list`.
@@ -473,13 +473,13 @@
ptype : string
The type of halo, either "Group" for the main halo or
"Subhalo" for subhalos.
- particle_identifier : int or tuple of (int, int)
+ particle_identifier : int or tuple of ints
The halo or subhalo id. If requesting a subhalo, the id
can also be given as a tuple of the main halo id and
subgroup id, such as (1, 4) for subgroup 4 of halo 1.
- Halo Container Attributes
- -------------------------
+ Attributes
+ ----------
particle_identifier : int
The id of the halo or subhalo.
group_identifier : int
@@ -496,14 +496,13 @@
velocity : array of floats
Halo velocity.
- Relevant Fields
- ---------------
- particle_number :
- number of particles
- subhalo_number :
- number of subhalos
- group_identifier :
- id of parent group for subhalos
+ Note
+ ----
+ Relevant Fields:
+
+ * particle_number - number of particles
+ * subhalo_number - number of subhalos
+ * group_identifier - id of parent group for subhalos
Examples
--------
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/frontends/stream/data_structures.py
--- a/yt/frontends/stream/data_structures.py
+++ b/yt/frontends/stream/data_structures.py
@@ -908,7 +908,7 @@
Parameters
----------
- base_ds : `~yt.data_objects.static_output.Dataset`
+ base_ds : ~yt.data_objects.static_output.Dataset
This is any static output. It can also be a stream static output, for
instance as returned by load_uniform_data.
refinement_critera : list of :class:`~yt.utilities.flagging_methods.FlaggingMethod`
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/units/unit_object.py
--- a/yt/units/unit_object.py
+++ b/yt/units/unit_object.py
@@ -729,7 +729,7 @@
----------
symbol : string
The symbol for the new unit.
- value : (value, unit) tuple or YTQuantity
+ value : tuple or ~yt.units.yt_array.YTQuantity
The definition of the new unit in terms of some other units. For example,
one would define a new "mph" unit with (1.0, "mile/hr")
tex_repr : string, optional
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/units/yt_array.py
--- a/yt/units/yt_array.py
+++ b/yt/units/yt_array.py
@@ -228,16 +228,16 @@
Parameters
----------
- input_array : Iterable
+ input_array : :obj:`!iterable`
A tuple, list, or array to attach units to
input_units : String unit specification, unit symbol object, or astropy units
The units of the array. Powers must be specified using python
syntax (cm**3, not cm^3).
- registry : A UnitRegistry object
+ registry : ~yt.units.unit_registry.UnitRegistry
The registry to create units from. If input_units is already associated
with a unit registry and this is specified, this will be used instead of
the registry associated with the unit object.
- dtype : string or NumPy dtype object
+ dtype : data-type
The dtype of the array data. Defaults to the dtype of the input data,
or, if none is found, uses np.float64
bypass_validation : boolean
@@ -1307,7 +1307,7 @@
The registry to create units from. If input_units is already associated
with a unit registry and this is specified, this will be used instead of
the registry associated with the unit object.
- dtype : string or NumPy dtype object
+ dtype : data-type
The dtype of the array data.
Examples
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/utilities/grid_data_format/writer.py
--- a/yt/utilities/grid_data_format/writer.py
+++ b/yt/utilities/grid_data_format/writer.py
@@ -40,8 +40,8 @@
The yt data to write out.
gdf_path : string
The path of the file to output.
- fields : field or list of fields
- The fields(s) to write out. If None, defaults to
+ fields
+ The field or list of fields to write out. If None, defaults to
ds.field_list.
data_author : string, optional
The name of the author who wrote the data. Default: None.
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/utilities/sdf.py
--- a/yt/utilities/sdf.py
+++ b/yt/utilities/sdf.py
@@ -1164,7 +1164,7 @@
"""Get floating point bounding box for a given midx cell
Returns:
- bbox: array-like, shape (3,2)
+ bbox: array-like of shape (3,2)
"""
cell_iarr = np.array(cell_iarr, dtype="int64")
@@ -1294,7 +1294,7 @@
"""
Returns:
- bbox: array-like, shape (3,2)
+ bbox: array-like of shape (3,2)
"""
bbox = self.get_cell_bbox(level, cell_iarr)
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/visualization/fits_image.py
--- a/yt/visualization/fits_image.py
+++ b/yt/visualization/fits_image.py
@@ -529,7 +529,7 @@
Parameters
----------
- ds : :class:`yt.data_objects.api.Dataset`
+ ds : :class:`~yt.data_objects.static_output.Dataset`
The dataset object.
axis : character or integer
The axis of the slice. One of "x","y","z", or 0,1,2.
@@ -584,7 +584,7 @@
Parameters
----------
- ds : :class:`yt.data_objects.api.Dataset`
+ ds : :class:`~yt.data_objects.static_output.Dataset`
The dataset object.
axis : character or integer
The axis along which to project. One of "x","y","z", or 0,1,2.
@@ -641,7 +641,7 @@
Parameters
----------
- ds : :class:`yt.data_objects.api.Dataset`
+ ds : :class:`~yt.data_objects.static_output.Dataset`
The dataset object.
normal : a sequence of floats
The vector normal to the projection plane.
@@ -700,7 +700,7 @@
Parameters
----------
- ds : :class:`yt.data_objects.api.Dataset`
+ ds : :class:`~yt.data_objects.static_output.Dataset`
This is the dataset object corresponding to the
simulation output to be plotted.
normal : a sequence of floats
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/visualization/particle_plots.py
--- a/yt/visualization/particle_plots.py
+++ b/yt/visualization/particle_plots.py
@@ -363,7 +363,7 @@
Parameters
----------
- ds : :class:`yt.data_objects.api.Dataset`
+ ds : :class:`yt.data_objects.static_output.Dataset`
This is the dataset object corresponding to the
simulation output to be plotted.
x_field : string
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -1536,7 +1536,7 @@
Parameters
----------
- ds : :class:`yt.data_objects.api.Dataset`
+ ds : :class:`yt.data_objects.static_output.Dataset`
This is the dataset object corresponding to the
simulation output to be plotted.
normal : a sequence of floats
@@ -1672,7 +1672,7 @@
Parameters
----------
- ds : :class:`yt.data_objects.api.Dataset`
+ ds : :class:`yt.data_objects.static_output.Dataset`
This is the dataset object corresponding to the
simulation output to be plotted.
normal : a sequence of floats
@@ -1855,7 +1855,7 @@
Parameters
----------
- ds : :class:`yt.data_objects.api.Dataset`
+ ds : :class:`yt.data_objects.static_output.Dataset`
This is the dataset object corresponding to the
simulation output to be plotted.
normal : int or one of 'x', 'y', 'z', or sequence of floats
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/visualization/streamlines.py
--- a/yt/visualization/streamlines.py
+++ b/yt/visualization/streamlines.py
@@ -37,17 +37,17 @@
Parameters
----------
- ds : `~yt.data_objects.Dataset`
+ ds : ~yt.data_objects.static_output.Dataset
This is the dataset to streamline
pos : array_like
An array of initial starting positions of the streamlines.
- xfield: field, optional
+ xfield : str or tuple of str, optional
The x component of the vector field to be streamlined.
Default:'velocity_x'
- yfield: field, optional
+ yfield : str or tuple of str, optional
The y component of the vector field to be streamlined.
Default:'velocity_y'
- zfield: field, optional
+ zfield : str or tuple of str, optional
The z component of the vector field to be streamlined.
Default:'velocity_z'
volume : `yt.extensions.volume_rendering.AMRKDTree`, optional
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/visualization/volume_rendering/camera.py
--- a/yt/visualization/volume_rendering/camera.py
+++ b/yt/visualization/volume_rendering/camera.py
@@ -163,7 +163,7 @@
Parameters
----------
- position : number, YTQuantity, iterable, or 3 element YTArray
+ position : number, YTQuantity, :obj:`!iterable`, or 3 element YTArray
If a scalar, assumes that the position is the same in all three
coordinates. If an iterable, must contain only scalars or
(length, unit) tuples.
@@ -192,7 +192,7 @@
Parameters
----------
- width : number, YTQuantity, iterable, or 3 element YTArray
+ width : number, YTQuantity, :obj:`!iterable`, or 3 element YTArray
The width of the volume rendering in the horizontal, vertical, and
depth directions. If a scalar, assumes that the width is the same in
all three directions. If an iterable, must contain only scalars or
@@ -220,7 +220,7 @@
Parameters
----------
- focus : number, YTQuantity, iterable, or 3 element YTArray
+ focus : number, YTQuantity, :obj:`!iterable`, or 3 element YTArray
The width of the volume rendering in the horizontal, vertical, and
depth directions. If a scalar, assumes that the width is the same in
all three directions. If an iterable, must contain only scalars or
@@ -357,7 +357,7 @@
Parameters
----------
- width : number, YTQuantity, iterable, or 3 element YTArray
+ width : number, YTQuantity, :obj:`!iterable`, or 3 element YTArray
The width of the volume rendering in the horizontal, vertical, and
depth directions. If a scalar, assumes that the width is the same in
all three directions. If an iterable, must contain only scalars or
@@ -376,7 +376,7 @@
Parameters
----------
- width : number, YTQuantity, iterable, or 3 element YTArray
+ width : number, YTQuantity, :obj:`!iterable`, or 3 element YTArray
If a scalar, assumes that the position is the same in all three
coordinates. If an iterable, must contain only scalars or
(length, unit) tuples.
@@ -400,7 +400,7 @@
Parameters
----------
- focus : number, YTQuantity, iterable, or 3 element YTArray
+ focus : number, YTQuantity, :obj:`!iterable`, or 3 element YTArray
If a scalar, assumes that the focus is the same is all three
coordinates. If an iterable, must contain only scalars or
(length, unit) tuples.
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/visualization/volume_rendering/interactive_vr.py
--- a/yt/visualization/volume_rendering/interactive_vr.py
+++ b/yt/visualization/volume_rendering/interactive_vr.py
@@ -86,11 +86,11 @@
Parameters
----------
- position : iterable, or 3 element array in code_length
+ position : :obj:`!iterable`, or 3 element array in code_length
The initial position of the camera.
- focus : iterable, or 3 element array in code_length
+ focus : :obj:`!iterable`, or 3 element array in code_length
A point in space that the camera is looking at.
- up : iterable, or 3 element array in code_length
+ up : :obj:`!iterable`, or 3 element array in code_length
The 'up' direction for the camera.
fov : float, optional
An angle defining field of view in degrees.
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/visualization/volume_rendering/off_axis_projection.py
--- a/yt/visualization/volume_rendering/off_axis_projection.py
+++ b/yt/visualization/volume_rendering/off_axis_projection.py
@@ -38,7 +38,7 @@
Parameters
----------
- data_source : `~yt.data_objects.static_output.Dataset` or `~yt.data_objects.data_containers.YTSelectionDataContainer`
+ data_source : ~yt.data_objects.static_output.Dataset or ~yt.data_objects.data_containers.YTSelectionDataContainer
This is the dataset or data object to volume render.
center : array_like
The current 'center' of the view port -- the focal point for the
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/visualization/volume_rendering/old_camera.py
--- a/yt/visualization/volume_rendering/old_camera.py
+++ b/yt/visualization/volume_rendering/old_camera.py
@@ -100,7 +100,7 @@
the volume rendering mechanism.
sub_samples : int, optional
The number of samples to take inside every cell per ray.
- ds : `~yt.data_objects.api.Dataset`
+ ds : ~yt.data_objects.static_output.Dataset
For now, this is a require parameter! But in the future it will become
optional. This is the dataset to volume render.
use_kd: bool, optional
@@ -258,9 +258,12 @@
Default : 0.3
cmap : string, optional
Colormap to be used mapping grid levels to colors.
- min_level, max_level : int, optional
- Optional parameters to specify the min and max level grid boxes
- to overplot on the image.
+ min_level : int, optional
+ Optional parameter to specify the min level grid boxes
+ to overplot on the image.
+ max_level : int, optional
+ Optional parameters to specify the max level grid boxes
+ to overplot on the image.
Returns
-------
@@ -1190,7 +1193,7 @@
the volume rendering mechanism.
sub_samples : int, optional
The number of samples to take inside every cell per ray.
- ds : `~yt.data_objects.api.Dataset`
+ ds : ~yt.data_objects.static_output.Dataset
For now, this is a require parameter! But in the future it will become
optional. This is the dataset to volume render.
use_kd: bool, optional
@@ -2155,7 +2158,7 @@
Parameters
----------
- ds : `~yt.data_objects.api.Dataset`
+ ds : ~yt.data_objects.static_output.Dataset
This is the dataset to volume render.
center : array_like
The current 'center' of the view port -- the focal point for the
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/visualization/volume_rendering/render_source.py
--- a/yt/visualization/volume_rendering/render_source.py
+++ b/yt/visualization/volume_rendering/render_source.py
@@ -735,7 +735,7 @@
Parameters
----------
- color: array of ints, shape (4), optional
+ color: array_like of shape (4,), optional
The RGBA value to use to draw the mesh lines.
Default is black.
alpha : float, optional
@@ -801,16 +801,16 @@
Parameters
----------
- positions: array, shape (N, 3)
+ positions: array_like of shape (N, 3)
The positions of points to be added to the scene. If specified with no
units, the positions will be assumed to be in code units.
- colors : array, shape (N, 4), optional
+ colors : array_like of shape (N, 4), optional
The colors of the points, including an alpha channel, in floating
point running from 0..1.
color_stride : int, optional
The stride with which to access the colors when putting them on the
scene.
- radii : array, shape (N), optional
+ radii : array_like of shape (N), optional
The radii of the points in the final image, in pixels (int)
Examples
@@ -922,12 +922,12 @@
Parameters
----------
- positions: array, shape (N, 2, 3)
+ positions: array_like of shape (N, 2, 3)
The positions of the starting and stopping points for each line.
For example,positions[0][0] and positions[0][1] would give the (x, y, z)
coordinates of the beginning and end points of the first line,
respectively. If specified with no units, assumed to be in code units.
- colors : array, shape (N, 4), optional
+ colors : array_like of shape (N, 4), optional
The colors of the points, including an alpha channel, in floating
point running from 0..1. The four channels correspond to r, g, b, and
alpha values. Note that they correspond to the line segment succeeding
@@ -1049,11 +1049,11 @@
Parameters
----------
- left_edge: array-like, shape (3,), float
+ left_edge: array-like of shape (3,), float
The left edge coordinates of the box.
- right_edge : array-like, shape (3,), float
+ right_edge : array-like of shape (3,), float
The right edge coordinates of the box.
- color : array-like, shape (4,), float, optional
+ color : array-like of shape (4,), float, optional
The colors (including alpha) to use for the lines.
Examples
@@ -1212,7 +1212,7 @@
Parameters
----------
- colors: array-like, shape (3,4), optional
+ colors: array-like of shape (3,4), optional
The x, y, z RGBA values to use to draw the vectors.
alpha : float, optional
The opacity of the vectors.
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/visualization/volume_rendering/scene.py
--- a/yt/visualization/volume_rendering/scene.py
+++ b/yt/visualization/volume_rendering/scene.py
@@ -640,7 +640,7 @@
Parameters
----------
- ds : :class:`yt.data_objects.api.Dataset`
+ ds : :class:`yt.data_objects.static_output.Dataset`
This is the dataset object corresponding to the
simulation being rendered. Used to get the domain bounds.
@@ -711,7 +711,7 @@
Parameters
----------
- colors: array of ints, shape (4), optional
+ colors: array_like of shape (4,), optional
The RGBA value to use to draw the mesh lines.
Default is black.
alpha : float, optional
@@ -732,7 +732,7 @@
Parameters
----------
- colors: array-like, shape (3,4), optional
+ colors: array-like of shape (3,4), optional
The x, y, z RGBA values to use to draw the axes.
alpha : float, optional
The opacity of the vectors.
diff -r 9038d396c6989cc82060470c19b077538c553921 -r 4409c8396c9ad1eafd15f08052aec9b2f2682a0a yt/visualization/volume_rendering/transfer_functions.py
--- a/yt/visualization/volume_rendering/transfer_functions.py
+++ b/yt/visualization/volume_rendering/transfer_functions.py
@@ -654,10 +654,10 @@
colormap : string, optional
An acceptable colormap. See either yt.visualization.color_maps or
http://www.scipy.org/Cookbook/Matplotlib/Show_colormaps .
- col_bounds: array_like [min, max], optional
- Limits the values over which the colormap spans to these
- values. Useful for sampling an entire colormap over a
- range smaller than the transfer function bounds.
+ col_bounds: array_like, optional
+ Limits ([min, max]) the values over which the colormap spans to
+ these values. Useful for sampling an entire colormap over a range
+ smaller than the transfer function bounds.
See Also
--------
@@ -702,7 +702,7 @@
colormap : string, optional
An acceptable colormap. See either yt.visualization.color_maps or
http://www.scipy.org/Cookbook/Matplotlib/Show_colormaps .
- scale_func: function(value, minval, maxval), optional
+ scale_func: function(:obj:`!value`, :obj:`!minval`, :obj:`!maxval`), optional
A user-defined function that can be used to scale the alpha channel
as a function of the TransferFunction field values. Function maps
value to somewhere between minval and maxval.
@@ -769,10 +769,10 @@
colormap : string, optional
An acceptable colormap. See either yt.visualization.color_maps or
http://www.scipy.org/Cookbook/Matplotlib/Show_colormaps .
- col_bounds: array_like [min, max], optional
- Limits the values over which the colormap spans to these
- values. Useful for sampling an entire colormap over a
- range smaller than the transfer function bounds.
+ col_bounds: array_like, optional
+ Limits ([min, max]) the values over which the colormap spans to
+ these values. Useful for sampling an entire colormap over a range
+ smaller than the transfer function bounds.
See Also
--------
Repository URL: https://bitbucket.org/yt_analysis/yt/
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