[yt-svn] commit/yt: ngoldbaum: Merged in xarthisius/yt (pull request #2526)
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Sat Mar 4 14:43:09 PST 2017
1 new commit in yt:
https://bitbucket.org/yt_analysis/yt/commits/e518ad9d8b5c/
Changeset: e518ad9d8b5c
Branch: yt
User: ngoldbaum
Date: 2017-03-04 22:43:01+00:00
Summary: Merged in xarthisius/yt (pull request #2526)
Prepopulate api docs before main sphinx build call
Approved-by: Nathan Goldbaum
Approved-by: Britton Smith
Approved-by: Matt Turk
Approved-by: chummels
Affected #: 32 files
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d doc/Makefile
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -47,6 +47,9 @@
-rm -rf _temp/*.done source/cookbook/_static/*
html:
+ sphinx-apidoc -o source/reference/api/ -e ../yt ../yt/extern/* \
+ $(shell find ../yt -name "*tests*" -type d) ../yt/utilities/voropp*
+ sed -e '/show-inheritance/ a\ \ \ \ :inherited-members:' -i source/reference/api/yt*.rst
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d doc/extensions/pythonscript_sphinxext.py
--- a/doc/extensions/pythonscript_sphinxext.py
+++ b/doc/extensions/pythonscript_sphinxext.py
@@ -1,4 +1,5 @@
import tempfile
+import time
import os
import glob
import shutil
@@ -37,12 +38,16 @@
f.write(content)
# Use sphinx logger?
+ uid = uuid.uuid4().hex[:8]
print("")
+ print(">> Contents of the script: %s" % uid)
print(content)
print("")
+ start = time.time()
subprocess.call(['python', 'temp.py'])
-
+ print(">> The execution of the script %s took %f s" %
+ (uid, time.time() - start))
text = ''
for im in sorted(glob.glob("*.png")):
text += get_image_tag(im, image_dir, image_rel_dir)
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d doc/source/analyzing/analysis_modules/xray_emission_fields.rst
--- a/doc/source/analyzing/analysis_modules/xray_emission_fields.rst
+++ b/doc/source/analyzing/analysis_modules/xray_emission_fields.rst
@@ -1,3 +1,6 @@
.. _xray_emission_fields:
+X-ray Emission Fields
+=====================
+
.. notebook:: XrayEmissionFields.ipynb
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d doc/source/reference/api/api.rst
--- a/doc/source/reference/api/api.rst
+++ b/doc/source/reference/api/api.rst
@@ -10,7 +10,6 @@
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. autosummary::
- :toctree: generated/
~yt.visualization.plot_window.SlicePlot
~yt.visualization.plot_window.AxisAlignedSlicePlot
@@ -24,7 +23,6 @@
^^^^^^^^^^^^^^^^^^^^^^^^^
.. autosummary::
- :toctree: generated/
~yt.visualization.profile_plotter.ProfilePlot
~yt.visualization.profile_plotter.PhasePlot
@@ -34,7 +32,6 @@
^^^^^^^^^^^^^^
.. autosummary::
- :toctree: generated/
~yt.visualization.particle_plots.ParticleProjectionPlot
~yt.visualization.particle_plots.ParticlePhasePlot
@@ -44,7 +41,6 @@
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. autosummary::
- :toctree: generated/
~yt.visualization.fixed_resolution.FixedResolutionBuffer
~yt.visualization.fixed_resolution.ParticleImageBuffer
@@ -69,7 +65,6 @@
These will almost never need to be instantiated on their own.
.. autosummary::
- :toctree: generated/
~yt.data_objects.data_containers.YTDataContainer
~yt.data_objects.data_containers.YTSelectionContainer
@@ -85,7 +80,6 @@
geometric.
.. autosummary::
- :toctree: generated/
~yt.data_objects.selection_data_containers.YTPoint
~yt.data_objects.selection_data_containers.YTOrthoRay
@@ -108,7 +102,6 @@
expensive set of intermediate data.
.. autosummary::
- :toctree: generated/
~yt.data_objects.construction_data_containers.YTStreamline
~yt.data_objects.construction_data_containers.YTQuadTreeProj
@@ -124,7 +117,6 @@
datasets.
.. autosummary::
- :toctree: generated/
~yt.data_objects.time_series.DatasetSeries
~yt.data_objects.time_series.DatasetSeriesObject
@@ -138,7 +130,6 @@
These objects generate an "index" into multiresolution data.
.. autosummary::
- :toctree: generated/
~yt.geometry.geometry_handler.Index
~yt.geometry.grid_geometry_handler.GridIndex
@@ -152,7 +143,6 @@
These classes and functions enable yt's symbolic unit handling system.
.. autosummary::
- :toctree: generated/
yt.data_objects.static_output.Dataset.arr
yt.data_objects.static_output.Dataset.quan
@@ -173,13 +163,11 @@
---------
.. autosummary::
- :toctree: generated/
ARTIO
^^^^^
.. autosummary::
- :toctree: generated/
~yt.frontends.artio.data_structures.ARTIOIndex
~yt.frontends.artio.data_structures.ARTIOOctreeSubset
@@ -194,7 +182,6 @@
^^^^^^
.. autosummary::
- :toctree: generated/
~yt.frontends.athena.data_structures.AthenaGrid
~yt.frontends.athena.data_structures.AthenaHierarchy
@@ -206,7 +193,6 @@
^^^^^^
.. autosummary::
- :toctree: generated/
~yt.frontends.boxlib.data_structures.BoxlibGrid
~yt.frontends.boxlib.data_structures.BoxlibHierarchy
@@ -225,7 +211,6 @@
^^^^^^
.. autosummary::
- :toctree: generated/
~yt.frontends.chombo.data_structures.ChomboGrid
~yt.frontends.chombo.data_structures.ChomboHierarchy
@@ -239,7 +224,6 @@
^^^^
.. autosummary::
- :toctree: generated/
~yt.frontends.enzo.answer_testing_support.ShockTubeTest
~yt.frontends.enzo.data_structures.EnzoGrid
@@ -264,7 +248,6 @@
^^^^
.. autosummary::
- :toctree: generated/
~yt.frontends.fits.data_structures.FITSGrid
~yt.frontends.fits.data_structures.FITSHierarchy
@@ -276,7 +259,6 @@
^^^^^
.. autosummary::
- :toctree: generated/
~yt.frontends.flash.data_structures.FLASHGrid
~yt.frontends.flash.data_structures.FLASHHierarchy
@@ -288,7 +270,6 @@
^^^
.. autosummary::
- :toctree: generated/
~yt.frontends.gdf.data_structures.GDFGrid
~yt.frontends.gdf.data_structures.GDFHierarchy
@@ -299,7 +280,6 @@
^^^^^^^^^^^^^
.. autosummary::
- :toctree: generated/
~yt.frontends.halo_catalog.data_structures.HaloCatalogHDF5File
~yt.frontends.halo_catalog.data_structures.HaloCatalogDataset
@@ -319,7 +299,6 @@
^^^^
.. autosummary::
- :toctree: generated/
~yt.frontends.moab.data_structures.MoabHex8Hierarchy
~yt.frontends.moab.data_structures.MoabHex8Mesh
@@ -334,7 +313,6 @@
^^^^^^^
.. autosummary::
- :toctree: generated/
~yt.frontends.open_pmd.data_structures.OpenPMDGrid
~yt.frontends.open_pmd.data_structures.OpenPMDHierarchy
@@ -349,7 +327,6 @@
^^^^^^
.. autosummary::
- :toctree: generated/
~yt.frontends.ramses.data_structures.RAMSESDomainFile
~yt.frontends.ramses.data_structures.RAMSESDomainSubset
@@ -362,7 +339,6 @@
^^^^^^^^^^^^^^^^^^^^^^
.. autosummary::
- :toctree: generated/
~yt.frontends.gadget.data_structures.GadgetBinaryFile
~yt.frontends.gadget.data_structures.GadgetHDF5Dataset
@@ -384,7 +360,6 @@
^^^^^^
.. autosummary::
- :toctree: generated/
~yt.frontends.stream.data_structures.StreamDictFieldHandler
~yt.frontends.stream.data_structures.StreamGrid
@@ -410,7 +385,6 @@
^^^^^^
.. autosummary::
- :toctree: generated/
~yt.frontends.ytdata.data_structures.YTDataContainerDataset
~yt.frontends.ytdata.data_structures.YTSpatialPlotDataset
@@ -434,7 +408,6 @@
------------
.. autosummary::
- :toctree: generated/
~yt.convenience.load
~yt.convenience.simulation
@@ -457,7 +430,6 @@
.. autosummary::
- :toctree: generated/
~yt.data_objects.profiles.ProfileND
~yt.data_objects.profiles.Profile1D
@@ -475,7 +447,6 @@
of topologically disconnected structures, i.e., clump finding.
.. autosummary::
- :toctree: generated/
~yt.analysis_modules.level_sets.clump_handling.Clump
~yt.analysis_modules.level_sets.clump_handling.Clump.add_info_item
@@ -495,7 +466,6 @@
on cosmological halos. It is also the primary interface for halo finding.
.. autosummary::
- :toctree: generated/
~yt.analysis_modules.halo_analysis.halo_catalog.HaloCatalog
~yt.analysis_modules.halo_analysis.halo_finding_methods.HaloFindingMethod
@@ -526,7 +496,6 @@
to use the ``HaloCatalog``.
.. autosummary::
- :toctree: generated/
~yt.analysis_modules.halo_finding.halo_objects.FOFHaloFinder
~yt.analysis_modules.halo_finding.halo_objects.HOPHaloFinder
@@ -541,7 +510,6 @@
.. autosummary::
- :toctree: generated/
~yt.analysis_modules.two_point_functions.two_point_functions.TwoPointFunctions
~yt.analysis_modules.two_point_functions.two_point_functions.FcnSet
@@ -550,7 +518,6 @@
-----------
.. autosummary::
- :toctree: generated/
~yt.fields.field_info_container.FieldInfoContainer
~yt.fields.derived_field.DerivedField
@@ -564,7 +531,6 @@
---------------
.. autosummary::
- :toctree: generated/
~yt.fields.field_info_container.FieldInfoContainer.add_field
~yt.data_objects.static_output.Dataset.add_field
@@ -574,7 +540,6 @@
----------------
.. autosummary::
- :toctree: generated/
~yt.data_objects.particle_filters.add_particle_filter
~yt.data_objects.particle_filters.particle_filter
@@ -587,7 +552,6 @@
writing to bitmaps.
.. autosummary::
- :toctree: generated/
~yt.data_objects.image_array.ImageArray
@@ -601,7 +565,6 @@
.. autosummary::
- :toctree: generated/
~yt.analysis_modules.star_analysis.sfr_spectrum.StarFormationRate
~yt.analysis_modules.star_analysis.sfr_spectrum.SpectrumBuilder
@@ -611,7 +574,6 @@
.. autosummary::
- :toctree: generated/
~yt.analysis_modules.cosmological_observation.light_cone.light_cone.LightCone
~yt.analysis_modules.cosmological_observation.light_ray.light_ray.LightRay
@@ -619,7 +581,6 @@
Absorption and X-ray spectra and spectral lines:
.. autosummary::
- :toctree: generated/
~yt.analysis_modules.absorption_spectrum.absorption_spectrum.AbsorptionSpectrum
~yt.fields.xray_emission_fields.XrayEmissivityIntegrator
@@ -628,14 +589,12 @@
Absorption spectra fitting:
.. autosummary::
- :toctree: generated/
~yt.analysis_modules.absorption_spectrum.absorption_spectrum_fit.generate_total_fit
Sunrise exporting:
.. autosummary::
- :toctree: generated/
~yt.analysis_modules.sunrise_export.sunrise_exporter.export_to_sunrise
~yt.analysis_modules.sunrise_export.sunrise_exporter.export_to_sunrise_from_halolist
@@ -643,7 +602,6 @@
RADMC-3D exporting:
.. autosummary::
- :toctree: generated/
~yt.analysis_modules.radmc3d_export.RadMC3DInterface.RadMC3DLayer
~yt.analysis_modules.radmc3d_export.RadMC3DInterface.RadMC3DWriter
@@ -657,7 +615,6 @@
Scene infrastructure:
.. autosummary::
- :toctree: generated/
~yt.visualization.volume_rendering.volume_rendering.volume_render
~yt.visualization.volume_rendering.volume_rendering.create_scene
@@ -669,7 +626,6 @@
The different kinds of sources:
.. autosummary::
- :toctree: generated/
~yt.visualization.volume_rendering.render_source.RenderSource
~yt.visualization.volume_rendering.render_source.VolumeSource
@@ -683,7 +639,6 @@
The different kinds of transfer functions:
.. autosummary::
- :toctree: generated/
~yt.visualization.volume_rendering.transfer_functions.TransferFunction
~yt.visualization.volume_rendering.transfer_functions.ColorTransferFunction
@@ -695,7 +650,6 @@
The different kinds of lenses:
.. autosummary::
- :toctree: generated/
~yt.visualization.volume_rendering.lens.Lens
~yt.visualization.volume_rendering.lens.PlaneParallelLens
@@ -712,7 +666,6 @@
.. autosummary::
- :toctree: generated/
~yt.visualization.streamlines.Streamlines
@@ -725,7 +678,6 @@
.. autosummary::
- :toctree: generated/
~yt.visualization.image_writer.multi_image_composite
~yt.visualization.image_writer.write_bitmap
@@ -740,7 +692,6 @@
particularly with complicated layouts.
.. autosummary::
- :toctree: generated/
~yt.visualization.eps_writer.DualEPS
~yt.visualization.eps_writer.single_plot
@@ -757,7 +708,6 @@
.. autosummary::
- :toctree: generated/
~yt.data_objects.derived_quantities.DerivedQuantity
~yt.data_objects.derived_quantities.DerivedQuantityCollection
@@ -783,7 +733,6 @@
See also :ref:`callbacks`.
.. autosummary::
- :toctree: generated/
~yt.visualization.plot_window.PWViewerMPL.annotate_clear
~yt.visualization.plot_modifications.ArrowCallback
@@ -817,7 +766,6 @@
See also :ref:`colormaps`.
.. autosummary::
- :toctree: generated/
~yt.visualization.color_maps.add_cmap
~yt.visualization.color_maps.make_colormap
@@ -828,7 +776,6 @@
.. autosummary::
- :toctree: generated/
~yt.convenience.load
~yt.frontends.ytdata.utilities.save_as_dataset
@@ -864,7 +811,6 @@
.. autosummary::
- :toctree: generated/
~yt.utilities.math_utils.periodic_position
~yt.utilities.math_utils.periodic_dist
@@ -899,7 +845,6 @@
.. autosummary::
- :toctree: generated/
~yt.config.YTConfigParser
~yt.utilities.parameter_file_storage.ParameterFileStore
@@ -913,7 +858,6 @@
--------------------
.. autosummary::
- :toctree: generated/
~yt.utilities.cosmology.Cosmology
~yt.utilities.cosmology.Cosmology.hubble_distance
@@ -937,7 +881,6 @@
The first set of functions are all provided by NumPy.
.. autosummary::
- :toctree: generated/
~yt.testing.assert_array_equal
~yt.testing.assert_almost_equal
@@ -953,7 +896,6 @@
These are yt-provided functions:
.. autosummary::
- :toctree: generated/
~yt.testing.assert_rel_equal
~yt.testing.amrspace
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/analysis_modules/halo_finding/halo_objects.py
--- a/yt/analysis_modules/halo_finding/halo_objects.py
+++ b/yt/analysis_modules/halo_finding/halo_objects.py
@@ -708,12 +708,12 @@
-------
tuple : (cm, mag_A, mag_B, mag_C, e0_vector, tilt)
The 6-tuple has in order:
- #. The center of mass as an array.
- #. mag_A as a float.
- #. mag_B as a float.
- #. mag_C as a float.
- #. e0_vector as an array.
- #. tilt as a float.
+ #. The center of mass as an array.
+ #. mag_A as a float.
+ #. mag_B as a float.
+ #. mag_C as a float.
+ #. e0_vector as an array.
+ #. tilt as a float.
Examples
--------
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/analysis_modules/halo_mass_function/halo_mass_function.py
--- a/yt/analysis_modules/halo_mass_function/halo_mass_function.py
+++ b/yt/analysis_modules/halo_mass_function/halo_mass_function.py
@@ -327,22 +327,22 @@
def sigmaM(self):
"""
- Written by BWO, 2006 (updated 25 January 2007).
- Converted to Python by Stephen Skory December 2009.
+ Written by BWO, 2006 (updated 25 January 2007).
+ Converted to Python by Stephen Skory December 2009.
- This routine takes in cosmological parameters and creates a file (array) with
- sigma(M) in it, which is necessary for various press-schechter type
- stuff. In principle one can calculate it ahead of time, but it's far,
- far faster in the long run to calculate your sigma(M) ahead of time.
+ This routine takes in cosmological parameters and creates a file (array) with
+ sigma(M) in it, which is necessary for various press-schechter type
+ stuff. In principle one can calculate it ahead of time, but it's far,
+ far faster in the long run to calculate your sigma(M) ahead of time.
- Inputs: cosmology, user must set parameters
+ Inputs: cosmology, user must set parameters
- Outputs: four columns of data containing the following information:
+ Outputs: four columns of data containing the following information:
- 1) mass (Msolar/h)
- 2) sigma (normalized) using Msun/h as the input
-
- The arrays output are used later.
+ 1) mass (Msolar/h)
+ 2) sigma (normalized) using Msun/h as the input
+
+ The arrays output are used later.
"""
# Set up the transfer function object.
@@ -446,13 +446,12 @@
def sigma_squared_of_R(self, R):
"""
- /* calculates sigma^2(R). This is the routine where the magic happens (or
- whatever it is that we do here). Integrates the sigma_squared_integrand
- parameter from R to infinity. Calls GSL (gnu scientific library) to do
- the actual integration.
+ calculates sigma^2(R). This is the routine where the magic happens (or
+ whatever it is that we do here). Integrates the sigma_squared_integrand
+ parameter from R to infinity. Calls GSL (gnu scientific library) to do
+ the actual integration.
- Note that R is in h^-1 Mpc (comoving)
- */
+ Note that R is in h^-1 Mpc (comoving)
"""
self.R = R
result = integrate_inf(self.sigma_squared_integrand)
@@ -463,7 +462,7 @@
def sigma_squared_integrand(self, k):
"""
- /* integrand for integral to get sigma^2(R). */
+ integrand for integral to get sigma^2(R).
"""
Rcom = self.R; # this is R in comoving Mpc/h
@@ -474,7 +473,7 @@
def PofK(self, k):
"""
- /* returns power spectrum as a function of wavenumber k */
+ returns power spectrum as a function of wavenumber k
"""
thisPofK = np.power(k, self.primordial_index) * np.power( self.TofK(k), 2.0);
@@ -483,7 +482,7 @@
def TofK(self, k):
"""
- /* returns transfer function as a function of wavenumber k. */
+ returns transfer function as a function of wavenumber k.
"""
thisTofK = self.TF.TFmdm_onek_hmpc(k);
@@ -503,9 +502,9 @@
def multiplicityfunction(self, sigma):
"""
- /* Multiplicity function - this is where the various fitting functions/analytic
+ Multiplicity function - this is where the various fitting functions/analytic
theories are different. The various places where I found these fitting functions
- are listed below. */
+ are listed below.
"""
nu = self.delta_c0 / sigma;
@@ -552,7 +551,7 @@
def sigmaof_M_z(self, sigmabin, redshift):
"""
- /* sigma(M, z) */
+ sigma(M, z)
"""
thissigma = self.Dofz(redshift) * self.sigmaarray[sigmabin];
@@ -561,7 +560,7 @@
def Dofz(self, redshift):
"""
- /* Growth function */
+ Growth function
"""
thisDofz = self.gofz(redshift) / self.gofz(0.0) / (1.0+redshift);
@@ -571,7 +570,7 @@
def gofz(self, redshift):
"""
- /* g(z) - I don't think this has any other name*/
+ g(z) - I don't think this has any other name
"""
thisgofz = 2.5 * self.omega_matter_of_z(redshift) / \
@@ -585,7 +584,7 @@
def omega_matter_of_z(self,redshift):
"""
- /* Omega matter as a function of redshift */
+ Omega matter as a function of redshift
"""
thisomofz = self.omega_matter0 * math.pow( 1.0+redshift, 3.0) / \
@@ -595,7 +594,7 @@
def omega_lambda_of_z(self,redshift):
"""
- /* Omega lambda as a function of redshift */
+ Omega lambda as a function of redshift
"""
thisolofz = self.omega_lambda0 / math.pow( self.Eofz(redshift), 2.0 )
@@ -604,7 +603,7 @@
def Eofz(self, redshift):
"""
- /* E(z) - I don't think this has any other name */
+ E(z) - I don't think this has any other name
"""
thiseofz = math.sqrt( self.omega_lambda0 \
+ (1.0 - self.omega_lambda0 - self.omega_matter0)*math.pow( 1.0+redshift, 2.0) \
@@ -614,15 +613,15 @@
"""
-/* Fitting Formulae for CDM + Baryon + Massive Neutrino (MDM) cosmologies. */
-/* Daniel J. Eisenstein & Wayne Hu, Institute for Advanced Study */
+Fitting Formulae for CDM + Baryon + Massive Neutrino (MDM) cosmologies.
+Daniel J. Eisenstein & Wayne Hu, Institute for Advanced Study
-/* There are two primary routines here, one to set the cosmology, the
+There are two primary routines here, one to set the cosmology, the
other to construct the transfer function for a single wavenumber k.
You should call the former once (per cosmology) and the latter as
-many times as you want. */
+many times as you want.
-/* TFmdm_set_cosm() -- User passes all the cosmological parameters as
+ TFmdm_set_cosm() -- User passes all the cosmological parameters as
arguments; the routine sets up all of the scalar quantites needed
computation of the fitting formula. The input parameters are:
1) omega_matter -- Density of CDM, baryons, and massive neutrinos,
@@ -634,7 +633,7 @@
6) hubble -- Hubble constant, in units of 100 km/s/Mpc
7) redshift -- The redshift at which to evaluate */
-/* TFmdm_onek_mpc() -- User passes a single wavenumber, in units of Mpc^-1.
+ TFmdm_onek_mpc() -- User passes a single wavenumber, in units of Mpc^-1.
Routine returns the transfer function from the Eisenstein & Hu
fitting formula, based on the cosmology currently held in the
internal variables. The routine returns T_cb (the CDM+Baryon
@@ -642,29 +641,40 @@
Baryon+Neutrino density-weighted transfer function) is stored
in the global variable tf_cbnu. */
-/* We also supply TFmdm_onek_hmpc(), which is identical to the previous
- routine, but takes the wavenumber in units of h Mpc^-1. */
+We also supply TFmdm_onek_hmpc(), which is identical to the previous
+routine, but takes the wavenumber in units of h Mpc^-1.
-/* We hold the internal scalar quantities in global variables, so that
-the user may access them in an external program, via "extern" declarations. */
+We hold the internal scalar quantities in global variables, so that
+the user may access them in an external program, via "extern" declarations.
-/* Please note that all internal length scales are in Mpc, not h^-1 Mpc! */
+Please note that all internal length scales are in Mpc, not h^-1 Mpc!
"""
class TransferFunction(object):
"""
- /* This routine takes cosmological parameters and a redshift and sets up
- all the internal scalar quantities needed to compute the transfer function. */
- /* INPUT: omega_matter -- Density of CDM, baryons, and massive neutrinos,
- in units of the critical density. */
- /* omega_baryon -- Density of baryons, in units of critical. */
- /* omega_hdm -- Density of massive neutrinos, in units of critical */
- /* degen_hdm -- (Int) Number of degenerate massive neutrino species */
- /* omega_lambda -- Cosmological constant */
- /* hubble -- Hubble constant, in units of 100 km/s/Mpc */
- /* redshift -- The redshift at which to evaluate */
- /* OUTPUT: Returns 0 if all is well, 1 if a warning was issued. Otherwise,
- sets many global variables for use in TFmdm_onek_mpc() */
+ This routine takes cosmological parameters and a redshift and sets up
+ all the internal scalar quantities needed to compute the transfer function.
+
+ Parameters
+ ----------
+ omega_matter : float
+ Density of CDM, baryons, and massive neutrinos, in units
+ of the critical density.
+ omega_baryon : float
+ Density of baryons, in units of critical.
+ omega_hdm : float
+ Density of massive neutrinos, in units of critical
+ degen_hdm : integer
+ Number of degenerate massive neutrino species
+ omega_lambda : float
+ Cosmological constant
+ hubble : float
+ Hubble constant, in units of 100 km/s/Mpc
+ redshift : float
+ The redshift at which to evaluate
+
+ Returns 0 if all is well, 1 if a warning was issued. Otherwise,
+ sets many global variables for use in TFmdm_onek_mpc()
"""
def __init__(self, omega_matter, omega_baryon, omega_hdm,
degen_hdm, omega_lambda, hubble, redshift):
@@ -751,15 +761,23 @@
def TFmdm_onek_mpc(self, kk):
"""
- /* Given a wavenumber in Mpc^-1, return the transfer function for the
- cosmology held in the global variables. */
- /* Input: kk -- Wavenumber in Mpc^-1 */
- /* Output: The following are set as global variables:
- growth_cb -- the transfer function for density-weighted
- CDM + Baryon perturbations.
- growth_cbnu -- the transfer function for density-weighted
- CDM + Baryon + Massive Neutrino perturbations. */
- /* The function returns growth_cb */
+ Given a wavenumber in Mpc^-1, return the transfer function for the
+ cosmology held in the global variables.
+
+ Parameters
+ ----------
+ kk : float
+ Wavenumber in Mpc^-1
+
+ Returns
+ -------
+ growth_cb : float
+ the transfer function for density-weighted
+ CDM + Baryon perturbations. (returned and set as a global var)
+ growth_cbnu : float
+ the transfer function for density-weighted
+ CDM + Baryon + Massive Neutrino perturbations.
+ (set as a global var)
"""
self.qq = kk/self.omhh*SQR(self.theta_cmb);
@@ -794,15 +812,22 @@
def TFmdm_onek_hmpc(self, kk):
"""
- /* Given a wavenumber in h Mpc^-1, return the transfer function for the
- cosmology held in the global variables. */
- /* Input: kk -- Wavenumber in h Mpc^-1 */
- /* Output: The following are set as global variables:
- growth_cb -- the transfer function for density-weighted
- CDM + Baryon perturbations.
- growth_cbnu -- the transfer function for density-weighted
- CDM + Baryon + Massive Neutrino perturbations. */
- /* The function returns growth_cb */
+ Given a wavenumber in h Mpc^-1, return the transfer function for the
+ cosmology held in the global variables.
+
+ Parameters
+ ----------
+ kk : float
+ Wavenumber in h Mpc^-1
+
+ Returns
+ -------
+ growth_cb : float
+ the transfer function for density-weighted
+ CDM + Baryon perturbations. (return and set as a global var)
+ growth_cbnu : float
+ the transfer function for density-weighted
+ CDM + Baryon + Massive Neutrino perturbations.
"""
return self.TFmdm_onek_mpc(kk*self.hhubble);
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/analysis_modules/sunyaev_zeldovich/projection.py
--- a/yt/analysis_modules/sunyaev_zeldovich/projection.py
+++ b/yt/analysis_modules/sunyaev_zeldovich/projection.py
@@ -78,7 +78,7 @@
Parameters
----------
- ds : Dataset
+ ds : ~yt.data_objects.static_output.Dataset
The dataset
freqs : array_like
The frequencies (in GHz) at which to compute the SZ spectral distortion.
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/data_objects/data_containers.py
--- a/yt/data_objects/data_containers.py
+++ b/yt/data_objects/data_containers.py
@@ -1957,7 +1957,7 @@
multiple data objects.
This object is not designed to be created directly; it is designed to be
- created implicitly by using one of the bitwise operations (&, |, ^, ~) on
+ created implicitly by using one of the bitwise operations (&, \|, ^, \~) on
one or two other data objects. These correspond to the appropriate boolean
operations, and the resultant object can be nested.
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/data_objects/static_output.py
--- a/yt/data_objects/static_output.py
+++ b/yt/data_objects/static_output.py
@@ -194,6 +194,8 @@
self.data = weakref.WeakKeyDictionary()
def __get__(self, instance, owner):
+ if not instance:
+ return None
ret = self.data.get(instance, None)
try:
ret = ret.copy()
@@ -1056,7 +1058,7 @@
Parameters
----------
- input_array : iterable
+ input_array : Iterable
A tuple, list, or array to attach units to
input_units : String unit specification, unit symbol or astropy object
The units of the array. Powers must be specified using python syntax
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/fields/species_fields.py
--- a/yt/fields/species_fields.py
+++ b/yt/fields/species_fields.py
@@ -126,8 +126,8 @@
"""
This takes a field registry, a fluid type, and two species names.
The first species name is one you wish to alias to an existing species
- name. For instance you might alias all "H_p0" fields to "H_" fields
- to indicate that "H_" fields are really just neutral hydrogen fields.
+ name. For instance you might alias all "H_p0" fields to "H\_" fields
+ to indicate that "H\_" fields are really just neutral hydrogen fields.
This function registers field aliases for the density, number_density,
mass, and fraction fields between the two species given in the arguments.
"""
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/fields/xray_emission_fields.py
--- a/yt/fields/xray_emission_fields.py
+++ b/yt/fields/xray_emission_fields.py
@@ -72,7 +72,7 @@
Parameters
----------
- table_type: string
+ table_type : string
The type of data to use when computing the emissivity values. If "cloudy",
a file called "cloudy_emissivity.h5" is used, for photoionized
plasmas. If, "apec", a file called "apec_emissivity.h5" is used for
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/frontends/chombo/io.py
--- a/yt/frontends/chombo/io.py
+++ b/yt/frontends/chombo/io.py
@@ -199,11 +199,9 @@
def parse_orion_sinks(fn):
'''
-
Orion sink particles are stored in text files. This function
is for figuring what particle fields are present based on the
- number of entries per line in the *.sink file.
-
+ number of entries per line in the \*.sink file.
'''
# Figure out the format of the particle file
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/frontends/fits/misc.py
--- a/yt/frontends/fits/misc.py
+++ b/yt/frontends/fits/misc.py
@@ -49,7 +49,7 @@
Parameters
----------
- ds : 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 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/frontends/stream/data_structures.py
--- a/yt/frontends/stream/data_structures.py
+++ b/yt/frontends/stream/data_structures.py
@@ -903,7 +903,7 @@
Parameters
----------
- base_ds : 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`
@@ -1167,7 +1167,7 @@
r"""Define the cell coordinates and cell neighbors of a hexahedral mesh
for a semistructured grid. Used to specify the connectivity and
coordinates parameters used in
- :function:`~yt.frontends.stream.data_structures.load_hexahedral_mesh`.
+ :func:`~yt.frontends.stream.data_structures.load_hexahedral_mesh`.
Parameters
----------
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/funcs.py
--- a/yt/funcs.py
+++ b/yt/funcs.py
@@ -747,6 +747,7 @@
With a name provided by the user, this will decide how to
appropriately name the output file by the following rules:
+
1. if name is None, the filename will be the keyword plus
the suffix.
2. if name ends with "/", assume name is a directory and
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/pmods.py
--- a/yt/pmods.py
+++ b/yt/pmods.py
@@ -79,13 +79,13 @@
# LLC, and shall not be used for advertising or product endorsement
# purposes.
-"""MPI_Import defines an mpi-aware import hook. The standard use of
-this module is as follows:
+"""``MPI_Import`` defines an mpi-aware import hook. The standard use of
+this module is as follows::
- from MPI_Import import mpi_import
- with mpi_import():
- import foo
- import bar
+ from MPI_Import import mpi_import
+ with mpi_import():
+ import foo
+ import bar
Within the with block, the standard import statement is replaced by an
MPI-aware import statement. The rank 0 process finds the location of
@@ -94,35 +94,35 @@
One CRITICAL detail: any code inside the mpi_import block must be
executed exactly the same on all of the MPI ranks. For example,
-consider this:
+consider this::
-def foo():
- import mpi
- if mpi.rank == 0:
- bar = someFunction()
- bar = mpi.bcast(bar,root=0)
+ def foo():
+ import mpi
+ if mpi.rank == 0:
+ bar = someFunction()
+ bar = mpi.bcast(bar,root=0)
+
+ def someFunction():
+ import os
+ return os.name
-def someFunction():
- import os
- return os.name
-
-If foo() is called during the import process, then things may go very
+If ``foo()`` is called during the import process, then things may go very
wrong. If the os module hasn't been loaded, then the rank 0 process
will find os and broadcast its location. Since there's no
-corresponding bcast for rank > 0, the other processes will receive
+corresponding bcast for ``rank > 0``, the other processes will receive
that broadcast instead of the broadcast for bar, resulting in
-undefined behavior. Similarly, if rank >0 process encounters an import
-that rank 0 does not encounter, that process will either hang waiting
+undefined behavior. Similarly, if ``rank > 0`` process encounters an import
+that ``rank`` 0 does not encounter, that process will either hang waiting
for the bcast, or it will receive an out-of-order bcast.
The import hook provides a way to test whether we're using this
importer, which can be used to disable rank-asymmetric behavior in a
-module import:
+module import::
-from yt.extern.six.moves import builtins
-hasattr(builtins.__import__,"mpi_import")
+ from yt.extern.six.moves import builtins
+ hasattr(builtins.__import__,"mpi_import")
-This evaluates to True only when we're in an mpi_import() context
+This evaluates to True only when we're in an ``mpi_import()`` context
manager.
There are some situations where rank-dependent code may be necessary.
@@ -130,66 +130,66 @@
tends to cause deadlocks when it is executed inside an mpi_imported
module. In that case, we provide a hook to execute a function after
the mpi_import hook has been replaced by the standard import hook.
-Here is an example showing the use of this feature:
-
-# encapsulate the rank-asymmetric code in a function
-def f():
- if mpi.rank == 0:
- doOneThing()
- else:
- doSomethingElse()
+Here is an example showing the use of this feature::
-# Either importer is None (standard import) or it's a reference to
-# the mpi_import object that owns the current importer.
-from yt.extern.six.moves import builtins
-importer = getattr(builtins.__import__,"mpi_import",None)
-if importer:
- importer.callAfterImport(f)
-else:
- # If we're using the standard import, then we'll execute the
- # code in f immediately
- f()
+ # encapsulate the rank-asymmetric code in a function
+ def f():
+ if mpi.rank == 0:
+ doOneThing()
+ else:
+ doSomethingElse()
-WARNING: the callAfterImport feature is not intended for casual use.
+ # Either importer is None (standard import) or it's a reference to
+ # the mpi_import object that owns the current importer.
+ from yt.extern.six.moves import builtins
+ importer = getattr(builtins.__import__,"mpi_import",None)
+ if importer:
+ importer.callAfterImport(f)
+ else:
+ # If we're using the standard import, then we'll execute the
+ # code in f immediately
+ f()
+
+WARNING: the ``callAfterImport`` feature is not intended for casual use.
Usually it will be sufficient (and preferable) to either remove the
rank-asymmetric code or explicitly move it outside of the 'with
mpi_import' block. callAfterImport is provided for the (hopefully
rare!) cases where this does not suffice.
-
-Some implementation details:
-
--This code is based on knee.py, which is an example of a pure Python
- hierarchical import that was included with Python 2.6 distributions.
-
--Python PEP 302 defines another way to override import by using finder
- and loader objects, which behave similarly to the imp.find_module and
- imp.load_module functions in __import_module__ below. Unfortunately,
- the implementation of PEP 302 is such that the path for the module
- has already been found by the time that the "finder" object is
- constructed, so it's not suitable for our purposes.
+Some implementation details
+---------------------------
--This module uses pyMPI. It was originally designed with mpi4py, and
- switching back to mpi4py requires only minor modifications. To
- quickly substitute mpi4py for pyMPI, the 'import mpi' line below can
- be replaced with the following wrapper:
+* This code is based on knee.py, which is an example of a pure Python
+ hierarchical import that was included with Python 2.6 distributions.
-from mpi4py import MPI
-class mpi(object):
- rank = MPI.COMM_WORLD.Get_rank()
- @staticmethod
- def bcast(obj=None,root=0):
- return MPI.COMM_WORLD.bcast(obj,root)
+* Python PEP 302 defines another way to override import by using finder
+ and loader objects, which behave similarly to the imp.find_module and
+ imp.load_module functions in __import_module__ below. Unfortunately,
+ the implementation of PEP 302 is such that the path for the module
+ has already been found by the time that the "finder" object is
+ constructed, so it's not suitable for our purposes.
--An alternate version of this module had rank 0 perform all of the
- lookups, and then broadcast the locations all-at-once when that
- process reached the end of the context manager. This was somewhat
- faster than the current implementation, but was prone to deadlock
- when loading modules containing MPI synchronization points.
+* This module uses pyMPI. It was originally designed with mpi4py, and
+ switching back to mpi4py requires only minor modifications. To
+ quickly substitute mpi4py for pyMPI, the 'import mpi' line below can
+ be replaced with the following wrapper::
--The 'level' parameter to the import hook is not handled correctly; we
- treat it as if it were -1 (try relative and absolute imports). For
- more information about the level parameter, run 'help(__import__)'.
+ from mpi4py import MPI
+ class mpi(object):
+ rank = MPI.COMM_WORLD.Get_rank()
+ @staticmethod
+ def bcast(obj=None,root=0):
+ return MPI.COMM_WORLD.bcast(obj,root)
+
+* An alternate version of this module had rank 0 perform all of the
+ lookups, and then broadcast the locations all-at-once when that
+ process reached the end of the context manager. This was somewhat
+ faster than the current implementation, but was prone to deadlock
+ when loading modules containing MPI synchronization points.
+
+* The ``level`` parameter to the import hook is not handled correctly; we
+ treat it as if it were -1 (try relative and absolute imports). For
+ more information about the level parameter, run ``help(__import__)``.
"""
from __future__ import print_function
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/testing.py
--- a/yt/testing.py
+++ b/yt/testing.py
@@ -353,13 +353,13 @@
This dataset allows you to easily explore orientations and
handiness in VR and other renderings
- Parameters:
- -----------
+ Parameters
+ ----------
- N: integer
+ N : integer
The number of cells along each direction
- scale: float
+ scale : float
A spatial scale, the domain boundaries will be multiplied by scale to
test datasets that have spatial different scales (e.g. data in CGS units)
@@ -811,17 +811,17 @@
Examples
--------
- @check_results
- def my_func(ds):
- return ds.domain_width
+ >>> @check_results
+ ... def my_func(ds):
+ ... return ds.domain_width
- my_func(ds)
+ >>> my_func(ds)
- @check_results
- def field_checker(dd, field_name):
- return dd[field_name]
+ >>> @check_results
+ ... def field_checker(dd, field_name):
+ ... return dd[field_name]
- field_cheker(ds.all_data(), 'density', result_basename='density')
+ >>> field_cheker(ds.all_data(), 'density', result_basename='density')
"""
def compute_results(func):
@@ -952,9 +952,12 @@
with the units of ``actual`` and ``desired``. If no units are attached,
assumes the same units as ``desired``. Defaults to zero.
+ Notes
+ -----
Also accepts additional keyword arguments accepted by
:func:`numpy.testing.assert_allclose`, see the documentation of that
function for details.
+
"""
# Create a copy to ensure this function does not alter input arrays
act = YTArray(actual)
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d 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 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/utilities/grid_data_format/writer.py
--- a/yt/utilities/grid_data_format/writer.py
+++ b/yt/utilities/grid_data_format/writer.py
@@ -50,11 +50,13 @@
dataset_units : dictionary, optional
A dictionary of (value, unit) tuples to set the default units
of the dataset. Keys can be:
- "length_unit"
- "time_unit"
- "mass_unit"
- "velocity_unit"
- "magnetic_unit"
+
+ * "length_unit"
+ * "time_unit"
+ * "mass_unit"
+ * "velocity_unit"
+ * "magnetic_unit"
+
If not specified, these will carry over from the parent
dataset.
particle_type_name : string, optional
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/utilities/hierarchy_inspection.py
--- a/yt/utilities/hierarchy_inspection.py
+++ b/yt/utilities/hierarchy_inspection.py
@@ -12,7 +12,7 @@
Parameters
----------
- candidates : iterable
+ candidates : Iterable
An interable object that is a collection of classes to find the lowest
subclass of.
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/utilities/math_utils.py
--- a/yt/utilities/math_utils.py
+++ b/yt/utilities/math_utils.py
@@ -61,7 +61,7 @@
pos : array
An array of floats.
- ds : Dataset
+ ds : ~yt.data_objects.static_output.Dataset
A simulation static output.
Examples
@@ -852,7 +852,7 @@
Parameters
----------
maxr : scalar
- should be max(|x|, |y|)
+ should be ``max(|x|, |y|)``
aspect : scalar
The aspect ratio of width / height for the projection.
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/utilities/parallel_tools/io_runner.py
--- a/yt/utilities/parallel_tools/io_runner.py
+++ b/yt/utilities/parallel_tools/io_runner.py
@@ -13,7 +13,7 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
-import np
+import numpy as np
from yt.utilities.logger import ytLogger as mylog
from .parallel_analysis_interface import \
ProcessorPool, parallel_objects
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/utilities/parallel_tools/parallel_analysis_interface.py
--- a/yt/utilities/parallel_tools/parallel_analysis_interface.py
+++ b/yt/utilities/parallel_tools/parallel_analysis_interface.py
@@ -434,7 +434,7 @@
Parameters
----------
- objects : iterable
+ objects : Iterable
The list of objects to dispatch to different processors.
njobs : int
How many jobs to spawn. By default, one job will be dispatched for
@@ -540,7 +540,7 @@
Parameters
----------
- objects : iterable
+ objects : Iterable
The list of objects to operate on.
generator_func : callable
This function will be called on each object, and the results yielded.
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/utilities/sdf.py
--- a/yt/utilities/sdf.py
+++ b/yt/utilities/sdf.py
@@ -431,17 +431,16 @@
Parameters
----------
- filename: string
- The filename associated with the data to be loaded.
- header: string, optional
- If separate from the data file, a file containing the
- header can be specified. Default: None.
+ filename : string
+ The filename associated with the data to be loaded.
+ header : string, optional
+ If separate from the data file, a file containing the
+ header can be specified. Default: None.
Returns
-------
self : SDFRead object
- Dict-like container of parameters and data.
-
+ Dict-like container of parameters and data.
References
----------
@@ -1270,11 +1269,15 @@
Return list of data chunks for a cell on the given level
plus a padding around the cell, for a list of fields.
- Returns:
- data: A list of dictionaries of data.
+ Returns
+ -------
+ data: list
+ A list of dictionaries of data.
- chunks = midx.get_padded_bbox_data(6, np.array([128]*3),
- 8.0, ['x','y','z','ident'])
+ Examples
+ --------
+ >>> chunks = midx.get_padded_bbox_data(6, np.array([128]*3),
+ ... 8.0, ['x','y','z','ident'])
"""
_ensure_xyz_fields(fields)
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/utilities/spatial/__init__.py
--- a/yt/utilities/spatial/__init__.py
+++ b/yt/utilities/spatial/__init__.py
@@ -1,12 +1,9 @@
"""
-=============================================================
Spatial algorithms and data structures (:mod:`scipy.spatial`)
-=============================================================
Nearest-neighbor queries:
.. autosummary::
- :toctree: generated/
KDTree -- class for efficient nearest-neighbor queries
cKDTree -- class for efficient nearest-neighbor queries (faster impl.)
@@ -15,7 +12,6 @@
Delaunay triangulation:
.. autosummary::
- :toctree: generated/
Delaunay
tsearch
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/utilities/spatial/ckdtree.pyx
--- a/yt/utilities/spatial/ckdtree.pyx
+++ b/yt/utilities/spatial/ckdtree.pyx
@@ -639,25 +639,31 @@
""" query the tree for the nearest neighbors, to get the density
of particles for chainHOP.
- Parameters:
- ===========
+ Parameters
+ ----------
- mass: A array-like list of the masses of the particles, in the same
+ mass : array
+ A array-like list of the masses of the particles, in the same
order as the data that went into building the kd tree.
- num_neighbors: Optional, the number of neighbors to search for and to
+ num_neighbors : integer, optional
+ The number of neighbors to search for and to
use in the density calculation. Default is 65, and is probably what
one should stick with.
- nMerge: The number of nearest neighbor tags to return for each particle.
+ nMerge: integer, optional
+ The number of nearest neighbor tags to return for each particle.
+ Defaults to 6.
- Returns:
- ========
+ Returns
+ -------
- dens: An array of the densities for each particle, in the same order
+ dens : array
+ An array of the densities for each particle, in the same order
as the input data.
- tags: A two-dimensional array of the indexes, nMerge nearest neighbors
+ tags : array
+ A two-dimensional array of the indexes, nMerge nearest neighbors
for each particle.
"""
@@ -723,20 +729,23 @@
""" query the tree in chunks, between start and finish, recording the
nearest neighbors.
- Parameters:
- ===========
-
- start: The starting point in the dataset for this search.
-
- finish: The ending point in the dataset for this search.
+ Parameters
+ ----------
- num_neighbors: Optional, the number of neighbors to search for.
- The default is 65.
+ start: integer
+ The starting point in the dataset for this search.
- Returns:
- ========
+ finish: integer
+ The ending point in the dataset for this search.
- chunk_tags: A two-dimensional array of the nearest neighbor tags for the
+ num_neighbors: integer, optional
+ The number of neighbors to search for. The default is 65.
+
+ Returns
+ -------
+
+ chunk_tags: array
+ A two-dimensional array of the nearest neighbor tags for the
points in this search.
"""
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/utilities/spatial/distance.py
--- a/yt/utilities/spatial/distance.py
+++ b/yt/utilities/spatial/distance.py
@@ -12,7 +12,6 @@
stored in a rectangular array.
.. autosummary::
- :toctree: generated/
pdist -- pairwise distances between observation vectors.
cdist -- distances between between two collections of observation vectors
@@ -23,7 +22,6 @@
for computing the number of observations in a distance matrix.
.. autosummary::
- :toctree: generated/
is_valid_dm -- checks for a valid distance matrix
is_valid_y -- checks for a valid condensed distance matrix
@@ -35,7 +33,6 @@
functions. Use ``pdist`` for this purpose.
.. autosummary::
- :toctree: generated/
braycurtis -- the Bray-Curtis distance.
canberra -- the Canberra distance.
@@ -383,9 +380,9 @@
def jaccard(u, v):
- """
+ r"""
Computes the Jaccard-Needham dissimilarity between two boolean
- n-vectors u and v, which is
+ ``n``-vectors ``u`` and ``v``, which is
.. math::
@@ -399,9 +396,9 @@
Parameters
----------
u : ndarray
- An :math:`n`-dimensional vector.
+ An ``n``-dimensional vector.
v : ndarray
- An :math:`n`-dimensional vector.
+ An ``n``-dimensional vector.
Returns
-------
@@ -417,9 +414,9 @@
def kulsinski(u, v):
- """
- Computes the Kulsinski dissimilarity between two boolean n-vectors
- u and v, which is defined as
+ r"""
+ Computes the Kulsinski dissimilarity between two boolean ``n``-vectors
+ ``u`` and ``v``, which is defined as
.. math::
@@ -433,9 +430,9 @@
Parameters
----------
u : ndarray
- An :math:`n`-dimensional vector.
+ An ``n``-dimensional vector.
v : ndarray
- An :math:`n`-dimensional vector.
+ An ``n``-dimensional vector.
Returns
-------
@@ -918,9 +915,9 @@
r"""
Computes the pairwise distances between m original observations in
n-dimensional space. Returns a condensed distance matrix Y. For
- each :math:`i` and :math:`j` (where :math:`i<j<n`), the
+ each ``i`` and ``j`` (where ``i < j < n``), the
metric ``dist(u=X[i], v=X[j])`` is computed and stored in the
- :math:`ij`th entry.
+ ``ij`` th entry.
See ``squareform`` for information on how to calculate the index of
this entry or to convert the condensed distance matrix to a
@@ -972,7 +969,7 @@
1 - \frac{uv^T}
{{|u|}_2 {|v|}_2}
- where |*|_2 is the 2 norm of its argument *.
+ where :math:`|*|_2` is the 2 norm of its argument \*.
7. ``Y = pdist(X, 'correlation')``
@@ -1361,49 +1358,45 @@
Parameters
----------
- X : ndarray
- Either a condensed or redundant distance matrix.
+ X : ndarray
+ Either a condensed or redundant distance matrix.
Returns
-------
- Y : ndarray
- If a condensed distance matrix is passed, a redundant
- one is returned, or if a redundant one is passed, a
- condensed distance matrix is returned.
+ Y : ndarray
+ If a condensed distance matrix is passed, a redundant
+ one is returned, or if a redundant one is passed, a
+ condensed distance matrix is returned.
+ force : string
+ As with MATLAB(TM), if force is equal to 'tovector' or
+ 'tomatrix', the input will be treated as a distance matrix
+ or distance vector respectively.
- force : string
- As with MATLAB(TM), if force is equal to 'tovector' or
- 'tomatrix', the input will be treated as a distance matrix
- or distance vector respectively.
+ checks : bool
+ If ``checks`` is set to ``False``, no checks will be made
+ for matrix symmetry nor zero diagonals. This is useful if
+ it is known that ``X - X.T1`` is small and ``diag(X)`` is
+ close to zero. These values are ignored any way so they do
+ not disrupt the squareform transformation.
- checks : bool
- If ``checks`` is set to ``False``, no checks will be made
- for matrix symmetry nor zero diagonals. This is useful if
- it is known that ``X - X.T1`` is small and ``diag(X)`` is
- close to zero. These values are ignored any way so they do
- not disrupt the squareform transformation.
-
-
- Calling Conventions
+ Notes
-------------------
1. v = squareform(X)
- Given a square d by d symmetric distance matrix ``X``,
- ``v=squareform(X)`` returns a :math:`d*(d-1)/2` (or
- `${n \choose 2}$`) sized vector v.
+ Given a square d by d symmetric distance matrix ``X``, ``v=squareform(X)``
+ returns a :math:`d*(d-1)/2` (or :math:`{n \choose 2}`) sized vector ``v``.
+ :math:`v[{n \choose 2}-{n-i \choose 2} + (j-i-1)]` is the distance between
+ points ``i`` and ``j``. If ``X`` is non-square or asymmetric, an error is
+ returned.
- v[{n \choose 2}-{n-i \choose 2} + (j-i-1)] is the distance
- between points i and j. If X is non-square or asymmetric, an error
- is returned.
+ 2. X = squareform(v)
- X = squareform(v)
-
- Given a d*d(-1)/2 sized v for some integer d>=2 encoding distances
- as described, X=squareform(v) returns a d by d distance matrix X. The
- X[i, j] and X[j, i] values are set to
- v[{n \choose 2}-{n-i \choose 2} + (j-u-1)] and all
- diagonal elements are zero.
+ Given a ``d*d(-1)/2`` sized ``v`` for some integer ``d>=2`` encoding
+ distances as described, ``X=squareform(v)`` returns a ``d`` by ``d``
+ distance matrix ``X``. The ``X[i, j]`` and ``X[j, i]`` values are set to
+ :math:`v[{n \choose 2}-{n-i \choose 2} + (j-u-1)]` and all diagonal
+ elements are zero.
"""
@@ -1489,7 +1482,7 @@
----------
D : ndarray
The candidate object to test for validity.
- tol : double
+ tol : float
The distance matrix should be symmetric. tol is the maximum
difference between the :math:`ij`th entry and the
:math:`ji`th entry for the distance metric to be
@@ -1750,7 +1743,7 @@
\frac{1 - uv^T}
{{|u|}_2 {|v|}_2}
- where :math:`|*|_2` is the 2-norm of its argument *.
+ where :math:`|*|_2` is the 2-norm of its argument \*.
7. ``Y = cdist(XA, XB, 'correlation')``
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/utilities/spatial/kdtree.py
--- a/yt/utilities/spatial/kdtree.py
+++ b/yt/utilities/spatial/kdtree.py
@@ -547,7 +547,7 @@
Parameters
==========
- other : KDTree
+ other : `~yt.utilities.spatial.kdtree.KDTree`
The tree containing points to search against
r : positive float
The maximum distance
@@ -719,7 +719,7 @@
Parameters
==========
- other : KDTree
+ other : `~yt.utilities.spatial.kdtree.KDTree`
r : float or one-dimensional array of floats
The radius to produce a count for. Multiple radii are searched with a single
@@ -790,14 +790,14 @@
any distance greater than max_distance.
Parameters
- ==========
+ ----------
- other : KDTree
+ other : `~yt.utilities.spatial.kdtree.KDTree`
max_distance : positive float
Returns
- =======
+ -------
result : dok_matrix
Sparse matrix representing the results in "dictionary of keys" format.
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -431,9 +431,9 @@
coordinate space can be given. If plain numeric types are input,
units of `code_length` are assumed. Further examples:
- ================================== ============================
- format example
- ================================== ============================
+ =============================================== ==================================
+ format example
+ =============================================== ==================================
'{space}' 'domain'
'{xloc}-{space}' 'left-window'
'{yloc}-{space}' 'upper-domain'
@@ -444,7 +444,7 @@
('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
((yloc, '{unit}'), (xloc, '{unit}'), '{space}') ((0.5, 'm'), (0.4, 'm'), 'window')
(xloc, yloc, '{space}') (0.23, 0.5, 'domain')
- ================================== ===========================
+ =============================================== ==================================
"""
self.origin = origin
@@ -1255,9 +1255,9 @@
coordinate space can be given. If plain numeric types are input,
units of `code_length` are assumed. Further examples:
- ================================== ============================
- format example
- ================================== ============================
+ =============================================== ==================================
+ format example
+ =============================================== ==================================
'{space}' 'domain'
'{xloc}-{space}' 'left-window'
'{yloc}-{space}' 'upper-domain'
@@ -1268,7 +1268,7 @@
('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
((yloc, '{unit}'), (xloc, '{unit}'), '{space}') ((0.5, 'm'), (0.4, 'm'), 'window')
(xloc, yloc, '{space}') (0.23, 0.5, 'domain')
- ================================== ===========================
+ =============================================== ==================================
axes_unit : A string
The name of the unit for the tick labels on the x and y axes.
Defaults to None, which automatically picks an appropriate unit.
@@ -1410,9 +1410,9 @@
coordinate space can be given. If plain numeric types are input,
units of `code_length` are assumed. Further examples:
- ================================== ============================
- format example
- ================================== ============================
+ =============================================== ==================================
+ format example
+ =============================================== ==================================
'{space}' 'domain'
'{xloc}-{space}' 'left-window'
'{yloc}-{space}' 'upper-domain'
@@ -1423,7 +1423,7 @@
('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
((yloc, '{unit}'), (xloc, '{unit}'), '{space}') ((0.5, 'm'), (0.4, 'm'), 'window')
(xloc, yloc, '{space}') (0.23, 0.5, 'domain')
- ================================== ===========================
+ =============================================== ==================================
right_handed : boolean
Whether the implicit east vector for the image generated is set to make a right
@@ -1930,9 +1930,9 @@
coordinate space can be given. If plain numeric types are input,
units of `code_length` are assumed. Further examples:
- ================================== ============================
- format example
- ================================== ============================
+ =============================================== ==================================
+ format example
+ =============================================== ==================================
'{space}' 'domain'
'{xloc}-{space}' 'left-window'
'{yloc}-{space}' 'upper-domain'
@@ -1943,7 +1943,7 @@
('{yloc}', '{xloc}', '{space}') ('lower', 'right', 'window')
((yloc, '{unit}'), (xloc, '{unit}'), '{space}') ((0.5, 'm'), (0.4, 'm'), 'window')
(xloc, yloc, '{space}') (0.23, 0.5, 'domain')
- ================================== ===========================
+ =============================================== ==================================
north_vector : a sequence of floats
A vector defining the 'up' direction in the `OffAxisSlicePlot`; not
used in `AxisAlignedSlicePlot`. This option sets the orientation of the
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/visualization/volume_rendering/interactive_vr.py
--- a/yt/visualization/volume_rendering/interactive_vr.py
+++ b/yt/visualization/volume_rendering/interactive_vr.py
@@ -455,7 +455,7 @@
Parameters
----------
- camera : :class:`yt.visualization.volume_rendering.interactive_vr.IDVCamera`
+ camera : :class:`~yt.visualization.volume_rendering.interactive_vr.IDVCamera`
A simple camera object.
"""
@@ -620,7 +620,7 @@
Parameters
----------
- camera : Camera
+ camera : :class:`~yt.visualization.volume_rendering.interactive_vr.IDVCamera`
"""
self.camera = camera
@@ -836,7 +836,7 @@
Parameters
----------
- camera : Camera
+ camera : :class:`~yt.visualization.volume_rendering.interactive_vr.IDVCamera`
"""
self.camera = camera
diff -r 3eca2ae80ab14a48b643d3055d7d3c0933fa77ae -r e518ad9d8b5c99f5841408ba2ee082797b1c727d yt/visualization/volume_rendering/scene.py
--- a/yt/visualization/volume_rendering/scene.py
+++ b/yt/visualization/volume_rendering/scene.py
@@ -796,7 +796,7 @@
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 object
Repository URL: https://bitbucket.org/yt_analysis/yt/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
More information about the yt-svn
mailing list