[yt-svn] commit/yt: 13 new changesets
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Sat Mar 4 14:43:11 PST 2017
13 new commits in yt:
https://bitbucket.org/yt_analysis/yt/commits/aa29bc66673a/
Changeset: aa29bc66673a
Branch: yt
User: xarthisius
Date: 2017-02-18 20:59:46+00:00
Summary: Prepopulate api doci before main sphinx build call
Affected #: 3 files
diff -r abf5a8eff1b2d0cd776a41a33e5d3f3d25232ecc -r aa29bc66673a573078c58dee9a9ab1e266053d30 doc/Makefile
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -47,6 +47,7 @@
-rm -rf _temp/*.done source/cookbook/_static/*
html:
+ sphinx-apidoc -o source/reference/api/ -e ../yt
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
diff -r abf5a8eff1b2d0cd776a41a33e5d3f3d25232ecc -r aa29bc66673a573078c58dee9a9ab1e266053d30 doc/source/conf.py
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -259,5 +259,6 @@
'http://matplotlib.org/': None,
}
+numpydoc_show_class_members = False
if not on_rtd:
autosummary_generate = glob.glob("reference/api/api.rst")
diff -r abf5a8eff1b2d0cd776a41a33e5d3f3d25232ecc -r aa29bc66673a573078c58dee9a9ab1e266053d30 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
https://bitbucket.org/yt_analysis/yt/commits/9410b7a9faa4/
Changeset: 9410b7a9faa4
Branch: yt
User: xarthisius
Date: 2017-02-19 01:41:39+00:00
Summary: Revert adding numpydoc_show_class_members
Affected #: 1 file
diff -r aa29bc66673a573078c58dee9a9ab1e266053d30 -r 9410b7a9faa494f0ccf2ef559a755b402ef14068 doc/source/conf.py
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -259,6 +259,5 @@
'http://matplotlib.org/': None,
}
-numpydoc_show_class_members = False
if not on_rtd:
autosummary_generate = glob.glob("reference/api/api.rst")
https://bitbucket.org/yt_analysis/yt/commits/0423aafb8fc4/
Changeset: 0423aafb8fc4
Branch: yt
User: xarthisius
Date: 2017-02-19 03:26:04+00:00
Summary: Add title xray_emission_fields
Affected #: 1 file
diff -r 9410b7a9faa494f0ccf2ef559a755b402ef14068 -r 0423aafb8fc4918e59c0601c9264962a34fe4aa2 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
https://bitbucket.org/yt_analysis/yt/commits/c156671d859e/
Changeset: c156671d859e
Branch: yt
User: xarthisius
Date: 2017-02-19 21:15:36+00:00
Summary: Exclude extern module and tests from api docs
Affected #: 1 file
diff -r 0423aafb8fc4918e59c0601c9264962a34fe4aa2 -r c156671d859e01726816735e43f7e56636fd3cc7 doc/Makefile
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -47,7 +47,8 @@
-rm -rf _temp/*.done source/cookbook/_static/*
html:
- sphinx-apidoc -o source/reference/api/ -e ../yt
+ sphinx-apidoc -o source/reference/api/ -e ../yt ../yt/extern/* \
+ $(shell find ../yt -name "*tests*" -type d)
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
https://bitbucket.org/yt_analysis/yt/commits/1935daff4e1e/
Changeset: 1935daff4e1e
Branch: yt
User: xarthisius
Date: 2017-02-22 21:54:41+00:00
Summary: Docstring fixes
Affected #: 12 files
diff -r c156671d859e01726816735e43f7e56636fd3cc7 -r 1935daff4e1ed395ecc678509a7efc38ee9abd01 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 c156671d859e01726816735e43f7e56636fd3cc7 -r 1935daff4e1ed395ecc678509a7efc38ee9abd01 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) \
@@ -653,18 +652,29 @@
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 c156671d859e01726816735e43f7e56636fd3cc7 -r 1935daff4e1ed395ecc678509a7efc38ee9abd01 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 c156671d859e01726816735e43f7e56636fd3cc7 -r 1935daff4e1ed395ecc678509a7efc38ee9abd01 yt/data_objects/static_output.py
--- a/yt/data_objects/static_output.py
+++ b/yt/data_objects/static_output.py
@@ -1056,7 +1056,7 @@
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 c156671d859e01726816735e43f7e56636fd3cc7 -r 1935daff4e1ed395ecc678509a7efc38ee9abd01 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 c156671d859e01726816735e43f7e56636fd3cc7 -r 1935daff4e1ed395ecc678509a7efc38ee9abd01 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 c156671d859e01726816735e43f7e56636fd3cc7 -r 1935daff4e1ed395ecc678509a7efc38ee9abd01 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 c156671d859e01726816735e43f7e56636fd3cc7 -r 1935daff4e1ed395ecc678509a7efc38ee9abd01 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
diff -r c156671d859e01726816735e43f7e56636fd3cc7 -r 1935daff4e1ed395ecc678509a7efc38ee9abd01 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 c156671d859e01726816735e43f7e56636fd3cc7 -r 1935daff4e1ed395ecc678509a7efc38ee9abd01 yt/utilities/spatial/__init__.py
--- a/yt/utilities/spatial/__init__.py
+++ b/yt/utilities/spatial/__init__.py
@@ -6,7 +6,6 @@
Nearest-neighbor queries:
.. autosummary::
- :toctree: generated/
KDTree -- class for efficient nearest-neighbor queries
cKDTree -- class for efficient nearest-neighbor queries (faster impl.)
@@ -15,7 +14,6 @@
Delaunay triangulation:
.. autosummary::
- :toctree: generated/
Delaunay
tsearch
diff -r c156671d859e01726816735e43f7e56636fd3cc7 -r 1935daff4e1ed395ecc678509a7efc38ee9abd01 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.
diff -r c156671d859e01726816735e43f7e56636fd3cc7 -r 1935daff4e1ed395ecc678509a7efc38ee9abd01 yt/visualization/volume_rendering/scene.py
--- a/yt/visualization/volume_rendering/scene.py
+++ b/yt/visualization/volume_rendering/scene.py
@@ -795,7 +795,7 @@
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
https://bitbucket.org/yt_analysis/yt/commits/814a908571fe/
Changeset: 814a908571fe
Branch: yt
User: xarthisius
Date: 2017-02-23 14:51:33+00:00
Summary: Don't build api docs for voropp
Affected #: 1 file
diff -r 1935daff4e1ed395ecc678509a7efc38ee9abd01 -r 814a908571fe207dc6ecdc5dd3b766939f8a6c51 doc/Makefile
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -48,7 +48,7 @@
html:
sphinx-apidoc -o source/reference/api/ -e ../yt ../yt/extern/* \
- $(shell find ../yt -name "*tests*" -type d)
+ $(shell find ../yt -name "*tests*" -type d) ../yt/utilities/voropp*
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
https://bitbucket.org/yt_analysis/yt/commits/79f348062569/
Changeset: 79f348062569
Branch: yt
User: xarthisius
Date: 2017-02-23 15:45:12+00:00
Summary: More docs fixes
Affected #: 14 files
diff -r 814a908571fe207dc6ecdc5dd3b766939f8a6c51 -r 79f34806256933803bc396bf8231adcdf2ea468d 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
@@ -613,15 +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,
@@ -633,7 +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
@@ -641,13 +641,13 @@
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):
@@ -818,7 +818,7 @@
Parameters
----------
kk : float
- Wavenumber in h Mpc^-1 */
+ Wavenumber in h Mpc^-1
Returns
-------
diff -r 814a908571fe207dc6ecdc5dd3b766939f8a6c51 -r 79f34806256933803bc396bf8231adcdf2ea468d 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 814a908571fe207dc6ecdc5dd3b766939f8a6c51 -r 79f34806256933803bc396bf8231adcdf2ea468d yt/frontends/stream/data_structures.py
--- a/yt/frontends/stream/data_structures.py
+++ b/yt/frontends/stream/data_structures.py
@@ -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 814a908571fe207dc6ecdc5dd3b766939f8a6c51 -r 79f34806256933803bc396bf8231adcdf2ea468d 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 814a908571fe207dc6ecdc5dd3b766939f8a6c51 -r 79f34806256933803bc396bf8231adcdf2ea468d 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
+"""``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
@@ -96,33 +96,33 @@
executed exactly the same on all of the MPI ranks. For example,
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:
-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.
@@ -132,64 +132,64 @@
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()
+ # encapsulate the rank-asymmetric code in a function
+ def f():
+ if mpi.rank == 0:
+ doOneThing()
+ else:
+ doSomethingElse()
-# 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()
+ # 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.
+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 814a908571fe207dc6ecdc5dd3b766939f8a6c51 -r 79f34806256933803bc396bf8231adcdf2ea468d 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 814a908571fe207dc6ecdc5dd3b766939f8a6c51 -r 79f34806256933803bc396bf8231adcdf2ea468d 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 814a908571fe207dc6ecdc5dd3b766939f8a6c51 -r 79f34806256933803bc396bf8231adcdf2ea468d yt/utilities/math_utils.py
--- a/yt/utilities/math_utils.py
+++ b/yt/utilities/math_utils.py
@@ -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 814a908571fe207dc6ecdc5dd3b766939f8a6c51 -r 79f34806256933803bc396bf8231adcdf2ea468d 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 814a908571fe207dc6ecdc5dd3b766939f8a6c51 -r 79f34806256933803bc396bf8231adcdf2ea468d 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
----------
diff -r 814a908571fe207dc6ecdc5dd3b766939f8a6c51 -r 79f34806256933803bc396bf8231adcdf2ea468d yt/utilities/spatial/__init__.py
--- a/yt/utilities/spatial/__init__.py
+++ b/yt/utilities/spatial/__init__.py
@@ -1,5 +1,4 @@
"""
-=============================================================
Spatial algorithms and data structures (:mod:`scipy.spatial`)
=============================================================
diff -r 814a908571fe207dc6ecdc5dd3b766939f8a6c51 -r 79f34806256933803bc396bf8231adcdf2ea468d 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 814a908571fe207dc6ecdc5dd3b766939f8a6c51 -r 79f34806256933803bc396bf8231adcdf2ea468d yt/utilities/spatial/distance.py
--- a/yt/utilities/spatial/distance.py
+++ b/yt/utilities/spatial/distance.py
@@ -380,9 +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::
@@ -396,9 +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
-------
@@ -414,9 +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::
@@ -430,9 +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
-------
@@ -915,9 +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
@@ -969,7 +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')``
@@ -1358,49 +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.
"""
@@ -1484,7 +1480,7 @@
Parameters
----------
- D : ndarray
+ D : `~np.ndarray`
The candidate object to test for validity.
tol : double
The distance matrix should be symmetric. tol is the maximum
@@ -1747,7 +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 814a908571fe207dc6ecdc5dd3b766939f8a6c51 -r 79f34806256933803bc396bf8231adcdf2ea468d 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
https://bitbucket.org/yt_analysis/yt/commits/1aaa20bf1356/
Changeset: 1aaa20bf1356
Branch: yt
User: xarthisius
Date: 2017-02-23 17:25:56+00:00
Summary: Fix docs issues with MutableAttribute
Affected #: 1 file
diff -r 79f34806256933803bc396bf8231adcdf2ea468d -r 1aaa20bf135687742555e66f571b67b0e9dc3dd3 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()
https://bitbucket.org/yt_analysis/yt/commits/c20e478b0d26/
Changeset: c20e478b0d26
Branch: yt
User: xarthisius
Date: 2017-02-23 17:50:29+00:00
Summary: More docsting fixes
Affected #: 5 files
diff -r 1aaa20bf135687742555e66f571b67b0e9dc3dd3 -r c20e478b0d2679173a3008d87eb46adb031ad6dd 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 1aaa20bf135687742555e66f571b67b0e9dc3dd3 -r c20e478b0d2679173a3008d87eb46adb031ad6dd yt/pmods.py
--- a/yt/pmods.py
+++ b/yt/pmods.py
@@ -80,7 +80,7 @@
# purposes.
"""``MPI_Import`` defines an mpi-aware import hook. The standard use of
-this module is as follows:
+this module is as follows::
from MPI_Import import mpi_import
with mpi_import():
@@ -94,7 +94,7 @@
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
@@ -117,7 +117,7 @@
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")
@@ -130,7 +130,7 @@
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:
+Here is an example showing the use of this feature::
# encapsulate the rank-asymmetric code in a function
def f():
@@ -172,7 +172,7 @@
* 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:
+ be replaced with the following wrapper::
from mpi4py import MPI
class mpi(object):
diff -r 1aaa20bf135687742555e66f571b67b0e9dc3dd3 -r c20e478b0d2679173a3008d87eb46adb031ad6dd yt/utilities/spatial/__init__.py
--- a/yt/utilities/spatial/__init__.py
+++ b/yt/utilities/spatial/__init__.py
@@ -1,6 +1,5 @@
"""
Spatial algorithms and data structures (:mod:`scipy.spatial`)
-=============================================================
Nearest-neighbor queries:
diff -r 1aaa20bf135687742555e66f571b67b0e9dc3dd3 -r c20e478b0d2679173a3008d87eb46adb031ad6dd yt/utilities/spatial/distance.py
--- a/yt/utilities/spatial/distance.py
+++ b/yt/utilities/spatial/distance.py
@@ -917,7 +917,7 @@
n-dimensional space. Returns a condensed distance matrix Y. For
each ``i`` and ``j`` (where ``i < j < n``), the
metric ``dist(u=X[i], v=X[j])`` is computed and stored in the
- ``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
@@ -1480,9 +1480,9 @@
Parameters
----------
- D : `~np.ndarray`
+ 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
diff -r 1aaa20bf135687742555e66f571b67b0e9dc3dd3 -r c20e478b0d2679173a3008d87eb46adb031ad6dd yt/visualization/plot_window.py
--- a/yt/visualization/plot_window.py
+++ b/yt/visualization/plot_window.py
@@ -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
https://bitbucket.org/yt_analysis/yt/commits/8597f7836026/
Changeset: 8597f7836026
Branch: yt
User: xarthisius
Date: 2017-02-23 19:07:13+00:00
Summary: More fixes
Affected #: 7 files
diff -r c20e478b0d2679173a3008d87eb46adb031ad6dd -r 8597f78360266542620a700455b85c90567c47e6 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 c20e478b0d2679173a3008d87eb46adb031ad6dd -r 8597f78360266542620a700455b85c90567c47e6 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`
diff -r c20e478b0d2679173a3008d87eb46adb031ad6dd -r 8597f78360266542620a700455b85c90567c47e6 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 c20e478b0d2679173a3008d87eb46adb031ad6dd -r 8597f78360266542620a700455b85c90567c47e6 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 c20e478b0d2679173a3008d87eb46adb031ad6dd -r 8597f78360266542620a700455b85c90567c47e6 yt/utilities/sdf.py
--- a/yt/utilities/sdf.py
+++ b/yt/utilities/sdf.py
@@ -1269,11 +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 c20e478b0d2679173a3008d87eb46adb031ad6dd -r 8597f78360266542620a700455b85c90567c47e6 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 c20e478b0d2679173a3008d87eb46adb031ad6dd -r 8597f78360266542620a700455b85c90567c47e6 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
https://bitbucket.org/yt_analysis/yt/commits/7b25d38d9c13/
Changeset: 7b25d38d9c13
Branch: yt
User: xarthisius
Date: 2017-03-04 19:39:30+00:00
Summary: Show inherited members
Affected #: 1 file
diff -r 8597f78360266542620a700455b85c90567c47e6 -r 7b25d38d9c1366fa42bbadc032004b4e03409fb3 doc/Makefile
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -49,6 +49,7 @@
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."
https://bitbucket.org/yt_analysis/yt/commits/37fdfb212c3c/
Changeset: 37fdfb212c3c
Branch: yt
User: xarthisius
Date: 2017-03-04 21:43:40+00:00
Summary: Add simple profiling for :python-script: directive
Affected #: 1 file
diff -r 7b25d38d9c1366fa42bbadc032004b4e03409fb3 -r 37fdfb212c3ccccb7df32632f0369968b06b6ec5 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)
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/
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