[yt-svn] commit/yt: xarthisius: Merged in ngoldbaum/yt (pull request #1745)
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Mon Sep 14 11:34:46 PDT 2015
1 new commit in yt:
https://bitbucket.org/yt_analysis/yt/commits/4c33cffa7ba9/
Changeset: 4c33cffa7ba9
Branch: yt
User: xarthisius
Date: 2015-09-14 18:34:33+00:00
Summary: Merged in ngoldbaum/yt (pull request #1745)
Linting yt.fields
Affected #: 20 files
diff -r 1e1fc6fb63d4dd5fc7183a3900902a0c0638ae9a -r 4c33cffa7ba96675a2cacaecf95a20eb15067413 yt/fields/angular_momentum.py
--- a/yt/fields/angular_momentum.py
+++ b/yt/fields/angular_momentum.py
@@ -15,12 +15,7 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
-import types
import numpy as np
-import inspect
-import copy
-
-from yt.units.yt_array import YTArray
from .derived_field import \
ValidateParameter
@@ -29,8 +24,8 @@
register_field_plugin
from .vector_operations import \
- create_magnitude_field
-
+ create_magnitude_field
+
from yt.utilities.lib.geometry_utils import \
obtain_rvec, obtain_rv_vec
@@ -78,7 +73,7 @@
create_magnitude_field(registry, "specific_angular_momentum",
"cm**2 / s", ftype=ftype)
-
+
def _angular_momentum_x(field, data):
return data[ftype, "cell_mass"] \
* data[ftype, "specific_angular_momentum_x"]
@@ -105,4 +100,3 @@
create_magnitude_field(registry, "angular_momentum",
"g * cm**2 / s", ftype=ftype)
-
diff -r 1e1fc6fb63d4dd5fc7183a3900902a0c0638ae9a -r 4c33cffa7ba96675a2cacaecf95a20eb15067413 yt/fields/astro_fields.py
--- a/yt/fields/astro_fields.py
+++ b/yt/fields/astro_fields.py
@@ -16,8 +16,7 @@
import numpy as np
from .derived_field import \
- ValidateParameter, \
- ValidateSpatial
+ ValidateParameter
from .field_exceptions import \
NeedsParameter
from .field_plugin_registry import \
@@ -30,7 +29,7 @@
clight, \
kboltz, \
G
-
+
@register_field_plugin
def setup_astro_fields(registry, ftype = "gas", slice_info = None):
# slice_info would be the left, the right, and the factor.
@@ -45,7 +44,7 @@
div_fac = 2.0
else:
sl_left, sl_right, div_fac = slice_info
-
+
def _dynamical_time(field, data):
"""
sqrt(3 pi / (16 G rho))
@@ -71,7 +70,7 @@
def _chandra_emissivity(field, data):
logT0 = np.log10(data[ftype, "temperature"].to_ndarray().astype(np.float64)) - 7
- # we get rid of the units here since this is a fit and not an
+ # we get rid of the units here since this is a fit and not an
# analytical expression
return data.ds.arr(data[ftype, "number_density"].to_ndarray().astype(np.float64)**2
* (10**(- 0.0103 * logT0**8 + 0.0417 * logT0**7
@@ -91,7 +90,7 @@
registry.add_field((ftype, "chandra_emissivity"),
function=_chandra_emissivity,
units="") # add correct units here
-
+
def _xray_emissivity(field, data):
# old scaling coefficient was 2.168e60
return data.ds.arr(data[ftype, "density"].to_ndarray().astype(np.float64)**2
@@ -110,7 +109,7 @@
registry.add_field((ftype,"mazzotta_weighting"),
function=_mazzotta_weighting,
units="keV**-0.25*cm**-6")
-
+
def _sz_kinetic(field, data):
scale = 0.88 * sigma_thompson / mh / clight
vel_axis = data.get_field_parameter("axis")
diff -r 1e1fc6fb63d4dd5fc7183a3900902a0c0638ae9a -r 4c33cffa7ba96675a2cacaecf95a20eb15067413 yt/fields/astro_simulations.py
--- a/yt/fields/astro_simulations.py
+++ b/yt/fields/astro_simulations.py
@@ -13,7 +13,6 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
-import numpy as np
from .domain_context import DomainContext
# Here's how this all works:
diff -r 1e1fc6fb63d4dd5fc7183a3900902a0c0638ae9a -r 4c33cffa7ba96675a2cacaecf95a20eb15067413 yt/fields/cosmology_fields.py
--- a/yt/fields/cosmology_fields.py
+++ b/yt/fields/cosmology_fields.py
@@ -14,21 +14,17 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
-import numpy as np
+from .derived_field import \
+ ValidateParameter
+from .field_exceptions import \
+ NeedsConfiguration, \
+ NeedsParameter
+from .field_plugin_registry import \
+ register_field_plugin
-from .derived_field import \
- ValidateParameter
-from .field_exceptions import \
- NeedsConfiguration, \
- NeedsParameter
-from .field_plugin_registry import \
- register_field_plugin
+from yt.utilities.physical_constants import \
+ speed_of_light_cgs
-from yt.utilities.cosmology import \
- Cosmology
-from yt.utilities.physical_constants import \
- speed_of_light_cgs
-
@register_field_plugin
def setup_cosmology_fields(registry, ftype = "gas", slice_info = None):
# slice_info would be the left, the right, and the factor.
@@ -49,7 +45,7 @@
data[ftype, "dark_matter_density"]
registry.add_field((ftype, "matter_density"),
- function=_matter_density,
+ function=_matter_density,
units="g/cm**3")
def _matter_mass(field, data):
@@ -67,7 +63,7 @@
co = data.ds.cosmology
return data[ftype, "matter_density"] / \
co.critical_density(data.ds.current_redshift)
-
+
registry.add_field((ftype, "overdensity"),
function=_overdensity,
units="")
@@ -116,7 +112,7 @@
function=_virial_radius_fraction,
validators=[ValidateParameter("virial_radius")],
units="")
-
+
# Weak lensing convergence.
# Eqn 4 of Metzler, White, & Loken (2001, ApJ, 547, 560).
# This needs to be checked for accuracy.
@@ -127,7 +123,7 @@
co = data.ds.cosmology
observer_redshift = data.get_field_parameter('observer_redshift')
source_redshift = data.get_field_parameter('source_redshift')
-
+
# observer to lens
dl = co.angular_diameter_distance(observer_redshift, data.ds.current_redshift)
# observer to source
@@ -135,11 +131,11 @@
# lens to source
dls = co.angular_diameter_distance(data.ds.current_redshift, source_redshift)
- # removed the factor of 1 / a to account for the fact that we are projecting
+ # removed the factor of 1 / a to account for the fact that we are projecting
# with a proper distance.
return (1.5 * (co.hubble_constant / speed_of_light_cgs)**2 * (dl * dls / ds) * \
data[ftype, "matter_overdensity"]).in_units("1/cm")
-
+
registry.add_field((ftype, "weak_lensing_convergence"),
function=_weak_lensing_convergence,
units="1/cm",
diff -r 1e1fc6fb63d4dd5fc7183a3900902a0c0638ae9a -r 4c33cffa7ba96675a2cacaecf95a20eb15067413 yt/fields/derived_field.py
--- a/yt/fields/derived_field.py
+++ b/yt/fields/derived_field.py
@@ -16,10 +16,7 @@
from yt.funcs import \
ensure_list
-from yt.units.yt_array import \
- YTArray
from .field_exceptions import \
- ValidationException, \
NeedsGridType, \
NeedsOriginalGrid, \
NeedsDataField, \
@@ -30,15 +27,9 @@
FieldDetector
from yt.units.unit_object import \
Unit
+from yt.utilities.exceptions import \
+ YTFieldNotFound
-def derived_field(**kwargs):
- def inner_decorator(function):
- if 'name' not in kwargs:
- kwargs['name'] = function.__name__
- kwargs['function'] = function
- add_field(**kwargs)
- return function
- return inner_decorator
def TranslationFunc(field_name):
def _TranslationFunc(field, data):
@@ -48,7 +39,7 @@
def NullFunc(field, data):
raise YTFieldNotFound(field.name)
-
+
class DerivedField(object):
"""
This is the base class used to describe a cell-by-cell derived field.
@@ -178,7 +169,7 @@
def __call__(self, data):
""" Return the value of the field in a given *data* object. """
- ii = self.check_available(data)
+ self.check_available(data)
original_fields = data.keys() # Copy
if self._function is NullFunc:
raise RuntimeError(
diff -r 1e1fc6fb63d4dd5fc7183a3900902a0c0638ae9a -r 4c33cffa7ba96675a2cacaecf95a20eb15067413 yt/fields/domain_context.py
--- a/yt/fields/domain_context.py
+++ b/yt/fields/domain_context.py
@@ -14,8 +14,6 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
-import numpy as np
-
domain_context_registry = {}
class DomainContext(object):
diff -r 1e1fc6fb63d4dd5fc7183a3900902a0c0638ae9a -r 4c33cffa7ba96675a2cacaecf95a20eb15067413 yt/fields/field_detector.py
--- a/yt/fields/field_detector.py
+++ b/yt/fields/field_detector.py
@@ -15,16 +15,9 @@
import numpy as np
from collections import defaultdict
-from yt.units.unit_object import Unit
from yt.units.yt_array import YTArray
from .field_exceptions import \
- ValidationException, \
- NeedsGridType, \
- NeedsOriginalGrid, \
- NeedsDataField, \
- NeedsProperty, \
- NeedsParameter, \
- FieldUnitsError
+ NeedsGridType
class FieldDetector(defaultdict):
Level = 1
@@ -87,27 +80,18 @@
return arr.reshape(self.ActiveDimensions, order="C")
def __missing__(self, item):
- if hasattr(self.ds, "field_info"):
- if not isinstance(item, tuple):
- field = ("unknown", item)
- finfo = self.ds._get_field_info(*field)
- #mylog.debug("Guessing field %s is %s", item, finfo.name)
- else:
- field = item
- finfo = self.ds._get_field_info(*field)
- # For those cases where we are guessing the field type, we will
- # need to re-update -- otherwise, our item will always not have the
- # field type. This can lead to, for instance, "unknown" particle
- # types not getting correctly identified.
- # Note that the *only* way this works is if we also fix our field
- # dependencies during checking. Bug #627 talks about this.
- item = self.ds._last_freq
+ if not isinstance(item, tuple):
+ field = ("unknown", item)
else:
- FI = getattr(self.ds, "field_info", FieldInfo)
- if item in FI:
- finfo = FI[item]
- else:
- finfo = None
+ field = item
+ finfo = self.ds._get_field_info(*field)
+ # For those cases where we are guessing the field type, we will
+ # need to re-update -- otherwise, our item will always not have the
+ # field type. This can lead to, for instance, "unknown" particle
+ # types not getting correctly identified.
+ # Note that the *only* way this works is if we also fix our field
+ # dependencies during checking. Bug #627 talks about this.
+ item = self.ds._last_freq
if finfo is not None and finfo._function.__name__ != 'NullFunc':
try:
vv = finfo(self)
@@ -171,10 +155,7 @@
def _read_data(self, field_name):
self.requested.append(field_name)
- if hasattr(self.ds, "field_info"):
- finfo = self.ds._get_field_info(*field_name)
- else:
- finfo = FieldInfo[field_name]
+ finfo = self.ds._get_field_info(*field_name)
if finfo.particle_type:
self.requested.append(field_name)
return np.ones(self.NumberOfParticles)
diff -r 1e1fc6fb63d4dd5fc7183a3900902a0c0638ae9a -r 4c33cffa7ba96675a2cacaecf95a20eb15067413 yt/fields/field_exceptions.py
--- a/yt/fields/field_exceptions.py
+++ b/yt/fields/field_exceptions.py
@@ -13,7 +13,6 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
-import numpy as np
class ValidationException(Exception):
pass
diff -r 1e1fc6fb63d4dd5fc7183a3900902a0c0638ae9a -r 4c33cffa7ba96675a2cacaecf95a20eb15067413 yt/fields/field_functions.py
--- a/yt/fields/field_functions.py
+++ b/yt/fields/field_functions.py
@@ -32,7 +32,7 @@
# it from a cm**2 array.
np.subtract(data["%s%s" % (field_prefix, ax)].in_units("cm"),
center[i], r)
- if data.ds.periodicity[i] == True:
+ if data.ds.periodicity[i] is True:
np.abs(r, r)
np.subtract(r, DW[i], rdw)
np.abs(rdw, rdw)
diff -r 1e1fc6fb63d4dd5fc7183a3900902a0c0638ae9a -r 4c33cffa7ba96675a2cacaecf95a20eb15067413 yt/fields/field_plugin_registry.py
--- a/yt/fields/field_plugin_registry.py
+++ b/yt/fields/field_plugin_registry.py
@@ -13,8 +13,6 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
-import numpy as np
-
field_plugins = {}
def register_field_plugin(func):
diff -r 1e1fc6fb63d4dd5fc7183a3900902a0c0638ae9a -r 4c33cffa7ba96675a2cacaecf95a20eb15067413 yt/fields/fluid_fields.py
--- a/yt/fields/fluid_fields.py
+++ b/yt/fields/fluid_fields.py
@@ -15,20 +15,16 @@
import numpy as np
-from yt.funcs import \
- just_one
-
from .derived_field import \
- ValidateParameter, \
ValidateSpatial
from .field_plugin_registry import \
register_field_plugin
from .vector_operations import \
- create_averaged_field, \
- create_magnitude_field, \
- create_vector_fields
+ create_averaged_field, \
+ create_magnitude_field, \
+ create_vector_fields
from yt.utilities.physical_constants import \
mh, \
@@ -37,20 +33,6 @@
from yt.utilities.physical_ratios import \
metallicity_sun
-from yt.units.yt_array import \
- YTArray
-
-from yt.utilities.math_utils import \
- get_sph_r_component, \
- get_sph_theta_component, \
- get_sph_phi_component, \
- get_cyl_r_component, \
- get_cyl_z_component, \
- get_cyl_theta_component, \
- get_cyl_r, get_cyl_theta, \
- get_cyl_z, get_sph_r, \
- get_sph_theta, get_sph_phi, \
- periodic_dist, euclidean_dist
@register_field_plugin
def setup_fluid_fields(registry, ftype = "gas", slice_info = None):
diff -r 1e1fc6fb63d4dd5fc7183a3900902a0c0638ae9a -r 4c33cffa7ba96675a2cacaecf95a20eb15067413 yt/fields/fluid_vector_fields.py
--- a/yt/fields/fluid_vector_fields.py
+++ b/yt/fields/fluid_vector_fields.py
@@ -16,10 +16,7 @@
import numpy as np
from yt.fields.derived_field import \
- ValidateGridType, \
- ValidateParameter, \
- ValidateSpatial, \
- NeedsParameter
+ ValidateSpatial
from .field_plugin_registry import \
register_field_plugin
@@ -28,8 +25,8 @@
just_one
from .vector_operations import \
- create_magnitude_field, \
- create_squared_field
+ create_magnitude_field, \
+ create_squared_field
@register_field_plugin
def setup_fluid_vector_fields(registry, ftype = "gas", slice_info = None):
diff -r 1e1fc6fb63d4dd5fc7183a3900902a0c0638ae9a -r 4c33cffa7ba96675a2cacaecf95a20eb15067413 yt/fields/interpolated_fields.py
--- a/yt/fields/interpolated_fields.py
+++ b/yt/fields/interpolated_fields.py
@@ -13,8 +13,6 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
-import numpy as np
-
from yt.fields.local_fields import add_field
from yt.utilities.linear_interpolators import \
diff -r 1e1fc6fb63d4dd5fc7183a3900902a0c0638ae9a -r 4c33cffa7ba96675a2cacaecf95a20eb15067413 yt/fields/local_fields.py
--- a/yt/fields/local_fields.py
+++ b/yt/fields/local_fields.py
@@ -13,8 +13,6 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
-import numpy as np
-
from yt.utilities.logger import \
ytLogger as mylog
diff -r 1e1fc6fb63d4dd5fc7183a3900902a0c0638ae9a -r 4c33cffa7ba96675a2cacaecf95a20eb15067413 yt/fields/magnetic_field.py
--- a/yt/fields/magnetic_field.py
+++ b/yt/fields/magnetic_field.py
@@ -15,11 +15,6 @@
import numpy as np
-from yt.units.yt_array import YTArray
-from yt.utilities.lib.misc_utilities import \
- obtain_rvec, obtain_rv_vec
-from yt.utilities.math_utils import resize_vector
-from yt.utilities.cosmology import Cosmology
from yt.fields.derived_field import \
ValidateParameter
@@ -27,16 +22,8 @@
register_field_plugin
from yt.utilities.math_utils import \
- get_sph_r_component, \
get_sph_theta_component, \
- get_sph_phi_component, \
- get_cyl_r_component, \
- get_cyl_z_component, \
- get_cyl_theta_component, \
- get_cyl_r, get_cyl_theta, \
- get_cyl_z, get_sph_r, \
- get_sph_theta, get_sph_phi, \
- periodic_dist, euclidean_dist
+ get_sph_phi_component
@register_field_plugin
def setup_magnetic_field_fields(registry, ftype = "gas", slice_info = None):
diff -r 1e1fc6fb63d4dd5fc7183a3900902a0c0638ae9a -r 4c33cffa7ba96675a2cacaecf95a20eb15067413 yt/fields/my_plugin_fields.py
--- a/yt/fields/my_plugin_fields.py
+++ b/yt/fields/my_plugin_fields.py
@@ -13,8 +13,6 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
-import numpy as np
-
from .field_plugin_registry import \
register_field_plugin
diff -r 1e1fc6fb63d4dd5fc7183a3900902a0c0638ae9a -r 4c33cffa7ba96675a2cacaecf95a20eb15067413 yt/fields/particle_fields.py
--- a/yt/fields/particle_fields.py
+++ b/yt/fields/particle_fields.py
@@ -16,8 +16,6 @@
import numpy as np
-from yt.funcs import *
-from yt.units.yt_array import YTArray
from yt.fields.derived_field import \
ValidateParameter, \
ValidateSpatial
@@ -125,7 +123,7 @@
def particle_density(field, data):
pos = data[ptype, coord_name].convert_to_units("code_length")
mass = data[ptype, mass_name].convert_to_units("code_mass")
- d = data.deposit(pos, [data[ptype, mass_name]], method = "sum")
+ d = data.deposit(pos, [mass], method = "sum")
d = data.ds.arr(d, "code_mass")
d /= data["index", "cell_volume"]
return d
@@ -827,7 +825,7 @@
field_name = (ptype, "smoothed_density")
else:
field_name = (ptype, "%s_smoothed_density" % (kernel_name))
- field_units = registry[ptype, mass_name].units
+
def _nth_neighbor(field, data):
pos = data[ptype, coord_name]
pos.convert_to_units("code_length")
diff -r 1e1fc6fb63d4dd5fc7183a3900902a0c0638ae9a -r 4c33cffa7ba96675a2cacaecf95a20eb15067413 yt/fields/setup.py
--- a/yt/fields/setup.py
+++ b/yt/fields/setup.py
@@ -1,8 +1,4 @@
#!/usr/bin/env python
-import setuptools
-import os
-import sys
-import os.path
def configuration(parent_package='', top_path=None):
diff -r 1e1fc6fb63d4dd5fc7183a3900902a0c0638ae9a -r 4c33cffa7ba96675a2cacaecf95a20eb15067413 yt/fields/species_fields.py
--- a/yt/fields/species_fields.py
+++ b/yt/fields/species_fields.py
@@ -17,12 +17,10 @@
import re
from yt.utilities.physical_constants import \
- mh, \
- mass_sun_cgs, \
amu_cgs
from yt.utilities.physical_ratios import \
primordial_H_mass_fraction
-from yt.funcs import *
+
from yt.utilities.chemical_formulas import \
ChemicalFormula
from .field_plugin_registry import \
diff -r 1e1fc6fb63d4dd5fc7183a3900902a0c0638ae9a -r 4c33cffa7ba96675a2cacaecf95a20eb15067413 yt/fields/tests/test_fields.py
--- a/yt/fields/tests/test_fields.py
+++ b/yt/fields/tests/test_fields.py
@@ -1,13 +1,20 @@
-from yt.testing import *
import numpy as np
+
+from yt.testing import \
+ fake_random_ds, \
+ assert_equal, \
+ assert_array_almost_equal_nulp, \
+ assert_array_equal, \
+ assert_raises
from yt.utilities.cosmology import \
- Cosmology
-from yt.utilities.definitions import \
- mpc_conversion, sec_conversion
+ Cosmology
from yt.frontends.stream.fields import \
StreamFieldInfo
from yt.units.yt_array import \
- YTArray, YTQuantity
+ YTArray, YTQuantity
+from yt.utilities.exceptions import \
+ YTFieldUnitError, \
+ YTFieldUnitParseError
def setup():
global base_ds
@@ -88,19 +95,6 @@
return field
return field[1]
-def _expand_field(field):
- if isinstance(field, tuple):
- return field
- if field in KnownStreamFields:
- fi = KnownStreamFields[field]
- if fi.particle_type:
- return ("all", field)
- else:
- return ("gas", field)
- # Otherwise, we just guess.
- if "particle" in field:
- return ("all", field)
- return ("gas", field)
class TestFieldAccess(object):
description = None
Repository URL: https://bitbucket.org/yt_analysis/yt/
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