[yt-svn] commit/yt: chummels: Merged in ngoldbaum/yt (pull request #1691)
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Thu Aug 20 09:41:35 PDT 2015
1 new commit in yt:
https://bitbucket.org/yt_analysis/yt/commits/4bfdb0ddccdb/
Changeset: 4bfdb0ddccdb
Branch: yt
User: chummels
Date: 2015-08-20 16:41:21+00:00
Summary: Merged in ngoldbaum/yt (pull request #1691)
Codebase linting: analysis modules and flake8 rules
Affected #: 47 files
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 setup.cfg
--- a/setup.cfg
+++ b/setup.cfg
@@ -7,3 +7,9 @@
where=yt
exclude=answer_testing
with-xunit=1
+
+[flake8]
+# if we include api.py files, we get tons of spurious "imported but unused" errors
+exclude = */api.py,*/__config__.py,yt/visualization/_mpl_imports.py
+max-line-length=999
+ignore = E111,E121,E122,E123,E124,E125,E126,E127,E128,E129,E131,E201,E202,E211,E221,E222,E228,E241,E301,E203,E225,E226,E231,E251,E261,E262,E265,E302,E303,E401,E502,E701,E703,W291,W293,W391
\ No newline at end of file
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/absorption_spectrum/absorption_line.py
--- a/yt/analysis_modules/absorption_spectrum/absorption_line.py
+++ b/yt/analysis_modules/absorption_spectrum/absorption_line.py
@@ -70,15 +70,6 @@
x = np.asarray(u).astype(np.float64)
y = np.asarray(a).astype(np.float64)
- w = np.array([0.462243670, 0.286675505, 0.109017206,
- 0.0248105209, 0.00324377334, 0.000228338636,
- 7.80255648e-6, 1.08606937e-7, 4.39934099e-10,
- 2.22939365e-13])
-
- t = np.array([0.245340708, 0.737473729, 1.23407622, 1.73853771,
- 2.25497400, 2.78880606, 3.34785457, 3.94476404,
- 4.60368245, 5.38748089])
-
# Hummer's Chebyshev Coefficients
c = ( 0.1999999999972224, -0.1840000000029998, 0.1558399999965025,
-0.1216640000043988, 0.0877081599940391, -0.0585141248086907,
@@ -195,7 +186,6 @@
## conversions
nu1 = speed_of_light_cgs / lam1 # line freq in Hz
nudop = v_doppler / speed_of_light_cgs * nu1 # doppler width in Hz
- lamdop = v_doppler / speed_of_light_cgs * lam1 # doppler width in Ang
## create wavelength
if lambda_bins is None:
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
--- a/yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
+++ b/yt/analysis_modules/absorption_spectrum/absorption_spectrum_fit.py
@@ -141,7 +141,7 @@
if flag and species=='lya' and min(yDatBounded)<.1:
newLinesP=_large_flag_fit(xBounded,yDatBounded,
yFitBounded,z,speciesDict,
- minSize,minError)
+ fitLim,minError)
if np.size(newLinesP)> 0:
@@ -226,7 +226,7 @@
"""
#Setup initial line guesses
- if initP==None: #Regular fit
+ if initP is None: #Regular fit
initP = [0,0,0]
if min(yDat)<.01: #Large lines get larger initial guess
initP[0] = speciesDict['init_N']*10**2
@@ -252,7 +252,7 @@
#Values to proceed through first run
errSq,prevErrSq,prevLinesP=1,10*len(x),[]
- if errBound == None:
+ if errBound is None:
errBound = len(yDat)*(max(1-yDat)*1E-2)**2
else:
errBound = errBound*len(yDat)
@@ -548,7 +548,7 @@
lb = _get_bounds(p[2],b,wl,x0,xRes)
xb,yb=x[lb[0]:lb[1]],y[lb[0]:lb[1]]
- if errBound == None:
+ if errBound is None:
errBound = 10*len(yb)*(max(1-yb)*1E-2)**2
else:
errBound = 10*errBound*len(yb)
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/cosmological_observation/cosmology_splice.py
--- a/yt/analysis_modules/cosmological_observation/cosmology_splice.py
+++ b/yt/analysis_modules/cosmological_observation/cosmology_splice.py
@@ -14,10 +14,11 @@
#-----------------------------------------------------------------------------
import numpy as np
+import os
from yt.convenience import \
simulation
-from yt.funcs import *
+from yt.funcs import mylog
from yt.utilities.cosmology import \
Cosmology
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/cosmological_observation/light_cone/light_cone.py
--- a/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py
+++ b/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py
@@ -24,8 +24,6 @@
CosmologySplice
from yt.convenience import \
load
-from yt.utilities.cosmology import \
- Cosmology
from yt.utilities.parallel_tools.parallel_analysis_interface import \
parallel_objects, \
parallel_root_only
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/cosmological_observation/light_cone/setup.py
--- a/yt/analysis_modules/cosmological_observation/light_cone/setup.py
+++ b/yt/analysis_modules/cosmological_observation/light_cone/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 deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/cosmological_observation/light_ray/light_ray.py
--- a/yt/analysis_modules/cosmological_observation/light_ray/light_ray.py
+++ b/yt/analysis_modules/cosmological_observation/light_ray/light_ray.py
@@ -13,7 +13,6 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
-import copy
import h5py
import numpy as np
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/cosmological_observation/light_ray/setup.py
--- a/yt/analysis_modules/cosmological_observation/light_ray/setup.py
+++ b/yt/analysis_modules/cosmological_observation/light_ray/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 deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/cosmological_observation/setup.py
--- a/yt/analysis_modules/cosmological_observation/setup.py
+++ b/yt/analysis_modules/cosmological_observation/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 deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/halo_analysis/enzofof_merger_tree.py
--- a/yt/analysis_modules/halo_analysis/enzofof_merger_tree.py
+++ b/yt/analysis_modules/halo_analysis/enzofof_merger_tree.py
@@ -35,13 +35,13 @@
import numpy as np
import h5py
-import time
-import pdb
+import glob
+import os
+
from yt.extern.six.moves import cPickle
-import glob
+from yt.extern.pykdtree import KDTree
+from yt.funcs import mylog, get_pbar
-from yt.funcs import *
-from yt.extern.pykdtree import KDTree
import yt.extern.pydot as pydot
# We don't currently use this, but we may again find a use for it in the
@@ -180,7 +180,7 @@
def calculate_parentage_fractions(self, other_catalog, radius = 0.10):
parentage_fractions = {}
- if self.halo_positions == None or other_catalog.halo_positions == None:
+ if self.halo_positions is None or other_catalog.halo_positions is None:
return parentage_fractions
mylog.debug("Ball-tree query with radius %0.3e", radius)
all_nearest = self.halo_kdtree.query_ball_tree(
@@ -320,7 +320,7 @@
for redshift in self.redshifts.values():
if redshift <= zrange[0] and redshift >= zrange[1]:
# some reverse lookup magic--assumes unique cycle/z pairs
- cycle = [key for key,value in mt.redshifts.items() \
+ cycle = [key for key,value in self.redshifts.items() \
if value == redshift][0]
del self.redshifts[cycle]
@@ -568,7 +568,7 @@
automatically. See GraphViz (e.g. "dot -v")
for a list of available output formats.
"""
- if filename == None:
+ if filename is None:
filename = "%s/tree_halo%5.5d.gv" % \
(self.FOF_directory, self.halonum)
# Create the pydot graph object.
@@ -598,7 +598,6 @@
# (lvl, br.halo_id, next_lvl, c[0], color)
#fp.write(line)
- last_level = (ii,lvl)
for ii,lvl in enumerate(sorted_lvl):
npart_max = 0
for br in self.levels[lvl]:
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/halo_analysis/halo_callbacks.py
--- a/yt/analysis_modules/halo_analysis/halo_callbacks.py
+++ b/yt/analysis_modules/halo_analysis/halo_callbacks.py
@@ -18,23 +18,22 @@
import os
from yt.analysis_modules.cosmological_observation.light_ray.light_ray import \
- periodic_distance
+ periodic_distance
from yt.data_objects.profiles import \
- create_profile
+ create_profile
from yt.units.yt_array import \
- YTArray, YTQuantity
+ YTArray
from yt.utilities.exceptions import \
- YTSphereTooSmall
+ YTSphereTooSmall
from yt.funcs import \
- ensure_list, is_root
-from yt.utilities.exceptions import YTUnitConversionError
+ ensure_list
from yt.utilities.logger import ytLogger as mylog
from yt.utilities.operator_registry import \
- OperatorRegistry
+ OperatorRegistry
from yt.utilities.parallel_tools.parallel_analysis_interface import \
parallel_root_only
from yt.visualization.profile_plotter import \
- PhasePlot
+ PhasePlot
callback_registry = OperatorRegistry()
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/halo_analysis/halo_catalog.py
--- a/yt/analysis_modules/halo_analysis/halo_catalog.py
+++ b/yt/analysis_modules/halo_analysis/halo_catalog.py
@@ -138,7 +138,7 @@
self.actions = []
# fields to be written to the halo catalog
self.quantities = []
- if not self.halos_ds is None:
+ if self.halos_ds is not None:
self.add_default_quantities()
def add_callback(self, callback, *args, **kwargs):
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/halo_analysis/halo_finding_methods.py
--- a/yt/analysis_modules/halo_analysis/halo_finding_methods.py
+++ b/yt/analysis_modules/halo_analysis/halo_finding_methods.py
@@ -17,8 +17,6 @@
from yt.analysis_modules.halo_finding.halo_objects import \
FOFHaloFinder, HOPHaloFinder
-from yt.frontends.halo_catalog.data_structures import \
- HaloCatalogDataset
from yt.frontends.stream.data_structures import \
load_particles
from yt.units.dimensions import length
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/halo_analysis/tests/test_halo_finders.py
--- a/yt/analysis_modules/halo_analysis/tests/test_halo_finders.py
+++ b/yt/analysis_modules/halo_analysis/tests/test_halo_finders.py
@@ -1,10 +1,7 @@
import os
import sys
-from yt.analysis_modules.halo_analysis.api import \
- HaloCatalog
from yt.convenience import load
-from yt.testing import *
from yt.utilities.answer_testing.framework import \
FieldValuesTest, \
requires_ds
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/halo_finding/fof/setup.py
--- a/yt/analysis_modules/halo_finding/fof/setup.py
+++ b/yt/analysis_modules/halo_finding/fof/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 deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 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
@@ -17,21 +17,15 @@
import h5py
import math
import numpy as np
-import random
-import sys
import glob
import os
import os.path as path
from functools import cmp_to_key
-from collections import defaultdict
from yt.extern.six import add_metaclass
from yt.extern.six.moves import zip as izip
from yt.config import ytcfg
from yt.funcs import mylog, ensure_dir_exists
-from yt.utilities.performance_counters import \
- time_function, \
- yt_counters
from yt.utilities.math_utils import \
get_rotation_matrix, \
periodic_dist
@@ -39,7 +33,7 @@
mass_sun_cgs, \
TINY
from yt.utilities.physical_ratios import \
- rho_crit_g_cm3_h2
+ rho_crit_g_cm3_h2
from .hop.EnzoHop import RunHOP
from .fof.EnzoFOF import RunFOF
@@ -282,7 +276,7 @@
return r.max()
def __getitem__(self, key):
- if ytcfg.getboolean("yt", "inline") == False:
+ if ytcfg.getboolean("yt", "inline") is False:
return self.data[key][self.indices]
else:
return self.data[key][self.indices]
@@ -339,8 +333,6 @@
if ('io','creation_time') in self.data.ds.field_list:
handle.create_dataset("/%s/creation_time" % gn,
data=self['creation_time'])
- n = handle["/%s" % gn]
- # set attributes on n
self._processing = False
def virial_mass(self, virial_overdensity=200., bins=300):
@@ -419,7 +411,7 @@
"""
self.virial_info(bins=bins)
over = (self.overdensity > virial_overdensity)
- if (over == True).any():
+ if over.any():
vir_bin = max(np.arange(bins + 1)[over])
return vir_bin
else:
@@ -1233,7 +1225,6 @@
fglob = path.join(basedir, 'halos_%d.*.bin' % n)
files = glob.glob(fglob)
halos = self._get_halos_binary(files)
- Jc = 1.0
length = 1.0 / ds['Mpchcm']
conv = dict(pos = np.array([length, length, length,
1, 1, 1]), # to unitary
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/halo_finding/hop/setup.py
--- a/yt/analysis_modules/halo_finding/hop/setup.py
+++ b/yt/analysis_modules/halo_finding/hop/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 deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/halo_finding/rockstar/rockstar.py
--- a/yt/analysis_modules/halo_finding/rockstar/rockstar.py
+++ b/yt/analysis_modules/halo_finding/rockstar/rockstar.py
@@ -16,23 +16,21 @@
from yt.config import ytcfg
from yt.data_objects.time_series import \
- DatasetSeries
+ DatasetSeries
from yt.funcs import \
- is_root
+ is_root, mylog
from yt.utilities.parallel_tools.parallel_analysis_interface import \
- ParallelAnalysisInterface, ProcessorPool, Communicator
-from yt.analysis_modules.halo_finding.halo_objects import * #Halos & HaloLists
+ ParallelAnalysisInterface, ProcessorPool
+from yt.analysis_modules.halo_finding.halo_objects import \
+ RockstarHaloList
from yt.utilities.exceptions import YTRockstarMultiMassNotSupported
from . import rockstar_interface
import socket
import time
-import threading
-import signal
import os
-from os import environ
-from os import mkdir
+import numpy as np
from os import path
class InlineRunner(ParallelAnalysisInterface):
@@ -202,7 +200,7 @@
mylog.info("http://adsabs.harvard.edu/abs/2013ApJ...762..109B")
ParallelAnalysisInterface.__init__(self)
# Decide how we're working.
- if ytcfg.getboolean("yt", "inline") == True:
+ if ytcfg.getboolean("yt", "inline") is True:
self.runner = InlineRunner()
else:
self.runner = StandardRunner(num_readers, num_writers)
@@ -247,8 +245,6 @@
dd = tds.all_data()
# Get DM particle mass.
- all_fields = set(tds.derived_field_list + tds.field_list)
- has_particle_type = ("particle_type" in all_fields)
particle_mass = self.particle_mass
if particle_mass is None:
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/halo_finding/rockstar/setup.py
--- a/yt/analysis_modules/halo_finding/rockstar/setup.py
+++ b/yt/analysis_modules/halo_finding/rockstar/setup.py
@@ -1,9 +1,7 @@
#!/usr/bin/env python
from __future__ import print_function
-import setuptools
-import os, sys, os.path
-
import os.path
+import sys
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/halo_finding/tests/test_rockstar.py
--- a/yt/analysis_modules/halo_finding/tests/test_rockstar.py
+++ b/yt/analysis_modules/halo_finding/tests/test_rockstar.py
@@ -2,7 +2,6 @@
import sys
from yt.convenience import load
-from yt.testing import *
from yt.utilities.answer_testing.framework import \
FieldValuesTest, \
requires_sim
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 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
@@ -14,7 +14,7 @@
#-----------------------------------------------------------------------------
import numpy as np
-import math, time
+import math
from yt.funcs import mylog
from yt.units.yt_array import \
@@ -184,7 +184,7 @@
if log_mass_max is None:
self.log_mass_max = 16
# If we're making the analytic function...
- if self.make_analytic == True:
+ if self.make_analytic is True:
# Try to set cosmological parameters from the simulation dataset
if simulation_ds is not None:
self.omega_matter0 = self.simulation_ds.omega_matter
@@ -623,27 +623,27 @@
many times as you want. */
/* 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,
- in units of the critical density.
- 2) omega_baryon -- Density of baryons, in units of critical.
- 3) omega_hdm -- Density of massive neutrinos, in units of critical
- 4) degen_hdm -- (Int) Number of degenerate massive neutrino species
- 5) omega_lambda -- Cosmological constant
- 6) hubble -- Hubble constant, in units of 100 km/s/Mpc
- 7) redshift -- The redshift at which to evaluate */
+ 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,
+ in units of the critical density.
+ 2) omega_baryon -- Density of baryons, in units of critical.
+ 3) omega_hdm -- Density of massive neutrinos, in units of critical
+ 4) degen_hdm -- (Int) Number of degenerate massive neutrino species
+ 5) omega_lambda -- Cosmological constant
+ 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.
- 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
- density-weighted transfer function), although T_cbn (the CDM+
- Baryon+Neutrino density-weighted transfer function) is stored
- in the global variable tf_cbnu. */
+ 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
+ density-weighted transfer function), although T_cbn (the CDM+
+ 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. */
+ 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. */
@@ -667,7 +667,7 @@
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):
+ degen_hdm, omega_lambda, hubble, redshift):
self.qwarn = 0;
self.theta_cmb = 2.728/2.7 # Assuming T_cmb = 2.728 K
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/halo_mass_function/setup.py
--- a/yt/analysis_modules/halo_mass_function/setup.py
+++ b/yt/analysis_modules/halo_mass_function/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 deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/level_sets/clump_handling.py
--- a/yt/analysis_modules/level_sets/clump_handling.py
+++ b/yt/analysis_modules/level_sets/clump_handling.py
@@ -19,7 +19,7 @@
from yt.fields.derived_field import \
ValidateSpatial
-from yt.funcs import mylog
+from yt.funcs import mylog, iterable
from yt.extern.six import string_types
from .clump_info_items import \
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/level_sets/clump_tools.py
--- a/yt/analysis_modules/level_sets/clump_tools.py
+++ b/yt/analysis_modules/level_sets/clump_tools.py
@@ -28,9 +28,9 @@
counter += 1
list.append(clump)
clump.level = level
- if clump.children != None:
+ if clump.children is not None:
for child in clump.children:
- x = recursive_all_clumps(child,list,level+1,clump.number)
+ recursive_all_clumps(child,list,level+1,clump.number)
return list
def return_all_clumps(clump):
@@ -64,8 +64,6 @@
Recursive. Prints the level and the number of cores to the screen."""
global counter
- if dbg > 0:
- print(tabs(level), "l =",level, "n_core",counter)
if ((clump.children is None) or (len(clump.children) == 0)):
counter += 1
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/level_sets/clump_validators.py
--- a/yt/analysis_modules/level_sets/clump_validators.py
+++ b/yt/analysis_modules/level_sets/clump_validators.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.data_point_utilities import FindBindingEnergy
from yt.utilities.operator_registry import \
OperatorRegistry
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/level_sets/contour_finder.py
--- a/yt/analysis_modules/level_sets/contour_finder.py
+++ b/yt/analysis_modules/level_sets/contour_finder.py
@@ -13,11 +13,11 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
-from itertools import chain
import numpy as np
-from yt.funcs import *
-import yt.utilities.data_point_utilities as data_point_utilities
+from collections import defaultdict
+
+from yt.funcs import mylog, get_pbar
from yt.utilities.lib.ContourFinding import \
ContourTree, TileContourTree, link_node_contours, \
update_joins
@@ -32,7 +32,6 @@
contours = {}
node_ids = []
DLE = data_source.ds.domain_left_edge
- selector = getattr(data_source, "base_object", data_source).selector
masks = dict((g.id, m) for g, m in data_source.blocks)
for (g, node, (sl, dims, gi)) in data_source.tiles.slice_traverse():
node.node_ind = len(node_ids)
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/level_sets/setup.py
--- a/yt/analysis_modules/level_sets/setup.py
+++ b/yt/analysis_modules/level_sets/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 deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/list_modules.py
--- a/yt/analysis_modules/list_modules.py
+++ b/yt/analysis_modules/list_modules.py
@@ -33,7 +33,7 @@
def __getattr__(self, attr):
try:
name = "yt.analysis_modules.%s.api" % (attr)
- nm = __import__(name, level=-1)
+ __import__(name, level=-1)
setattr(self, attr, sys.modules[name])
except ImportError:
raise AttributeError(attr)
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/particle_trajectories/particle_trajectories.py
--- a/yt/analysis_modules/particle_trajectories/particle_trajectories.py
+++ b/yt/analysis_modules/particle_trajectories/particle_trajectories.py
@@ -16,7 +16,7 @@
from yt.utilities.lib.CICDeposit import CICSample_3
from yt.utilities.parallel_tools.parallel_analysis_interface import \
parallel_root_only
-from yt.funcs import *
+from yt.funcs import mylog, get_pbar
from yt.units.yt_array import array_like_field
from yt.config import ytcfg
from collections import OrderedDict
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/particle_trajectories/setup.py
--- a/yt/analysis_modules/particle_trajectories/setup.py
+++ b/yt/analysis_modules/particle_trajectories/setup.py
@@ -1,8 +1,5 @@
#!/usr/bin/env python
-import setuptools
-import os
-import sys
-import os.path
+
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/photon_simulator/photon_models.py
--- a/yt/analysis_modules/photon_simulator/photon_models.py
+++ b/yt/analysis_modules/photon_simulator/photon_models.py
@@ -24,7 +24,8 @@
from yt.extern.six import string_types
import numpy as np
-from yt.funcs import *
+from yt.funcs import mylog, get_pbar
+from yt.units.yt_array import YTArray
from yt.utilities.physical_constants import mp
from yt.utilities.parallel_tools.parallel_analysis_interface import \
parallel_objects
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/photon_simulator/photon_simulator.py
--- a/yt/analysis_modules/photon_simulator/photon_simulator.py
+++ b/yt/analysis_modules/photon_simulator/photon_simulator.py
@@ -26,14 +26,15 @@
#-----------------------------------------------------------------------------
from yt.extern.six import string_types
import numpy as np
-from yt.funcs import *
+from yt.funcs import \
+ mylog, get_pbar, iterable, ensure_list
from yt.utilities.physical_constants import clight
from yt.utilities.cosmology import Cosmology
from yt.utilities.orientation import Orientation
from yt.utilities.fits_image import assert_same_wcs
from yt.utilities.parallel_tools.parallel_analysis_interface import \
- communication_system, parallel_root_only, get_mpi_type, \
- parallel_capable
+ communication_system, parallel_root_only, get_mpi_type, \
+ parallel_capable
from yt.units.yt_array import YTQuantity, YTArray, uconcatenate
import h5py
from yt.utilities.on_demand_imports import _astropy
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/photon_simulator/setup.py
--- a/yt/analysis_modules/photon_simulator/setup.py
+++ b/yt/analysis_modules/photon_simulator/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 deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/photon_simulator/spectral_models.py
--- a/yt/analysis_modules/photon_simulator/spectral_models.py
+++ b/yt/analysis_modules/photon_simulator/spectral_models.py
@@ -11,11 +11,12 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
+import h5py
import numpy as np
import os
-from yt.funcs import *
-from yt.units.yt_array import YTQuantity
-import h5py
+
+from yt.funcs import mylog
+from yt.units.yt_array import YTArray, YTQuantity
from yt.utilities.on_demand_imports import _astropy, _scipy
from yt.utilities.physical_constants import hcgs, clight, erg_per_keV, amu_cgs
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/photon_simulator/tests/test_cluster.py
--- a/yt/analysis_modules/photon_simulator/tests/test_cluster.py
+++ b/yt/analysis_modules/photon_simulator/tests/test_cluster.py
@@ -10,11 +10,13 @@
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
-from yt.testing import *
+from yt.analysis_modules.photon_simulator.api import \
+ TableApecModel, TableAbsorbModel, \
+ ThermalPhotonModel, PhotonList
from yt.config import ytcfg
-from yt.analysis_modules.photon_simulator.api import *
+from yt.testing import requires_file
from yt.utilities.answer_testing.framework import requires_ds, \
- GenericArrayTest, data_dir_load
+ GenericArrayTest, data_dir_load
import numpy as np
def setup():
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/ppv_cube/setup.py
--- a/yt/analysis_modules/ppv_cube/setup.py
+++ b/yt/analysis_modules/ppv_cube/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 deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/ppv_cube/tests/test_ppv.py
--- a/yt/analysis_modules/ppv_cube/tests/test_ppv.py
+++ b/yt/analysis_modules/ppv_cube/tests/test_ppv.py
@@ -15,7 +15,7 @@
import yt.units as u
from yt.utilities.physical_constants import kboltz, mh, clight
import numpy as np
-from yt.testing import *
+from yt.testing import assert_allclose_units
def setup():
"""Test specific setup."""
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/radmc3d_export/tests/test_radmc3d_exporter.py
--- a/yt/analysis_modules/radmc3d_export/tests/test_radmc3d_exporter.py
+++ b/yt/analysis_modules/radmc3d_export/tests/test_radmc3d_exporter.py
@@ -11,13 +11,13 @@
#-----------------------------------------------------------------------------
import yt
-from yt.testing import *
+from yt.testing import assert_allclose
from yt.analysis_modules.radmc3d_export.api import RadMC3DWriter
from yt.utilities.answer_testing.framework import \
AnswerTestingTest, \
requires_ds
-from yt.config import ytcfg
import tempfile
+import numpy as np
import os
import shutil
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/setup.py
--- a/yt/analysis_modules/setup.py
+++ b/yt/analysis_modules/setup.py
@@ -1,5 +1,6 @@
#!/usr/bin/env python
-import sys
+
+
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('analysis_modules', parent_package, top_path)
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/spectral_integrator/setup.py
--- a/yt/analysis_modules/spectral_integrator/setup.py
+++ b/yt/analysis_modules/spectral_integrator/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 deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/star_analysis/setup.py
--- a/yt/analysis_modules/star_analysis/setup.py
+++ b/yt/analysis_modules/star_analysis/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 deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/star_analysis/sfr_spectrum.py
--- a/yt/analysis_modules/star_analysis/sfr_spectrum.py
+++ b/yt/analysis_modules/star_analysis/sfr_spectrum.py
@@ -18,7 +18,6 @@
import numpy as np
import h5py
import math
-import itertools
from yt.config import ytcfg
from yt.extern.six.moves import zip as izip
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/sunrise_export/sunrise_exporter.py
--- a/yt/analysis_modules/sunrise_export/sunrise_exporter.py
+++ b/yt/analysis_modules/sunrise_export/sunrise_exporter.py
@@ -19,14 +19,17 @@
except ImportError:
pass
+import os
import time
import numpy as np
-from yt.funcs import *
+
import yt.utilities.lib.api as amr_utils
+
+from yt import add_field
+from yt.funcs import get_pbar, mylog
from yt.utilities.physical_constants import \
kpc_per_cm, \
sec_per_year
-from yt.mods import *
def export_to_sunrise(ds, fn, star_particle_type, fc, fwidth, ncells_wide=None,
debug=False,dd=None,**kwargs):
@@ -492,7 +495,7 @@
idxst = dd["particle_type"] == star_type
#make sure we select more than a single particle
- assert na.sum(idxst)>0
+ assert np.sum(idxst)>0
if pos is None:
pos = np.array([dd["particle_position_%s" % ax]
for ax in 'xyz']).transpose()
@@ -543,7 +546,7 @@
#make sure we have nonzero particle number
assert pd_table.data.shape[0]>0
- return pd_table,na.sum(idx)
+ return pd_table,np.sum(idx)
def add_fields():
@@ -559,12 +562,8 @@
# SFR in a cell. This assumes stars were created by the Cen & Ostriker algorithm
# Check Grid_AddToDiskProfile.C and star_maker7.src
star_mass_ejection_fraction = data.ds.get_parameter("StarMassEjectionFraction",float)
- star_maker_minimum_dynamical_time = 3e6 # years, which will get divided out
- dtForSFR = star_maker_minimum_dynamical_time / data.ds["years"]
xv1 = ((data.ds["InitialTime"] - data["creation_time"])
/ data["dynamical_time"])
- xv2 = ((data.ds["InitialTime"] + dtForSFR - data["creation_time"])
- / data["dynamical_time"])
denom = (1.0 - star_mass_ejection_fraction * (1.0 - (1.0 + xv1)*np.exp(-xv1)))
minitial = data["ParticleMassMsun"] / denom
return minitial
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/sunyaev_zeldovich/setup.py
--- a/yt/analysis_modules/sunyaev_zeldovich/setup.py
+++ b/yt/analysis_modules/sunyaev_zeldovich/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 deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
--- a/yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
+++ b/yt/analysis_modules/sunyaev_zeldovich/tests/test_projection.py
@@ -11,12 +11,12 @@
#-----------------------------------------------------------------------------
from yt.frontends.stream.api import load_uniform_grid
-from yt.funcs import get_pbar, mylog
+from yt.funcs import get_pbar
from yt.utilities.physical_constants import cm_per_kpc, K_per_keV, \
- mh, cm_per_km, kboltz, Tcmb, hcgs, clight, sigma_thompson
-from yt.testing import *
+ mh, cm_per_km, kboltz, Tcmb, hcgs, clight, sigma_thompson
+from yt.testing import requires_module, assert_almost_equal
from yt.utilities.answer_testing.framework import requires_ds, \
- GenericArrayTest, data_dir_load, GenericImageTest
+ GenericArrayTest, data_dir_load, GenericImageTest
try:
from yt.analysis_modules.sunyaev_zeldovich.projection import SZProjection, I0
except ImportError:
diff -r deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/two_point_functions/setup.py
--- a/yt/analysis_modules/two_point_functions/setup.py
+++ b/yt/analysis_modules/two_point_functions/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 deeb92e93357a433dd56e83a339a2192ca42e9e1 -r 4bfdb0ddccdb3bad26724484a89149b5a7ecfe51 yt/analysis_modules/two_point_functions/two_point_functions.py
--- a/yt/analysis_modules/two_point_functions/two_point_functions.py
+++ b/yt/analysis_modules/two_point_functions/two_point_functions.py
@@ -14,17 +14,19 @@
#-----------------------------------------------------------------------------
import h5py
-from yt.mods import *
-#from yt.utilities.math_utils import *
-from yt.utilities.performance_counters import yt_counters, time_function
+import numpy as np
+
+from yt.funcs import mylog
+from yt.utilities.performance_counters import yt_counters
from yt.utilities.parallel_tools.parallel_analysis_interface import ParallelAnalysisInterface, parallel_blocking_call, parallel_root_only
try:
- from yt.utilities.kdtree.api import *
+ from yt.utilities.kdtree.api import \
+ fKD, free_tree, create_tree
except ImportError:
mylog.debug("The Fortran kD-Tree did not import correctly.")
-import math, sys, itertools, inspect, types, time
+import math, inspect, time
from collections import defaultdict
sep = 12
@@ -117,7 +119,7 @@
self.index = ds.index
self.center = (ds.domain_right_edge + ds.domain_left_edge)/2.0
# Figure out the range of ruler lengths.
- if length_range == None:
+ if length_range is None:
length_range = [math.sqrt(3) * self.ds.index.get_smallest_dx(),
self.min_edge/2.]
else:
@@ -679,7 +681,7 @@
"""
for fset in self._fsets:
# Only operate on correlation functions.
- if fset.corr_norm == None: continue
+ if fset.corr_norm is None: continue
fp = self.comm.write_on_root("%s_correlation.txt" % fset.function.__name__)
line = "# length".ljust(sep)
line += "\\xi".ljust(sep)
Repository URL: https://bitbucket.org/yt_analysis/yt/
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