diff --git a/hyperion/__init__.py b/hyperion/__init__.py index 27f93673..d9e8cca9 100644 --- a/hyperion/__init__.py +++ b/hyperion/__init__.py @@ -1,3 +1,2 @@ -from __future__ import print_function, division from .version import __version__ diff --git a/hyperion/conf/conf_files.py b/hyperion/conf/conf_files.py index 0413a18c..0ff36c8f 100644 --- a/hyperion/conf/conf_files.py +++ b/hyperion/conf/conf_files.py @@ -1,13 +1,13 @@ -from __future__ import print_function, division import warnings import numpy as np -from astropy import log as logger -import six +import logging from ..util.functions import FreezableClass, bool2str, str2bool, is_numpy_array from ..filter import Filter +logger = logging.getLogger(__name__) + class OutputConf(FreezableClass): @@ -89,7 +89,7 @@ def set_propagation_check_frequency(self, frequency): How often the photon position and cell should be double-checked (1 is always, 0 is never). ''' - if not np.isscalar(frequency) or isinstance(frequency, six.string_types): + if not np.isscalar(frequency) or isinstance(frequency, str): raise TypeError("frequency should be a scalar value") if frequency < 0. or frequency > 1.: raise ValueError("frequency should be between 0 and 1") diff --git a/hyperion/conf/tests/test_conf_io.py b/hyperion/conf/tests/test_conf_io.py index e4a5dc10..cb067497 100644 --- a/hyperion/conf/tests/test_conf_io.py +++ b/hyperion/conf/tests/test_conf_io.py @@ -1,6 +1,5 @@ # Test that parameters are preserved when written out and read in again -from __future__ import print_function, division from itertools import product diff --git a/hyperion/densities/alpha_disk.py b/hyperion/densities/alpha_disk.py index a1df4959..96df3acb 100644 --- a/hyperion/densities/alpha_disk.py +++ b/hyperion/densities/alpha_disk.py @@ -1,8 +1,6 @@ -from __future__ import print_function, division import numpy as np -from astropy import log as logger -import six +import logging from ..dust import SphericalDust from ..util.constants import pi, G @@ -12,6 +10,8 @@ from .core import Disk +logger = logging.getLogger(__name__) + class AlphaDisk(Disk): r''' @@ -350,7 +350,7 @@ def dust(self): @dust.setter def dust(self, value): - if isinstance(value, six.string_types): + if isinstance(value, str): self._dust = SphericalDust(value) else: self._dust = value diff --git a/hyperion/densities/ambient_medium.py b/hyperion/densities/ambient_medium.py index 2c5c22f3..c927ab4d 100644 --- a/hyperion/densities/ambient_medium.py +++ b/hyperion/densities/ambient_medium.py @@ -1,7 +1,5 @@ -from __future__ import print_function, division import numpy as np -import six from ..dust import SphericalDust from ..grid import SphericalPolarGrid @@ -128,7 +126,7 @@ def subtract(self, value): @dust.setter def dust(self, value): - if isinstance(value, six.string_types): + if isinstance(value, str): self._dust = SphericalDust(value) else: self._dust = value diff --git a/hyperion/densities/bipolar_cavity.py b/hyperion/densities/bipolar_cavity.py index 12516411..a91fedfa 100644 --- a/hyperion/densities/bipolar_cavity.py +++ b/hyperion/densities/bipolar_cavity.py @@ -1,8 +1,6 @@ -from __future__ import print_function, division import numpy as np -from astropy import log as logger -import six +import logging from ..util.functions import FreezableClass from ..dust import SphericalDust @@ -11,6 +9,8 @@ from .core import Envelope, Density +logger = logging.getLogger(__name__) + class BipolarCavity(Density): r''' @@ -132,7 +132,7 @@ def dust(self): @dust.setter def dust(self, value): - if isinstance(value, six.string_types): + if isinstance(value, str): self._dust = SphericalDust(value) else: self._dust = value diff --git a/hyperion/densities/core.py b/hyperion/densities/core.py index 0358be89..21cfdc77 100644 --- a/hyperion/densities/core.py +++ b/hyperion/densities/core.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division from ..util.functions import FreezableClass diff --git a/hyperion/densities/flared_disk.py b/hyperion/densities/flared_disk.py index 6131a377..9d636d4f 100644 --- a/hyperion/densities/flared_disk.py +++ b/hyperion/densities/flared_disk.py @@ -1,8 +1,6 @@ -from __future__ import print_function, division import numpy as np -from astropy import log as logger -import six +import logging from ..dust import SphericalDust from ..util.constants import pi @@ -12,6 +10,8 @@ from .core import Disk +logger = logging.getLogger(__name__) + class FlaredDisk(Disk): r''' @@ -248,7 +248,7 @@ def dust(self): @dust.setter def dust(self, value): - if isinstance(value, six.string_types): + if isinstance(value, str): self._dust = SphericalDust(value) else: self._dust = value diff --git a/hyperion/densities/power_law_envelope.py b/hyperion/densities/power_law_envelope.py index b47579ad..f9bf386a 100644 --- a/hyperion/densities/power_law_envelope.py +++ b/hyperion/densities/power_law_envelope.py @@ -1,8 +1,6 @@ -from __future__ import print_function, division import numpy as np -from astropy import log as logger -import six +import logging from ..dust import SphericalDust from ..grid import SphericalPolarGrid, CylindricalPolarGrid @@ -14,6 +12,8 @@ from .core import Envelope from .bipolar_cavity import BipolarCavity +logger = logging.getLogger(__name__) + class PowerLawEnvelope(Envelope): r''' @@ -175,7 +175,7 @@ def dust(self): @dust.setter def dust(self, value): - if isinstance(value, six.string_types): + if isinstance(value, str): self._dust = SphericalDust(value) else: self._dust = value diff --git a/hyperion/densities/tests/test_densities.py b/hyperion/densities/tests/test_densities.py index 4d57a7cf..d24f66af 100644 --- a/hyperion/densities/tests/test_densities.py +++ b/hyperion/densities/tests/test_densities.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import pytest import numpy as np diff --git a/hyperion/densities/ulrich_envelope.py b/hyperion/densities/ulrich_envelope.py index 3ddcc3fc..6935c6b2 100644 --- a/hyperion/densities/ulrich_envelope.py +++ b/hyperion/densities/ulrich_envelope.py @@ -1,8 +1,6 @@ -from __future__ import print_function, division import numpy as np -from astropy import log as logger -import six +import logging from ..dust import SphericalDust from ..grid import SphericalPolarGrid, CylindricalPolarGrid @@ -14,6 +12,8 @@ from .core import Envelope from .bipolar_cavity import BipolarCavity +logger = logging.getLogger(__name__) + def delta_neg(r, q): @@ -294,7 +294,7 @@ def dust(self): @dust.setter def dust(self, value): - if isinstance(value, six.string_types): + if isinstance(value, str): self._dust = SphericalDust(value) else: self._dust = value diff --git a/hyperion/dust/dust_type.py b/hyperion/dust/dust_type.py index 9c012f77..69d0b122 100644 --- a/hyperion/dust/dust_type.py +++ b/hyperion/dust/dust_type.py @@ -9,15 +9,13 @@ # ############################################################################## -from __future__ import print_function, division import os import hashlib import h5py import numpy as np -from astropy import log as logger -import six +import logging from ..version import __version__ @@ -31,6 +29,8 @@ from .emissivities import Emissivities from .mean_opacities import MeanOpacities +logger = logging.getLogger(__name__) + def henyey_greenstein(mu, g, p_lin_max): P1 = (1. - g * g) / (1. + g * g - 2. * g * mu) ** 1.5 @@ -264,7 +264,7 @@ def write(self, filename, compression=True): self.emissivities.set_lte(self.optical_properties, self.mean_opacities) # Create dust table set - if isinstance(filename, six.string_types): + if isinstance(filename, str): dt = h5py.File(filename, 'w') else: dt = filename @@ -305,7 +305,7 @@ def read(self, filename): from ..util.functions import asstr - if isinstance(filename, six.string_types): + if isinstance(filename, str): # Check file exists if not os.path.exists(filename): diff --git a/hyperion/dust/emissivities.py b/hyperion/dust/emissivities.py index 3b9513dd..27b0b59d 100644 --- a/hyperion/dust/emissivities.py +++ b/hyperion/dust/emissivities.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import hashlib @@ -9,7 +8,9 @@ from ..util.interpolate import interp1d_fast_loglog from ..util.functions import (B_nu, FreezableClass, nu_common, planck_nu_range, bool2str, is_numpy_array, monotonically_increasing) -from astropy import log as logger +import logging + +logger = logging.getLogger(__name__) class Emissivities(FreezableClass): diff --git a/hyperion/dust/mean_opacities.py b/hyperion/dust/mean_opacities.py index dc80d901..6455869b 100644 --- a/hyperion/dust/mean_opacities.py +++ b/hyperion/dust/mean_opacities.py @@ -1,16 +1,17 @@ -from __future__ import print_function, division import hashlib import numpy as np from astropy.table import Table, Column -from astropy import log as logger +import logging from ..util.integrate import integrate_loglog from ..util.interpolate import interp1d_fast_loglog from ..util.functions import FreezableClass, nu_common, B_nu, dB_nu_dT, planck_nu_range from ..util.constants import sigma +logger = logging.getLogger(__name__) + class MeanOpacities(FreezableClass): diff --git a/hyperion/dust/optical_properties.py b/hyperion/dust/optical_properties.py index 111dfb3f..ebccbd56 100644 --- a/hyperion/dust/optical_properties.py +++ b/hyperion/dust/optical_properties.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import hashlib @@ -11,7 +10,9 @@ from ..util.functions import (extrap1d_log10, FreezableClass, is_numpy_array, monotonically_increasing) from ..util.constants import c, sigma -from astropy import log as logger +import logging + +logger = logging.getLogger(__name__) class OpticalProperties(FreezableClass): diff --git a/hyperion/dust/tests/test_emissivities.py b/hyperion/dust/tests/test_emissivities.py index 3a0a4317..59d5292a 100644 --- a/hyperion/dust/tests/test_emissivities.py +++ b/hyperion/dust/tests/test_emissivities.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import matplotlib.pyplot as plt diff --git a/hyperion/dust/tests/test_mean_opacities.py b/hyperion/dust/tests/test_mean_opacities.py index d6a4c5e9..9c7dacb1 100644 --- a/hyperion/dust/tests/test_mean_opacities.py +++ b/hyperion/dust/tests/test_mean_opacities.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import matplotlib.pyplot as plt diff --git a/hyperion/dust/tests/test_optical_properties.py b/hyperion/dust/tests/test_optical_properties.py index 510cdd82..5a9fd919 100644 --- a/hyperion/dust/tests/test_optical_properties.py +++ b/hyperion/dust/tests/test_optical_properties.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import matplotlib.pyplot as plt diff --git a/hyperion/filter/filter.py b/hyperion/filter/filter.py index 91e89f7b..5242a6e4 100644 --- a/hyperion/filter/filter.py +++ b/hyperion/filter/filter.py @@ -1,8 +1,6 @@ -from __future__ import print_function, division import numpy as np -import six from astropy import units as u from ..util.integrate import integrate @@ -46,7 +44,7 @@ def name(self): @name.setter def name(self, value): - if value is None or isinstance(value, six.string_types): + if value is None or isinstance(value, str): self._name = value else: raise TypeError("name should be given as a string") diff --git a/hyperion/grid/amr_grid.py b/hyperion/grid/amr_grid.py index 2309f60f..e36b8d8d 100644 --- a/hyperion/grid/amr_grid.py +++ b/hyperion/grid/amr_grid.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import os import posixpath @@ -11,9 +10,11 @@ from ..util.meshgrid import meshgrid_nd from ..util.functions import FreezableClass, link_or_copy, as_str -from astropy import log as logger +import logging from .grid_helpers import single_grid_dims +logger = logging.getLogger(__name__) + def zero_density(amr_grid, xmin=-np.inf, xmax=np.inf, ymin=-np.inf, ymax=np.inf, zmin=-np.inf, zmax=np.inf): for level in amr_grid.levels: diff --git a/hyperion/grid/cartesian_grid.py b/hyperion/grid/cartesian_grid.py index d614bb82..fd98d0fa 100644 --- a/hyperion/grid/cartesian_grid.py +++ b/hyperion/grid/cartesian_grid.py @@ -1,16 +1,17 @@ -from __future__ import print_function, division import hashlib from copy import deepcopy import h5py import numpy as np -from astropy import log as logger +import logging from ..util.meshgrid import meshgrid_nd from ..util.functions import FreezableClass, is_numpy_array, monotonically_increasing, link_or_copy, as_str from .grid_helpers import single_grid_dims +logger = logging.getLogger(__name__) + class CartesianGrid(FreezableClass): ''' diff --git a/hyperion/grid/cylindrical_polar_grid.py b/hyperion/grid/cylindrical_polar_grid.py index 9b20af18..3fa00196 100644 --- a/hyperion/grid/cylindrical_polar_grid.py +++ b/hyperion/grid/cylindrical_polar_grid.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import hashlib from copy import deepcopy @@ -8,9 +7,11 @@ from ..util.meshgrid import meshgrid_nd from ..util.functions import FreezableClass, is_numpy_array, monotonically_increasing, link_or_copy, as_str -from astropy import log as logger +import logging from .grid_helpers import single_grid_dims +logger = logging.getLogger(__name__) + class CylindricalPolarGrid(FreezableClass): ''' diff --git a/hyperion/grid/grid_helpers.py b/hyperion/grid/grid_helpers.py index a60dd8d8..7068bdf0 100644 --- a/hyperion/grid/grid_helpers.py +++ b/hyperion/grid/grid_helpers.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import h5py import numpy as np @@ -22,7 +21,7 @@ def single_grid_dims(data, ndim=3): ''' if type(data) in [list, tuple]: - + n_pop = len(data) shape = None for item in data: diff --git a/hyperion/grid/octree_grid.py b/hyperion/grid/octree_grid.py index 565a1d2b..f558c06a 100644 --- a/hyperion/grid/octree_grid.py +++ b/hyperion/grid/octree_grid.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import struct import hashlib @@ -8,9 +7,11 @@ import numpy as np from ..util.functions import FreezableClass, is_numpy_array, link_or_copy, as_str -from astropy import log as logger +import logging from .grid_helpers import single_grid_dims +logger = logging.getLogger(__name__) + class OctreeGrid(FreezableClass): ''' diff --git a/hyperion/grid/spherical_polar_grid.py b/hyperion/grid/spherical_polar_grid.py index f4a71523..73807b8b 100644 --- a/hyperion/grid/spherical_polar_grid.py +++ b/hyperion/grid/spherical_polar_grid.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import hashlib from copy import deepcopy @@ -8,9 +7,11 @@ from ..util.meshgrid import meshgrid_nd from ..util.functions import FreezableClass, is_numpy_array, monotonically_increasing, link_or_copy, as_str -from astropy import log as logger +import logging from .grid_helpers import single_grid_dims +logger = logging.getLogger(__name__) + class SphericalPolarGrid(FreezableClass): ''' diff --git a/hyperion/grid/tests/test_grid.py b/hyperion/grid/tests/test_grid.py index 2d7b12b2..fd381c90 100644 --- a/hyperion/grid/tests/test_grid.py +++ b/hyperion/grid/tests/test_grid.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import pytest import numpy as np diff --git a/hyperion/grid/tests/test_io.py b/hyperion/grid/tests/test_io.py index b2b21e18..05868804 100644 --- a/hyperion/grid/tests/test_io.py +++ b/hyperion/grid/tests/test_io.py @@ -3,7 +3,6 @@ import h5py import numpy as np import pytest -import six from ...util.functions import virtual_file from .. import (CartesianGrid, @@ -16,7 +15,7 @@ def exc_msg(exc): - if isinstance(exc.value, six.string_types): + if isinstance(exc.value, str): return exc.value elif type(exc.value) is tuple: return exc.value[0] diff --git a/hyperion/grid/tests/test_views.py b/hyperion/grid/tests/test_views.py index 77820ec3..c25e04cd 100644 --- a/hyperion/grid/tests/test_views.py +++ b/hyperion/grid/tests/test_views.py @@ -2,7 +2,6 @@ import numpy as np import pytest -import six from hyperion.grid import CartesianGrid, CylindricalPolarGrid, SphericalPolarGrid, AMRGrid, OctreeGrid @@ -10,7 +9,7 @@ def exc_msg(exc): - if isinstance(exc.value, six.string_types): + if isinstance(exc.value, str): return exc.value elif type(exc.value) is tuple: return exc.value[0] diff --git a/hyperion/grid/tests/test_voronoi.py b/hyperion/grid/tests/test_voronoi.py index 1e3fce53..31819e7c 100644 --- a/hyperion/grid/tests/test_voronoi.py +++ b/hyperion/grid/tests/test_voronoi.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import os import random @@ -110,11 +109,11 @@ def test_io(tmpdir): np.testing.assert_allclose(g1._sparse_neighbors[0], g2._sparse_neighbors[0]) np.testing.assert_allclose(g1._sparse_neighbors[1], g2._sparse_neighbors[1]) - - + + def test_init_sparse(tmpdir): - + # Regression test for a bug that caused VoronoiGrid._sparse_neighbors to not be defined # when writing out a Voronoi grid. @@ -129,7 +128,7 @@ def test_init_sparse(tmpdir): f2 = h5py.File(file_1, 'r') g2 = VoronoiGrid() g2.read(f2) - + f3 = h5py.File(file_2, 'w') g3 = VoronoiGrid(g2) g3.write(f3) diff --git a/hyperion/grid/voronoi_grid.py b/hyperion/grid/voronoi_grid.py index 24f42b1e..4320fd77 100644 --- a/hyperion/grid/voronoi_grid.py +++ b/hyperion/grid/voronoi_grid.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import struct import hashlib @@ -7,12 +6,14 @@ import h5py import numpy as np -from astropy import log as logger +import logging from astropy.table import Table from ..util.functions import FreezableClass, is_numpy_array, link_or_copy, as_str from .grid_helpers import single_grid_dims +logger = logging.getLogger(__name__) + class VoronoiGrid(FreezableClass): ''' diff --git a/hyperion/grid/voronoi_helpers.py b/hyperion/grid/voronoi_helpers.py index 1669bee1..7058f075 100644 --- a/hyperion/grid/voronoi_helpers.py +++ b/hyperion/grid/voronoi_helpers.py @@ -1,4 +1,6 @@ -from astropy import log as logger +import logging + +logger = logging.getLogger(__name__) class voronoi_grid(object): diff --git a/hyperion/grid/yt3_wrappers.py b/hyperion/grid/yt3_wrappers.py index ef2eb1ce..921e50cc 100644 --- a/hyperion/grid/yt3_wrappers.py +++ b/hyperion/grid/yt3_wrappers.py @@ -1,8 +1,8 @@ -from __future__ import print_function, division import numpy as np -import six -from astropy import log as logger +import logging + +logger = logging.getLogger(__name__) def almost_equal(a, b): @@ -262,8 +262,8 @@ def yt_dataset_to_amr_grid(ds, quantity_mapping={}): "in Hyperion and value is the name of the field in the " "yt dataset. Available quantities are: \n\n {0}".format(field_list)) - for output_quantity, input_field in six.iteritems(quantity_mapping): - if not isinstance(output_quantity, six.string_types): + for output_quantity, input_field in quantity_mapping.items(): + if not isinstance(output_quantity, str): raise ValueError("quantity_mapping keys should be strings") if input_field not in ds.derived_field_list: raise ValueError("yt field {0} does not exist. Available fields " @@ -312,7 +312,7 @@ def yt_dataset_to_amr_grid(ds, quantity_mapping={}): grid.nz, grid.ny, grid.nx = yt_grid.shape - for output_quantity, input_field in six.iteritems(quantity_mapping): + for output_quantity, input_field in quantity_mapping.items(): grid.quantities[output_quantity] = yt_grid[input_field].in_units('g/cm**3').ndarray_view() return amr diff --git a/hyperion/importers/orion.py b/hyperion/importers/orion.py index 96b4476a..8cd7fab0 100644 --- a/hyperion/importers/orion.py +++ b/hyperion/importers/orion.py @@ -1,9 +1,7 @@ -from __future__ import print_function, division import numpy as np -from astropy import log as logger -import six +import logging from ..grid.amr_grid import Grid, Level, AMRGrid @@ -110,7 +108,7 @@ def __init__(self, dirname, quantities, verbose=False, max_level=None): available_quantities = [f.readline().strip() for i in range(n_quantities)] # If a single quantity is requested as a string, make it into a list - if isinstance(quantities, six.string_types): + if isinstance(quantities, str): if quantities == 'all': quantities = available_quantities else: diff --git a/hyperion/model/analytical_yso_model.py b/hyperion/model/analytical_yso_model.py index 939ad670..5a0a3374 100644 --- a/hyperion/model/analytical_yso_model.py +++ b/hyperion/model/analytical_yso_model.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division try: from collections.abc import Mapping @@ -8,7 +7,7 @@ from copy import deepcopy import numpy as np -from astropy import log as logger +import logging from ..densities import FlaredDisk, AlphaDisk, PowerLawEnvelope, UlrichEnvelope, AmbientMedium from ..util.interpolate import interp1d_fast_loglog @@ -19,6 +18,8 @@ from . import Model +logger = logging.getLogger(__name__) + def _min_none(*args): "Minimum of several arguments, ignoring None values" diff --git a/hyperion/model/image.py b/hyperion/model/image.py index 232ea345..f318a008 100644 --- a/hyperion/model/image.py +++ b/hyperion/model/image.py @@ -1,6 +1,5 @@ import numpy as np -import six from ..util.functions import FreezableClass, is_numpy_array from ..util.constants import c @@ -127,7 +126,7 @@ def unit(self): @unit.setter def unit(self, value): - if value is None or isinstance(value, six.string_types): + if value is None or isinstance(value, str): self._unit = value else: raise ValueError("unit should be a string") diff --git a/hyperion/model/model.py b/hyperion/model/model.py index b5a75c7b..8052699d 100644 --- a/hyperion/model/model.py +++ b/hyperion/model/model.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import os import subprocess @@ -8,8 +7,7 @@ import h5py import numpy as np -from astropy import log as logger -import six +import logging from ..version import __version__ from ..util.functions import delete_file @@ -24,6 +22,8 @@ from .model_output import ModelOutput +logger = logging.getLogger(__name__) + class Configuration(FreezableClass): @@ -648,7 +648,7 @@ def write(self, filename=None, compression=True, copy=True, if copy: - if isinstance(dust, six.string_types): + if isinstance(dust, str): dust = SphericalDust(dust) if dust.hash() in present: @@ -826,7 +826,7 @@ class (e.g. ``SphericalDust``, ``IsotropicDust``, ...). # Only consider this if the specific energy is not specified if specific_energy is None: - if isinstance(dust, six.string_types): + if isinstance(dust, str): if dust in self.dust: @@ -840,7 +840,7 @@ class (e.g. ``SphericalDust``, ``IsotropicDust``, ...). dust_hashes = [] for d in self.dust: - if not isinstance(d, six.string_types): + if not isinstance(d, str): dust_hashes.append(d.hash()) else: dust_hashes.append(None) diff --git a/hyperion/model/model_output.py b/hyperion/model/model_output.py index b367f36e..02f7d914 100644 --- a/hyperion/model/model_output.py +++ b/hyperion/model/model_output.py @@ -1,11 +1,9 @@ -from __future__ import print_function, division import os import warnings import numpy as np -from astropy import log as logger -import six +import logging from ..util.constants import c, pi from ..util.functions import FreezableClass @@ -13,6 +11,8 @@ from ..util.otf_hdf5 import on_the_fly_hdf5 from ..grid import CartesianGrid, SphericalPolarGrid, CylindricalPolarGrid, OctreeGrid, AMRGrid, VoronoiGrid +logger = logging.getLogger(__name__) + STOKESD = {} STOKESD['I'] = 0 STOKESD['Q'] = 1 @@ -151,7 +151,7 @@ def _get_origin_slice(self, group, component, source_id=None, dust_id=None, n_sc if track_origin == 'detailed': - if isinstance(source_id, six.string_types) and source_id != 'all': + if isinstance(source_id, str) and source_id != 'all': try: source_id = self.get_available_sources().index(source_id) except ValueError: @@ -330,7 +330,7 @@ def get_sed(self, stokes='I', group=0, technique='peeled', ''' # Check argument types - if not isinstance(stokes, six.string_types): + if not isinstance(stokes, str): raise ValueError("stokes argument should be a string") # Check for inconsistent parameters @@ -654,7 +654,7 @@ def get_image(self, stokes='I', group=0, technique='peeled', ''' # Check argument types - if not isinstance(stokes, six.string_types): + if not isinstance(stokes, str): raise ValueError("stokes argument should be a string") # Check for inconsistent parameters diff --git a/hyperion/model/sed.py b/hyperion/model/sed.py index 12d2d3e4..17e2f9b4 100644 --- a/hyperion/model/sed.py +++ b/hyperion/model/sed.py @@ -1,6 +1,5 @@ import numpy as np -import six from ..util.functions import FreezableClass from ..util.constants import c @@ -118,7 +117,7 @@ def unit(self): @unit.setter def unit(self, value): - if value is None or isinstance(value, six.string_types): + if value is None or isinstance(value, str): self._unit = value else: raise ValueError("unit should be a string") diff --git a/hyperion/model/tests/test_analytical_yso.py b/hyperion/model/tests/test_analytical_yso.py index 73ee9630..bd6e895f 100644 --- a/hyperion/model/tests/test_analytical_yso.py +++ b/hyperion/model/tests/test_analytical_yso.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import pytest import numpy as np diff --git a/hyperion/model/tests/test_bit_level.py b/hyperion/model/tests/test_bit_level.py index 3826f547..01aaaaa4 100644 --- a/hyperion/model/tests/test_bit_level.py +++ b/hyperion/model/tests/test_bit_level.py @@ -8,12 +8,12 @@ import os import shutil import itertools +from io import StringIO import pytest import numpy as np -from six import StringIO from .test_helpers import random_id, assert_identical_results from .. import Model, AnalyticalYSOModel from ...util.constants import pc, lsun, c, au, msun, pi, sigma, rsun diff --git a/hyperion/model/tests/test_filters.py b/hyperion/model/tests/test_filters.py index fce7a41c..08b46854 100644 --- a/hyperion/model/tests/test_filters.py +++ b/hyperion/model/tests/test_filters.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import os import shutil diff --git a/hyperion/model/tests/test_grid_geometry.py b/hyperion/model/tests/test_grid_geometry.py index f3426c78..9f69d5c1 100644 --- a/hyperion/model/tests/test_grid_geometry.py +++ b/hyperion/model/tests/test_grid_geometry.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import os import tempfile diff --git a/hyperion/model/tests/test_helpers.py b/hyperion/model/tests/test_helpers.py index 30869a3e..290dc536 100644 --- a/hyperion/model/tests/test_helpers.py +++ b/hyperion/model/tests/test_helpers.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import os import tempfile diff --git a/hyperion/model/tests/test_image.py b/hyperion/model/tests/test_image.py index 81ee17ec..e7bd0b1c 100644 --- a/hyperion/model/tests/test_image.py +++ b/hyperion/model/tests/test_image.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import os import shutil diff --git a/hyperion/model/tests/test_model.py b/hyperion/model/tests/test_model.py index 9d192776..1e812ee0 100644 --- a/hyperion/model/tests/test_model.py +++ b/hyperion/model/tests/test_model.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import os import tempfile diff --git a/hyperion/model/tests/test_model_copy_link.py b/hyperion/model/tests/test_model_copy_link.py index 84759c0d..75422b08 100644 --- a/hyperion/model/tests/test_model_copy_link.py +++ b/hyperion/model/tests/test_model_copy_link.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import os import shutil diff --git a/hyperion/model/tests/test_model_io.py b/hyperion/model/tests/test_model_io.py index 991c1372..65ca24a1 100644 --- a/hyperion/model/tests/test_model_io.py +++ b/hyperion/model/tests/test_model_io.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division from numpy.testing import assert_equal import pytest diff --git a/hyperion/model/tests/test_output_physical.py b/hyperion/model/tests/test_output_physical.py index 911f2d47..40d2b2da 100644 --- a/hyperion/model/tests/test_output_physical.py +++ b/hyperion/model/tests/test_output_physical.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import pytest import numpy as np diff --git a/hyperion/model/tests/test_sed.py b/hyperion/model/tests/test_sed.py index 6e86526e..33d60f75 100644 --- a/hyperion/model/tests/test_sed.py +++ b/hyperion/model/tests/test_sed.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import os import shutil @@ -8,7 +7,6 @@ from numpy.testing import assert_array_almost_equal_nulp import pytest -import six from .. import Model from ..sed import SED @@ -121,7 +119,7 @@ def test_sed_stokes(self, stokes): def test_sed_stokes_invalid(self, stokes): with pytest.raises(ValueError) as exc: wav, nufnu = self.m.get_sed(stokes=stokes) - if isinstance(stokes, six.string_types): + if isinstance(stokes, str): assert exc.value.args[0] == "Unknown Stokes parameter: %s" % stokes else: assert exc.value.args[0] == "stokes argument should be a string" diff --git a/hyperion/model/tests/test_specific_energy_spectrum.py b/hyperion/model/tests/test_specific_energy_spectrum.py index 132a22fe..f47f1e0c 100644 --- a/hyperion/model/tests/test_specific_energy_spectrum.py +++ b/hyperion/model/tests/test_specific_energy_spectrum.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import shutil diff --git a/hyperion/model/tests/test_spot_source.py b/hyperion/model/tests/test_spot_source.py index bf0c5a04..ba67c165 100644 --- a/hyperion/model/tests/test_spot_source.py +++ b/hyperion/model/tests/test_spot_source.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import os import tempfile diff --git a/hyperion/model/tests/test_use_previous.py b/hyperion/model/tests/test_use_previous.py index 43a30ea5..4aacd19f 100644 --- a/hyperion/model/tests/test_use_previous.py +++ b/hyperion/model/tests/test_use_previous.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division from itertools import product diff --git a/hyperion/sources/source.py b/hyperion/sources/source.py index 21d9d6c0..a2de325e 100644 --- a/hyperion/sources/source.py +++ b/hyperion/sources/source.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import numpy as np from astropy.table import Table, Column @@ -9,7 +8,9 @@ is_numpy_array, bool2str, str2bool, monotonically_increasing from ..util.integrate import integrate_loglog from ..util.validator import validate_scalar -from astropy import log as logger +import logging + +logger = logging.getLogger(__name__) def read_source(handle): diff --git a/hyperion/sources/tests/test_source.py b/hyperion/sources/tests/test_source.py index bc42710d..7780e487 100644 --- a/hyperion/sources/tests/test_source.py +++ b/hyperion/sources/tests/test_source.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import pytest import numpy as np diff --git a/hyperion/sources/tests/test_source_io.py b/hyperion/sources/tests/test_source_io.py index 85d226f6..9f641423 100644 --- a/hyperion/sources/tests/test_source_io.py +++ b/hyperion/sources/tests/test_source_io.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import numpy as np from numpy.testing import assert_equal diff --git a/hyperion/util/constants.py b/hyperion/util/constants.py index 66eb5612..8889de02 100644 --- a/hyperion/util/constants.py +++ b/hyperion/util/constants.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division # Numerical constants, in cgs diff --git a/hyperion/util/convenience.py b/hyperion/util/convenience.py index 0772d50f..5d670838 100644 --- a/hyperion/util/convenience.py +++ b/hyperion/util/convenience.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import numpy as np diff --git a/hyperion/util/functions.py b/hyperion/util/functions.py index c5b684d8..433487e7 100644 --- a/hyperion/util/functions.py +++ b/hyperion/util/functions.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import string import random @@ -11,7 +10,9 @@ import numpy as np from .constants import h, c, k -from astropy import log as logger +import logging + +logger = logging.getLogger(__name__) MAX_FLOAT = np.log(np.finfo('d').max) @@ -274,4 +275,3 @@ def asstr(s): return str(s) else: asstr = str - diff --git a/hyperion/util/integrate.py b/hyperion/util/integrate.py index 19a3b6d0..1f8f5619 100644 --- a/hyperion/util/integrate.py +++ b/hyperion/util/integrate.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import numpy as np diff --git a/hyperion/util/interpolate.py b/hyperion/util/interpolate.py index e68475a0..43da83f6 100644 --- a/hyperion/util/interpolate.py +++ b/hyperion/util/interpolate.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import numpy as np diff --git a/hyperion/util/meshgrid.py b/hyperion/util/meshgrid.py index 4f7b8fe3..2f0ce351 100644 --- a/hyperion/util/meshgrid.py +++ b/hyperion/util/meshgrid.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import numpy as np diff --git a/hyperion/util/parfile.py b/hyperion/util/parfile.py index 8e7b4a89..15635d98 100644 --- a/hyperion/util/parfile.py +++ b/hyperion/util/parfile.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import os diff --git a/hyperion/util/polyhedra.py b/hyperion/util/polyhedra.py index be35fc05..48fc237d 100644 --- a/hyperion/util/polyhedra.py +++ b/hyperion/util/polyhedra.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division from math import sqrt, atan2, degrees diff --git a/hyperion/util/tests/test_convenience.py b/hyperion/util/tests/test_convenience.py index 4285572c..3162c67d 100644 --- a/hyperion/util/tests/test_convenience.py +++ b/hyperion/util/tests/test_convenience.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division from ..convenience import OptThinRadius diff --git a/hyperion/util/tests/test_integrate.py b/hyperion/util/tests/test_integrate.py index b3f8b715..5bee74ac 100644 --- a/hyperion/util/tests/test_integrate.py +++ b/hyperion/util/tests/test_integrate.py @@ -1,4 +1,3 @@ -from __future__ import print_function, division import struct @@ -6,7 +5,6 @@ from numpy.testing import assert_array_almost_equal_nulp import pytest -import six from ..integrate import * @@ -123,7 +121,7 @@ def test_linear_not_monotonic(): y = 2. * x - 1. with pytest.raises(ValueError) as exc: integrate(x, y) - if isinstance(exc.value, six.string_types): + if isinstance(exc.value, str): assert exc.value == 'x is not monotonically increasing' else: assert exc.value.args[0] == 'x is not monotonically increasing' @@ -134,7 +132,7 @@ def test_loglog_not_monotonic(): y = 2. * x - 1. with pytest.raises(ValueError) as exc: integrate_loglog(x, y) - if isinstance(exc.value, six.string_types): + if isinstance(exc.value, str): assert exc.value == 'x is not monotonically increasing' else: assert exc.value.args[0] == 'x is not monotonically increasing' @@ -145,7 +143,7 @@ def test_loglin_not_monotonic(): y = 2. * x - 1. with pytest.raises(ValueError) as exc: integrate_loglin(x, y) - if isinstance(exc.value, six.string_types): + if isinstance(exc.value, str): assert exc.value == 'x is not monotonically increasing' else: assert exc.value.args[0] == 'x is not monotonically increasing' @@ -156,7 +154,7 @@ def test_linlog_not_monotonic(): y = 2. * x - 1. with pytest.raises(ValueError) as exc: integrate_linlog(x, y) - if isinstance(exc.value, six.string_types): + if isinstance(exc.value, str): assert exc.value == 'x is not monotonically increasing' else: assert exc.value.args[0] == 'x is not monotonically increasing' diff --git a/hyperion/util/validator.py b/hyperion/util/validator.py index 307fc82c..52d40c97 100644 --- a/hyperion/util/validator.py +++ b/hyperion/util/validator.py @@ -1,14 +1,13 @@ import numpy as np from astropy import units as u -import six def validate_physical_type(name, value, physical_type): if physical_type is not None: if not isinstance(value, u.Quantity): raise TypeError("{0} should be given as a Quantity object".format(name)) - if isinstance(physical_type, six.string_types): + if isinstance(physical_type, str): if value.unit.physical_type != physical_type: raise TypeError("{0} should be given in units of {1}".format(name, physical_type)) else: