Switch from astropy logger to python logging module and other cleanup

hyperion/__init__.py

@@ -1,3 +1,2 @@
-from __future__ import print_function, division
 
 from .version import __version__

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")

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
 

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

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

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

hyperion/densities/core.py

@@ -1,4 +1,3 @@
-from __future__ import print_function, division
 
 from ..util.functions import FreezableClass
 

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

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

hyperion/densities/tests/test_densities.py

@@ -1,4 +1,3 @@
-from __future__ import print_function, division
 
 import pytest
 import numpy as np

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

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):

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):

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):
 

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):

hyperion/dust/tests/test_emissivities.py

@@ -1,4 +1,3 @@
-from __future__ import print_function, division
 
 import matplotlib.pyplot as plt
 

hyperion/dust/tests/test_mean_opacities.py

@@ -1,4 +1,3 @@
-from __future__ import print_function, division
 
 import matplotlib.pyplot as plt
 

hyperion/dust/tests/test_optical_properties.py

@@ -1,4 +1,3 @@
-from __future__ import print_function, division
 
 import matplotlib.pyplot as plt
 

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")

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:

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):
     '''

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):
     '''