Import six standalone and gfortran9(?) bugfix

.gitignore

@@ -12,3 +12,7 @@ htmlcov
 *.rtin
 *.rtout
 build_cmake
+.vscode
+dist
+Hyperion.egg-info
+

hyperion/conf/conf_files.py

@@ -3,7 +3,7 @@
 import warnings
 import numpy as np
 from astropy import log as logger
-from astropy.extern import six
+import six
 
 from ..util.functions import FreezableClass, bool2str, str2bool, is_numpy_array
 from ..filter import Filter

hyperion/densities/alpha_disk.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 from astropy import log as logger
-from astropy.extern import six
+import six
 
 from ..dust import SphericalDust
 from ..util.constants import pi, G

hyperion/densities/ambient_medium.py

@@ -1,7 +1,7 @@
 from __future__ import print_function, division
 
 import numpy as np
-from astropy.extern import six
+import six
 
 from ..dust import SphericalDust
 from ..grid import SphericalPolarGrid

hyperion/densities/bipolar_cavity.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 from astropy import log as logger
-from astropy.extern import six
+import six
 
 from ..util.functions import FreezableClass
 from ..dust import SphericalDust

hyperion/densities/flared_disk.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 from astropy import log as logger
-from astropy.extern import six
+import six
 
 from ..dust import SphericalDust
 from ..util.constants import pi

hyperion/densities/power_law_envelope.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 from astropy import log as logger
-from astropy.extern import six
+import six
 
 from ..dust import SphericalDust
 from ..grid import SphericalPolarGrid, CylindricalPolarGrid

hyperion/densities/ulrich_envelope.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 from astropy import log as logger
-from astropy.extern import six
+import six
 
 from ..dust import SphericalDust
 from ..grid import SphericalPolarGrid, CylindricalPolarGrid

hyperion/dust/dust_type.py

@@ -17,7 +17,7 @@
 import h5py
 import numpy as np
 from astropy import log as logger
-from astropy.extern import six
+import six
 
 from ..version import __version__
 

hyperion/filter/filter.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 
-from astropy.extern import six
+import six
 from astropy import units as u
 
 from ..util.integrate import integrate

hyperion/grid/tests/test_io.py

@@ -3,7 +3,7 @@
 import h5py
 import numpy as np
 import pytest
-from astropy.extern import six
+import six
 
 from ...util.functions import random_id
 from .. import (CartesianGrid,

hyperion/grid/tests/test_views.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 import pytest
-from astropy.extern import six
+import six
 
 from hyperion.grid import CartesianGrid, CylindricalPolarGrid, SphericalPolarGrid, AMRGrid, OctreeGrid
 

hyperion/grid/yt3_wrappers.py

@@ -1,7 +1,7 @@
 from __future__ import print_function, division
 
 import numpy as np
-from astropy.extern import six
+import six
 from astropy import log as logger
 
 

hyperion/importers/orion.py

@@ -3,7 +3,7 @@
 import numpy as np
 
 from astropy import log as logger
-from astropy.extern import six
+import six
 
 from ..grid.amr_grid import Grid, Level, AMRGrid
 

hyperion/model/image.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-from astropy.extern import six
+import six
 
 from ..util.functions import FreezableClass, is_numpy_array
 from ..util.constants import c

hyperion/model/model.py

@@ -9,7 +9,7 @@
 import numpy as np
 
 from astropy import log as logger
-from astropy.extern import six
+import six
 
 from ..version import __version__
 from ..util.functions import delete_file

hyperion/model/model_output.py

@@ -5,7 +5,7 @@
 
 import numpy as np
 from astropy import log as logger
-from astropy.extern import six
+import six
 
 from ..util.constants import c, pi
 from ..util.functions import FreezableClass

hyperion/model/sed.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-from astropy.extern import six
+import six
 
 from ..util.functions import FreezableClass
 from ..util.constants import c

hyperion/model/tests/test_bit_level.py

@@ -9,10 +9,13 @@
 import shutil
 import itertools
 
-import pytest
+try:
+    import pytest
+except:
+    from astropy.tests.helper import pytest
 import numpy as np
 
-from astropy.extern.six import StringIO
+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
@@ -25,7 +28,6 @@
 
 bit_level = pytest.mark.skipif(str(not pytest.config.getoption('enable_bit_level_tests')))
 
-
 @pytest.fixture(scope="module")
 def generate(request):
     generate_reference = request.config.getvalue("generate_reference")

hyperion/model/tests/test_sed.py

@@ -8,7 +8,7 @@
 from numpy.testing import assert_array_almost_equal_nulp
 
 import pytest
-from astropy.extern import six
+import six
 
 from .. import Model
 from ..sed import SED

hyperion/util/tests/test_integrate.py

@@ -6,7 +6,7 @@
 from numpy.testing import assert_array_almost_equal_nulp
 
 import pytest
-from astropy.extern import six
+import six
 
 from ..integrate import *
 

hyperion/util/validator.py

@@ -1,7 +1,7 @@
 import numpy as np
 
 from astropy import units as u
-from astropy.extern import six
+import six
 
 
 def validate_physical_type(name, value, physical_type):

setup.py

@@ -100,6 +100,6 @@ def run(self):
       cmdclass=cmdclass,
       ext_modules=ext_modules,
       setup_requires=['numpy>=1.11'],
-      install_requires=['numpy>=1.11', 'matplotlib>=1.5', 'astropy>=1.2', 'h5py>=2.4', 'yt>=3.2'],
+      install_requires=['numpy>=1.11', 'matplotlib>=1.5', 'astropy>=1.2', 'h5py>=2.4', 'yt>=3.2', 'six'],
       extras_require={'test': ['pytest'],
                       'docs': ['sphinx', 'numpydoc']})

src/dust/dust_interact.f90

@@ -28,7 +28,10 @@ subroutine interact(p, force_scatter)
     real(dp) :: xi,albedo
     real(dp) :: energy_scaling
     logical,optional :: force_scatter
+    logical :: force_scatter_val = .false.
 
+    if(present(force_scatter)) force_scatter_val = force_scatter
+
     ! given the density and energy of each dust type, process a photon
     ! this means finding out whether to scatter or aborb the photon, and to do
     ! whatever needs doing
@@ -43,7 +46,7 @@ subroutine interact(p, force_scatter)
     p%s_prev = p%s
 
     ! Decide whether to absorb or scatter
-    if(present(force_scatter) .and. force_scatter) then
+    if(force_scatter_val) then
       xi = 0._dp
     else
       call random(xi)
@@ -69,7 +72,7 @@ subroutine interact(p, force_scatter)
 
     call angle3d_to_vector3d(p%a,p%v)
 
-    if(present(force_scatter) .and. force_scatter) then
+    if(force_scatter_val) then
       p%energy = p%energy * albedo
     end if
 

src/grid/grid_physics_3d.f90

@@ -453,7 +453,7 @@ logical function specific_energy_converged() result(converged)
 
     write(*,*)
     write(*,'("     -> Percentile: ",F7.2)') convergence_percentile
-    write(*,'("     -> Value @ Percentile: ",F10.2)') value
+    write(*,'("     -> Value @ Percentile: ",E10.3)') value
     if(value_prev < huge(1._dp)) then
        if(value == 0._dp) then
           write(*,'("     -> Exact convergence")')