Switch from Travis to GitHub actions

.github/workflows/main.yml

@@ -0,0 +1,54 @@
+name: Continuous Integration
+
+on:
+  push:
+    branches:
+    - '*'
+    tags:
+    - '*'
+  pull_request:
+
+jobs:
+  tests:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: Python 3.6
+            os: ubuntu-latest
+            python: '3.6'
+          - name: Python 3.7
+            os: ubuntu-latest
+            python: '3.7'
+          - name: Python 3.8
+            os: ubuntu-latest
+            python: '3.8'
+          - name: Python 3.9
+            os: ubuntu-latest
+            python: '3.9'
+          - name: Python 3.10
+            os: ubuntu-latest
+            python: '3.10'
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+      with:
+        submodules: 'true'
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python }}
+    - name: Install HDF5 and MPI
+      if: startsWith(matrix.os, 'ubuntu')
+      run: sudo apt-get install libhdf5-serial-dev libmpich-dev
+    - name: Install Hyperion Fortran executables
+      run: |
+        ./configure
+        make serial
+        sudo make install
+    - name: Install Hyperion Python package
+      run: pip install -e .[test]
+    - name: Run tests
+      run: pytest hyperion

hyperion/grid/amr_grid.py

@@ -9,7 +9,7 @@
 import numpy as np
 
 from ..util.meshgrid import meshgrid_nd
-from ..util.functions import FreezableClass, link_or_copy
+from ..util.functions import FreezableClass, link_or_copy, as_str
 from astropy import log as logger
 from .grid_helpers import single_grid_dims
 
@@ -245,7 +245,7 @@ def read_geometry(self, group):
         '''
 
         # Check that grid is indeed AMR
-        if group.attrs['grid_type'].decode('utf-8') != 'amr':
+        if as_str(group.attrs['grid_type']) != 'amr':
             raise Exception("Grid is not an AMR grid")
 
         # Initialize levels list
@@ -285,7 +285,7 @@ def read_geometry(self, group):
                 grid.nz = int(g_grid.attrs['n3'])
 
         # Check that advertised hash matches real hash
-        if group.attrs['geometry'].decode('utf-8') != self.get_geometry_id():
+        if as_str(group.attrs['geometry']) != self.get_geometry_id():
             raise Exception("Calculated geometry hash does not match hash in file")
 
     def read_quantities(self, group, quantities='all'):

hyperion/grid/cartesian_grid.py

@@ -8,7 +8,7 @@
 from astropy import log as logger
 
 from ..util.meshgrid import meshgrid_nd
-from ..util.functions import FreezableClass, is_numpy_array, monotonically_increasing, link_or_copy
+from ..util.functions import FreezableClass, is_numpy_array, monotonically_increasing, link_or_copy, as_str
 from .grid_helpers import single_grid_dims
 
 
@@ -252,15 +252,15 @@ def read_geometry(self, group):
             The HDF5 group to read the grid geometry from.
         '''
 
-        if group.attrs['grid_type'].decode('utf-8') != 'car':
+        if as_str(group.attrs['grid_type']) != 'car':
             raise ValueError("Grid is not cartesian")
 
         self.set_walls(group['walls_1']['x'],
                        group['walls_2']['y'],
                        group['walls_3']['z'])
 
         # Check that advertised hash matches real hash
-        if group.attrs['geometry'].decode('utf-8') != self.get_geometry_id():
+        if as_str(group.attrs['geometry']) != self.get_geometry_id():
             raise Exception("Calculated geometry hash does not match hash in file")
 
     def read_quantities(self, group, quantities='all'):

hyperion/grid/cylindrical_polar_grid.py

@@ -7,7 +7,7 @@
 import numpy as np
 
 from ..util.meshgrid import meshgrid_nd
-from ..util.functions import FreezableClass, is_numpy_array, monotonically_increasing, link_or_copy
+from ..util.functions import FreezableClass, is_numpy_array, monotonically_increasing, link_or_copy, as_str
 from astropy import log as logger
 from .grid_helpers import single_grid_dims
 
@@ -280,15 +280,15 @@ def read_geometry(self, group):
             The HDF5 group to read the grid geometry from.
         '''
 
-        if group.attrs['grid_type'].decode('utf-8') != 'cyl_pol':
+        if as_str(group.attrs['grid_type']) != 'cyl_pol':
             raise ValueError("Grid is not cylindrical polar")
 
         self.set_walls(group['walls_1']['w'],
                        group['walls_2']['z'],
                        group['walls_3']['p'])
 
         # Check that advertised hash matches real hash
-        if group.attrs['geometry'].decode('utf-8') != self.get_geometry_id():
+        if as_str(group.attrs['geometry']) != self.get_geometry_id():
             raise Exception("Calculated geometry hash does not match hash in file")
 
     def read_quantities(self, group, quantities='all'):

hyperion/grid/octree_grid.py

@@ -7,7 +7,7 @@
 import h5py
 import numpy as np
 
-from ..util.functions import FreezableClass, is_numpy_array, link_or_copy
+from ..util.functions import FreezableClass, is_numpy_array, link_or_copy, as_str
 from astropy import log as logger
 from .grid_helpers import single_grid_dims
 
@@ -341,7 +341,7 @@ def read_geometry(self, group):
             The HDF5 group to read the grid geometry from.
         '''
 
-        if group.attrs['grid_type'].decode('utf-8') != 'oct':
+        if as_str(group.attrs['grid_type']) != 'oct':
             raise ValueError("Grid is not an octree")
 
         self.set_walls(group.attrs['x'],
@@ -353,7 +353,7 @@ def read_geometry(self, group):
                        group['cells']['refined'].astype(bool))
 
         # Check that advertised hash matches real hash
-        if group.attrs['geometry'].decode('utf-8') != self.get_geometry_id():
+        if as_str(group.attrs['geometry']) != self.get_geometry_id():
             raise Exception("Calculated geometry hash does not match hash in file")
 
     def read_quantities(self, group, quantities='all'):

hyperion/grid/spherical_polar_grid.py

@@ -7,7 +7,7 @@
 import numpy as np
 
 from ..util.meshgrid import meshgrid_nd
-from ..util.functions import FreezableClass, is_numpy_array, monotonically_increasing, link_or_copy
+from ..util.functions import FreezableClass, is_numpy_array, monotonically_increasing, link_or_copy, as_str
 from astropy import log as logger
 from .grid_helpers import single_grid_dims
 
@@ -290,15 +290,15 @@ def read_geometry(self, group):
             The HDF5 group to read the grid geometry from.
         '''
 
-        if group.attrs['grid_type'].decode('utf-8') != 'sph_pol':
+        if as_str(group.attrs['grid_type']) != 'sph_pol':
             raise ValueError("Grid is not spherical polar")
 
         self.set_walls(group['walls_1']['r'],
                        group['walls_2']['t'],
                        group['walls_3']['p'])
 
         # Check that advertised hash matches real hash
-        if group.attrs['geometry'].decode('utf-8') != self.get_geometry_id():
+        if as_str(group.attrs['geometry']) != self.get_geometry_id():
             raise Exception("Calculated geometry hash does not match hash in file")
 
     def read_quantities(self, group, quantities='all'):

hyperion/grid/tests/test_io.py

@@ -5,7 +5,7 @@
 import pytest
 import six
 
-from ...util.functions import random_id
+from ...util.functions import virtual_file
 from .. import (CartesianGrid,
                 CylindricalPolarGrid,
                 SphericalPolarGrid,
@@ -75,7 +75,7 @@ def setup_method(self, method):
     @pytest.mark.parametrize(('grid_type'), ALL_GRID_TYPES)
     def test_write_read_empty(self, grid_type):
         g = self.grid[grid_type]
-        f = h5py.File(random_id(), driver='core', backing_store=False)
+        f = virtual_file()
         g.write(f)
         h = self.grid_empty[grid_type]()
         h.read(f)
@@ -85,7 +85,7 @@ def test_write_read_empty(self, grid_type):
     @pytest.mark.parametrize(('grid_type'), ALL_GRID_TYPES)
     def test_write_read_single(self, grid_type):
         g = self.grid[grid_type]
-        f = h5py.File(random_id(), driver='core', backing_store=False)
+        f = virtual_file()
         g['density'] = []
         g['density'].append(self.density[grid_type])
         g.write(f)
@@ -101,7 +101,7 @@ def test_write_read_single(self, grid_type):
     @pytest.mark.parametrize(('grid_type'), ALL_GRID_TYPES)
     def test_write_read_double(self, grid_type):
         g = self.grid[grid_type]
-        f = h5py.File(random_id(), driver='core', backing_store=False)
+        f = virtual_file()
         g['density'] = []
         g['density'].append(self.density[grid_type])
         g['density'].append(self.density[grid_type])
@@ -118,7 +118,7 @@ def test_write_read_double(self, grid_type):
     @pytest.mark.parametrize(('grid_type'), ALL_GRID_TYPES)
     def test_write_read_double_multiple(self, grid_type):
         g = self.grid[grid_type]
-        f = h5py.File(random_id(), driver='core', backing_store=False)
+        f = virtual_file()
         g['density'] = []
         g['density'].append(self.density[grid_type])
         g['density'].append(self.density[grid_type])
@@ -140,7 +140,7 @@ def test_write_read_double_multiple(self, grid_type):
     @pytest.mark.parametrize(('grid_type'), ALL_GRID_TYPES)
     def test_write_read_type_mismatch(self, grid_type):
         g = self.grid[grid_type]
-        f = h5py.File(random_id(), driver='core', backing_store=False)
+        f = virtual_file()
         g['density'] = []
         g['density'].append(self.density[grid_type])
         g.write(f)
@@ -162,7 +162,7 @@ def test_write_read_type_mismatch(self, grid_type):
     @pytest.mark.parametrize(('grid_type'), ALL_GRID_TYPES)
     def test_write_read_hash_mismatch(self, grid_type):
         g = self.grid[grid_type]
-        f = h5py.File(random_id(), driver='core', backing_store=False)
+        f = virtual_file()
         g['density'] = []
         g['density'].append(self.density[grid_type])
         g.write(f)
@@ -176,7 +176,7 @@ def test_write_read_hash_mismatch(self, grid_type):
     @pytest.mark.parametrize(('grid_type'), ALL_GRID_TYPES)
     def test_write_read_groups_exist(self, grid_type):
         g = self.grid[grid_type]
-        f = h5py.File(random_id(), driver='core', backing_store=False)
+        f = virtual_file()
         f.create_group('Geometry')
         f.create_group('Quantities')
         g['density'] = []

hyperion/grid/voronoi_grid.py

@@ -10,7 +10,7 @@
 from astropy import log as logger
 from astropy.table import Table
 
-from ..util.functions import FreezableClass, is_numpy_array, link_or_copy
+from ..util.functions import FreezableClass, is_numpy_array, link_or_copy, as_str
 from .grid_helpers import single_grid_dims
 
 
@@ -362,7 +362,7 @@ def read_geometry(self, group):
             The HDF5 group to read the grid geometry from.
         '''
 
-        if group.attrs['grid_type'].decode('utf-8') != 'vor':
+        if as_str(group.attrs['grid_type']) != 'vor':
             raise ValueError("Grid is not an voronoi")
 
         coords = group['cells']['coordinates']
@@ -373,7 +373,7 @@ def read_geometry(self, group):
                         zmin=group.attrs['zmin'], zmax=group.attrs['zmax'])
 
         # Check that advertised hash matches real hash
-        if group.attrs['geometry'].decode('utf-8') != self.get_geometry_id():
+        if as_str(group.attrs['geometry']) != self.get_geometry_id():
             raise Exception("Calculated geometry hash does not match hash in file")
 
         # Avoid re-computing Voronoi table

hyperion/util/functions.py

@@ -21,7 +21,7 @@ def random_id(length=32):
 
 
 def virtual_file():
-    return h5py.File(random_id(), driver='core', backing_store=False)
+    return h5py.File(random_id(), driver='core', backing_store=False, mode='w')
 
 
 def str2bool(value):
@@ -32,6 +32,13 @@ def bool2str(value):
     return np.string_('yes'.encode('utf-8')) if value else np.string_('no'.encode('utf-8'))
 
 
+def as_str(value):
+    if isinstance(value, bytes):
+        return value.decode('utf-8')
+    else:
+        return value
+
+
 def link_or_copy(group, name, link, copy, absolute_paths=False):
     '''
     Link or copy a dataset or group

setup.cfg

@@ -10,7 +10,7 @@ description = Monte-Carlo Radiative Transfer Code
 zip_safe = True
 packages = find:
 include_package_data = True
-setup_requires = numpy>=1.11
+setup_requires = oldest-supported-numpy
 install_requires =
     numpy>=1.11
     matplotlib>=1.5