Merge branch 'hyperion-rt:main' into master

Author: dnarayanan

.circleci/config.yml

@@ -0,0 +1,50 @@
+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-20.04
+            python: '3.6'
+          - name: Python 3.7
+            os: ubuntu-20.04
+            python: '3.7'
+          - name: Python 3.8
+            os: ubuntu-20.04
+            python: '3.8'
+          - name: Python 3.9
+            os: ubuntu-20.04
+            python: '3.9'
+          - name: Python 3.10
+            os: ubuntu-20.04
+            python: '3.10'
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+      with:
+        submodules: 'true'
+        fetch-depth: 0
+    - 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 tox
+      run: pip install tox
+    - name: Run tests
+      run: tox -e test-bitlevel

.github/workflows/main.yml

@@ -1,8 +1,7 @@
 About
 -----
 
-[![Build Status](https://travis-ci.org/hyperion-rt/hyperion.svg)](https://travis-ci.org/hyperion-rt/hyperion?branch=master)
-[![CircleCI](https://circleci.com/gh/hyperion-rt/hyperion/tree/master.svg?style=svg)](https://circleci.com/gh/hyperion-rt/hyperion/tree/master)
+[![Continuous Integration](https://github.com/hyperion-rt/hyperion/actions/workflows/main.yml/badge.svg)](https://github.com/hyperion-rt/hyperion/actions/workflows/main.yml)
 [![Documentation Status](https://readthedocs.org/projects/hyperion/badge/?version=stable)](http://docs.hyperion-rt.org/en/stable/?badge=stable)
 
 Hyperion is a 3D Monte-Carlo radiation transfer code - see http://www.hyperion-rt.org

.travis.yml

@@ -2,22 +2,6 @@
 
 from .version import __version__
 
-try:
-    _HYPERION_SETUP_
-except NameError:  # we are not currently running setup.py
-    try:
-        from .util import integrate
-    except ImportError:  # indicates the C extension failed to build
-        import os
-        import sys
-        if os.path.exists('setup.py'):
-            print("\nYou appear to be importing Hyperion from the source code "
-                  "directory. Try changing to a different directory and try "
-                  "importing Hyperion again.\n")
-            sys.exit(0)
-        else:
-            raise
-
 # Set up the test function
 _test_runner = None
 

README.md

@@ -1,23 +1,7 @@
 import warnings
 
-import pytest
-
 from .util.nans import NaNWarning
 
 
-def pytest_addoption(parser):
-    parser.addoption('--generate-reference', help="generate reference results for bit-level tests", type="string")
-    parser.addoption('--enable-bit-level-tests', help="enable bit-level tests", action="store_true")
-
-
 def pytest_configure(config):
     warnings.simplefilter('error', NaNWarning)
-
-
-def pytest_collection_modifyitems(config, items):
-    if config.getoption("--enable-bit-level-tests"):
-        return
-    skip_bit_level = pytest.mark.skip(reason="need --enable-bit-level-tests option to run")
-    for item in items:
-        if "bitlevel" in item.keywords:
-            item.add_marker(skip_bit_level)

hyperion/__init__.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/conftest.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/amr_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/cartesian_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'):