Update CI to use Python versions 3.7 and 3.10 (#1926)

* Update CI to use Python versions 3.7 and 3.10

* surround 3.10 with quotes to treat as string

* unpin coverage version

* remove obsolete Python 2 related imports

* pin coverage package due to nedbat/coveragepy#916

* pin coveragepy to 5.0.3

* run coverage in parallel mode, combine coverage report, and add type annotation for chunk_layout

* append coverage data only during combine and not run

* output test logs if make check fails

.github/workflows/build-ci.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.6, 3.9]
+        python-version: [3.7, '3.10']
         enable-mpi: [false, true]
 
     steps:
@@ -126,8 +126,8 @@ jobs:
       run: pip install -r python/requirements.txt
 
     - name: Install coverage
-      if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.6 }}
-      run: pip install coverage==4.5.4
+      if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.7 }}
+      run: pip install coverage
 
     - name: Install mpi4py
       if: ${{ matrix.enable-mpi && steps.cache.outputs.cache-hit != true }}
@@ -140,66 +140,67 @@ jobs:
         echo "MEEP_VERSION=${MEEP_VERSION}" >> $GITHUB_ENV
 
     - name: Run configure with OpenMP
-      if: ${{ !(matrix.enable-mpi == false && matrix.python-version == 3.6) && !(matrix.enable-mpi == true && matrix.python-version == 3.9) }}
+      if: ${{ !(matrix.enable-mpi == false && matrix.python-version == 3.7) && !(matrix.enable-mpi == true && matrix.python-version == 3.10) }}
       run: |
         mkdir -p build &&
         pushd build &&
         ../configure --enable-maintainer-mode --prefix=${HOME}/local --with-libctl=${HOME}/local/share/libctl ${MPICONF} --with-openmp &&
         popd
 
     - name: Run configure with coverage
-      if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.6 }}
+      if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.7 }}
       run: ./configure --enable-maintainer-mode --with-coverage --prefix=${HOME}/local --with-libctl=${HOME}/local/share/libctl ${MPICONF}
 
     - name: Run configure with single-precision floating point and swig threads
-      if: ${{ matrix.enable-mpi == true && matrix.python-version == 3.9 }}
+      if: ${{ matrix.enable-mpi == true && matrix.python-version == 3.10 }}
       run: |
         mkdir -p build &&
         pushd build &&
         ../configure --enable-maintainer-mode --prefix=${HOME}/local --with-libctl=${HOME}/local/share/libctl ${MPICONF} --enable-single --enable-swig-python-threads &&
         popd
 
     - name: Run make
-      if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.6 }}
+      if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.7 }}
       run: make ${MKCHECKFLAGS}
 
     - name: Run make check
-      if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.6 }}
+      if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.7 }}
       run: |
         pushd python/ &&
-        make ${MKCHECKFLAGS} check &&
+        { make ${MKCHECKFLAGS} check || cat test-suite.log; } &&
         popd
 
     - name: Run make distcheck
-      if: ${{ !(matrix.enable-mpi == false && matrix.python-version == 3.6) }}
+      if: ${{ !(matrix.enable-mpi == false && matrix.python-version == 3.7) }}
       run: |
         pushd build &&
         make ${MKCHECKFLAGS} distcheck DISTCHECK_CONFIGURE_FLAGS="--with-libctl=${HOME}/local/share/libctl ${MPICONF}" &&
         popd
 
     - name: Generate coverage report
-      if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.6 }}
+      if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.7 }}
       run: |
         pushd python/ &&
+        coverage combine -a &&
         coverage report -i &&
         coverage xml -i &&
         popd
 
     - name: Upload coverage to Codecov
-      if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.6 }}
+      if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.7 }}
       uses: codecov/codecov-action@v1
       with:
         files: ${{ github.workspace }}/python/coverage.xml
 
     - name: Archive C++ test logs
-      if: ${{ failure() && !(matrix.enable-mpi == false && matrix.python-version == 3.6) }}
+      if: ${{ failure() && !(matrix.enable-mpi == false && matrix.python-version == 3.7) }}
       uses: actions/upload-artifact@v2
       with:
         name: cpp-tests-mpi-${{ matrix.enable-mpi }}-log
         path: ${{ github.workspace }}/build/meep-${{ env.MEEP_VERSION }}/_build/sub/tests/test-suite.log
 
     - name: Archive Python test logs
-      if: ${{ failure() && !(matrix.enable-mpi == false && matrix.python-version == 3.6) }}
+      if: ${{ failure() && !(matrix.enable-mpi == false && matrix.python-version == 3.7) }}
       uses: actions/upload-artifact@v2
       with:
         name: py${{ matrix.python-version }}-tests-mpi-${{ matrix.enable-mpi }}-log

doc/docs/Python_User_Interface.md

@@ -87,40 +87,40 @@ control various parameters of the Meep computation.
 
 ```python
 def __init__(self,
-             cell_size: Union[meep.geom.Vector3, Tuple[float, ...], Tuple[int, ...], NoneType] = None,
-             resolution: float = None,
-             geometry: Optional[List[meep.geom.GeometricObject]] = None,
-             sources: Optional[List[meep.source.Source]] = None,
-             eps_averaging: bool = True,
-             dimensions: int = 3,
-             boundary_layers: Optional[List[meep.simulation.PML]] = None,
-             symmetries: Optional[List[meep.simulation.Symmetry]] = None,
-             force_complex_fields: bool = False,
-             default_material: meep.geom.Medium = Medium(),
-             m: float = 0,
-             k_point: Union[meep.geom.Vector3, Tuple[float, ...], Tuple[int, ...], bool] = False,
-             kz_2d: str = 'complex',
-             extra_materials: Optional[List[meep.geom.Medium]] = None,
-             material_function: Optional[Callable[[Union[meep.geom.Vector3, Tuple[float, ...], Tuple[int, ...]]], meep.geom.Medium]] = None,
-             epsilon_func: Optional[Callable[[Union[meep.geom.Vector3, Tuple[float, ...], Tuple[int, ...]]], float]] = None,
-             epsilon_input_file: str = '',
-             progress_interval: float = 4,
-             subpixel_tol: float = 0.0001,
-             subpixel_maxeval: int = 100000,
-             loop_tile_base_db: int = 0,
-             loop_tile_base_eh: int = 0,
-             ensure_periodicity: bool = True,
-             num_chunks: int = 0,
-             Courant: float = 0.5,
-             accurate_fields_near_cylorigin: bool = False,
-             filename_prefix: Optional[str] = None,
-             output_volume: Optional[meep.simulation.Volume] = None,
-             output_single_precision: bool = False,
-             geometry_center: Union[meep.geom.Vector3, Tuple[float, ...], Tuple[int, ...]] = Vector3<0.0, 0.0, 0.0>,
-             force_all_components: bool = False,
-             split_chunks_evenly: bool = True,
-             chunk_layout=None,
-             collect_stats: bool = False):
+             cell_size: 'Optional[Vector3Type]' = None,
+             resolution: 'float' = None,
+             geometry: 'Optional[List[GeometricObject]]' = None,
+             sources: 'Optional[List[Source]]' = None,
+             eps_averaging: 'bool' = True,
+             dimensions: 'int' = 3,
+             boundary_layers: 'Optional[List[PML]]' = None,
+             symmetries: 'Optional[List[Symmetry]]' = None,
+             force_complex_fields: 'bool' = False,
+             default_material: 'Medium' = Medium(),
+             m: 'float' = 0,
+             k_point: 'Union[Vector3Type, bool]' = False,
+             kz_2d: 'str' = 'complex',
+             extra_materials: 'Optional[List[Medium]]' = None,
+             material_function: 'Optional[Callable[[Vector3Type], Medium]]' = None,
+             epsilon_func: 'Optional[Callable[[Vector3Type], float]]' = None,
+             epsilon_input_file: 'str' = '',
+             progress_interval: 'float' = 4,
+             subpixel_tol: 'float' = 0.0001,
+             subpixel_maxeval: 'int' = 100000,
+             loop_tile_base_db: 'int' = 0,
+             loop_tile_base_eh: 'int' = 0,
+             ensure_periodicity: 'bool' = True,
+             num_chunks: 'int' = 0,
+             Courant: 'float' = 0.5,
+             accurate_fields_near_cylorigin: 'bool' = False,
+             filename_prefix: 'Optional[str]' = None,
+             output_volume: 'Optional[Volume]' = None,
+             output_single_precision: 'bool' = False,
+             geometry_center: 'Vector3Type' = Vector3<0.0, 0.0, 0.0>,
+             force_all_components: 'bool' = False,
+             split_chunks_evenly: 'bool' = True,
+             chunk_layout: 'Optional[str, Simulation, BinaryPartition]' = None,
+             collect_stats: 'bool' = False):
 ```
 
 <div class="method_docstring" markdown="1">

python/Makefile.am

@@ -95,7 +95,7 @@ TESTS =                                        \
     $(WVG_SRC_TEST)
 
 if WITH_COVERAGE
-  PY_LOG_COMPILER = coverage run -a --source=$(top_srcdir)/python/meep --omit=$(top_srcdir)/python/tests/*,$(top_srcdir)/python/examples/*,$(top_srcdir)/python/meep/materials.py
+  PY_LOG_COMPILER = coverage run -p --source=$(top_srcdir)/python/meep --omit=$(top_srcdir)/python/tests/*,$(top_srcdir)/python/examples/*,$(top_srcdir)/python/meep/materials.py
 else
   PY_LOG_COMPILER = $(RUNCODE) $(PYTHON)
 endif

python/geom.py

@@ -1,6 +1,4 @@
 # -*- coding: utf-8 -*-
-from __future__ import division
-
 import functools
 import math
 import numbers

python/mpb_data.py

@@ -1,8 +1,5 @@
 # -*- coding: utf-8 -*-
-from __future__ import division
-
 import math
-
 import numpy as np
 import meep as mp
 from . import map_data

python/simulation.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-from __future__ import division, print_function
+from __future__ import annotations
 
 from typing import Callable, List, Tuple, Union, Optional
 
@@ -170,7 +170,7 @@ def p(self):
         return self._p
 
 DefaultPMLProfile = lambda u: u * u
-Vector3Type = Union[Vector3, Tuple[float, ...], Tuple[int, ...]]
+Vector3Type = Union[Vector3, Tuple[float, ...]]
 
 class PML(object):
     """
@@ -968,7 +968,7 @@ def __init__(self,
                  geometry_center: Vector3Type = Vector3(),
                  force_all_components: bool = False,
                  split_chunks_evenly: bool = True,
-                 chunk_layout = None,
+                 chunk_layout: Optional[str, Simulation, BinaryPartition] = None,
                  collect_stats: bool = False):
         """
         All `Simulation` attributes are described in further detail below. In brackets

python/solver.py

@@ -1,6 +1,4 @@
 # -*- coding: utf-8 -*-
-from __future__ import division, print_function
-
 import functools
 import math
 import os

python/source.py

@@ -1,8 +1,5 @@
 # -*- coding: utf-8 -*-
-from __future__ import division
-
 import warnings
-
 import meep as mp
 from meep.geom import Vector3, check_nonnegative
 

python/tests/test_absorber_1d.py

@@ -1,5 +1,3 @@
-from __future__ import division
-
 import unittest
 import meep as mp
 from meep.materials import Al

python/tests/test_antenna_radiation.py

@@ -1,5 +1,3 @@
-from __future__ import division
-
 import meep as mp
 import math
 import numpy as np

python/tests/test_binary_grating.py

@@ -1,5 +1,3 @@
-from __future__ import division
-
 import unittest
 import meep as mp
 import math
@@ -9,7 +7,7 @@
 class TestEigCoeffs(unittest.TestCase):
 
   def run_binary_grating_oblique(self, theta):
-  
+
     resolution = 30        # pixels/um
 
     dpml = 1.0             # PML thickness
@@ -25,7 +23,7 @@ def run_binary_grating_oblique(self, theta):
     cell_size = mp.Vector3(sx,sy,0)
 
     # replace anisotropic PML with isotropic Absorber to attenuate parallel-directed fields of oblique source
-    abs_layers = [mp.Absorber(thickness=dpml,direction=mp.X)] 
+    abs_layers = [mp.Absorber(thickness=dpml,direction=mp.X)]
 
     wvl = 0.5              # center wavelength
     fcen = 1/wvl           # center frequency
@@ -46,7 +44,7 @@ def run_binary_grating_oblique(self, theta):
       k = mp.Vector3(0,0,0)
       symmetries = [mp.Mirror(mp.Y)]
       eig_parity += mp.EVEN_Y
-  
+
     def pw_amp(k,x0):
       def _pw_amp(x):
         return cmath.exp(1j*2*math.pi*k.dot(x+x0))
@@ -71,7 +69,7 @@ def _pw_amp(x):
     refl_flux = sim.add_flux(fcen, 0, 1, mp.FluxRegion(center=refl_pt, size=mp.Vector3(0,sy,0)))
 
     sim.run(until_after_sources=100)
-  
+
     input_flux = mp.get_fluxes(refl_flux)
     input_flux_data = sim.get_flux_data(refl_flux)
 

python/tests/test_cyl_ellipsoid.py

@@ -1,5 +1,3 @@
-from __future__ import division
-
 import unittest
 import meep as mp
 

python/tests/test_diffracted_planewave.py

@@ -1,5 +1,3 @@
-from __future__ import division
-
 import unittest
 import meep as mp
 import math

python/tests/test_faraday_rotation.py

@@ -1,5 +1,3 @@
-from __future__ import division
-
 import unittest
 import numpy as np
 import meep as mp

python/tests/test_fragment_stats.py

@@ -1,5 +1,3 @@
-from __future__ import division
-
 import unittest
 import meep as mp
 

python/tests/test_gaussianbeam.py

@@ -1,5 +1,3 @@
-from __future__ import division
-
 import unittest
 import meep as mp
 import math

python/tests/test_kdom.py

@@ -1,5 +1,3 @@
-from __future__ import division
-
 import unittest
 import meep as mp
 import math
@@ -30,7 +28,7 @@ def run_kdom(self, theta, num_band):
       k = mp.Vector3(0,0,0)
       eig_parity += mp.EVEN_Y
       symmetries = [mp.Mirror(mp.Y)]
-  
+
     sim = mp.Simulation(resolution=resolution,
                         cell_size=cell_size,
                         k_point=k,

python/tests/test_material_dispersion.py

@@ -1,5 +1,3 @@
-from __future__ import division
-
 import unittest
 import numpy as np
 import meep as mp

python/tests/test_medium_evaluations.py

@@ -3,12 +3,10 @@
 # Checks materials with lorentizian, drude, and non uniform diagonals.
 # The extracted values are compared against actual datapoints pulled from
 #   refractiveindex.info.
-# TODO: 
+# TODO:
 #  * check materials with off diagonal components
 #  * check magnetic profiles
 
-from __future__ import division
-
 import unittest
 import meep as mp
 import numpy as np

python/tests/test_mpb.py

@@ -1,5 +1,3 @@
-from __future__ import division, print_function
-
 import glob
 import math
 import os

python/tests/test_oblique_source.py

@@ -1,5 +1,3 @@
-from __future__ import division
-
 import meep as mp
 import math
 import unittest

python/tests/test_physical.py

@@ -1,5 +1,3 @@
-from __future__ import division
-
 import unittest
 import meep as mp
 

python/tests/test_prism.py

@@ -1,5 +1,3 @@
-from __future__ import division
-
 import os
 import unittest
 import numpy as np

python/tests/test_ring.py

@@ -1,7 +1,5 @@
 # Python port of meep/examples/ring.ctl
 # Calculating 2d ring-resonator modes, from the Meep tutorial.
-from __future__ import division
-
 import unittest
 import meep as mp
 

python/tests/test_ring_cyl.py

@@ -1,5 +1,3 @@
-from __future__ import division
-
 import unittest
 import meep as mp
 from utils import ApproxComparisonTestCase