Merge pull request #20 from scientificcomputing/finsberg/fixes-for-conda

Fixes for conda

Author: finsberg

tests/conftest.py

@@ -41,6 +41,7 @@ def backend(request):
 def cluster():
     cluster = ipp.Cluster(engines="mpi", n=2)
     rc = cluster.start_and_connect_sync()
+    rc.wait_for_engines(n=2)
     yield rc
     cluster.stop_cluster_sync()
 

tests/test_legacy_readers.py

@@ -14,7 +14,6 @@
 import numpy as np
 import pytest
 import ufl
-from dolfinx.fem.petsc import LinearProblem
 
 from io4dolfinx import (
     read_cell_data,
@@ -110,6 +109,11 @@ def test_legacy_function(backend):
     f = ufl.conditional(ufl.gt(x[0], 0.5), x[1], 2 * x[0])
     L = ufl.inner(f, v) * ufl.dx
 
+    if not dolfinx.has_petsc4py:
+        pytest.skip("dolfinx not configured with PETSc4py")
+
+    from dolfinx.fem.petsc import LinearProblem
+
     uh = dolfinx.fem.Function(V)
     if "petsc_options_prefix" in inspect.signature(LinearProblem.__init__).parameters.keys():
         extra_options = {"petsc_options_prefix": "legacy_test"}
@@ -139,6 +143,8 @@ def test_read_legacy_function_from_checkpoint(backend):
     if not path.exists():
         pytest.skip(f"{path} does not exist")
 
+    from dolfinx.fem.petsc import LinearProblem
+
     mesh = read_mesh_from_legacy_h5(path, comm, "/Mesh/mesh", backend=backend)
 
     V = dolfinx.fem.functionspace(mesh, ("DG", 2))
@@ -149,6 +155,9 @@ def test_read_legacy_function_from_checkpoint(backend):
     f = ufl.conditional(ufl.gt(x[0], 0.5), x[1], 2 * x[0])
     L = ufl.inner(f, v) * ufl.dx
 
+    if not dolfinx.has_petsc4py:
+        pytest.skip("dolfinx not configured with PETSc4py")
+
     uh = dolfinx.fem.Function(V)
     if "petsc_options_prefix" in inspect.signature(LinearProblem.__init__).parameters.keys():
         extra_options = {"petsc_options_prefix": "legacy_checkpoint_test"}

tests/test_vtkhdf.py

@@ -105,7 +105,7 @@ def test_write_point_data(dtype, tmp_path, cell_type):
             filename=filename, name="u", mesh=grid, time=tj, backend="vtkhdf"
         )
         v_ref = Function(u.function_space, dtype=u.x.array.dtype)
-        atol = 10 * np.finfo(u.x.array.dtype).eps
+        atol = 15 * np.finfo(u.x.array.dtype).eps
         v_ref.interpolate(lambda x: f(x, tj))
         np.testing.assert_allclose(u.x.array, v_ref.x.array, atol=atol)
 
@@ -124,7 +124,7 @@ def test_write_point_data(dtype, tmp_path, cell_type):
             filename=blocked_file, name="u", mesh=grid, time=tk, backend="vtkhdf"
         )
         v_ref = Function(u.function_space, dtype=u.x.array.dtype)
-        atol = 10 * np.finfo(u.x.array.dtype).eps
+        atol = 15 * np.finfo(u.x.array.dtype).eps
         v_ref.interpolate(lambda x: g(x, tk))
         np.testing.assert_allclose(u.x.array, v_ref.x.array, atol=atol)
 
@@ -160,7 +160,7 @@ def test_write_cell_data(dtype, tmp_path, cell_type):
             filename=filename, name="u", mesh=grid, time=tj, backend="vtkhdf"
         )
         v_ref = Function(u.function_space, dtype=u.x.array.dtype)
-        atol = 10 * np.finfo(u.x.array.dtype).eps
+        atol = 15 * np.finfo(u.x.array.dtype).eps
         v_ref.interpolate(lambda x: f(x, tj))
         np.testing.assert_allclose(u.x.array, v_ref.x.array, atol=atol)
 
@@ -179,7 +179,7 @@ def test_write_cell_data(dtype, tmp_path, cell_type):
             filename=blocked_file, name="u", mesh=grid, time=tk, backend="vtkhdf"
         )
         v_ref = Function(u.function_space, dtype=u.x.array.dtype)
-        atol = 10 * np.finfo(u.x.array.dtype).eps
+        atol = 15 * np.finfo(u.x.array.dtype).eps
         v_ref.interpolate(lambda x: g(x, tk))
         np.testing.assert_allclose(u.x.array, v_ref.x.array, atol=atol)
 
@@ -254,7 +254,7 @@ def test_write_meshtags(dtype, tmp_path, generate_reference_map):
         )
         org_maps[dim] = generate_reference_map(mesh, et, comm, root)
 
-    tol = 10 * np.finfo(dtype).eps
+    tol = 15 * np.finfo(dtype).eps
     # Read in hex grid from second time step
     hex_mesh = io4dolfinx.read_mesh(
         filename, comm, time=1.0, backend_args={"name": "hex"}, backend="vtkhdf"
@@ -288,7 +288,7 @@ def test_write_meshtags(dtype, tmp_path, generate_reference_map):
 
 @pytest.mark.parametrize("dtype", [np.float32, np.float64])
 def test_read_write_pointdata(dtype, tmp_path):
-    tol = 10 * np.finfo(dtype).eps
+    tol = 15 * np.finfo(dtype).eps
 
     comm = MPI.COMM_WORLD
     tmp_path = comm.bcast(tmp_path, root=0)
@@ -360,7 +360,7 @@ def f(x, t):
 
 @pytest.mark.parametrize("dtype", [np.float32, np.float64])
 def test_read_write_celldata(dtype, tmp_path):
-    tol = 10 * np.finfo(dtype).eps
+    tol = 15 * np.finfo(dtype).eps
 
     comm = MPI.COMM_WORLD
     tmp_path = comm.bcast(tmp_path, root=0)
@@ -436,7 +436,7 @@ def f(x, t):
 
 @pytest.mark.parametrize("dtype", [np.float32, np.float64])
 def test_read_write_mix_data(dtype, tmp_path):
-    tol = 10 * np.finfo(dtype).eps
+    tol = 15 * np.finfo(dtype).eps
 
     mesh = create_unit_square(MPI.COMM_WORLD, 5, 7, dtype=dtype)