Fix ENV

Signed-off-by: Umberto Zerbinati <zerbinati@maths.ox.ac.uk>
NGSolve · Oct 28, 2023 · 4cffdd7 · 4cffdd7
1 parent e2273d8
commit 4cffdd7
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Showing 7 changed files with 91 additions and 38 deletions.
diff --git a/.github/workflows/FEniCSx.yml b/.github/workflows/FEniCSx.yml
@@ -0,0 +1,35 @@
+# .github/workflows/app.yaml
+name: ngsPETSc FEniCSx tests
+on: 
+    push:
+      branches-ignore:    
+      - 'no-ci/*'
+
+    schedule:
+    - cron:  '30 10 7,14,21,28 * *'
+
+jobs:
+  ngsolve_tests:
+    runs-on: ubuntu-latest
+    container: dolfinx/dolfinx:latest
+    timeout-minutes: 20
+
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v2
+
+      - name: Install Netgen and ngsPETSc
+        run: |
+          pip3 install netgen-mesher \
+          && pip3 install pylint \
+          && export PYTHONPATH=$PYTHONPATH:/usr/local/lib/python3.10/site-packages \
+          && NGSPETSC_NO_INSTALL_REQUIRED=ON pip install .
+
+      - name: Check formatting
+        run: |
+          make lint
+          make lint_test
+
+      - name: Run test suite in serial
+        run: |
+          pytest -v tests/test_fenicsx.py
diff --git a/.github/workflows/ngsPETSc.yml → .github/workflows/NGSolve.yml b/.github/workflows/ngsPETSc.yml → .github/workflows/NGSolve.yml
@@ -1,5 +1,5 @@
 # .github/workflows/app.yaml
-name: ngsPETSc
+name: ngsPETSc NGsolve tests
 on: 
     push:
       branches-ignore:    

diff --git a/Makefile b/Makefile
@@ -1,9 +1,9 @@
 MPI_EXEC = ${PETSC_DIR}/${PETSC_ARCH}/bin/mpiexec
 lint:
-	pylint --disable=C0412,C0103,C0415,C0321,E1101,E0611,R1736,R0401,R0801,R0902,R1702,R0913,R0914,R0903,R0205,R0912,R0915,I1101,W0201,C0209 --variable-naming-style=camelCase --class-naming-style=PascalCase --argument-naming-style=camelCase --attr-naming-style=camelCase ngsPETSc
-	pylint --disable=C0412,C0103,C0415,C0321,C3001,E1101,E0611,R1736,R0401,R0801,R0902,R1702,R0913,R0914,R0903,R0205,R0912,R0915,I1101,W0201,W0406,W0212,C0209 --variable-naming-style=camelCase --class-naming-style=PascalCase --argument-naming-style=camelCase --attr-naming-style=camelCase ngsPETSc/utils
+	pylint --disable=C0412,C0103,C0415,C0321,E0401,E1101,E0611,R1736,R0401,R0801,R0902,R1702,R0913,R0914,R0903,R0205,R0912,R0915,I1101,W0201,C0209 --variable-naming-style=camelCase --class-naming-style=PascalCase --argument-naming-style=camelCase --attr-naming-style=camelCase ngsPETSc
+	pylint --disable=C0412,C0103,C0415,C0321,C3001,E0401,E1101,E0611,R1736,R0401,R0801,R0902,R1702,R0913,R0914,R0903,R0205,R0912,R0915,I1101,W0201,W0406,W0212,C0209 --variable-naming-style=camelCase --class-naming-style=PascalCase --argument-naming-style=camelCase --attr-naming-style=camelCase ngsPETSc/utils
 lint_test:
-	pylint --disable=C0412,C0103,C0415,C0321,E1101,E0611,R1736,R0401,R0914,R0801,R0902,R1702,R0913,R0903,R0205,R0912,R0915,I1101,W0201,C0209 --variable-naming-style=camelCase --class-naming-style=PascalCase --argument-naming-style=camelCase --attr-naming-style=camelCase tests
+	pylint --disable=C0412,C0103,C0415,C0321,E0401,E1101,E0611,R1736,R0401,R0914,R0801,R0902,R1702,R0913,R0903,R0205,R0912,R0915,I1101,W0201,C0209 --variable-naming-style=camelCase --class-naming-style=PascalCase --argument-naming-style=camelCase --attr-naming-style=camelCase tests
 test:
 	pytest tests/test_env.py
 	pytest tests/test_vec.py
@@ -13,6 +13,7 @@ test:
 	pytest tests/test_pc.py
 	pytest tests/test_eps.py
 	pytest tests/test_snes.py
+	pytest tests/test_fenicsx.py
 test_mpi:
 	$(MPI_EXEC) --allow-run-as-root -n 2 pytest --with-mpi tests/test_env.py
 	$(MPI_EXEC) --allow-run-as-root -n 2 pytest --with-mpi tests/test_vec.py
@@ -22,6 +23,7 @@ test_mpi:
 	$(MPI_EXEC) --allow-run-as-root -n 2 pytest --with-mpi tests/test_pc.py
 	$(MPI_EXEC) --allow-run-as-root -n 2 pytest --with-mpi tests/test_eps.py
 	$(MPI_EXEC) --allow-run-as-root -n 2 pytest --with-mpi tests/test_snes.py
+	$(MPI_EXEC) --allow-run-as-root -n 2 pytest --with-mpi tests/test_fenicsx.py
 doc:
 	rm docs/src/notebooks/*.rst
 	jupyter nbconvert --to rst docs/src/notebooks/*.ipynb

diff --git a/ngsPETSc/__init__.py b/ngsPETSc/__init__.py
@@ -2,14 +2,34 @@
 ngsPETSc is a NGSolve/Netgen interface to PETSc
 '''
 import warnings
+
 from ngsPETSc.plex import *
-from ngsPETSc.utils.firedrake import *
-from ngsPETSc.utils.fenicsx import *
+
+#Firedrake
+try:
+    import firedrake
+except ImportError:
+    firedrake = None
+
+if firedrake:
+    from ngsPETSc.utils.firedrake import *
+
+#FEniCSx
+try:
+    import dolfinx
+except ImportError:
+    dolfinx = None
+
+if dolfinx:
+    from ngsPETSc.utils.fenicsx import *
+
+#Netgen
 try:
     import ngsolve
 except ImportError:
     warnings.warn("No NGSolve installed, only working with Netgen.")
     ngsolve = None
+
 if ngsolve:
     from ngsPETSc.mat import *
     from ngsPETSc.vec import *
@@ -18,6 +38,6 @@
     from ngsPETSc.eps import *
     from ngsPETSc.snes import *
 
-VERSION = "0.0.3"
+VERSION = "0.0.4"
 
 __all__ = ["Matrix","VectorMapping","MeshMapping","KrylovSolver","EigenSolver","FiredrakeMesh"]
diff --git a/ngsPETSc/utils/fenicsx.py b/ngsPETSc/utils/fenicsx.py
@@ -3,21 +3,10 @@
 We adopt the same docstring conventiona as the FEniCSx project, since this part of
 the package will only be used in combination with FEniCSx.
 '''
-try:
-    import dolfinx
-    import basix
-    import ufl
-except ImportError:
-    dolfinx = None
-    basix = None
-    ufl = None
-
-import typing 
+import typing
+import dolfinx
 import numpy as np
 
-import netgen as ng
-import netgen.meshing as ngm
-
 from mpi4py import MPI as _MPI
 
 from ngsPETSc import MeshMapping
@@ -33,15 +22,16 @@ class GeometricModel:
             comm: The MPI communicator to use for mesh creation
     """
     def __init__(self,geo, comm: _MPI.Comm):
-            self.geo = geo
-            self.comm = comm
-    
+        self.geo = geo
+        self.comm = comm
+
     def model_to_mesh(self, hmax: float, gdim: int = 2,
-                        partitioner: typing.Callable[
-            [_MPI.Comm, int, int, dolfinx.cpp.graph.AdjacencyList_int32], dolfinx.cpp.graph.AdjacencyList_int32] =
-            dolfinx.mesh.create_cell_partitioner(dolfinx.mesh.GhostMode.none), transform: typing.Any = None,
-            routine: typing.Any = None) -> typing.Tuple[dolfinx.mesh.Mesh, dolfinx.cpp.mesh.MeshTags_int32,
-            dolfinx.cpp.mesh.MeshTags_int32]:
+        partitioner: typing.Callable[
+        [_MPI.Comm, int, int, dolfinx.cpp.graph.AdjacencyList_int32],
+        dolfinx.cpp.graph.AdjacencyList_int32] =
+        dolfinx.mesh.create_cell_partitioner(dolfinx.mesh.GhostMode.none),
+        transform: typing.Any = None, routine: typing.Any = None) -> typing.Tuple[dolfinx.mesh.Mesh,
+        dolfinx.cpp.mesh.MeshTags_int32,dolfinx.cpp.mesh.MeshTags_int32]:
         """Given a NetGen model, take all physical entities of the highest
         topological dimension and create the corresponding DOLFINx mesh.
         
@@ -65,10 +55,10 @@ def model_to_mesh(self, hmax: float, gdim: int = 2,
         ngmesh = self.geo.GenerateMesh(maxh=hmax)
         # Apply any ngs routine post meshing
         if routine is not None:
-            ngmesh, geo = routine(ngmesh, geo)
+            ngmesh, self.geo = routine(ngmesh, self.geo)
         # Applying any PETSc Transform
         if transform is not None:
-            meshMap = MeshMapping(ngmesh) 
+            meshMap = MeshMapping(ngmesh)
             transform.setDM(meshMap.plex)
             transform.setUp()
             newplex = transform.apply(meshMap.plex)
@@ -84,8 +74,8 @@ def model_to_mesh(self, hmax: float, gdim: int = 2,
             T = ngmesh.Elements3D().NumPy()["nodes"]
             T = np.array([list(np.trim_zeros(a, 'b')) for a in list(T)])-1
         ufl_domain = dolfinx.io.gmshio.ufl_mesh(_ngs_to_cells[(gdim,T.shape[1])],gdim)
-        cell_perm = dolfinx.cpp.io.perm_gmsh(dolfinx.cpp.mesh.to_type(str(ufl_domain.ufl_cell())), T.shape[1])
+        cell_perm = dolfinx.cpp.io.perm_gmsh(dolfinx.cpp.mesh.to_type(str(ufl_domain.ufl_cell())),
+                                             T.shape[1])
         T = T[:, cell_perm]
         mesh = dolfinx.mesh.create_mesh(self.comm, T, V, ufl_domain, partitioner)
         return mesh
-
diff --git a/tests/test_env.py b/tests/test_env.py
@@ -38,4 +38,4 @@ def test_ngsPETSc():
     '''
     Testing that ngsPETSc can be imported correctly
     '''
-    assert ngsPETSc.VERSION == "0.0.3"
+    assert ngsPETSc.VERSION == "0.0.4"
diff --git a/tests/test_fenicsx.py b/tests/test_fenicsx.py
@@ -1,13 +1,19 @@
+'''
+This module test the utils.fenicsx class
+'''
 import pytest
 
 def test_square_netgen():
+    '''
+    Testing FEniCSx interface with Netgen generating a square mesh
+    '''
+    from mpi4py import MPI
+    import ngsPETSc.utils.fenicsx as fx
+    from dolfinx.io import XDMFFile
     try:
-        from mpi4py import MPI
-        import ngsPETSc.utils.fenicsx as fx
-        from dolfinx.io import XDMFFile
+        pass
     except ImportError:
         pytest.skip(msg="DOLFINx unavailable, skipping FENICSx test")
-    import numpy as np
 
     from netgen.geom2d import SplineGeometry
     geo = SplineGeometry()
@@ -18,4 +24,4 @@ def test_square_netgen():
         xdmf.write_mesh(domain)
 
 if __name__ == "__main__":
-    test_square_netgen()
+    test_square_netgen()