Release v2.2.0

.github/workflows/build-and-test.yml

@@ -22,13 +22,13 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install setuptools wheel twine
+          pip3 install --break-system-packages setuptools wheel twine
       - name: Build distribution
         run:  python3 setup.py sdist
   test:
     name: Run mock unit tests
     runs-on: ubuntu-latest
-    container: quay.io/fenicsproject/stable:current
+    container: benjaminrodenberg/fenics
     steps:
       - name: Checkout Repository
         uses: actions/checkout@v2      
@@ -37,7 +37,7 @@ jobs:
           mkdir -p precice
           echo "from setuptools import setup" >> precice/setup.py
           echo "setup(name='pyprecice', version='3.0.0.0')" >> precice/setup.py
-          python3 -m pip install ./precice/
+          pip3 install --break-system-packages ./precice/
       - name: Run unit tests
         run:  python3 setup.py test -s tests.unit
       - name: Run integration tests

CHANGELOG.md

@@ -1,5 +1,12 @@
 # FEniCS-preCICE adapter changelog
 
+## v2.2.0
+
+* Use `copy(deepcopy=True)` when checkpointing to make checkpointing more user-friendly and secure. IMPORTANT: might increase runtime, please open an issue if you face serious problems. [#172](https://github.com/precice/fenics-adapter/pull/172)
+* Add unit tests for checkpointing. [#173](https://github.com/precice/fenics-adapter/pull/173)
+* Add required version of `mpi4py` to `<4` to avoid crash during installation. [#181](https://github.com/precice/fenics-adapter/pull/181)
+* Remove checks for FEniCS installation and python3 from `setup.py` since the approach is deprecated. [#182](https://github.com/precice/fenics-adapter/pull/182)
+
 ## 2.1.0
 
 * Additionally support checkpoints being provided as a list or tuple (of FEniCS Functions). [#170](https://github.com/precice/fenics-adapter/pull/170)

CITATION.cff

@@ -32,7 +32,7 @@ abstract: >-
   preCICE-adapter for the open source computing platform
   FEniCS.
 license: LGPL-3.0
-version: 2.1.0
+version: 2.2.0
 preferred-citation:
   title: "FEniCS-preCICE: Coupling FEniCS to other Simulation Software"
   type: "article"

README.md

@@ -86,7 +86,7 @@ To create and install the `fenicsprecice` python package the following instructi
 
 ## Development history
 
-The initial version of this adapter was developed by [Benjamin Rodenberg](https://www.cs.cit.tum.de/sccs/personen/benjamin-rodenberg/) during his research stay at Lund University in the group for [Numerical Analysis](http://www.maths.lu.se/english/research/research-divisions/numerical-analysis/) in close collaboration with Peter Meisrimel.
+The initial version of this adapter was developed by [Benjamin Rodenberg](https://www.cs.cit.tum.de/sccs/personen/benjamin-rodenberg/) during his research stay at Lund University in the group for [Numerical Analysis (Philipp Birken)](https://www.maths.lu.se/forskning/forskningsavdelningar/numerisk-analys/forskning/) in close collaboration with Peter Meisrimel.
 
 [Richard Hertrich](https://github.com/richahert) contributed the possibility to perform FSI simulations using the adapter in his [Bachelor thesis](https://mediatum.ub.tum.de/node?id=1520579).
 

fenicsprecice/solverstate.py

@@ -13,9 +13,9 @@ def __init__(self, payload, t, n):
             Iteration number.
         """
         try:
-            self.payload = payload.copy()
-        except AttributeError:  # if .copy() does not exist, it probably is a list
-            self.payload = [item.copy() for item in payload]
+            self.payload = payload.copy(deepcopy=True)
+        except (AttributeError, TypeError):  # AttributeError, if .copy() does not exist; TypeError, if .copy(deepcopy) does not exist. -> Probably a list
+            self.payload = [item.copy(deepcopy=True) for item in payload]
 
         self.t = t
         self.n = n
@@ -34,9 +34,9 @@ def get_state(self):
             Iteration number.
         """
         try:
-            return self.payload.copy(), self.t, self.n
-        except AttributeError:  # if .copy() does not exist, it probably is a list
-            return [item.copy() for item in self.payload], self.t, self.n
+            return self.payload.copy(deepcopy=True), self.t, self.n
+        except (AttributeError, TypeError):  # AttributeError, if .copy() does not exist; TypeError, if .copy(deepcopy) does not exist. -> Probably a list
+            return [item.copy(deepcopy=True) for item in self.payload], self.t, self.n
 
     def print_state(self):
         payload, t, n = self.get_state()

setup.py

@@ -1,29 +1,6 @@
 import os
 from setuptools import setup
 import versioneer
-import warnings
-
-# from https://stackoverflow.com/a/9079062
-import sys
-if sys.version_info[0] < 3:
-    raise Exception("fenicsprecice only supports Python3. Did you run $python setup.py <option>.? "
-                    "Try running $python3 setup.py <option>.")
-
-if sys.version_info[1] == 6 and sys.version_info[2] == 9:
-    warnings.warn("It seems like you are using Python version 3.6.9. There is a known bug with this Python version "
-                  "when running the tests (see https://github.com/precice/fenics-adapter/pull/61). If you want to "
-                  "run the tests, please install a different Python version.")
-
-try:
-    from fenics import *
-except ModuleNotFoundError:
-    warnings.warn("No FEniCS installation found on system. Please install FEniCS and check the installation.\n\n"
-                  "You can check this by running the command\n\n"
-                  "python3 -c 'from fenics import *'\n\n"
-                  "Please check https://fenicsproject.org/download/ for installation guidance.\n"
-                  "The installation will continue, but please be aware that your installed version of the "
-                  "fenics-adapter might not work as expected.")
-
 this_directory = os.path.abspath(os.path.dirname(__file__))
 with open(os.path.join(this_directory, 'README.md'), encoding='utf-8') as f:
     long_description = f.read()
@@ -39,6 +16,6 @@
       author_email='[email protected]',
       license='LGPL-3.0',
       packages=['fenicsprecice'],
-      install_requires=['pyprecice>=3.0.0.0', 'scipy', 'numpy>=1.13.3', 'mpi4py'],
+      install_requires=['pyprecice>=3.0.0.0', 'scipy', 'numpy>=1.13.3, <2', 'mpi4py<4'],
       test_suite='tests',
       zip_safe=False)

tests/integration/test_fenicsprecice.py

@@ -25,7 +25,11 @@ def assign(self, new_value):
         """
         self.value = new_value.value
 
-    def copy(self):
+    def copy(self, deepcopy=False):
+        """
+        mock of dolfin.Function.copy
+        :param deepcopy: has no effect but we need to provide it to avoid throwing TypeError if copy(deepcopy=True) is called
+        """
         returned_array = MockedArray()
         returned_array.value = self.value
         return returned_array

tests/unit/test_checkpointing.py

@@ -0,0 +1,96 @@
+from unittest.mock import MagicMock
+from unittest import TestCase
+from fenics import FunctionSpace, UnitSquareMesh, Expression, interpolate
+from fenicsprecice.solverstate import SolverState
+
+
+class TestCheckpointing(TestCase):
+    def test_solverstate_basic(self):
+        """
+        Check if correct values are read from the checkpoint, while the state of the object that is copied is not changed
+        """
+        n = 1
+        size = 5
+        mesh = UnitSquareMesh(size, size)
+        V = FunctionSpace(mesh, 'P', 2)
+        dummy_value = 1
+        E = Expression("t", t=dummy_value, degree=2)
+        u = interpolate(E, V)
+
+        # "write checkpoint"
+        sstate = SolverState(u, dummy_value, n)
+        # "read checkpoint"
+        u_cp, t_cp, n_cp = sstate.get_state()
+
+        # check values
+        self.assertEqual(t_cp, dummy_value)
+        self.assertEqual(n, n_cp)
+        # function should be the same everywhere (-> check vector values of the function)
+        vec_u = u.vector()
+        vec_u_cp = u_cp.vector()
+        for i in range(size * size):
+            self.assertAlmostEqual(vec_u[i], vec_u_cp[i])
+
+    def test_solverstate_modification_vector(self):
+        """
+        Check if correct values are read from the checkpoint, if the dof vector of the dolfin functions are changed directly
+
+        Motivation for this test: Related to https://github.com/precice/fenics-adapter/pull/172 and https://github.com/precice/tutorials/pull/554
+        """
+        n = 1
+        size = 5
+        mesh = UnitSquareMesh(size, size)
+        V = FunctionSpace(mesh, 'P', 2)
+        ref_value = 1
+        E = Expression("t", t=ref_value, degree=2)
+        u = interpolate(E, V)
+
+        # "write checkpoint"
+        sstate = SolverState(u, ref_value, n)
+
+        # modify state of u
+        dummy_value = ref_value + 2
+        u.vector()[:] = dummy_value
+
+        # "read checkpoint"
+        u_cp, _, _ = sstate.get_state()
+
+        # check values
+        # function should be the same everywhere
+        # (so the vector values should all be ref_value)
+        vec_u_cp = u_cp.vector()
+        for i in range(size * size):
+            self.assertAlmostEqual(ref_value, vec_u_cp[i])
+
+    def test_solverstate_modification_assign(self):
+        """
+        Check if correct values are read from the checkpoint, if the dof of the dolfin functions are changed with the assign function
+        and not directly via the dof vector
+        """
+        n = 1
+        size = 5
+        mesh = UnitSquareMesh(size, size)
+        V = FunctionSpace(mesh, 'P', 2)
+        ref_value = 1
+        E = Expression("t", t=ref_value, degree=2)
+        u = interpolate(E, V)
+
+        # "write checkpoint"
+        sstate = SolverState(u, ref_value, n)
+
+        # modify state of u
+        # "compute" new solution
+        dummy_value = ref_value + 2
+        E.t = dummy_value
+        u2 = interpolate(E, V)
+        u.assign(u2)
+
+        # "read checkpoint"
+        u_cp, _, _ = sstate.get_state()
+
+        # check values
+        # function should be the same everywhere
+        # (so the vector values should all be ref_value)
+        vec_u_cp = u_cp.vector()
+        for i in range(size * size):
+            self.assertAlmostEqual(ref_value, vec_u_cp[i])

tools/testing/docker/Dockerfile

@@ -0,0 +1,14 @@
+# Dockerfile to build a ubuntu image containing the installed Debian package of a release 
+FROM ubuntu:24.04
+
+# Add the precice user to run test with mpi
+RUN useradd -m -s /bin/bash precice
+ENV PRECICE_USER=precice
+
+# Installing necessary dependencies
+RUN apt-get -qq update && \
+    apt-get -qq install software-properties-common && \
+    add-apt-repository -y ppa:fenics-packages/fenics && \
+    apt-get -qq update && \
+    apt-get -qq install --no-install-recommends fenics python3-pip && \
+    rm -rf /var/lib/apt/lists/*