Make t and n optional arguments in store_checkpoint

CHANGELOG.md

@@ -1,9 +1,11 @@
 # FEniCS-preCICE adapter changelog
 
-## latest
+## 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
 

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

@@ -27,9 +27,18 @@ preCICE-adapter for the open source computing platform FEniCS.
 It is recommended to install [fenicsprecice from PyPI](https://pypi.org/project/fenicsprecice/) via
 
 ```bash
-pip3 install --user fenicsprecice
+pip3 install fenicsprecice
 ```
 
+For more recent pip versions you may encounter the error `error: externally-managed-environment` during installation of the fenicsprecice. You can read why [here](https://packaging.python.org/en/latest/specifications/externally-managed-environments/). In this case, it is recommended to create a virtual environment and install the package in the virtual environment. The following commands will create the virtual environment `venv_name` at the location `path/of/your/venv/`:
+
+```bash
+python3 -m venv --system-site-packages path/of/your/venv/venv_name
+. path/of/your/venv/venv_name/bin/activate
+```
+
+You can replace `path/of/your/venv/venv_name` with the location and name you want to use for your virtual environment. The command `--system-size-packages` will allow the virtual environment to access the FEniCS installation on your system. Refer to the [Python documentation](https://docs.python.org/3/library/venv.html) for further details on virtual environments.
+
 This should work out of the box, if all dependencies are installed correctly. If you face problems during installation or you want to run the tests, see below for a list of dependencies and alternative installation procedures
 
 ### Clone this repository and use pip3

docs/ReleaseGuide.md

@@ -19,10 +19,39 @@ Before starting this process make sure to check that all relevant changes are in
 
     a) If a pre-release is made: Directly hit the "Publish release" button in your Release Draft. Now you can check the artifacts (e.g. release on [PyPI](https://pypi.org/project/fenicsprecice/#history)) of the release. *Note:* As soon as a new tag is created github actions will take care of deploying the new version on PyPI using [this workflow](https://github.com/precice/fenics-adapter/actions?query=workflow%3A%22Upload+Python+Package%22).
 
-    b) If this is a "real" release: As soon as one approving review is made, merge the release PR (`fenics-adapter-vX.X.X`) into `master`.
+    b) If this is a "real" release: As soon as one approving review is made, merge the release PR (`fenics-adapter-vX.X.X`) into `master`. Use **Merge pull request**, don't squash the commits.
 
 5. Merge `master` into `develop` for synchronization of `develop`.
 
 6. If everything is in order up to this point then the new version can be released by hitting the "Publish release" button in your Release Draft.
 
 7. Now there should be a tag for the release. Re-run the [docker release workflow `build-docker.yml` via dispatch](https://github.com/precice/fenics-adapter/actions/workflows/build-docker.yml) such that the correct version is picked up by `versioneer`. Check the version in the container via `docker pull precice/fenics-adapter`, then `docker run -ti precice/fenics-adapter`, and inside the container `$ python3 -c "import fenicsprecice; print(fenicsprecice.__version__)"`.
+
+8. Add an empty commit (details see [here](https://github.com/precice/python-bindings/issues/109)) on master by running the steps:
+
+    ```bash
+    git checkout master
+    git commit --allow-empty -m "post-tag bump"
+    git push
+    ```
+
+    Check that everything is in order via `git log`. Important: The `tag` and `origin/master` should not point to the same commit. For example:
+
+    ```bash
+    commit 9d0d6bf978b2363c7ee041201df4322f930dd456 (HEAD -> master)
+    Author: Benjamin Rodenberg <[email protected]>
+    Date:   Thu Oct 31 08:52:07 2024 +0100
+
+        post-tag bump
+
+    commit 0d8eecb54b4bc582f33f5f38fca77dfe6161a237 (origin/master)
+    Merge: f3abeb0 8ca28ae
+    Author: Benjamin Rodenberg <[email protected]>
+    Date:   Thu Oct 31 08:41:36 2024 +0100
+
+        Merge pull request #184 from precice/fenics-adapter-v2.2.0
+
+        Release v2.2.0
+    ```
+
+    For more details refer to [this issue](https://github.com/precice/python-bindings/issues/109) and [this issue](https://github.com/python-versioneer/python-versioneer/issues/217).

fenicsprecice/fenicsprecice.py

@@ -432,17 +432,17 @@ def initialize(self, coupling_subdomain, read_function_space=None, write_object=
 
         self._participant.initialize()
 
-    def store_checkpoint(self, payload, t, n):
+    def store_checkpoint(self, payload, t = None, n = None):
         """
         Defines an object of class SolverState which stores the current state of the variable and the time stamp.
 
         Parameters
         ----------
         payload : fenics.function or a list of fenics.functions
             Current state of the physical variable(s) of interest for this participant.
-        t : double
+        t : double (optional)
             Current simulation time.
-        n : int
+        n : int (optional)
             Current time window (iteration) number.
         """
         if self._first_advance_done:
@@ -459,14 +459,25 @@ def retrieve_checkpoint(self):
         -------
         u : FEniCS Function
             Current state of the physical variable of interest for this participant.
-        t : double
+        t : double (optional)
             Current simulation time.
-        n : int
+        n : int (optional)
             Current time window (iteration) number.
         """
         assert (not self.is_time_window_complete())
         logger.debug("Restore solver state")
-        return self._checkpoint.get_state()
+
+        # since t and n are optional, they should not be returned, if not specified
+        payload, t, n = self._checkpoint.get_state()
+        match (t, n):
+            case (None, None):
+                return payload
+            case (_, None):
+                return payload, t
+            case (None, _):
+                return payload, n
+            case _:
+                return payload, t, n
 
     def advance(self, dt):
         """

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, <2', '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_write_read.py

@@ -1,7 +1,7 @@
 from unittest.mock import MagicMock, patch
 from unittest import TestCase
 from tests import MockedPrecice
-from fenics import Expression, UnitSquareMesh, FunctionSpace, VectorFunctionSpace, interpolate, SubDomain, near
+from fenics import Expression, UnitSquareMesh, FunctionSpace, VectorFunctionSpace, interpolate, SubDomain, near, UnitIntervalMesh
 import numpy as np
 
 x_left, x_right = 0, 1
@@ -185,3 +185,78 @@ def return_dummy_data(n_points):
                 self.fail(f"Unexpected combination of arg: {arg}, expected_arg: {expected_arg}")
 
         np.testing.assert_almost_equal(list(read_data.values()), return_dummy_data(self.n_vertices))
+
+    def test_optional_parameters(self):
+        from precice import Participant
+        import fenicsprecice
+
+        def test_all_parameters(adapter):
+            #init variables that are tested against
+            nx = 10
+            mesh = UnitIntervalMesh(nx)
+            V = FunctionSpace(mesh, 'P', 2)
+            dummy_value = 1
+            E = Expression("t", t=dummy_value, degree=2)
+            u = interpolate(E, V)
+            t = 0.5
+            n = 42
+            # test adapter
+            adapter.store_checkpoint(u, t, n) # is the old implementation still working?
+            res_u, res_t, res_n = adapter.retrieve_checkpoint()
+            self.assertEqual(res_t, t)
+            self.assertEqual(res_n, n)
+            np.testing.assert_array_equal(res_u.vector(), u.vector())
+
+        def test_opt_parameters(adapter):
+            #init variables that are tested against
+            nx = 10
+            mesh = UnitIntervalMesh(nx)
+            V = FunctionSpace(mesh, 'P', 2)
+            dummy_value = 1
+            E = Expression("t", t=dummy_value, degree=2)
+            u = interpolate(E, V)
+            t = 0.5
+            n = 42
+            # test adapter
+            adapter.store_checkpoint(u, t) # without n
+            res = adapter.retrieve_checkpoint()
+            self.assertEqual(len(res), 2) # correct number of return values
+            res_u, res_t = res
+            self.assertEqual(res_t, t)
+            np.testing.assert_array_equal(res_u.vector(), u.vector())
+
+            adapter.store_checkpoint(u, n) # without t
+            res = adapter.retrieve_checkpoint()
+            self.assertEqual(len(res), 2) # correct number of return values
+            res_u, res_n = res
+            self.assertEqual(res_n, n)
+            np.testing.assert_array_equal(res_u.vector(), u.vector())
+
+        def test_payload_only(adapter):
+            nx = 10
+            mesh = UnitIntervalMesh(nx)
+            V = FunctionSpace(mesh, 'P', 2)
+            dummy_value = 1
+            E = Expression("t", t=dummy_value, degree=2)
+            u = interpolate(E, V)
+            # test adapter
+            adapter.store_checkpoint(u) # no optional parameters
+            res = adapter.retrieve_checkpoint()
+            np.testing.assert_array_equal(res.vector(), u.vector())
+
+
+
+        Participant.is_time_window_complete = MagicMock(return_value=False)
+
+        precice = fenicsprecice.Adapter(self.dummy_config)
+
+        # call the tests
+        test_all_parameters(precice)
+        test_opt_parameters(precice)
+        test_payload_only(precice)
+
+
+
+
+
+