Merge pull request #122 from precice/fenics-adapter-v1.1.0

Release v1.1.0

Author: IshaanDesai

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

@@ -18,9 +18,11 @@ jobs:
         uses: actions/checkout@v2      
       - name: Install fake precice
         run:  |
-          mkdir -p precice 
+          mkdir -p precice
           echo "from setuptools import setup" >> precice/setup.py
           echo "setup(name='pyprecice', version='2.0.2.1')" >> precice/setup.py
           python3 -m pip install ./precice/
       - name: Run unit tests
-        run:  python3 setup.py test
+        run:  python3 setup.py test -s tests.unit
+      - name: Run integration tests
+        run:  python3 setup.py test -s tests.integration

.github/workflows/check-pep8.yml

@@ -0,0 +1,15 @@
+name: autopep8
+on: push
+jobs:
+  autopep8:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: autopep8 
+        id: autopep8
+        uses: peter-evans/autopep8@v1
+        with:
+          args: --recursive --diff --aggressive --aggressive --exit-code --ignore E402 --max-line-length 120 .
+      - name: Fail if autopep8 made changes
+        if: ${{ steps.autopep8.outputs.exit-code == 2 }}
+        run: exit 1

.github/workflows/run-tutorials.yml

@@ -0,0 +1,60 @@
+name: Run preCICE Tutorials
+on:
+  push:
+    branches:
+      - master
+      - develop
+  pull_request:
+    paths:
+      - '**'
+      
+jobs:  
+  run_ht_simple:
+    name: Run HT, simple
+    runs-on: ubuntu-latest
+    container: precice/precice
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v2      
+      - name: Install Dependencies & FEniCS
+        run: |
+          apt-get -qq update
+          apt-get -qq install software-properties-common python3-dev python3-pip git apt-utils
+          add-apt-repository -y ppa:fenics-packages/fenics
+          apt-get -qq install --no-install-recommends fenics
+          rm -rf /var/lib/apt/lists/*
+      - name: Install adapter
+        run:  pip3 install --user .
+      - name: Fix broken FEniCS installation (see https://fenicsproject.discourse.group/t/installing-python-package-with-fenics-dependency-breaks-fenics-installation/4476)
+        run: pip3 uninstall -y fenics-ufl
+      - name: Get tutorials
+        run: git clone -b develop https://github.com/precice/tutorials.git
+      - name: Run tutorial
+        run: | 
+          cd tutorials/partitioned-heat-conduction/fenics
+          python3 heat.py -d & python3 heat.py -n
+        
+  run_ht_complex:
+    name: Run HT, complex
+    runs-on: ubuntu-latest
+    container: precice/precice
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v2      
+      - name: Install Dependencies & FEniCS
+        run: |
+          apt-get -qq update
+          apt-get -qq install software-properties-common python3-dev python3-pip git apt-utils
+          add-apt-repository -y ppa:fenics-packages/fenics
+          apt-get -qq install --no-install-recommends fenics
+          rm -rf /var/lib/apt/lists/*
+      - name: Install adapter
+        run:  pip3 install --user .
+      - name: Fix broken FEniCS installation (see https://fenicsproject.discourse.group/t/installing-python-package-with-fenics-dependency-breaks-fenics-installation/4476)
+        run: pip3 uninstall -y fenics-ufl
+      - name: Get tutorials
+        run: git clone -b develop https://github.com/precice/tutorials.git
+      - name: Run tutorial
+        run: |
+          cd tutorials/partitioned-heat-conduction-complex/fenics
+          python3 heat.py -d -i complex & python3 heat.py -n -i complex

.travis.yml

@@ -1,7 +1,9 @@
-matrix: 
+matrix:
+  allow_failures:
+  - name: "Systemtests [failure allowed]"
   include: 
   - os: linux
-    name: "Systemtests"
+    name: "Systemtests [failure allowed]"
     if: fork = false AND ( branch = master OR branch = develop )
     python: "3.6" 
     env: PY=python3

CHANGELOG.md

@@ -1,5 +1,10 @@
 # FEniCS-preCICE adapter changelog
 
+## 1.1.0
+
+* Only warn during initialization, if duplicate boundary point is found for point sources.
+* Remove deprecated package `fenicsadapter`. Don't use `import fenicsadapter`. Please use `import fenicsprecice`. https://github.com/precice/fenics-adapter/pull/121
+
 ## 1.0.1
 
 * Bugfix for PointSources https://github.com/precice/fenics-adapter/issues/109

README.md

@@ -1,21 +1,24 @@
 FEniCS-preCICE adapter
 ----------------------
 
-<a style="text-decoration: none" href="https://travis-ci.com/precice/fenics-adapter" target="_blank">
-    <img src="https://travis-ci.com/precice/fenics-adapter.svg?branch=master" alt="Build status">
-</a>
 <a style="text-decoration: none" href="https://github.com/precice/fenics-adapter/blob/master/LICENSE" target="_blank">
     <img src="https://img.shields.io/github/license/precice/fenics-adapter.svg" alt="GNU LGPL license">
 </a>
 
-preCICE-adapter for the open source computing platform FEniCS
+<a style="text-decoration: none" href="https://github.com/precice/fenics-adapter/actions/workflows/build-and-test.yml" target="_blank">
+    <img src="https://github.com/precice/fenics-adapter/actions/workflows/build-and-test.yml/badge.svg" alt="Build and Test">
+</a>
+<a style="text-decoration: none" href="https://github.com/precice/fenics-adapter/actions/workflows/run-tutorials.yml" target="_blank">
+    <img src="https://github.com/precice/fenics-adapter/actions/workflows/run-tutorials.yml/badge.svg" alt="Run preCICE Tutorials">
+</a>
+<a style="text-decoration: none" href="https://pypi.org/project/fenicsprecice/" target="_blank">
+    <img src="https://github.com/precice/fenics-adapter/actions/workflows/pythonpublish.yml/badge.svg" alt="Upload Python Package">
+</a> 
 
-_**Note:** This adapter is currently purely expermental and limited in functionality. If you are interested in using it or you want to contribute, feel free to contact us via the [preCICE mailing list](https://mailman.informatik.uni-stuttgart.de/mailman/listinfo/precice)._
+preCICE-adapter for the open source computing platform FEniCS
 
 **currently only supports 2D simulations in FEniCS**
 
-This adapter was developed by [Benjamin Rüth](https://www5.in.tum.de/wiki/index.php/Benjamin_R%C3%BCth,_M.Sc._(hons)) 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](https://www.lunduniversity.lu.se/lucat/user/09d80f0367a060bcf2a22d7c22e5e504).
-
 # Installing the package
 
 ## Using pip3 to install from PyPI
@@ -53,18 +56,27 @@ Single tests can be also be run. For example the test `test_vector_write` in the
 python3 -m unittest tests.test_write_read.TestWriteandReadData.test_vector_write
 ```
 
-# Use the adapter
+### Troubleshooting
 
-Add ``from fenicsprecice import Adapter`` in your FEniCS code. Please refer to the examples in the [tutorials repository](https://github.com/precice/tutorials) for usage examples:
+**FEniCS is suddenly broken:** There are two known issues with preCICE, fenicsprecice and FEniCS:
 
-The adapter is configured via a `json` configuration file. For example configuration files and usage refer to the tutorials ([fenics-fenics](https://github.com/precice/tutorials/tree/master/HT/partitioned-heat/fenics-fenics)).
+* If you see `ImportError: cannot import name 'sub_forms_by_domain'` run `pip3 uninstall -y fenics-ufl`. For details, refer to [issue #103](https://github.com/precice/fenics-adapter/issues/103).
+* If you see `ModuleNotFoundError: No module named 'dolfin'` and have installed PETSc from source, refer to [this forum post](https://fenicsproject.discourse.group/t/modulenotfounderror-no-module-named-dolfin-if-petsc-dir-is-set/4407). Short version: Try to use the PETSc that comes with your system, if possible. Note that you can also [compile preCICE without PETSc](https://www.precice.org/installation-source-configuration.html), if necessary.
+
+If this does not help, you can contact us on [gitter](https://gitter.im/precice/lobby) or [open an issue](https://github.com/precice/fenics-adapter/issues/new).
+
+# Use the adapter
+
+Please refer to [our website](https://www.precice.org/adapter-fenics.html#how-can-i-use-my-own-solver-with-the-adapter-).
 
 # Packaging
 
 To create and install the `fenicsprecice` python package the following instructions were used: https://python-packaging.readthedocs.io/en/latest/index.html.
 
 # Citing
 
+If you are using this adapter, please refer to the [citing information on the FEniCS adapter](https://www.precice.org/adapter-fenics.html#how-to-cite).
+
 preCICE is an academic project, developed at the [Technical University of Munich](https://www5.in.tum.de/) and at the [University of Stuttgart](https://www.ipvs.uni-stuttgart.de/). If you use preCICE, please [cite us](https://www.precice.org/publications/):
 
 *H.-J. Bungartz, F. Lindner, B. Gatzhammer, M. Mehl, K. Scheufele, A. Shukaev, and B. Uekermann: preCICE - A Fully Parallel Library for Multi-Physics Surface Coupling. Computers and Fluids, 141, 250–258, 2016.*
@@ -74,3 +86,12 @@ If you are using FEniCS, please also consider the information on https://fenicsp
 # Disclaimer
 
 This offering is not approved or endorsed by the FEniCS Project, producer and distributor of the FEniCS software via https://fenicsproject.org/.
+
+# Development history
+
+The initial version of this adapter was developed by [Benjamin Rodenberg](https://www.in.tum.de/i05/personen/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](https://www.lunduniversity.lu.se/lucat/user/09d80f0367a060bcf2a22d7c22e5e504).
+
+[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).
+
+[Ishaan Desai](https://www.ipvs.uni-stuttgart.de/institute/team/Desai/) improved the user interface and extended the adapter to also allow for parallel FEniCS computations.
+

docs/ReleaseGuide.md

@@ -1,22 +1,23 @@
 ## Guide to release new version of the FEniCS-preCICE adapter
 
-The developer who is releasing a new version of FEniCS-preCICE adapter is expected to follow this work flow
+Before starting this process make sure to check that all relevant changes are included in the `CHANGELOG.md`. The developer who is releasing a new version of FEniCS-preCICE adapter is expected to follow this workflow:
 
-1. If it does not already exist, create a release branch with the version number of the planned release. Use develop as base for the branch. `git checkout develop`; `git checkout -b release_vX.X.X`. Perform the following steps only on the release branch, if not indicated differently.
+1. If it does not already exist, create a release branch with the version number of the planned release. Use develop as base for the branch. `git checkout develop`; `git checkout -b fenics-adapter-vX.X.X`. Perform the following steps only on the release branch, if not indicated differently.  
 
-2. [Open a Pull Request from the branch `release_vX.X.X` to `master`](https://github.com/precice/fenics-adapter/compare) named after the version (i.e. `Release v1.0.0`) and briefly describe the new features of the release in the PR description.
+2. [Open a Pull Request from the branch `fenics-adapter-vX.X.X` to `master`](https://github.com/precice/fenics-adapter/compare) named after the version (i.e. `Release v1.0.0`) and briefly describe the new features of the release in the PR description.
 
-    a) Check `CHANGELOG.md`, if necessary, update `CHANGELOG.md` on `develop` and merge into `release_vX.X.X`
-    
-    b) Before merging the PR, make sure to bump the version in `CHANGELOG.md` on `release_vX.X.X`
+3. Bump the version in the following places:
 
-3. [Draft a New Release](https://github.com/precice/fenics-adapter/releases/new) in the `Releases` section of the repository page in a web browser. The release tag needs to be the exact version number (i.e.`v1.0.0` or `v1.0.0rc1`, compare to [existing tags](https://github.com/precice/fenics-adapter/tags)). Use `@target:master`. Release title is also the version number (i.e. `v1.0.0` or `v1.0.0rc1`, compare to [existing releases](https://github.com/precice/fenics-adapter/tags)).
-*Note:* If it is a pre-release then the option *This is a pre-release* needs to be selected at the bottom of the page. Use `@target:release_vX.X.X` for a pre-release, since we will never merge a pre-release into master.
+    a) Before merging the PR, make sure to bump the version in `CHANGELOG.md` on `fenics-adapter-vX.X.X`  
+    b) There is no need to bump the version anywhere else, since we use the [python-versioneer](https://github.com/python-versioneer/python-versioneer/) for maintaining the version everywhere else.
+
+4. [Draft a New Release](https://github.com/precice/fenics-adapter/releases/new) in the `Releases` section of the repository page in a web browser. The release tag needs to be the exact version number (i.e.`v1.0.0` or `v1.0.0rc1`, compare to [existing tags](https://github.com/precice/fenics-adapter/tags)). Use `@target:master`. Release title is also the version number (i.e. `v1.0.0` or `v1.0.0rc1`, compare to [existing releases](https://github.com/precice/fenics-adapter/tags)).
+*Note:* If it is a pre-release then the option *This is a pre-release* needs to be selected at the bottom of the page. Use `@target:fenics-adapter-vX.X.X` for a pre-release, since we will never merge a pre-release into master.
 
     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 (`release_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`.
 
-4. Merge `master` into `develop` for synchronization of `develop`.
+5. Merge `master` into `develop` for synchronization of `develop`.
 
-5. 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.
+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.

fenicsadapter/__init__.py

@@ -32,6 +32,7 @@ class Vertices:
     Vertices class provides a generic skeleton for vertices. A set of vertices has a set of global IDs, local IDs and
     coordinates as defined in FEniCS.
     """
+
     def __init__(self, vertex_type):
         self._vertex_type = vertex_type
         self._global_ids = None
@@ -91,12 +92,12 @@ def determine_function_type(input_obj):
     tag : bool
         0 if input_function is SCALAR and 1 if input_function is VECTOR.
     """
-    if type(input_obj) == FunctionSpace:  # scalar-valued functions have rank 0 is FEniCS
+    if isinstance(input_obj, FunctionSpace):  # scalar-valued functions have rank 0 is FEniCS
         if input_obj.num_sub_spaces() == 0:
             return FunctionType.SCALAR
         elif input_obj.num_sub_spaces() == 2:
             return FunctionType.VECTOR
-    elif type(input_obj) == Function:
+    elif isinstance(input_obj, Function):
         if input_obj.value_rank() == 0:
             return FunctionType.SCALAR
         elif input_obj.value_rank() == 1:
@@ -107,7 +108,7 @@ def determine_function_type(input_obj):
         raise Exception("Error determining type of given dolfin FunctionSpace")
 
 
-def filter_point_sources(point_sources, filter_out):
+def filter_point_sources(point_sources, filter_out, warn_duplicate=True):
     """
     Filter dictionary of PointSources (point_sources) with respect to a given domain (filter_out). If a PointSource
     is applied at a point inside of the given domain (filter_out), this PointSource will be removed from dictionary.
@@ -118,6 +119,8 @@ def filter_point_sources(point_sources, filter_out):
         Dictionary containing coordinates and associated PointSources {(point_x, point_y): PointSource, ...}.
     filter_out: FEniCS domain
         Defines the domain where PointSources should be filtered out.
+    warn_duplicate: bool
+        Set False to surpress warnings, if double-boundary points are filtered out.
 
     Returns
     -------
@@ -128,10 +131,10 @@ def filter_point_sources(point_sources, filter_out):
 
     for point in point_sources.keys():
         # Filter double boundary points to avoid instabilities and create PointSource
-        if filter_out.inside(point, 1):
-            print("Found a double-boundary point at {location}.".format(location=point))
-        else:
+        if not filter_out.inside(point, 1):
             filtered_point_sources[point] = point_sources[point]
+        elif warn_duplicate:
+            logger.warning("Found a double-boundary point at {location}.".format(location=point))
 
     return filtered_point_sources
 
@@ -153,7 +156,7 @@ def convert_fenics_to_precice(fenics_function, local_ids):
         Array of FEniCS function values at each point on the boundary.
     """
 
-    if type(fenics_function) is not Function:
+    if not isinstance(fenics_function, Function):
         raise Exception("Cannot handle data type {}".format(type(fenics_function)))
 
     precice_data = []
@@ -382,8 +385,8 @@ def get_forces_as_point_sources(fixed_boundary, function_space, data):
         y_forces[key] = PointSource(function_space.sub(1), Point(px, py), nodal_data[i, 1])
 
     # Avoid application of PointSource and Dirichlet boundary condition at the same point by filtering
-    x_forces = filter_point_sources(x_forces, fixed_boundary)
-    y_forces = filter_point_sources(y_forces, fixed_boundary)
+    x_forces = filter_point_sources(x_forces, fixed_boundary, warn_duplicate=False)
+    y_forces = filter_point_sources(y_forces, fixed_boundary, warn_duplicate=False)
 
     return x_forces.values(), y_forces.values()  # don't return dictionary, but list of PointSources
 

fenicsprecice/adapter_core.py

@@ -13,6 +13,7 @@ class Config:
     configuration file. Initializer calls read_json() method. Instance attributes
     can be accessed by provided getter functions.
     """
+
     def __init__(self, adapter_config_filename):
 
         self._config_file_name = None
@@ -42,12 +43,12 @@ def read_json(self, adapter_config_filename):
 
         try:
             self._write_data_name = data["interface"]["write_data_name"]
-        except:
+        except KeyError:
             self._write_data_name = None  # not required for one-way coupling, if this participant reads data
 
         try:
             self._read_data_name = data["interface"]["read_data_name"]
-        except:
+        except KeyError:
             self._read_data_name = None  # not required for one-way coupling, if this participant writes data
 
         read_file.close()