Merge pull request #167 from precice/fenics-adapter-v2.0.0

Release v2.0.0

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

@@ -36,7 +36,7 @@ jobs:
         run:  |
           mkdir -p precice
           echo "from setuptools import setup" >> precice/setup.py
-          echo "setup(name='pyprecice', version='2.0.2.1')" >> precice/setup.py
+          echo "setup(name='pyprecice', version='3.0.0.0')" >> precice/setup.py
           python3 -m pip install ./precice/
       - name: Run unit tests
         run:  python3 setup.py test -s tests.unit

.github/workflows/build-docker.yml

@@ -1,10 +1,18 @@
 name: Update docker image
 
 on:
-  workflow_dispatch:      # Trigger by hand from the UI
+  workflow_dispatch: # Trigger by hand from the UI
+    inputs:
+      branch:
+        type: choice
+        description: branch to build the container from
+        options:
+          - develop
+          - master     
   push:
     branches:
       - develop
+      - master
 
 jobs:
   build-and-release-docker-image:
@@ -13,10 +21,28 @@ jobs:
     env:
         docker_username: precice
     steps:
-      - name: Get branch name
-        if: github.event_name != 'pull_request'
+      - name: Set branch name for manual triggering
+        if: github.event_name == 'workflow_dispatch'
         shell: bash
-        run: echo "branch=$(echo ${GITHUB_REF#refs/heads/} | tr / -)" >> $GITHUB_ENV    
+        run: | 
+          echo "ADAPTER_REF=${{ inputs.branch }}" >> $GITHUB_ENV 
+      - name: Set branch name for on pull triggering
+        if: github.event_name != 'pull_request' && github.event_name != 'workflow_dispatch'
+        shell: bash
+        run: |
+          echo "ADAPTER_REF=${{ github.ref_name }}" >> $GITHUB_ENV
+      - name: Set PYTHON_BINDINGS_REF and the TAG depending on branch
+        shell: bash
+        run: |
+          if [[ '${{ env.ADAPTER_REF }}' == 'master' ]]; then
+              echo "PYTHON_BINDINGS_REF=latest" >> "$GITHUB_ENV"
+              echo "TAG=latest" >> "$GITHUB_ENV"
+              echo "Building TAG: latest"
+          else
+              echo "PYTHON_BINDINGS_REF=${{ env.ADAPTER_REF }}" >> "$GITHUB_ENV"
+              echo "TAG=${{ env.ADAPTER_REF }}" >> "$GITHUB_ENV"
+              echo "Building TAG: ${{ env.ADAPTER_REF }}"
+          fi   
       - name: Checkout Repository
         uses: actions/checkout@v2
       - name: Set up Docker Buildx
@@ -31,6 +57,7 @@ jobs:
         with:
           push: true
           file: "./tools/releasing/packaging/docker/Dockerfile"
-          tags: ${{ env.docker_username }}/fenics-adapter:${{ env.branch }},${{ env.docker_username }}/fenics-adapter:latest
+          tags: ${{ env.docker_username }}/fenics-adapter:${{ env.TAG }}
           build-args: |
-            branch=${{ env.branch }}
+            FENICS_ADAPTER_REF=${{ env.ADAPTER_REF }}
+            PYTHON_BINDINGS_REF=${{ env.PYTHON_BINDINGS_REF }}

.github/workflows/pythonpublish.yml

@@ -20,8 +20,8 @@ jobs:
         pip install setuptools wheel twine
     - name: Build and publish
       env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
       run: |
         python setup.py sdist
         twine upload dist/*

.github/workflows/run-tutorials.yml

@@ -7,15 +7,15 @@ on:
   pull_request:
     paths:
       - '**'
-      
-jobs:  
+
+jobs:
   run_ht_simple:
     name: Run HT, simple
     runs-on: ubuntu-latest
-    container: precice/precice
+    container: precice/precice:develop
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v2      
+        uses: actions/checkout@v2
       - name: Install Dependencies & FEniCS
         run: |
           apt-get -qq update
@@ -30,17 +30,17 @@ jobs:
       - 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: |
+          cd tutorials/partitioned-heat-conduction
+          cd dirichlet-fenics && ./run.sh & cd neumann-fenics && ./run.sh
+
   run_ht_complex:
     name: Run HT, complex
     runs-on: ubuntu-latest
-    container: precice/precice
+    container: precice/precice:develop
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v2      
+        uses: actions/checkout@v2
       - name: Install Dependencies & FEniCS
         run: |
           apt-get -qq update
@@ -56,5 +56,5 @@ jobs:
         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
+          cd tutorials/partitioned-heat-conduction-complex
+          cd dirichlet-fenics && ./run.sh & cd neumann-fenics && ./run.sh

CHANGELOG.md

@@ -1,5 +1,11 @@
 # FEniCS-preCICE adapter changelog
 
+## 2.0.0
+
+* Drop support for preCICE 2.x version, as this is a breaking release.
+* Update adapter to use preCICE v3 API [#153](https://github.com/precice/fenics-adapter/pull/153).
+* Remove functionality to define mesh connectivity in 2D cases in the form of triangles due to lack of testing and compatibility problems (might be added again). See [#162](https://github.com/precice/fenics-adapter/issues/162).
+
 ## 1.4.0
 
 * Adding CITATION.cff to link the adapter repository to the relevant publication in the journal SoftwareX.

CITATION.cff

@@ -1,45 +1,63 @@
-# YAML 1.2
----
-abstract: "The new software FEniCS-preCICE is a middle software layer, sitting in between the existing finite-element library FEniCS and the coupling library preCICE. The middle layer simplifies coupling (existing) FEniCS application codes to other simulation software via preCICE. To this end, FEniCS-preCICE converts between FEniCS and preCICE mesh and data structures, provides easy-to-use coupling conditions, and manages data checkpointing for implicit coupling. The new software is a library itself and follows a FEniCS-native style. Only a few lines of additional code are necessary to prepare a FEniCS application code for coupling. We illustrate the functionality of FEniCS-preCICE by two examples: a FEniCS heat conduction code coupled to OpenFOAM and a FEniCS linear elasticity code coupled to SU2. The results of both scenarios are compared with other simulation software showing good agreement."
-authors: 
-  -
-    affiliation: "Technical University of Munich"
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: FEniCS-preCICE
+message: >-
+  If you use this software, please cite it using the metadata from this file. When using or referring to preCICE in
+  academic publications, please follow the [citation guidelines](https://precice.org/fundamentals-literature-guide.html). 
+type: software
+authors:
+  - given-names: Benjamin
     family-names: Rodenberg
-    given-names: Benjamin
-    orcid: "https://orcid.org/0000-0002-3116-0133"
-  -
-    affiliation: "University Stuttgart"
+    orcid: 'https://orcid.org/0000-0002-3116-0133'
+    affiliation: Technical University of Munich
+  - given-names: Ishaan
     family-names: Desai
-    given-names: Ishaan
-    orcid: "https://orcid.org/0000-0002-2552-7509"
-  -
-    family-names: Hertrich
+    orcid: 'https://orcid.org/0000-0002-2552-7509'
+    affiliation: University Stuttgart
+  - family-names: Hertrich
     given-names: Richard
-    orcid: "https://orcid.org/0000-0003-1722-2841"
-  -
-    affiliation: "University of Stuttgart"
-    family-names: Jaust
-    given-names: Alexander
-    orcid: "https://orcid.org/0000-0002-6082-105X"
-  -
-    affiliation: "University of Stuttgart"
-    family-names: Uekermann
-    given-names: Benjamin
-    orcid: "https://orcid.org/0000-0002-1314-9969"
-cff-version: "1.1.0"
-date-released: 2021-01-10
-keywords: 
-  - FEniCS
-  - "Fluid-Structure Interaction"
-  - "Conjugate Heat Transfer"
-  - Multiphysics
-  - "Coupled Problems"
-  - "Finite Element Method"
-  - preCICE
-license: "LGPL-3.0"
-message: "If you use this software, please cite it using these metadata."
-repository-code: "https://github.com/precice/fenics-adapter"
-title: "FEniCS-preCICE: Coupling FEniCS to other Simulation Software"
-version: 1.2.0
-doi: 10.1016/j.softx.2021.100807
-...
+    orcid: 'https://orcid.org/0000-0003-1722-2841'
+  - affiliation: University of Stuttgart
+    given-names: Jaust
+    family-names: Alexander
+    orcid: 'https://orcid.org/0000-0002-6082-105X'
+  - affiliation: University of Stuttgart
+    given-names: Uekermann
+    family-names: Benjamin
+    orcid: 'https://orcid.org/0000-0002-1314-9969'
+repository-code: 'https://github.com/precice/fenics-adapter'
+abstract: >-
+  preCICE-adapter for the open source computing platform
+  FEniCS.
+license: LGPL-3.0
+version: 2.0.0
+preferred-citation:
+  title: "FEniCS-preCICE: Coupling FEniCS to other Simulation Software"
+  type: "article"
+  authors: 
+    - affiliation: "Technical University of Munich"
+      family-names: Rodenberg
+      given-names: Benjamin
+      orcid: "https://orcid.org/0000-0002-3116-0133"
+    - affiliation: "University Stuttgart"
+      family-names: Desai
+      given-names: Ishaan
+      orcid: "https://orcid.org/0000-0002-2552-7509"
+    - family-names: Hertrich
+      given-names: Richard
+      orcid: "https://orcid.org/0000-0003-1722-2841"
+    - affiliation: "University of Stuttgart"
+      family-names: Jaust
+      given-names: Alexander
+      orcid: "https://orcid.org/0000-0002-6082-105X"
+    - affiliation: "University of Stuttgart"
+      family-names: Uekermann
+      given-names: Benjamin
+      orcid: "https://orcid.org/0000-0002-1314-9969"
+  doi: 10.1016/j.softx.2021.100807
+  journal: "SoftwareX"
+  volume: 16
+  pages: 100807
+  year: 2021

README.md

@@ -65,6 +65,7 @@ python3 -m unittest tests.test_write_read.TestWriteandReadData.test_vector_write
 **FEniCS is suddenly broken:** There are two known issues with preCICE, fenicsprecice and 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 `ImportError: cannot import name 'cellname2facetname' from 'ufl.cell'`, refer to [issue #154](https://github.com/precice/fenics-adapter/issues/154).
 * 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).
@@ -85,7 +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.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).
+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.
 
 [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).
 

docs/ReleaseGuide.md

@@ -2,14 +2,17 @@
 
 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 fenics-adapter-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 `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.
 
 3. Bump the version in the following places:
 
-    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.
+    a) Before merging the PR, make sure to bump the version in `CHANGELOG.md` on `fenics-adapter-vX.X.X`.
+
+    b) Update the version in `CITATION.cff` and update the release date.
+
+    c) 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.

fenicsprecice/__init__.py

@@ -7,6 +7,5 @@
                   "The FEniCS adapter might not work as expected.\n\n")
 
 from .fenicsprecice import Adapter
-from ._version import get_versions
-__version__ = get_versions()['version']
-del get_versions
+from . import _version
+__version__ = _version.get_versions()['version']