Merge pull request #136 from precice/fenics-adapter-v1.2.0

Release v1.2.0

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

@@ -9,6 +9,22 @@ on:
       - '**'
 
 jobs:  
+  sdist:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: '3.x'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools wheel twine
+      - name: Build distribution
+        run:  python3 setup.py sdist
   test:
     name: Run mock unit tests
     runs-on: ubuntu-latest

.github/workflows/build-docker.yml

@@ -0,0 +1,36 @@
+name: Update docker image
+
+on:
+  workflow_dispatch:      # Trigger by hand from the UI
+  push:
+    branches:
+      - develop
+
+jobs:
+  build-and-release-docker-image:
+    name: Builds a dockerimage with the fenics adapter of preCICE
+    runs-on: ubuntu-latest
+    env:
+        docker_username: precice
+    steps:
+      - name: Get branch name
+        if: github.event_name != 'pull_request'
+        shell: bash
+        run: echo "branch=$(echo ${GITHUB_REF#refs/heads/} | tr / -)" >> $GITHUB_ENV    
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      - name: Login to DockerHub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ env.docker_username }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - name: Build and push Dockerfile
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          file: "./tools/releasing/packaging/docker/Dockerfile"
+          tags: ${{ env.docker_username }}/fenics-adapter:${{ env.branch }},${{ env.docker_username }}/fenics-adapter:latest
+          build-args: |
+            branch=${{ env.branch }}

.github/workflows/check-links.yml

@@ -0,0 +1,21 @@
+name: Lint scripts and docs
+on: [push, pull_request]
+jobs:
+  check_markdown_files:
+    name: Lint scripts and docs
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v2
+      - name: Lint markdown files (markdownlint)
+        uses: articulate/actions-markdownlint@v1
+        with:
+          config: .markdownlint.json
+          files: '.'
+          ignore: changelog-entries
+      - name: Check links in markdown files (markdown-link-check)
+        uses: gaurav-nelson/github-action-markdown-link-check@v1
+        with:
+          use-quiet-mode: 'yes'
+          use-verbose-mode: 'no'
+          config-file: '.markdown-link-check-config.json'

.markdown-link-check-config.json

@@ -0,0 +1,3 @@
+{
+  "aliveStatusCodes": [429, 200]
+}

.markdownlint.json

@@ -0,0 +1,4 @@
+{
+    "MD013": false,
+    "MD033": false
+}

CHANGELOG.md

@@ -1,25 +1,31 @@
 # FEniCS-preCICE adapter changelog
 
+## 1.2.0
+
+* Reduce complexity of initialization to reduce runtime for large cases. [See PR #135](https://github.com/precice/fenics-adapter/pull/135)
+* Raise warning, if FEniCS is not found on system. [See PR #130](https://github.com/precice/fenics-adapter/pull/130)
+* Add test for python3 setup.py sdist. [See PR #127](https://github.com/precice/fenics-adapter/pull/127)
+
 ## 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
+* Remove deprecated package `fenicsadapter`. Don't use `import fenicsadapter`. Please use `import fenicsprecice`. [See PR #121](https://github.com/precice/fenics-adapter/pull/121)
 
 ## 1.0.1
 
-* Bugfix for PointSources https://github.com/precice/fenics-adapter/issues/109
-* Bugfix in parallelization https://github.com/precice/fenics-adapter/pull/110
+* Bugfix for PointSources in [PR #109](https://github.com/precice/fenics-adapter/issues/109)
+* Bugfix in parallelization in [PR #110](https://github.com/precice/fenics-adapter/pull/110)
 
 ## 1.0.0
 
 * The paper *FEniCS-preCICE: Coupling FEniCS to other Simulation Software* (in preparation) describes features, usage and API of the adapter.
-* The software is called FEniCS-preCICE adapter, the corresponding python package `fenicsprecice`. Our software uses the naming proposed in https://github.com/precice/fenics-adapter/issues/85.
-* `fenicsprecice` is published via PyPI https://github.com/precice/fenics-adapter/pull/94.
+* The software is called FEniCS-preCICE adapter, the corresponding python package `fenicsprecice`. Our software uses the naming proposed in [PR #85](https://github.com/precice/fenics-adapter/issues/85).
+* `fenicsprecice` is published via PyPI. [See PR #94](https://github.com/precice/fenics-adapter/pull/94).
 * FEniCS PointSource and Expressions are used to create boundary conditions for coupling.
-* The adapter uses a `SegregatedRBFinterpolationExpression` for interpolation, if an Expression is used https://github.com/precice/fenics-adapter/pull/83.
+* The adapter uses a `SegregatedRBFinterpolationExpression` for interpolation, if an Expression is used. [See PR #83](https://github.com/precice/fenics-adapter/pull/83).
 * The adapter supports one-way coupling and two-way coupling.
 * The adapter supports explicit and implicit coupling schemes.
 * The adapter supports checkpointing and subcycling.
 * The adapter supports up to one read and one write data set.
-* The current state of the adapter API was mainly designed in https://github.com/precice/fenics-adapter/pull/59.
-* Supports parallel solvers for Expressions, but not for PointSources as coupling boundary conditions. See https://github.com/precice/fenics-adapter/pull/71.
+* The current state of the adapter API was mainly designed in [PR #59](https://github.com/precice/fenics-adapter/pull/59).
+* Supports parallel solvers for Expressions, but not for PointSources as coupling boundary conditions. [See PR #71](https://github.com/precice/fenics-adapter/pull/71).

README.md

@@ -1,5 +1,4 @@
-FEniCS-preCICE adapter
-----------------------
+# FEniCS-preCICE adapter
 
 <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">
@@ -13,25 +12,25 @@ FEniCS-preCICE adapter
 </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> 
-
-preCICE-adapter for the open source computing platform FEniCS
+</a>
 
-**currently only supports 2D simulations in FEniCS**
+preCICE-adapter for the open source computing platform FEniCS. Note: The adapter **currently only supports 2D simulations in FEniCS.**
 
-# Installing the package
+## Installing the package
 
-## Using pip3 to install from PyPI
+### Using pip3 to install from PyPI
 
 It is recommended to install [fenicsprecice from PyPI](https://pypi.org/project/fenicsprecice/) via
+
+```bash
+pip3 install --user fenicsprecice
 ```
-$ pip3 install --user fenicsprecice
-```
+
 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
+### Clone this repository and use pip3
 
-### Required dependencies
+#### Required dependencies
 
 Make sure to install the following dependencies:
 
@@ -41,22 +40,23 @@ Make sure to install the following dependencies:
 * [FEniCS](https://fenicsproject.org/) (with python interface, installed by default)
 * and scipy (`pip3 install scipy`)
 
-### Build and install the adapter
+#### Build and install the adapter
 
 After cloning this repository and switching to the root directory (`fenics-adapter`), run ``pip3 install --user .`` from your shell.
 
-### Test the adapter
+#### Test the adapter
 
 As a first test, try to import the adapter via `python3 -c "import fenicsprecice"`.
 
 You can run the other tests via `python3 setup.py test`.
 
 Single tests can be also be run. For example the test `test_vector_write` in the file `test_write_read.py` can be run as follows:
-```
+
+```bash
 python3 -m unittest tests.test_write_read.TestWriteandReadData.test_vector_write
 ```
 
-### Troubleshooting
+#### Troubleshooting
 
 **FEniCS is suddenly broken:** There are two known issues with preCICE, fenicsprecice and FEniCS:
 
@@ -65,33 +65,28 @@ python3 -m unittest tests.test_write_read.TestWriteandReadData.test_vector_write
 
 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
+## 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
+## Packaging
 
-To create and install the `fenicsprecice` python package the following instructions were used: https://python-packaging.readthedocs.io/en/latest/index.html.
+To create and install the `fenicsprecice` python package the following instructions were used: [How To Package Your Python Code from python-packaging.readthedocs.io](https://python-packaging.readthedocs.io/en/latest/index.html).
 
-# Citing
+## 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.*
 
-If you are using FEniCS, please also consider the information on https://fenicsproject.org/citing/.
-
-# Disclaimer
+If you are using FEniCS, please also consider the information on [the official FEniCS website on citing](https://fenicsproject.org/citing/).
 
-This offering is not approved or endorsed by the FEniCS Project, producer and distributor of the FEniCS software via https://fenicsproject.org/.
-
-# Development history
+## 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

@@ -1,4 +1,4 @@
-## Guide to release new version of the FEniCS-preCICE adapter
+# Guide to release new version of the FEniCS-preCICE adapter
 
 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:
 

fenicsprecice/__init__.py

@@ -1,3 +1,11 @@
+import warnings
+
+try:
+    from fenics import *
+except ModuleNotFoundError:
+    warnings.warn("No FEniCS installation found on system. Please check whether it is found correctly. "
+                  "The FEniCS adapter might not work as expected.\n\n")
+
 from .fenicsprecice import Adapter
 from ._version import get_versions
 __version__ = get_versions()['version']