Merge pull request #218 from ImperialCollegeLondon/dev_docker

SHARPy Docker now releases to GitHub Packages

.github/workflows/docker_build.yaml

@@ -0,0 +1,45 @@
+name: Create and publish Docker image
+
+on:
+  push:
+    branches: 
+      - develop
+      - master
+    tags:
+      - 'v*'
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v2
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v3.2.0
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/docker_build_test.yaml

@@ -0,0 +1,49 @@
+name: Test Docker image build
+
+on:
+  pull_request:
+    branches:
+      - master
+      - develop
+      - 'rc*'
+  push:
+    paths:
+      - 'utils/*'
+      - 'Dockerfile'
+      - '.github/workflows/docker*'
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  test_image_build:
+    runs-on: ubuntu-latest
+    name: Test Docker image build
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v2
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build Docker image
+        uses: docker/build-push-action@v3.2.0
+        with:
+          context: .
+          push: false
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/readme.md

@@ -0,0 +1,23 @@
+# SHARPy GitHub Workflows
+
+There are 4 automated workflows for SHARPy's CI/CD.
+
+## SHARPy Tests
+
+The related to the SHARPy tests that run the `SHARPy Tests` job are:
+
+    * `sharpy_tests.yaml`: when Python or the submodules files are edited
+    * `sharpy_no_test_needed.yaml`: otherwise
+
+This avoids running the full set of tests for changes in the documentation etc.
+Since the merge to `develop` and `master` is protected by the tests passing, the 
+second workflow ensures a positive result for those PRs that did not change the 
+Python code, hence allowing the merge.
+
+## Docker
+
+Two nearly identical workflows, the only difference is that one pushes the Docker 
+image to the SHARPy packages. Therefore:
+
+    * `docker_build.yaml`: Builds the Docker image but does not push. Runs on changes to the `docker*` workflows, changes to the `utils/` directory (environments) and changes to the `Dockerfile`. Required test for PRs to merge to `develop` and `master`.
+    * `docker_build.yaml`: Builds and pushes the Docker image. Runs on pushes to `develop`, `master` and annotated tags.

.github/workflows/sharpy_no_test_needed.yaml

@@ -1,4 +1,4 @@
-name: Python package
+name: SHARPy Tests
 
 on:
   pull_request:

.github/workflows/sharpy_tests.yaml

@@ -1,11 +1,11 @@
-name: Python package
+name: SHARPy Tests
 
 on:
   push:
     paths:
       - '*.py'
       - 'lib/*'
-      - '.github/workflows/*'
+      - '.github/workflows/sharpy*'
   pull_request:
     branches:
       - master

Dockerfile

@@ -5,6 +5,13 @@ ENV BASH_ENV ~/.bashrc
 SHELL ["/bin/bash", "-c"]
 ENV PATH=${PATH}:/miniconda3/bin
 
+# CENTOS 8 has reached end of life - Not yet an updated Docker base for CentOS stream
+# Point to the CentOS 8 vault in order to download dependencies
+RUN cd /etc/yum.repos.d/ && \
+    sed -i 's/mirrorlist/#mirrorlist/g' /etc/yum.repos.d/CentOS-* && \
+    sed -i 's|#baseurl=http://mirror.centos.org|baseurl=http://vault.centos.org|g' /etc/yum.repos.d/CentOS-* && \
+    cd /
+
 # Development tools including compilers
 RUN yum groupinstall "Development Tools" -y --nogpgcheck && \
     yum install -y --nogpgcheck mesa-libGL libXt libXt-devel wget gcc-gfortran lapack vim tmux && \
@@ -34,11 +41,13 @@ RUN ln -s /sharpy_dir/utils/docker/* /root/
 
 RUN cd sharpy_dir && \
     conda activate sharpy_minimal && \
+    git submodule update --init --recursive && \
     mkdir build && \
     cd build && \
     CXX=g++ FC=gfortran cmake .. && make install -j 2 && \
     cd .. && \
+    pip install . && \
     rm -rf build
-
+    
 ENTRYPOINT ["/bin/bash", "--init-file", "/root/bashrc"]
 

README.md

@@ -117,6 +117,7 @@ is:
 
 Master
 ![Build Status](/~https://github.com/ImperialCollegeLondon/sharpy/actions/workflows/sharpy_tests.yaml/badge.svg)
+![Docker Status](/~https://github.com/ImperialCollegeLondon/sharpy/actions/workflows/docker_build.yaml/badge.svg)
 
 Develop
 ![Build Status](/~https://github.com/ImperialCollegeLondon/sharpy/actions/workflows/sharpy_tests.yaml/badge.svg?branch=develop)

docs/source/content/installation.md

@@ -97,7 +97,7 @@ you would like to install a develop build or modify the compilation settings of
     cd sharpy
     ```
 
-1. Ensure that the SHARPy environment is active in the session. Your terminal prompt line should begin with
+2. Ensure that the SHARPy environment is active in the session. Your terminal prompt line should begin with
     ```bash
     (sharpy) [usr@host] $
     ```
@@ -107,30 +107,35 @@ you would like to install a develop build or modify the compilation settings of
     conda activate sharpy
     ```
 
-1. Create a directory `build` that will be used during CMake's building process and `cd` into it:
+3. Create a directory `build` that will be used during CMake's building process and `cd` into it:
     ```bash
     mkdir build
     cd build
     ```
 
-2. Prepare UVLM and xbeam for compilation using `gfortran` and `g++` in their release builds running. If you'd like to
+4. Prepare UVLM and xbeam for compilation using `gfortran` and `g++` in their release builds running. If you'd like to
 change compilers see the Custom Installation.
     ```bash
     cmake ..
     ```
 
-3. Compile the libraries
+5. Compile the libraries
     ```bash
     make install -j 4
     ```
     where the number after the `-j` flag will specify how many cores to use during installation.
 
-4. Finally, leave the build directory and install SHARPy
+6. Finally, leave the build directory and install SHARPy
     ```bash
     cd ..
     pip install .
     ```
 
+7. You can check the version of SHARPy you are running with
+    ```bash
+    sharpy --version
+    ```
+
 __You are ready to run SHARPy__. Continue reading the [Running SHARPy](#running-sharpy) section.
 
 ### Custom installation
@@ -218,16 +223,25 @@ If this works, you're good to go!
 
 First, obtain the SHARPy docker container:
 ```
-docker pull fonsocarre/sharpy:stable
+docker pull ghcr.io/imperialcollegelondon/sharpy:master
 ```
+You can obtain other versions as well, check those available in the [containers](/~https://github.com/ImperialCollegeLondon/sharpy/pkgs/container/sharpy) page.
+
+This will donwload a Docker image of SHARPy to your machine, from where you can create and run Docker containers. To create and run a container from the downloaded image use:
 
-Now you can run it:
 ```
-docker run --name sharpy -it fonsocarre/sharpy:stable
+docker run --name sharpy -it -p 8080:8080 ghcr.io/imperialcollegelondon/sharpy:master
 ```
-You should see a welcome dialog such as:
+
+A few details about the above command, although if in doubt please check the Docker documentation. The `--name` argument gives a name to the container. Note you can create multiple containers from a single image. 
+
+The `-it` is an important command as it runs the container in interactive mode with a terminal attached. Thus you can use it an navigate it. Otherwise the container will finish as soon as it is created. 
+
+The `-p 8080:8080` argument connects the container to your machine through port `8080` (it could be any other) which may be useful for some applications. For instance, running SHARPy as hardware-in-the-loop through UDP.
+
+Once you run it, you should see a welcome dialog such as:
 ```
->>>> docker run -it fonsocarre/sharpy:stable
+>>>> docker run --name sharpy -it -p 8080:8080 ghcr.io/imperialcollegelondon/sharpy:master
 SHARPy added to PATH from the directory: /sharpy_dir/bin
 =======================================================================
 Welcome to the Docker image of SHARPy
@@ -239,6 +253,11 @@ SHARPy>
 ```
 You are now good to go.
 
+You can check the version of SHARPy you are running with
+```
+sharpy --version
+```
+
 It is important to note that a docker container runs as an independent
 operating system with no access to your hard drive. If you want to copy your own
 files, run the container and from another terminal run:
@@ -254,11 +273,6 @@ cd sharpy_dir
 python -m unittest
 ```
 
-We make available two different releases: `stable` and `experimental`. The former is the latest SHARPy
-release. The latter is our latest development work which will include new features but with higher chances
-of encountering some bugs along the way. To obtain the experimental build, follow the instructions
-above replacing the `stable` tag for `experimental`.
-
 **Enjoy!**
 
 

docs/source/content/publications.md

@@ -5,18 +5,22 @@ Here we present a list of past papers which have used SHARPy for research purpos
 
 ## 2022
 
-* Goizueta, N., Wynn, A., Palacios, R., Drachinsky, A., Raveh, D. E. (2022). Flutter Predictions for Very Flexible Wing Wind Tunnel Test. Journal of Aircraft. Article in Advance. [https://doi.org/10.2514/1.C036710](https://doi.org/10.2514/1.C036710)
+* Goizueta, N. (2022). Parametric reduced-order aeroelastic modelling for analysis, dynamic system interpolation and control of flexible aircraft. PhD Thesis. [http://doi.org/10.25560/100137](http://doi.org/10.25560/100137)
 
-* Muñoz-Simón A, Wynn A, Palacios R (2022). Some modelling improvements for prediction of wind turbine rotor loads in turbulent wind. Wind Energy: 25(2), pp. 333-353. [https://doi.org/10.1002/we.2675](https://doi.org/10.1002/we.2675)
+* Goizueta, N., Wynn, A., & Palacios, R. (2022). Adaptive sampling for interpolation of reduced-order aeroelastic dynamical systems. AIAA Journal. Article in Advance. [https://doi.org/10.2514/1.J062050](https://doi.org/10.2514/1.J062050)
 
-* Goizueta, N., Wynn, A., Palacios, R. (2022). Fast flutter evaluation of very flexible wing using interpolation on an optimal training dataset. AIAA SciTech Forum. [https://doi.org/10.2514/6.2022-1345](https://doi.org/10.2514/6.2022-1345)
+* Muñoz Simón, A. (2022). Vortex-lattice-based nonlinear aeroservoelastic modelling and analysis of large floating wind turbines. PhD Thesis. [https://doi.org/10.25560/96986](https://doi.org/10.25560/96986)
+
+* Goizueta, N., Wynn, A., Palacios, R., Drachinsky, A., & Raveh, D. E. (2022). Flutter Predictions for Very Flexible Wing Wind Tunnel Test. Journal of Aircraft: 59(4), pp. 1082-1097. [https://doi.org/10.2514/1.C036710](https://doi.org/10.2514/1.C036710)
 
 * Düssler, S., Goizueta, N., Muñoz-Simón, A., & Palacios, R. (2022). Modelling and Numerical Enhancements on a UVLM for Nonlinear Aeroelastic Simulation. AIAA SciTech Forum. [https://doi.org/10.2514/6.2022-2455](https://doi.org/10.2514/6.2022-2455)
 
 * Cea, A., Palacios, R. (2022). Parametric Reduced Order Models for Aeroelastic Design of Very Flexible Aircraft. AIAA SciTech Forum. [https://doi.org/10.2514/6.2022-0727](https://doi.org/10.2514/6.2022-0727)
 
 * Wynn, A., Artola, M., Palacios, R. (2022). Nonlinear optimal control for gust load alleviation with a physics-constrained data-driven internal model. AIAA SciTech Forum. [https://doi.org/10.2514/6.2022-0442](https://doi.org/10.2514/6.2022-0442)
 
+* Goizueta, N., Wynn, A., Palacios, R. (2022). Fast flutter evaluation of very flexible wing using interpolation on an optimal training dataset. In AIAA SciTech Forum, AIAA Paper 2022-1345. [https://doi.org/10.2514/6.2022-1345](https://doi.org/10.2514/6.2022-1345)
+
 ## 2021
 
 * Artola, M., Goizueta, N., Wynn, A., & Palacios, R. (2021). Aeroelastic Control and Estimation with a Minimal 
@@ -34,6 +38,8 @@ models. In AIAA SciTech Forum (pp. 1–25). [https://doi.org/10.2514/6.2021-1798
 
 ## 2020
 
+* del Carre, A. (2020). Aeroelasticity of very flexible aircraft at low altitudes. PhD Thesis. [https://doi.org/10.25560/88269](https://doi.org/10.25560/88269)
+
 * Muñoz-Simón, A., Palacios, R., & Wynn, A. (2020). Benchmarking different fidelities in wind turbine aerodynamics 
 under yaw. Journal of Physics: Conference Series, 1618, 42017. 
 [https://doi.org/10.1088/1742-6596/1618/4/042017](https://doi.org/10.1088/1742-6596/1618/4/042017)

setup.py

@@ -2,12 +2,12 @@
 import re
 import os
 
+this_directory = os.path.abspath(os.path.dirname(__file__))
 __version__ = re.findall(
     r"""__version__ = ["']+([0-9\.]*)["']+""",
-    open("sharpy/__init__.py").read(),
+    open(os.path.join(this_directory, "sharpy/version.py")).read(),
 )[0]
 
-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()
 

sharpy/__init__.py

@@ -1 +1 @@
-__version__ = "2.0"
+from .version import __version__

sharpy/sharpy_main.py

@@ -5,6 +5,7 @@
 import sys
 import dill as pickle
 import sharpy.utils.cout_utils as cout
+from .version import __version__
 
 
 def main(args=None, sharpy_input_dict=None):
@@ -56,12 +57,14 @@ def main(args=None, sharpy_input_dict=None):
         if sharpy_input_dict is None:
             parser = argparse.ArgumentParser(prog='SHARPy', description=
             """This is the executable for Simulation of High Aspect Ratio Planes.\n
-            Imperial College London 2021""")
+            Imperial College London 2022""")
             parser.add_argument('input_filename', help='path to the *.sharpy input file', type=str, default='')
             parser.add_argument('-r', '--restart', help='restart the solution with a given snapshot', type=str,
                                 default=None)
             parser.add_argument('-d', '--docs', help='generates the solver documentation in the specified location. '
                                                      'Code does not execute if running this flag', action='store_true')
+            parser.add_argument('-v', '--version', action='version', 
+                version='Running %(prog)s version {version}'.format(version=__version__))
             if args is not None:
                 args = parser.parse_args(args[1:])
             else:

sharpy/version.py

@@ -0,0 +1,2 @@
+# version stored here to don't load dependencies by storing it in __init__.py
+__version__ = '2.0'

utils/docker/bashrc

@@ -27,7 +27,6 @@ unset __conda_setup
 # <<< conda initialize <<<
 
 conda activate sharpy_minimal
-source /sharpy_dir/bin/sharpy_vars.sh
 
 # custom prompt
 PS1="SHARPy> "