Merge branch 'develop' into gust_vanes

Author: sduess

.github/workflows/pypi_build.yaml

@@ -0,0 +1,90 @@
+name: Create and publish pypi image
+
+on:
+  # only runs when there are pushes to develop and main for publishing
+  # and for testing, pull requests to develop and main
+  # and if there are changes to the build process and github action
+  push:
+    branches: 
+      - develop
+      - main
+    paths:
+      - 'setup.py'
+      - '.github/workflows/pypi*'  
+  pull_request:
+    branches:
+      - main
+      - develop
+      - 'rc*'
+
+jobs:
+  create-pypi-image:
+    name: >-
+      Create .whl 🛞 from SHARPy distribution
+    runs-on: ubuntu-20.04
+    env:
+      python-version-chosen: "3.10.8"
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ env.python-version-chosen }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ env.python-version-chosen }}
+      - name: Set up GCC
+        uses: egor-tensin/setup-gcc@v1
+        with:
+          version: 7
+          platform: x64
+      - name: Pre-Install dependencies
+        run: |
+          export QT_QPA_PLATFORM='offscreen'
+          sudo apt install libeigen3-dev
+          git submodule init
+          git submodule update
+      - name: Install pypa/build
+        run: >-
+          python3 -m
+          pip install
+          build
+          --user    
+      - name: Install wheel
+        run: python3 -m pip install wheel --user
+      - name: Build a source tarball
+        run: python setup.py sdist
+      - name: Build a binary wheel
+        run: python3 setup.py bdist_wheel        
+      - name: Find the wheel created during pip install
+        run: 
+          python3 -m pip cache dir
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    if: startsWith(github.ref, 'refs/tags/v')  # only publish to PyPI on tag pushes
+    needs:
+    - create-pypi-image
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/ic_sharpy  # Replace <package-name> with your PyPI project name
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      # with:
+      #   path: dist/*

.github/workflows/readme.md

@@ -1,6 +1,6 @@
 # SHARPy GitHub Workflows
 
-There are 4 automated workflows for SHARPy's CI/CD.
+There are 4(+1 experimental) automated workflows for SHARPy's CI/CD.
 
 ## SHARPy Tests
 
@@ -19,5 +19,12 @@ Python code, hence allowing the merge.
 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 `main`.
+    * `docker_build_test.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 `main`.
     * `docker_build.yaml`: Builds and pushes the Docker image. Runs on pushes to `develop`, `main` and annotated tags.
+
+## Pypi (experimental!)
+
+One workflow with two jobs, the first creates and the second pushes the wheel 
+artifact to ic-sharpy @ pypi. Therefore:
+
+    * `pypi_build.yaml`: Builds and pushes the pypi wheel according to conditions. Runs on changes to the `pypi*` workflow, changes to the `setup.py`, and PRs and pushes to main and develop. Required test for PRs to merge to `develop` and `main`. Publishes on annotated tags.    

.github/workflows/sharpy_tests.yaml

@@ -21,16 +21,20 @@ jobs:
         python-version: [3.7]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+        with:
+          submodules: "recursive"
+          fetch-tags: true
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Set up GCC
         uses: egor-tensin/setup-gcc@v1
         with:
           version: 10
           platform: x64
+<<<<<<< HEAD
       - name: Setup conda
         uses: s-weigand/setup-conda@v1
         with:
@@ -57,8 +61,19 @@ jobs:
           git fetch -t
           mkdir build && cd build
           cmake .. && make install -j 4 && cd ..
+=======
+      - name: Check that gfortran works
+        run: gfortran --version
+      - name: Install build package dependencies
+        run: sudo apt install libblas-dev liblapack-dev libeigen3-dev
+      - name: Install sharpy and coverage using pip
+        run: |
+          export QT_QPA_PLATFORM='offscreen'
+>>>>>>> develop
           pip install .
           pip install coverage
+      - name: Run coverage
+        run: |
           coverage run -m unittest discover
       - name: Upload Coverage to Codecov
         uses: codecov/codecov-action@v2

.readthedocs.yaml

@@ -0,0 +1,26 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
+python:
+  install:
+    - requirements: docs/requirements_rtd
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# We recommend specifying your dependencies to enable reproducible builds:
+# https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+# python:
+#   install:
+#   - requirements: docs/requirements.txt

.version.json

@@ -1,6 +1,6 @@
 {
   "schemaVersion": 1,
   "label": "release version",
-  "message": "2.1",
+  "message": "2.4",
   "color": "green"
 }

CHANGELOG.md

@@ -1,5 +1,79 @@
 # Changelog
 
+## [2.3](https://github.com/imperialcollegelondon/sharpy/tree/2.3) (2024-05-10)
+
+[Full Changelog](https://github.com/imperialcollegelondon/sharpy/compare/2.2...2.3)
+
+**Implemented enhancements:**
+
+- Version 2.3 update [\#289](https://github.com/ImperialCollegeLondon/sharpy/pull/289) ([ben-l-p](https://github.com/ben-l-p))
+- Update develop branch with main [\#284](https://github.com/ImperialCollegeLondon/sharpy/pull/284) ([ben-l-p](https://github.com/ben-l-p))
+- Added pip install \(with docs\) [\#280](https://github.com/ImperialCollegeLondon/sharpy/pull/280) ([ben-l-p](https://github.com/ben-l-p))
+- Update beamplot.py to have stride option, consistent with aerogridplot.py [\#279](https://github.com/ImperialCollegeLondon/sharpy/pull/279) ([kccwing](https://github.com/kccwing))
+
+**Fixed bugs:**
+
+- Fix Github Runner Docker build failing [\#285](https://github.com/ImperialCollegeLondon/sharpy/pull/285) ([ben-l-p](https://github.com/ben-l-p))
+- Add scipy version info to env yml [\#277](https://github.com/ImperialCollegeLondon/sharpy/pull/277) ([SJ-Innovation](https://github.com/SJ-Innovation))
+
+**Closed issues:**
+
+- Scipy 1.12.0 Incompatible [\#276](https://github.com/ImperialCollegeLondon/sharpy/issues/276)
+- BeamLoader postprocessor squishing answers [\#270](https://github.com/ImperialCollegeLondon/sharpy/issues/270)
+- Solving Environment gets killed. [\#268](https://github.com/ImperialCollegeLondon/sharpy/issues/268)
+- Error when running sharpy unittest: module scipy.sparse.\_sputils not found [\#227](https://github.com/ImperialCollegeLondon/sharpy/issues/227)
+- Potential bug in /sharpy/structure/utils/modalutils.py [\#208](https://github.com/ImperialCollegeLondon/sharpy/issues/208)
+
+**Merged pull requests:**
+
+- Added ability to turn aligned grid off [\#288](https://github.com/ImperialCollegeLondon/sharpy/pull/288) ([ben-l-p](https://github.com/ben-l-p))
+- Update with main for mamba fixes [\#286](https://github.com/ImperialCollegeLondon/sharpy/pull/286) ([ben-l-p](https://github.com/ben-l-p))
+- Correct typos caught by Divya Sanghi [\#283](https://github.com/ImperialCollegeLondon/sharpy/pull/283) ([bbahiam](https://github.com/bbahiam))
+- Develop: Update environment.yml to fix scipy version issue [\#282](https://github.com/ImperialCollegeLondon/sharpy/pull/282) ([kccwing](https://github.com/kccwing))
+- Update noaero.py for consistency in function input [\#275](https://github.com/ImperialCollegeLondon/sharpy/pull/275) ([kccwing](https://github.com/kccwing))
+- A few minor bug fixes [\#273](https://github.com/ImperialCollegeLondon/sharpy/pull/273) ([sduess](https://github.com/sduess))
+- Update XBeam version to include compiler optimisation [\#272](https://github.com/ImperialCollegeLondon/sharpy/pull/272) ([ben-l-p](https://github.com/ben-l-p))
+- Update XBeam version to include compiler optimisation [\#271](https://github.com/ImperialCollegeLondon/sharpy/pull/271) ([ben-l-p](https://github.com/ben-l-p))
+- Improve docs and code of newmark\_ss [\#267](https://github.com/ImperialCollegeLondon/sharpy/pull/267) ([bbahiam](https://github.com/bbahiam))
+- Changed Github runner from Conda to Mamba [\#266](https://github.com/ImperialCollegeLondon/sharpy/pull/266) ([ben-l-p](https://github.com/ben-l-p))
+- Changed Github runner from Conda to Mamba [\#265](https://github.com/ImperialCollegeLondon/sharpy/pull/265) ([ben-l-p](https://github.com/ben-l-p))
+- Hotfix for documentation search [\#264](https://github.com/ImperialCollegeLondon/sharpy/pull/264) ([kccwing](https://github.com/kccwing))
+- Hotfix for documentation - develop [\#263](https://github.com/ImperialCollegeLondon/sharpy/pull/263) ([kccwing](https://github.com/kccwing))
+- Hotfix for documentation - main [\#262](https://github.com/ImperialCollegeLondon/sharpy/pull/262) ([kccwing](https://github.com/kccwing))
+- Merging v2.2 into develop [\#261](https://github.com/ImperialCollegeLondon/sharpy/pull/261) ([kccwing](https://github.com/kccwing))
+
+
+## [2.2](https://github.com/imperialcollegelondon/sharpy/tree/2.2) (2023-10-18)
+
+[Full Changelog](https://github.com/imperialcollegelondon/sharpy/compare/2.1...2.2)
+
+**Implemented enhancements:**
+
+- Added environment for Apple Silicon \(ARM64\) [\#254](https://github.com/ImperialCollegeLondon/sharpy/pull/254) ([ben-l-p](https://github.com/ben-l-p))
+- New Fuselage Model plus Minor Improvements [\#249](https://github.com/ImperialCollegeLondon/sharpy/pull/249) ([sduess](https://github.com/sduess))
+
+**Fixed bugs:**
+
+- fix polars concatenation in assembly of aeroinformation - develop [\#253](https://github.com/ImperialCollegeLondon/sharpy/pull/253) ([kccwing](https://github.com/kccwing))
+- fix polars concatenation in assembly of aeroinformation - main [\#252](https://github.com/ImperialCollegeLondon/sharpy/pull/252) ([kccwing](https://github.com/kccwing))
+- Minor bug fixes in aero util functions and save data postprocessor [\#247](https://github.com/ImperialCollegeLondon/sharpy/pull/247) ([sduess](https://github.com/sduess))
+
+**Closed issues:**
+
+- Automated tests failed : UnicodeEncodeError: 'ascii' codec can't encode character '\xe9' in position 47: ordinal not in range\(128\) [\#245](https://github.com/ImperialCollegeLondon/sharpy/issues/245)
+- Wrong key in settings for /cases/templates/flying\_wings.py [\#205](https://github.com/ImperialCollegeLondon/sharpy/issues/205)
+
+**Merged pull requests:**
+
+- merging develop into main for v2.2 [\#259](https://github.com/ImperialCollegeLondon/sharpy/pull/259) ([kccwing](https://github.com/kccwing))
+- fix \[docker\] use correct environment name in docker bashrc [\#257](https://github.com/ImperialCollegeLondon/sharpy/pull/257) ([sduess](https://github.com/sduess))
+- Update docker environment  [\#255](https://github.com/ImperialCollegeLondon/sharpy/pull/255) ([sduess](https://github.com/sduess))
+- Update README.md [\#246](https://github.com/ImperialCollegeLondon/sharpy/pull/246) ([rafapalacios](https://github.com/rafapalacios))
+- bringing commits to main into develop [\#244](https://github.com/ImperialCollegeLondon/sharpy/pull/244) ([rafapalacios](https://github.com/rafapalacios))
+- Updates to plotutils.py and the cantilever\_wing demo [\#242](https://github.com/ImperialCollegeLondon/sharpy/pull/242) ([boltyboi](https://github.com/boltyboi))
+- Small additions to the installation guide. [\#241](https://github.com/ImperialCollegeLondon/sharpy/pull/241) ([boltyboi](https://github.com/boltyboi))
+- Tutorial for closed-Loop Simulation with SHARPy as a hardware-in-the-loop system [\#240](https://github.com/ImperialCollegeLondon/sharpy/pull/240) ([sduess](https://github.com/sduess))
+
 ## [2.1](https://github.com/imperialcollegelondon/sharpy/tree/2.1) (2023-05-31)
 
 [Full Changelog](https://github.com/imperialcollegelondon/sharpy/compare/2.0...2.1)

Dockerfile

@@ -3,7 +3,7 @@ FROM centos:8
 ENV PYTHONDONTWRITEBYTECODE=true
 ENV BASH_ENV ~/.bashrc
 SHELL ["/bin/bash", "-c"]
-ENV PATH=${PATH}:/miniconda3/bin
+ENV PATH=${PATH}:/mamba/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
@@ -14,40 +14,38 @@ RUN cd /etc/yum.repos.d/ && \
 
 # 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 && \
+    yum install dnf-plugins-core && \
+    yum config-manager --set-enabled powertools && \
+    yum install -y --nogpgcheck mesa-libGL libXt libXt-devel wget gcc-gfortran lapack vim tmux eigen3-devel && \
     yum clean all
 
-# Install miniconda
-RUN wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /miniconda.sh && \
-    chmod +x /miniconda.sh && \
-    /miniconda.sh -b -p /miniconda3/ && \
-    rm /miniconda.sh && hash -r
+# Install Mamba - swapped from Conda to Mamba due to Github runner memory constraint
+# Mambaforge is deprecated in latest miniforge https://github.com/conda-forge/miniforge/pull/704
+RUN wget --no-check-certificate https://github.com/conda-forge/miniforge/releases/download/24.7.1-0/Mambaforge-Linux-x86_64.sh -O /mamba.sh && \
+    chmod +x /mamba.sh && \
+    /mamba.sh -b -p /mamba/ && \
+    rm /mamba.sh && hash -r
 
 ADD / /sharpy_dir/
 
-# Update conda and make it run with no user interaction
-# Cleanup conda installation
-RUN conda init bash && \
-    conda config --set always_yes yes --set changeps1 no && \
-    conda update -q conda && \
-    conda config --set auto_activate_base false && \
-    conda env create -f /sharpy_dir/utils/environment_minimal.yml && conda clean -afy && \
-    find /miniconda3/ -follow -type f -name '*.a' -delete && \
-    find /miniconda3/ -follow -type f -name '*.pyc' -delete && \
-    find /miniconda3/ -follow -type f -name '*.js.map' -delete
-
-#COPY /utils/docker/* /root/
+# Initialise mamba installation
+RUN mamba init bash && \
+    mamba update -q conda && \
+    mamba env create -f /sharpy_dir/utils/environment.yml && \
+    find /mamba/ -follow -type f -name '*.a' -delete && \
+    find /mamba/ -follow -type f -name '*.pyc' -delete && \
+    find /mamba/ -follow -type f -name '*.js.map' -delete
+
 RUN ln -s /sharpy_dir/utils/docker/* /root/
 
 RUN cd sharpy_dir && \
-    conda activate sharpy_minimal && \
+    mamba activate sharpy && \
     git submodule update --init --recursive && \
     mkdir build && \
     cd build && \
-    CXX=g++ FC=gfortran cmake .. && make install -j 2 && \
+    CXX=g++ FC=gfortran cmake .. && make install -j 4 && \
     cd .. && \
     pip install . && \
     rm -rf build
 
 ENTRYPOINT ["/bin/bash", "--init-file", "/root/bashrc"]
-

README.md

@@ -9,7 +9,7 @@
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3531965.svg)](https://doi.org/10.5281/zenodo.3531965)
 
 SHARPy is a nonlinear aeroelastic analysis package originally developed at the Department of Aeronautics, Imperial
-College London. It can be used for the structural, aerodynamic and aeroelastic analysis of flexible wings, aircraft and wind turbines.
+College London. It can be used for the structural, aerodynamic and aeroelastic analysis of flexible wings, aircraft and wind turbines. It is shared here under a BSD 3-Clause permissive license.
 
 ![XHALE](./docs/source/_static/XHALE-render.jpg)
 
@@ -33,6 +33,8 @@ vortex ring lattice with the boundary conditions enforced at the collocation poi
 The Kutta condition is also enforced at the trailing edge. The wake can be simulated by either additional vortex rings
 or by infinitely long horseshoe vortices, which are ideally suited for steady simulations only.
 
+The aerodynamic model has recently been extended by a linear source panel method (SPM) to model nonlifting bodies for example fuselages. The SPM and UVLM can be coupled to model fuselage-wing configuration and a junction handling approach, based on phantom panels and circulation interpolation, has been added.
+
 The input problems can be structural, aerodynamic or coupled, yielding an aeroelastic system.
 
 ## [Capabilities](http://ic-sharpy.readthedocs.io/en/latest/content/capabilities.html)
@@ -42,7 +44,7 @@ wings and wind turbines. In addition, it supports linearisation of these nonline
 arbitrary conditions and includes various tools such as: model reduction or frequency analysis.
 
 In short, SHARPy offers (amongst others) the following solutions to the user:
-* Static aerodynamic, structural and aeroelastic solutions
+* Static aerodynamic, structural and aeroelastic solutions including fuselage effects
 * Finding trim conditions for aeroelastic configurations
 * Nonlinear, dynamic time domain simulations under a large number of conditions such as:
     + Prescribed trajectories.

docs/requirements_rtd

@@ -1,4 +1,5 @@
-sphinx>=3.0
+sphinx>=3.0,<7
 ipykernel
 nbsphinx
-sphinx-rtd-theme==0.5.0
+sphinx-rtd-theme>=1.2.2
+recommonmark