Merge branch 'develop' into dev_pip2

.github/workflows/docker_build.yaml

@@ -4,7 +4,7 @@ on:
   push:
     branches: 
       - develop
-      - master
+      - main
     tags:
       - 'v*'
 

.github/workflows/docker_build_test.yaml

@@ -3,7 +3,7 @@ name: Test Docker image build
 on:
   pull_request:
     branches:
-      - master
+      - main
       - develop
       - 'rc*'
   push:

.github/workflows/readme.md

@@ -10,7 +10,7 @@ The related to the SHARPy tests that run the `SHARPy Tests` job are:
     * `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 
+Since the merge to `develop` and `main` 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.
 
@@ -19,5 +19,5 @@ 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 `master`.
-    * `docker_build.yaml`: Builds and pushes the Docker image. Runs on pushes to `develop`, `master` and annotated tags.
+    * `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.yaml`: Builds and pushes the Docker image. Runs on pushes to `develop`, `main` and annotated tags.

.github/workflows/sharpy_no_test_needed.yaml

@@ -3,7 +3,7 @@ name: SHARPy Tests
 on:
   pull_request:
     branches:
-      - master
+      - main
       - develop
       - 'rc*'
     paths-ignore:

.github/workflows/sharpy_tests.yaml

@@ -8,7 +8,7 @@ on:
       - '.github/workflows/sharpy*'
   pull_request:
     branches:
-      - master
+      - main
       - develop
       - 'rc*'
 
@@ -31,28 +31,25 @@ jobs:
         with:
           version: 10
           platform: x64
-      - name: Setup conda
-        uses: s-weigand/setup-conda@v1
-        with:
-          python-version: 3.9
+        #Swapped from Conda to Mamba due to Github runner memory constraint
+      - name: Setup Mamba
+        uses: mamba-org/setup-micromamba@v1
       - name: Pre-Install dependencies
         run: |
           gfortran --version
-          wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-          # wget https://repo.anaconda.com/archive/Anaconda3-2022.10-Linux-x86_64.sh -O miniconda.sh;
-          bash miniconda.sh -b -p $HOME/miniconda
-          export PATH="$HOME/miniconda/bin:$PATH"
+          wget --no-check-certificate https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh -O mamba.sh
+          bash mamba.sh -b -p $HOME/mamba
+          export PATH="$HOME/mamba/bin:$PATH"
           hash -r
-          conda config --set always_yes yes --set changeps1 no
-          # conda config --append channels conda-forge
-          conda update --name base conda
-          conda list --name base conda
-          conda init bash
+          mamba config --set always_yes yes --set changeps1 no
+          mamba update --name base mamba
+          mamba list --name base mamba
+          mamba init bash
           hash -r
           export QT_QPA_PLATFORM='offscreen'
           sudo apt install libeigen3-dev
-          conda env create -f utils/environment_new.yml
-          conda init bash
+          mamba env create -f utils/environment.yml
+          mamba init bash
           source activate sharpy
           git submodule init
           git submodule update

.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": "2.2",
   "color": "green"
 }

CHANGELOG.md

@@ -1,8 +1,39 @@
 # Changelog
 
-## [2.0.1](https://github.com/imperialcollegelondon/sharpy/tree/2.0.1) (2023-05-31)
+## [2.2](https://github.com/imperialcollegelondon/sharpy/tree/2.2) (2023-10-18)
 
-[Full Changelog](https://github.com/imperialcollegelondon/sharpy/compare/2.0...2.0.1)
+[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)
 
 **Implemented enhancements:**
 
@@ -17,10 +48,13 @@
 
 **Closed issues:**
 
+- No such file or directory during: source bin/sharpy\_vars.sh [\#233](https://github.com/ImperialCollegeLondon/sharpy/issues/233)
 - Twist direction inconsistent [\#212](https://github.com/ImperialCollegeLondon/sharpy/issues/212)
 
 **Merged pull requests:**
 
+- Version number updates for 2.1 from develop [\#237](https://github.com/ImperialCollegeLondon/sharpy/pull/237) ([kccwing](https://github.com/kccwing))
+- Merge to main for version 2.0.1 release [\#236](https://github.com/ImperialCollegeLondon/sharpy/pull/236) ([kccwing](https://github.com/kccwing))
 - Updates to Goland wing example [\#234](https://github.com/ImperialCollegeLondon/sharpy/pull/234) ([rafapalacios](https://github.com/rafapalacios))
 - A bit of clean-up of the readme file of the repo [\#231](https://github.com/ImperialCollegeLondon/sharpy/pull/231) ([rafapalacios](https://github.com/rafapalacios))
 - Dev internals [\#223](https://github.com/ImperialCollegeLondon/sharpy/pull/223) ([ACea15](https://github.com/ACea15))

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
@@ -17,30 +17,32 @@ RUN yum groupinstall "Development Tools" -y --nogpgcheck && \
     yum install -y --nogpgcheck mesa-libGL libXt libXt-devel wget gcc-gfortran lapack vim tmux && \
     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
+RUN wget --no-check-certificate https://github.com/conda-forge/miniforge/releases/latest/download/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
+# Update mamba and make it run with no user interaction
+# Cleanup mamba installation
+RUN mamba init bash
+RUN mamba config --set always_yes yes --set changeps1 no
+RUN mamba update -q conda
+RUN mamba config --set auto_activate_base false
+RUN mamba env create -f /sharpy_dir/utils/environment.yml && mamba clean -afy && \
+
+    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
 
 #COPY /utils/docker/* /root/
 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 && \

README.md

@@ -1,15 +1,15 @@
 # Simulation of High Aspect Ratio aeroplanes in Python [SHARPy]
 
-![Version badge](https://img.shields.io/endpoint.svg?url=https%3A%2F%2Fraw.githubusercontent.com%2FImperialCollegeLondon%2Fsharpy%2Fmaster%2F.version.json)
+![Version badge](https://img.shields.io/endpoint.svg?url=https%3A%2F%2Fraw.githubusercontent.com%2FImperialCollegeLondon%2Fsharpy%2Fmain%2F.version.json)
 ![Build Status](https://github.com/ImperialCollegeLondon/sharpy/actions/workflows/sharpy_tests.yaml/badge.svg)
-[![Documentation Status](https://readthedocs.org/projects/ic-sharpy/badge/?version=master)](https://ic-sharpy.readthedocs.io/en/master/?badge=master)
-[![codecov](https://codecov.io/gh/ImperialCollegeLondon/sharpy/branch/master/graph/badge.svg)](https://codecov.io/gh/ImperialCollegeLondon/sharpy)
+[![Documentation Status](https://readthedocs.org/projects/ic-sharpy/badge/?version=main)](https://ic-sharpy.readthedocs.io/en/main/?badge=main)
+[![codecov](https://codecov.io/gh/ImperialCollegeLondon/sharpy/branch/main/graph/badge.svg)](https://codecov.io/gh/ImperialCollegeLondon/sharpy)
 [![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 [![status](https://joss.theoj.org/papers/f7ccd562160f1a54f64a81e90f5d9af9/status.svg)](https://joss.theoj.org/papers/f7ccd562160f1a54f64a81e90f5d9af9)
 [![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.
@@ -115,7 +117,7 @@ journal = {Journal of Open Source Software}
 SHARPy uses Continuous Integration to control the integrity of its code. The status in the release and develop branches
 is:
 
-Master
+Main
 ![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)
 

docs/JOSS/paper.md

@@ -107,7 +107,7 @@ structural or aerodynamic simulation are supported natively.
 The nonlinear system can also be linearised taking an arbitrary reference condition. The linearised system can be used
 for frequency domain analysis, linear model order reduction methods and controller design.
 
-![Aerodynamic grid and forces in the static aeroelastic equilibrium configuration on the XHALE aircraft [@del2019ifasd]](https://github.com/ImperialCollegeLondon/sharpy/raw/master/docs/source/_static/XHALE-render.jpg)
+![Aerodynamic grid and forces in the static aeroelastic equilibrium configuration on the XHALE aircraft [@del2019ifasd]](https://github.com/ImperialCollegeLondon/sharpy/raw/main/docs/source/_static/XHALE-render.jpg)
 
 
 # Acknowledgements

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

docs/source/conf.py

@@ -47,6 +47,7 @@
     'sphinx.ext.napoleon',
     'nbsphinx',
     'sphinx.ext.autosectionlabel',
+    'sphinxcontrib.jquery',
     'recommonmark'
 ]
 
@@ -82,9 +83,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '2.1'
+version = '2.2'
 # The full version, including alpha/beta/rc tags.
-release = '2.1'
+release = '2.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/source/content/casefiles.rst

@@ -321,6 +321,55 @@ Item by item:
     should be included for each airfoil defined. Each entry consists of a 4-column table. The first column corresponds
     to the angle of attack (in radians) and then the ``C_L``, ``C_D`` and ``C_M``. 
 
+Nonlifting Body file
+-----------------
+
+All the nonlifting body data is contained in ``case.nonlifting_body.h5``.
+
+The idea behind the structure of the model definition of nonlifting bodies in SHARPy is similiar to the aerodynamic 
+one for lifting surfaces. Again for each node or element we define several parameters.
+
+Item by item:
+
+* ``shape``: Type of geometrical form of 3D nonlifting body.
+
+    In the ``nonlifting_body.h5`` file, there is a Group called ``shape``. The shape indicates the geometrical form of the 
+    nonlifting body. Common options for this parameter are ``'cylindrical'`` and ``'specific'``. For the former, SHARPy 
+    expects rotational symmetric cross-section for which only a radius is required for each node. For the ``'specific'`` 
+    option, SHARPy can create a more unique nonlifting body geometry by creating an ellipse at each fuselage defined by 
+    :math:`\frac{y^2}{a^2}+\frac{z^2}{b^2}=1` with the given ellipse axis lengths :math:`a`  and :math:`b`. Further, SHARPy 
+    lets define the user to create a vertical offset from the node with :math:`z_0`.
+
+* ``radius [num_node]``: Cross-sectional radius.
+
+    Is an array with the radius of specified for each fuselage node.
+
+* ``a_ellipse [num_node]``: Elliptical axis lengths along the local y-axis.
+
+    Is an array with the length of the elliptical axis along the y-axis.
+
+* ``b_ellipse [num_node]``: Elliptical axis lengths along the local z-axis.
+
+    Is an array with the length of the elliptical axis along the z-axis.
+
+* ``z_0_ellipse [num_node]``: Vertical offset of the ellipse center from the beam node.
+
+    Is an array with the vertical offset of the center of the elliptical cross-sectoin from the fuselage node.
+
+*  ``surface_m [num_surfaces]``: Radial panelling.
+
+    Is an integer array with the number of radial panels for every surface.
+
+*  ``nonlifting_body_node [num_node]``: Nonlifting body node definition.
+
+    Is a boolean (``True`` or ``False``) array that indicates if that node has a nonlifting body
+    attached to it.
+
+*  ``surface_distribution [num_elem]``:  Nonlifting Surface integer array.
+
+    It contains the index of the surface the element belongs to. Surfaces need to be continuous, so please note 
+    that if your beam numbering is not continuous, you need to make a surface per continuous section.
+
 
 Time-varying force input file (``.dyn.h5``)
 -------------------------------------------