Merge pull request #236 from ImperialCollegeLondon/develop

Merge to main for version 2.0.1 release

.codecov.yml

@@ -1,2 +1,2 @@
 ignore:
-  - "*/tests/*”
+  - '*/tests/*'

.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
@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7]
+        python-version: [3.10.8]
 
     steps:
       - uses: actions/checkout@v2
@@ -34,24 +34,26 @@ jobs:
       - name: Setup conda
         uses: s-weigand/setup-conda@v1
         with:
-          python-version: 3.7
+          python-version: 3.9
       - 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"
           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
           hash -r
           export QT_QPA_PLATFORM='offscreen'
           sudo apt install libeigen3-dev
-          conda env create -f utils/environment_minimal.yml
+          conda env create -f utils/environment_new.yml
           conda init bash
-          source activate sharpy_minimal
+          source activate sharpy
           git submodule init
           git submodule update
           git fetch --tags -f
@@ -60,7 +62,8 @@ jobs:
           pip install .
           pip install coverage
           coverage run -m unittest discover
+          coverage json
       - name: Upload Coverage to Codecov
-        uses: codecov/codecov-action@v2
+        uses: codecov/codecov-action@v3
         with:
           verbose: true

.gitignore

@@ -118,3 +118,7 @@ figs/*
 
 # sharpy extension
 *.sharpy
+
+# Exceptions
+# !tests/coupled/multibody/floating_wind_turbine/oc3_cs_v07.floating.h5 
+!tests/coupled/multibody/floating_wind_turbine/oc3_cs_v07.floating.h*

.version.json

@@ -1,6 +1,6 @@
 {
   "schemaVersion": 1,
   "label": "release version",
-  "message": "2.0",
+  "message": "2.0.1",
   "color": "green"
 }

CHANGELOG.md

@@ -1,5 +1,13 @@
 # Changelog
 
+## [2.0.1](/~https://github.com/imperialcollegelondon/sharpy/tree/2.0.1) (2023-05-31)
+
+[Full Changelog](/~https://github.com/imperialcollegelondon/sharpy/compare/2.0...2.0.1)
+
+**Closed issues:**
+
+- Twist direction inconsistent [\#212](/~https://github.com/ImperialCollegeLondon/sharpy/issues/212)
+
 ## [2.0](/~https://github.com/imperialcollegelondon/sharpy/tree/2.0) (2022-07-04)
 
 [Full Changelog](/~https://github.com/imperialcollegelondon/sharpy/compare/1.3...2.0)
@@ -102,11 +110,16 @@
 - Simple post-processor to save simulation parameters for batch runs [\#91](/~https://github.com/ImperialCollegeLondon/sharpy/pull/91) ([ngoiz](/~https://github.com/ngoiz))
 - SHARPy support for external inputs via UDP network [\#90](/~https://github.com/ImperialCollegeLondon/sharpy/pull/90) ([ngoiz](/~https://github.com/ngoiz))
 - Vortex radius as input parameter [\#86](/~https://github.com/ImperialCollegeLondon/sharpy/pull/86) ([ArturoMS13](/~https://github.com/ArturoMS13))
+- Enhanced Frequency Response post-processor and linear system input/output options [\#83](/~https://github.com/ImperialCollegeLondon/sharpy/pull/83) ([ngoiz](/~https://github.com/ngoiz))
+- Pazi wing added to flying\_wing template [\#82](/~https://github.com/ImperialCollegeLondon/sharpy/pull/82) ([outoforderdev](/~https://github.com/outoforderdev))
+- Several new aerodynamic enhancements [\#79](/~https://github.com/ImperialCollegeLondon/sharpy/pull/79) ([ArturoMS13](/~https://github.com/ArturoMS13))
 
 **Fixed bugs:**
 
 - libss.py disc2cont doesn't accept SISO systems [\#88](/~https://github.com/ImperialCollegeLondon/sharpy/issues/88)
 - Dimension mismatch when assembling linear UVLM with "shortened" wake [\#71](/~https://github.com/ImperialCollegeLondon/sharpy/issues/71)
+- Fix bug wake shape generator StaticCoupled [\#85](/~https://github.com/ImperialCollegeLondon/sharpy/pull/85) ([ArturoMS13](/~https://github.com/ArturoMS13))
+- Rework of direct balancing [\#74](/~https://github.com/ImperialCollegeLondon/sharpy/pull/74) ([outoforderdev](/~https://github.com/outoforderdev))
 
 **Closed issues:**
 
@@ -130,6 +143,9 @@
 - New SHARPy examples in the documentation [\#94](/~https://github.com/ImperialCollegeLondon/sharpy/pull/94) ([ArturoMS13](/~https://github.com/ArturoMS13))
 - Add support for offline use of UDPout postproc [\#93](/~https://github.com/ImperialCollegeLondon/sharpy/pull/93) ([ngoiz](/~https://github.com/ngoiz))
 - Option to transform rigid modes given at A FoR to centre of gravity and aligned with principal axes of inertia [\#92](/~https://github.com/ImperialCollegeLondon/sharpy/pull/92) ([ngoiz](/~https://github.com/ngoiz))
+- Pazy wing modified to include the tip weight [\#87](/~https://github.com/ImperialCollegeLondon/sharpy/pull/87) ([outoforderdev](/~https://github.com/outoforderdev))
+- Minor output clean up [\#81](/~https://github.com/ImperialCollegeLondon/sharpy/pull/81) ([ngoiz](/~https://github.com/ngoiz))
+- Fixes assembly of linUVLM after plotting wake with minus m\_star  [\#72](/~https://github.com/ImperialCollegeLondon/sharpy/pull/72) ([ngoiz](/~https://github.com/ngoiz))
 
 ## [v1.1.1](/~https://github.com/imperialcollegelondon/sharpy/tree/v1.1.1) (2020-02-03)
 
@@ -154,6 +170,10 @@
 - Update README.md [\#63](/~https://github.com/ImperialCollegeLondon/sharpy/pull/63) ([rafapalacios](/~https://github.com/rafapalacios))
 - Clean up linear SHARPy's interface with UVLM [\#60](/~https://github.com/ImperialCollegeLondon/sharpy/pull/60) ([ngoiz](/~https://github.com/ngoiz))
 
+## [v1.1.0-2](/~https://github.com/imperialcollegelondon/sharpy/tree/v1.1.0-2) (2019-12-12)
+
+[Full Changelog](/~https://github.com/imperialcollegelondon/sharpy/compare/v1.1.0...v1.1.0-2)
+
 ## [v1.1.0](/~https://github.com/imperialcollegelondon/sharpy/tree/v1.1.0) (2019-12-12)
 
 [Full Changelog](/~https://github.com/imperialcollegelondon/sharpy/compare/v1.0.1...v1.1.0)
@@ -214,6 +234,70 @@
 
 - Version v1.0.1 released [\#29](/~https://github.com/ImperialCollegeLondon/sharpy/pull/29) ([fonsocarre](/~https://github.com/fonsocarre))
 
+## [1.0.0](/~https://github.com/imperialcollegelondon/sharpy/tree/1.0.0) (2019-11-07)
+
+[Full Changelog](/~https://github.com/imperialcollegelondon/sharpy/compare/v1.0.0-rc...1.0.0)
+
+**Implemented enhancements:**
+
+- WriteVariablesTime output global beam variables and consistent out dir [\#19](/~https://github.com/ImperialCollegeLondon/sharpy/pull/19) ([ngoiz](/~https://github.com/ngoiz))
+- Autodocumenter [\#16](/~https://github.com/ImperialCollegeLondon/sharpy/pull/16) ([ngoiz](/~https://github.com/ngoiz))
+
+**Closed issues:**
+
+- Tests not passing due to them being outdated + test refactoring. [\#11](/~https://github.com/ImperialCollegeLondon/sharpy/issues/11)
+
+**Merged pull requests:**
+
+- Release of v1.0.0!!! [\#20](/~https://github.com/ImperialCollegeLondon/sharpy/pull/20) ([fonsocarre](/~https://github.com/fonsocarre))
+- Documentation fixes/updates [\#18](/~https://github.com/ImperialCollegeLondon/sharpy/pull/18) ([ngoiz](/~https://github.com/ngoiz))
+- Fix dynamic control surface and settings for aerogridloader [\#15](/~https://github.com/ImperialCollegeLondon/sharpy/pull/15) ([ngoiz](/~https://github.com/ngoiz))
+
+## [v1.0.0-rc](/~https://github.com/imperialcollegelondon/sharpy/tree/v1.0.0-rc) (2019-08-22)
+
+[Full Changelog](/~https://github.com/imperialcollegelondon/sharpy/compare/V0.2.1...v1.0.0-rc)
+
+**Closed issues:**
+
+- Output table [\#10](/~https://github.com/ImperialCollegeLondon/sharpy/issues/10)
+
+**Merged pull requests:**
+
+- Remove H5pyDeprecationWarning [\#14](/~https://github.com/ImperialCollegeLondon/sharpy/pull/14) ([ArturoMS13](/~https://github.com/ArturoMS13))
+- Lagrange multipliers for Catapult Take Off works + clean tests [\#13](/~https://github.com/ImperialCollegeLondon/sharpy/pull/13) ([fonsocarre](/~https://github.com/fonsocarre))
+
+## [V0.2.1](/~https://github.com/imperialcollegelondon/sharpy/tree/V0.2.1) (2019-03-14)
+
+[Full Changelog](/~https://github.com/imperialcollegelondon/sharpy/compare/v0.2...V0.2.1)
+
+## [v0.2](/~https://github.com/imperialcollegelondon/sharpy/tree/v0.2) (2019-03-14)
+
+[Full Changelog](/~https://github.com/imperialcollegelondon/sharpy/compare/v0.1...v0.2)
+
+**Closed issues:**
+
+- Add recovery options [\#9](/~https://github.com/ImperialCollegeLondon/sharpy/issues/9)
+
+## [v0.1](/~https://github.com/imperialcollegelondon/sharpy/tree/v0.1) (2018-09-03)
+
+[Full Changelog](/~https://github.com/imperialcollegelondon/sharpy/compare/bd2b65974d57d2d6486ea90cdb68ef6324efbac8...v0.1)
+
+**Implemented enhancements:**
+
+- Hinge definition for control surface [\#8](/~https://github.com/ImperialCollegeLondon/sharpy/issues/8)
+- sharpy\_main.main does not return output [\#5](/~https://github.com/ImperialCollegeLondon/sharpy/issues/5)
+
+**Fixed bugs:**
+
+- Aerofoil data associated to the nodes instead of the elements [\#6](/~https://github.com/ImperialCollegeLondon/sharpy/issues/6)
+
+**Merged pull requests:**
+
+- Trimming routine working [\#4](/~https://github.com/ImperialCollegeLondon/sharpy/pull/4) ([fonsocarre](/~https://github.com/fonsocarre))
+- Feature coupled dynamic [\#3](/~https://github.com/ImperialCollegeLondon/sharpy/pull/3) ([fonsocarre](/~https://github.com/fonsocarre))
+- Refactored storage finished [\#2](/~https://github.com/ImperialCollegeLondon/sharpy/pull/2) ([fonsocarre](/~https://github.com/fonsocarre))
+- Settings files are ConfigObjs now, not ConfigParser anymore [\#1](/~https://github.com/ImperialCollegeLondon/sharpy/pull/1) ([fonsocarre](/~https://github.com/fonsocarre))
+
 
 
 \* *This Changelog was automatically generated by [github_changelog_generator](/~https://github.com/github-changelog-generator/github-changelog-generator)*

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"]