From d1fb710b22bf86c6a331c5924b5d49a888a5004b Mon Sep 17 00:00:00 2001 From: Anne Koelewijn Date: Mon, 9 Dec 2024 08:46:30 +0100 Subject: [PATCH] Doxygen documentation --- .github/workflows/main | 39 -------------------------------------- .github/workflows/main.yml | 6 +++--- paper.md | 6 +++--- 3 files changed, 6 insertions(+), 45 deletions(-) delete mode 100644 .github/workflows/main diff --git a/.github/workflows/main b/.github/workflows/main deleted file mode 100644 index 1382e20..0000000 --- a/.github/workflows/main +++ /dev/null @@ -1,39 +0,0 @@ -# This is a basic workflow to help you get started with Actions - -name: Doxygen Action - -# Controls when the action will run. Triggers the workflow on push or pull request -# events but only for the master branch -on: - push: - branches: [ master ] - - - -# A workflow run is made up of one or more jobs that can run sequentially or in parallel -jobs: - # This workflow contains a single job called "build" - build: - # The type of runner that the job will run on - runs-on: ubuntu-latest - - # Steps represent a sequence of tasks that will be executed as part of the job - steps: - # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - - uses: actions/checkout@v2 - - - name: Doxygen Action - uses: mattnotmitt/doxygen-action@v1.1.0 - with: - # Path to Doxyfile - doxyfile-path: "./docs/Doxygen/Doxyfile" # default is ./Doxyfile - # Working directory - working-directory: "./docs/Doxygen" # default is . - - - name: Deploy - uses: peaceiris/actions-gh-pages@v3 - with: - github_token: ${{ secrets.GITHUB_TOKEN }} - # Default Doxyfile build documentation to html directory. - # Change the directory if changes in Doxyfile - publish_dir: ./docs/Doxygen/html diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 5f170ab..1382e20 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -26,9 +26,9 @@ jobs: uses: mattnotmitt/doxygen-action@v1.1.0 with: # Path to Doxyfile - doxyfile-path: "./Doxyfile" # default is ./Doxyfile + doxyfile-path: "./docs/Doxygen/Doxyfile" # default is ./Doxyfile # Working directory - working-directory: "." # default is . + working-directory: "./docs/Doxygen" # default is . - name: Deploy uses: peaceiris/actions-gh-pages@v3 @@ -36,4 +36,4 @@ jobs: github_token: ${{ secrets.GITHUB_TOKEN }} # Default Doxyfile build documentation to html directory. # Change the directory if changes in Doxyfile - publish_dir: ./html + publish_dir: ./docs/Doxygen/html diff --git a/paper.md b/paper.md index c66069e..34e1eca 100644 --- a/paper.md +++ b/paper.md @@ -1,5 +1,5 @@ --- -title: 'Biomech-Sim-Toolbox: A MATLAB toolbox for human movement simulation and analysis' +title: 'BioMAC-Sim-Toolbox: A MATLAB toolbox for human movement simulation and analysis' tags: - MATLAB - Biomechanics @@ -57,7 +57,7 @@ On the one hand, we can use so-called predictive simulations [@ackermann:2010; @ On the other hand, we can use so-called reconstructive simulations to estimate variables that cannot or were not measured directly by minimizing a data tracking error [@dorschky:2019a;@nitschke:2023;@nitschke:2024]. Such wide-spread measurements and their biomechanical analysis are vital to be able to reach this understanding of human movement. -Here, we present `Biomech-Sim-Toolbox`, a MATLAB toolbox that can be used to create simulations of human movement +Here, we present `BioMAC-Sim-Toolbox`, a MATLAB toolbox that can be used to create simulations of human movement and analyse human movements. The main functionality of the toolbox is that it solves trajectory optimization problems, or optimal control problems, for human musculoskeletal dynamics models. These dynamics models combine multibody dynamics to model the movements of the skeleton with muscle dynamics models to model the dynamics of muscular contraction and activation. In the trajectory optimization problem, the muscle stimulations are found that minimize an objective. This objective generally includes terms to minimize muscular effort and to minimize a tracking error @@ -138,7 +138,7 @@ Figure sizes can be customized by adding an optional second parameter: # Acknowledgements -We acknowledge contributions from Marko Ackermann, Dieter Heinrich, Maria Eleni Athanasiadou, Chuyi Wang, Christopher Löffelmann, Linus Hötzel, Utkarsha Shukla, Tobias Luckfiel, Heiko Schlarb. The development of the Biomech-Sim-Toolbox was supported by adidas AG and by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through Project-ID442419336, SFB 1483 - EmpkinS and through Project-ID520189992 +We acknowledge contributions from Marko Ackermann, Dieter Heinrich, Maria Eleni Athanasiadou, Chuyi Wang, Christopher Löffelmann, Linus Hötzel, Utkarsha Shukla, Tobias Luckfiel, Heiko Schlarb. The development of the BioMAC-Sim-Toolbox was supported by adidas AG and by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through Project-ID442419336, SFB 1483 - EmpkinS and through Project-ID520189992 # TODOS - Check mu in 2D normal and 3D contact model