Tutorial updates for Finite Element interfacing and other small tutorial updates (#26)

* Tutorial snippet updates

* Tutorial images and text changes

* Tutorial snippets in Getting started

* Tutorial snippets in Modeling the human body

* Created whole folders for snippet files

* Update tests

* Used cmd.exe to create lib in ci test

* Merge commit '118df158da292f4b7f185ff8d0172692779da1e9'

* Updates to tutorial Modeling the Human Body. New folder structure

* Final updates to the first 4 tutorials.

* Update file paths in lesson1.md

* rename1

* rename2

* Tutorial updates - file structure, images and more

* Update file path in lesson2.md

* Different updates to the first few tutorials

* Text and general structure updates to the first few tutorials

* Updates of code snippets, images and other stuff in A Study of Studies

* Mainly changes to Parameter Studies and Optimization Tutorial. Many files created due to Code Snippets.

* Setup of making Python optimization tutorial in Jupyter notebook and changes to the tutorial

* Small extra update to Python Optimization Tutorial

* Final changes in Python optimization tutorial - made download files an more

* One small extra update to Python optimization Study

* Update instructions for installing python

* Fixed download link

* Fix download link

* Add exclusion pattern for Jupyter Notebook execution in conf.py

* Updates to Finite element analysis interfacing tutorials (Not finished work yet)

* Minor changes to other tutorials and all changes to FEM interfacing lesson 1 tutorial (which is not finished yet)

* Updates for FE interfacing tutorial to use FEBio

* Small grammar changes to Getting Started and A Study of Studies tutorials

* Fixed mistakes with insertion of notes in tutorials

* Update build workflow to checkout ammr4-beta branch instead of master

---------

Signed-off-by: Morten Enemark Lund <melund@gmail.com>
Co-authored-by: Jacob Hilmar Adamsen <jha@anybodytech.com>
Co-authored-by: Morten Enemark Lund <mel@anybodytech.com>
Co-authored-by: Morten Enemark Lund <melund@gmail.com>

Author: 3 people

.github/workflows/build.yaml

@@ -73,12 +73,20 @@ jobs:
           repository: anybody/ammr
           ref: master
           path: ammr
-      
+      - uses: actions/checkout@v4
+        name: Checkout AMMR4
+        with:
+          repository: anybody/ammr4-beta
+          ref: ammr4-beta
+          path: ammr4
+        
+        
+        
       - name: Link AMMR
         shell: cmd
         run: | 
             echo #include "%GITHUB_WORKSPACE%/ammr/libdef.any" > libdef.any
-
+            echo #include "%GITHUB_WORKSPACE%/ammr4/libdef.any" > libdef-ammr4.any
           
       - uses: prefix-dev/setup-pixi@v0.8.1
         with:

A_Getting_started/intro.md

@@ -3,61 +3,64 @@
 
 # Getting Started Tutorial
 
-:::{note}
-The AnyBody software comes with an inbuilt model repository - The AnyBody Managed Model Repository (AMMR). This tutorial starts with unpacking a local version of the AMMR. You can skip to {doc}`lesson 1 <lesson1>` if you have already done this. 
+:::{note} The AnyBody software comes with an inbuilt model repository - The
+AnyBody Managed Model Repository (AMMR). This tutorial starts with unpacking a
+local version of the AMMR. You can skip to {doc}`lesson 1 <lesson1>` if you have
+already done this. 
 :::
 
-
 ## Goals for this tutorial
 
-This tutorial takes the top-down approach and aims to accomplish the following:
+This tutorial takes a top-down approach and aims to accomplish the following:
 
 1. Create a new standing model using the Human Standing template model
-2. Learn how to load & change the posture of the human model, and use the model view window
-3. Run an inverse dynamics analysis and review the results.
+2. Learn how to load & change the posture of the human model, and use 
+the model view window
+3. Run an inverse dynamics analysis and review the results
 
-This entire tutorial relies heavily on using the AnyBody Managed Model Respository (AMMR). 
+This tutorial relies heavily on using the AnyBody Managed Model Repository (AMMR). 
 Follow the steps below to unpack a local version of the AMMR.
 
 # Setup the AMMR
 
-
-Before you continue you must unpack the entire repository and save it on
-your hard disk. To get a copy of the AMMR press the Demo tab in the
-AnyBody assistant dialog box.
+Before you continue, you must unpack the entire repository and save it on your
+hard disk. To get a copy of the AMMR, press the Demo tab in the AnyBody
+assistant dialog box.
 
 ![...](_static/intro/image1.png)
 
-Following the instructions in the Demo tab will install a copy of the AMMR in your documents folder by
-default. It is good practice to create a second local copy of the AMMR
-so that you do not overwrite the original AMMR folder by accident.
+Following the instructions in the Demo tab will install a copy of the AMMR in
+your documents folder by default. It is good practice to create a second local
+copy of the AMMR so that you do not overwrite the original AMMR folder by
+accident.
 
 # AMMR structure
 
 Open a file manager and navigate to the directory where you unpacked the
-repository. You should see a folder structure that includes the
-following subfolders:
+repository. You should see a folder structure that includes the following
+subfolders:
 
-- **Application** includes demo simulations of activities such as cycling, lifting
-  a box or propelling a wheelchair.
-- **Body** contains models of body parts and collections of body parts such as the lumbar spine model, leg models etc.
-  which are used by the applications.
+- **Application**: Includes demo simulations of activities such as cycling,
+  lifting a box, or propelling a wheelchair.
+- **Body**: Contains models of body parts and collections of body parts such as
+  the lumbar spine model, leg models, etc., which are used by the applications.
 
 A closer inspection of the Application branch reveals that it has four subfolders:
 
-- The **Beta** folder contains models that are unfinished, but may still be useful.
-- The **Examples** folder contains many models of various activities of daily living, and it is likely that you
-  will find a model that is similar to your own end goal.
-- The **MocapExamples** folder contains models utilizing the AnyMoCap framework. If you have your own motion capture data this is a good place to start,
-  whether you want to analyze multi trial/subject MoCap data or a single subject wearing an inertial MoCap suit.
-- The **Validation** folder contains models that have been used for validation purposes, typically by comparison of the model predictions
-  with experimental measurements.
-
+- The **Beta** folder contains models that are unfinished but may still be useful.
+- The **Examples** folder contains many models of various activities of daily
+  living, and it is likely that you will find a model that is similar to your
+  own end goal.
+- The **MocapExamples** folder contains models utilizing the AnyMoCap framework.
+  If you have your own motion capture data, this is a good place to start,
+  whether you want to analyze multi-trial/subject MoCap data or a single subject
+  wearing an inertial MoCap suit.
+- The **Validation** folder contains models that have been used for validation
+  purposes, typically by comparison of the model predictions with experimental
+  measurements.
 
 :::{admonition} **Continue**
 :class: seealso
 
 With that knowledge, you are all set to go, and you can proceed with
-{doc}`Lesson 1: Creating the standing model <lesson1>` using
-template.
-:::
+{doc}`Lesson 1: Creating the standing model <lesson1>` using the template. :::

A_Getting_started/lesson1.md

@@ -3,25 +3,30 @@
 
 # Lesson 1: Creating a Standing Model
 
-The standing model can be found in the AMMR folder under
-Applications/Examples. The main file is called StandingModel.Main.any.
+The standing model can be found in the AMMR folder under Applications/Examples.
+The main file is called StandingModel.Main.any.
 
-**While this file can be opened with the "File->Open" menu in AnyBody, do not do this! This tutorial will teach you an easier way
-to use the Standing Model as a starting template.**
+**While this file can be opened with the "File->Open" menu in AnyBody, do not do
+this! This tutorial will teach you an easier way to use the Standing Model as a
+starting template.**
 
 Key (modifiable) features of the standing model are:
 
 - Both feet are always connected to the ground.
 - The posture is defined by the joint angles for all major joints except the ankles.
-- The model automatically balances itself by maintaining its center of mass vertically above the ankle joints.
-  E.g., if the arms move forward, the entire body moves backwards to maintain the balance.
-- External forces can be applied to predefined nodes on the model. Muscle forces may change, to resist these forces and maintain balance.
+- The model automatically balances itself by maintaining its center of mass
+  vertically above the ankle joints. For example, if the arms move forward, the
+  entire body moves backward to maintain balance.
+- External forces can be applied to predefined nodes on the model. Muscle forces
+  may change to resist these forces and maintain balance.
 
 (model-templates)=
 
 ## Model templates
 
-To create a new standing model using the template model in the AMMR, click the "Create New from template" button ![Model_button](_static/lesson1/image_1.png) in the toolbar:
+To create a new standing model using the template model in the AMMR, click the
+"Create New from template" button ![Model_button](_static/lesson1/image_1.png)
+in the toolbar:
 
 ```{image} _static/lesson1/image_2.png
 :alt: Toolbar
@@ -66,11 +71,13 @@ to AMMR repository you want to use.
 
 To see the 3D graphical representation of the model you need to load.
 
-**Load/reload is a frequent operation and has been assigned to function
-key F7. You may also load your model by clicking** ![Load](_static/lesson1/image_6.png) **in the toolbar.**
+**Load/reload is a frequent operation and has been assigned to function key F7.
+You may also load your model by clicking** ![Load](_static/lesson1/image_6.png)
+**in the toolbar.**
 
-This action will load whatever file is chosen in the text editor. If a file is already loaded, the
-above action will simply reload the file until you give another file loading priority by right-clicking its tab and select “Load Model”.
+This action will load whatever file is chosen in the text editor. If a file is
+already loaded, the above action will simply reload the file until you give
+another file loading priority by right-clicking its tab and select “Load Model”.
 
 ```{image} _static/lesson1/image_7.png
 :alt: Load Model
@@ -80,19 +87,19 @@ above action will simply reload the file until you give another file loading pri
 
 ## The model view
 
-When loading is completed, the Model View window opens and shows the
-standing model: (You can open it manually from View -> Model Views).
+When loading is completed, the Model View window opens and shows the standing
+model: (You can open it manually from View -> Model Views).
 
 ```{image} _static/lesson1/image_5.png
 :alt: Model view
 :class: bg-primary
 :align: center
 ```
 
-The icons in the toolbar at the top of the Model View window allow you
-to modify the image: zoom, pan, rotate, etc. They should be mostly
-self-explanatory. Now is a good time to play a bit around with them and
-to familiarize yourself with the options.
+The icons in the toolbar at the top of the Model View window allow you to modify
+the image: zoom, pan, rotate, etc. They should be mostly self-explanatory. Now
+is a good time to play a bit around with them and to familiarize yourself with
+the options.
 
 In practical use it is often necessary to change quickly between these
 functions, so keyboard shortcuts have been provided:

A_Getting_started/lesson2.md

@@ -20,8 +20,8 @@ Scroll down to the line that says `#include "Model\Mannequin.any"`.
 :end-before: //# END SNIPPET 1
 ```
 
-**This line means that your model will include the content of the "Mannequin.any" file located in the Model folder,
-within the main file.**
+**This line means that your model will include the content of the
+"Mannequin.any" file located in the Model folder, within the main file.**
 
 Double-clicking the file name in the editor window after loading
 your model opens the mannequin file in a new tab. Then you see the
@@ -34,9 +34,11 @@ of the lines):
 :end-before: //# END SNIPPET 1
 ```
 
-**The section between each pair of braces creates a Folder, with all variables defined within forming the folder contents.**
+**The section between each pair of braces creates a Folder, with all variables
+defined within forming the folder contents.**
 
-Once the loading process is complete, you can see this folder structure being replicated in "Model tree" on the left of your screen. All contents of this file
+Once the loading process is complete, you can see this folder structure being
+replicated in "Model tree" on the left of your screen. All contents of this file
 can be seen by expanding the "Mannequin" folder icon in the tree.
 
 ```{image} _static/lesson2/image1.png
@@ -45,38 +47,44 @@ can be seen by expanding the "Mannequin" folder icon in the tree.
 :align: center
 ```
 
-There are sub-folders for postural joint angles (in degrees) and angular velocities (in degrees/second),
-for the right and left halves of the body.
+There are sub-folders for postural joint angles (in degrees) and angular
+velocities (in degrees/second), for the right and left halves of the body.
 
-Changing any of the joint angles and reloading the model, will change the model's posture at load time. To start with, ensure that the contents of the `Right`
-and `Left` sub-folders are as follows.
+Changing any of the joint angles and reloading the model, will change the
+model's posture at load time. To start with, ensure that the contents of the
+`Right` and `Left` sub-folders are as follows.
 
 ```{literalinclude} Snippets/lesson2/MyStandingHuman-3/Model/Mannequin.any
 :language: AnyScriptDoc
 :start-after: //# BEGIN SNIPPET 1
 :end-before: //# END SNIPPET 1
 ```
 
-If you scroll down, you'll see that the contents of `Left` folder are set to be equal
-to those from the `Right` folder, in order to create a symmetric posture.
+If you scroll down, you'll see that the contents of `Left` folder are set to be
+equal to those from the `Right` folder, in order to create a symmetric posture.
 
-**This is an important feature of the AnyScript language. Instead of numbers, you can create references to other variables or write
-mathematical expressions wherever necessary.**
+**This is an important feature of the AnyScript language. Instead of numbers,
+you can create references to other variables or write mathematical expressions
+wherever necessary.**
 
-To create a non-symmetric posture, you would have to replace some of the expressions in the `Left` folder with numbers of your choice.
+To create a non-symmetric posture, you would have to replace some of the
+expressions in the `Left` folder with numbers of your choice.
 
-Scrolling further below, you will find the `PosturVel folder`. This is organized exactly like Posture, but the numbers here specify
-joint angular velocities in degrees per second. For now, please leave all the values in this folder as zero.
+Scrolling further below, you will find the `PosturVel folder`. This is organized
+exactly like Posture, but the numbers here specify joint angular velocities in
+degrees per second. For now, please leave all the values in this folder as zero.
 
 (running-analysis)=
 
 ## Running a simulation analysis
 
 Simulation based analyses in AnyBody are termed "Studies".
 
-**Step 1**: Click on the operations drop-down menu at the top (see figure). Select “Main.RunApplication”
+**Step 1**: Click on the operations drop-down menu at the top (see figure).
+Select “Main.RunApplication”
 
-"RunApplication" is a readymade package of some pre-processing steps and the "InverseDynamics" analysis. Other drop-down operations include:
+"RunApplication" is a readymade package of some pre-processing steps and the
+"InverseDynamics" analysis. Other drop-down operations include:
 
 - **Kinematics**: Runs Kinematic analysis
 - **InverseDynamics**: Runs Inverse dynamic analysis
@@ -92,7 +100,8 @@ useful for testing and debugging.
 :align: center
 ```
 
-**Step 2**: Click the "Execute" button on the Execute toolbar. This toolbar is next to the drop-down menu, and contains three buttons:
+**Step 2**: Click the "Execute" button on the Execute toolbar. This toolbar is
+next to the drop-down menu, and contains three buttons:
 
 - **Run operation**: Starts or pauses the chosen operation. Shortcut
   F5.