Fix error in syntax due to migration to myst

AnyBody · Sep 29, 2021 · 458ee45 · 458ee45
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diff --git a/A_Getting_started/intro.md b/A_Getting_started/intro.md
@@ -13,9 +13,7 @@ tool, or even as the foundations for your own modeling studies.**
 
 Building models from the bottom-up is described further in "{doc}`Getting Started AnyScript Programming </A_Getting_started_anyscript/intro>`".
 
-Modifying the postures and motion of an existing model is introduced in "{doc}`Getting Started:
-Modeling <../A_Getting_started_modeling/intro>`" and the "{doc}`Making
-Things Move <../Making_things_move/intro>`" tutorials.
+Modifying the postures and motion of an existing model is introduced in "{doc}`Getting Started:Modeling <../A_Getting_started_modeling/intro>`" and the "{doc}`MakingThings Move <../Making_things_move/intro>`" tutorials.
 
 ```{rubric} Goals for this tutorial
 ```

diff --git a/A_Getting_started/lesson2.md b/A_Getting_started/lesson2.md
@@ -139,5 +139,4 @@ awarded the following message:
 You have just completed your first analysis with an AnyBody model. In the
 next lesson, we will examine the effects of posture on the results
 
-+++{doc}`Lesson 3: Reviewing analysis
-results <lesson3>`.
++++{doc}`Lesson 3: Reviewing analysisresults <lesson3>`.
diff --git a/A_Getting_started_anyscript/lesson5.md b/A_Getting_started_anyscript/lesson5.md
@@ -113,8 +113,7 @@ AnyDrawMuscle DrwMus = {};
 ```
 
 Upon re-loading the model, you should see a thick, red line connecting the muscle's origin and
-insertion points. There are other ways to visualize muscles, and these are described here in a {doc}`dedicated muscle
-tutorial <../Muscle_modeling/intro>`.
+insertion points. There are other ways to visualize muscles, and these are described here in a {doc}`dedicated muscletutorial <../Muscle_modeling/intro>`.
 
 The muscle path may appear strange because the mechanism hasn't been assembled by a kinematic analysis.
 
@@ -316,8 +315,7 @@ movement and drops off again.
 
 :::{note}
 Applied forces do not have to be constant. They can change with time
-and other properties in the model.  Please refer to the {doc}`tutorial on
-forces <../The_mechanical_elements/intro>` for more
+and other properties in the model.  Please refer to the {doc}`tutorial onforces <../The_mechanical_elements/intro>` for more
 details.
 :::
 

diff --git a/A_Getting_started_anyscript/lesson6.md b/A_Getting_started_anyscript/lesson6.md
@@ -30,8 +30,7 @@ option during the export process.
 Since the bone models shown in the above tutorial may be a bit too elaborate for a
 basic tutorial, we will demonstrate this by adding an STL file for the dumbbel in the arm model.
 
-Download the following model {download}`here
-(dumbell.stl) <Downloads/dumbbell.stl>`.
+Download the following model {download}`here(dumbell.stl) <Downloads/dumbbell.stl>`.
 
 The dumbbell STL should be added to the forearm, so add the following code - which imports the STL
 file into AnyBody - within the "ArmModel.Segs.ForeArm" object:

diff --git a/A_Getting_started_modeling/lesson3.md b/A_Getting_started_modeling/lesson3.md
@@ -506,7 +506,5 @@ can still run the kinematics of your model.
 :::
 
 :::{seealso}
-**Next lesson:** Now that the kinematics is in order let us move on to the {doc}`kinetic
-analysis in Lesson 4 and see what the model is good
-for. <lesson4>`
+**Next lesson:** Now that the kinematics is in order let us move on to the {doc}`kineticanalysis in Lesson 4 and see what the model is goodfor. <lesson4>`
 :::
diff --git a/A_study_of_studies/intro.md b/A_study_of_studies/intro.md
@@ -172,8 +172,7 @@ studies can easily be made with references to the common part and their
 respective distinctive part. Special studies that are used to initialize
 properties in the model, is also a case where it is indeed useful to be
 able to point to parts of the model. Muscle property calibration is such
-a case, which we shall look at in a special lesson of the {doc}`Inverse
-Dynamics of Muscle Systems tutorial </MuscleRecruitment/index>`.
+a case, which we shall look at in a special lesson of the {doc}`InverseDynamics of Muscle Systems tutorial </MuscleRecruitment/index>`.
 
 ## The elements of a study
 

diff --git a/A_study_of_studies/lesson1.md b/A_study_of_studies/lesson1.md
@@ -87,8 +87,7 @@ AnyBody allows for the definition of joints that only provide kinematic
 constraints but not the associated reaction forces. In fact, the system
 also allows the opposite: Reaction forces without kinematic constraints.
 For an in-depth discussion of some of these issues, please refer to the
-{doc}`tutorial on mechanical
-elements <../The_mechanical_elements/intro>`. For now, the
+{doc}`tutorial on mechanical  elements <../The_mechanical_elements/intro>`. For now, the
 bottom line is that counting reactions can sometimes be tricky, and the
 Mechanical System Information in Object Description is helpful in this
 respect.

diff --git a/A_study_of_studies/lesson2.md b/A_study_of_studies/lesson2.md
@@ -67,8 +67,7 @@ is used for positioning muscles wrapping over surfaces. It is just not
 visible in this simple model.
 
 The InitialConditions study can be thought of as the first step of a
-kinematic analysis, which will be the subject of {doc}`the next
-lesson. <lesson3>`
+kinematic analysis, which will be the subject of {doc}`the next lesson. <lesson3>`
 
 :::{rst-class} without-title
 :::

diff --git a/A_study_of_studies/lesson3.md b/A_study_of_studies/lesson3.md
@@ -105,8 +105,7 @@ the purpose:
 
 ![demo.SliderCrank3D.any](_static/lesson3/image1.png)
 
-When you load it and open a {doc}`Model
-View <../Interface_features/lesson3>` you will see that
+When you load it and open a {doc}`Model View <../Interface_features/lesson3>` you will see that
 this is a very simple mechanism comprising only three segments. They are
 not yet connected correctly at their joints, but they will be if you run
 the Kinematics operation. Go to the Study tree, pick Kinematics and

diff --git a/A_study_of_studies/lesson4.md b/A_study_of_studies/lesson4.md
@@ -48,5 +48,4 @@ balance the moments exerted about the elbow and shoulder joints by the
 external load.
 
 Much more details about inverse dynamics of musculoskeletal systems are
-found {doc}`the special tutorial on the
-topic <../MuscleRecruitment/Inverse_dynamics>`.
+found {doc}`the special tutorial on the topic <../MuscleRecruitment/Inverse_dynamics>`.
diff --git a/AnyExp4SOLIDWORKS/lesson1.md b/AnyExp4SOLIDWORKS/lesson1.md
@@ -1,7 +1,6 @@
 # Translating a SOLIDWORKS CAD model to AnyBody
 
-Start by downloading the {download}`example SOLIDWORKS CAD assembly
-<Downloads/FitnessMachine_SolidWorks.zip>`
+Start by downloading the {download}`example SOLIDWORKS CAD assembly<Downloads/FitnessMachine_SolidWorks.zip>`
 
 After having downloaded and opened this model in your SOLIDWORKS
 environment, you will see the following image.

diff --git a/Finite_element_analysis/lesson1.md b/Finite_element_analysis/lesson1.md
@@ -460,5 +460,4 @@ selected commercial FE packages using small interface tools
 
 Click here to continue to
 
-- {doc}`Lesson 2: ANSYS interface <lesson2>`.
-- {doc}`Lesson 3: ABAQUS interface <lesson3>`
+- {doc}`Lesson 2: ANSYS interface <lesson2>`. - {doc}`Lesson 3: ABAQUS interface <lesson3>`
diff --git a/Interface_features/intro.md b/Interface_features/intro.md
@@ -7,8 +7,7 @@ substitutions:
 
 # Using the AnyBody Modeling System
 
-Please complete the “{doc}`Getting Started: AnyScript
-Programming” tutorial </A_Getting_started_anyscript/intro>`
+Please complete the “{doc}`Getting Started: AnyScript Programming” tutorial </A_Getting_started_anyscript/intro>`
 before proceeding.
 
 :::{note}
@@ -48,12 +47,10 @@ following lessons:
 - {doc}`Lesson 1: Editor Window Facilities <lesson1>`
 - {doc}`Lesson 2: The Model View Window <lesson2>`
 - {doc}`Lesson 3: The Chart View <lesson3>`
-- {doc}`Lesson 4: Browsing the Model via Model Tree and Object
-  Description <lesson4>`
+- {doc}`Lesson 4: Browsing the Model via Model Tree and Object Description <lesson4>`
 - {doc}`Lesson 5: The Command Line Application <lesson5>`
 - {doc}`Lesson 6: Modifying the Loaded Model <lesson6>`
-- {doc}`Lesson 7: Wrapping the Model with AnyBody
-  Project <lesson7>`
+- {doc}`Lesson 7: Wrapping the Model with AnyBody Project <lesson7>`
 
 :::{rst-class} without-title
 :::

diff --git a/Interface_features/lesson1.md b/Interface_features/lesson1.md
@@ -105,8 +105,7 @@ If you are unsure on how to write the code for an object of a certain
 class, first position your cursor appropriately in the AnyScript Window.
 Then right click on a class name from the list and select “Insert Class
 Template” (see image below). Remember to replace any placeholder text in
-the inserted template as required. Read more from {doc}`Getting Started:
-AnyScript Programming tutorial <../A_Getting_started_anyscript/intro>`.
+the inserted template as required. Read more from {doc}`Getting Started:AnyScript Programming tutorial <../A_Getting_started_anyscript/intro>`.
 
 ![Class tree](_static/lesson1/image7.png)
 

diff --git a/Interface_features/lesson4.md b/Interface_features/lesson4.md
@@ -9,8 +9,7 @@ These functions make it easier to navigate between the three different
 modes in which the model is represented in AnyBody - the Model View,
 AnyScript, and the Model Tree.
 
-Watch the video mentioned in the {doc}`User Interface Introduction
-tutorial <intro>` to learn more.
+Watch the video mentioned in the {doc}`User Interface Introduction tutorial <intro>` to learn more.
 
 ## The Object Description
 

diff --git a/Interface_features/lesson6.md b/Interface_features/lesson6.md
@@ -17,8 +17,7 @@ dependents are marked with an **(Editable\*)**. The procedure for
 re-computing these dependencies is described in the next section.
 
 “Set Value” is a Class Operation, which means that it can be summoned
-from the console application if needed, as defined in the {doc}`previous
-chapter <lesson5>`.
+from the console application if needed, as defined in the {doc}`previous chapter <lesson5>`.
 
 ## Resetting values
 
@@ -28,8 +27,7 @@ reset all values in the model. This action is also available from the
 menu Operations > Reset All Values.
 
 “Reset values” is a Class Operation, which means that it can be summoned
-from the console application if needed, as defined in the {doc}`previous
-chapter <lesson5>`.
+from the console application if needed, as defined in the {doc}`previous chapter <lesson5>`.
 
 ![Operations menu](_static/lesson6/image1.png)
 

diff --git a/Making_things_move/lesson5.md b/Making_things_move/lesson5.md
@@ -14,7 +14,7 @@ for data processing.
 
 :::{note}
 Make sure you have installed your own copy of the AnyBody Model repository (AMMR).
-See the {ammr:ref}`AMMR documentation <installing_ammr>`.
+See the {ref}`AMMR documentation <ammr:installing-ammr>`.
 :::
 
 1. Go to the folder {file}`Application/MocapExamples/Plug-in-gait_Simple`.

diff --git a/MuscleRecruitment/Inverse_dynamics.md b/MuscleRecruitment/Inverse_dynamics.md
@@ -66,8 +66,7 @@ general mathematical software. The only viable solution is to use a
 computer system designed for this particular purpose, so here we are.
 With the AnyBody Modeling System you can easily define very complex
 musculoskeletal systems and analyze them dynamically as you have
-probably already done in the {doc}`Getting
-Started <../A_Getting_started/intro>` tutorial. If not, now would
+probably already done in the {doc}`Getting Started <../A_Getting_started/intro>` tutorial. If not, now would
 be a good time to do it and familiarize yourself with the mouse clicks
 necessary to conduct the InverseDynamics operation and inspect the
 results before continuing with the next steps of this tutorial.

diff --git a/MuscleRecruitment/lesson3.md b/MuscleRecruitment/lesson3.md
@@ -30,8 +30,7 @@ energy stored in a muscle would be a quadratic function of the force it
 carries.
 
 Before we try it out, let us set up a model that makes more
-physiological sense than the previous one. Please {download}`download and save
-this zip file <Downloads/Bike2D.zip>` and unpack it into some working
+physiological sense than the previous one. Please {download}`download and savethis zip file <Downloads/Bike2D.zip>` and unpack it into some working
 directory. Then open AnyBody and load the file Bike2D.main.any. After
 you have compiled the model into memory you can open up a Model View
 window and see this picture:

diff --git a/MuscleRecruitment/lesson_calibration.md b/MuscleRecruitment/lesson_calibration.md
@@ -3,7 +3,7 @@
 :::{note}
 The following tutorial will explain how to set up your simple
 calibration study. Calibration is already built into the AMMR,
-{ammr:doc}`see the AMMR documentation <index>` for more details.
+{doc}`see the AMMR documentation <ammr:index>` for more details.
 :::
 
 One of the challenges in body modeling is that models must be able to change

diff --git a/Muscle_modeling/lesson1.md b/Muscle_modeling/lesson1.md
@@ -260,8 +260,7 @@ Notice that we have added an AnyDrawMuscle object to the definition.
 Like other classes in AnyScript, muscles are not drawn in the Model View
 window unless you specifically ask for it. When you load the model and
 run the SetInitialConditions study you will get the following picture
-(if your model does not load, and you cannot find the error, {download}`click
-here to download a model that works <Downloads/MuscleDemo.1.any>`):
+(if your model does not load, and you cannot find the error, {download}`clickhere to download a model that works <Downloads/MuscleDemo.1.any>`):
 
 ![simple model with muscle](_static/lesson1/image4.jpeg)
 

diff --git a/Muscle_modeling/lesson3.md b/Muscle_modeling/lesson3.md
@@ -132,8 +132,7 @@ move around with the different segments.
 
 From-the-point of view of kinematic robustness, the wrapping muscles are
 easier to handle than via point muscles, but the price is much higher
-computationally. Wrapping muscles is the subject of {doc}`Lesson
-4 <lesson4>`.
+computationally. Wrapping muscles is the subject of {doc}`Lesson 4 <lesson4>`.
 
 :::{rst-class} without-title
 :::

diff --git a/Muscle_modeling/lesson4.md b/Muscle_modeling/lesson4.md
@@ -19,8 +19,7 @@ surface.
 
 Enough talk! Let us prepare for addition of a wrapping muscle to our
 model. If for some reason you do not have a working model from the
-previous lessons, {download}`you can download one
-here <Downloads/MuscleDemo.4.any>`.
+previous lessons, {download}`you can download onehere <Downloads/MuscleDemo.4.any>`.
 
 A wrapping muscle needs one or several surfaces to wrap on, so the first
 thing to do is to define a surface. For convenience we shall attach the
@@ -326,8 +325,7 @@ AnyShortestPathMuscle Muscle2 = {
 Notice that the InitWrapPosVectors like the StringMesh is part of an
 object called SPLine. This is an object in its own right that gets
 defined automatically inside a shortest path muscle. It is a special
-kind of {doc}`kinematic
-measure <../The_mechanical_elements/lesson4>` that is
+kind of {doc}`kinematic measure <../The_mechanical_elements/lesson4>` that is
 really a string that wraps just like a muscle but does nothing else than
 measure its own length. These objects can be used outside the muscle
 definition for various purposes in the model, for instance for
@@ -344,8 +342,7 @@ If you keep pressing the step button you will see how the muscle now
 wraps on the other side of the cylinder.
 
 With the kinematics of muscles well under control, we can proceed to
-another important and interesting topic, {doc}`Lesson 5: Muscle
-models <lesson5>`.
+another important and interesting topic, {doc}`Lesson 5: Muscle models <lesson5>`.
 
 :::{rst-class} without-title
 :::

diff --git a/Muscle_modeling/lesson5.md b/Muscle_modeling/lesson5.md
@@ -920,11 +920,9 @@ time, where all the muscles in a set are calibrated at the same joint
 postures. This way, all the muscles in a complicated system can be
 calibrated with a reasonable number of operations.
 
-Detailed muscle parameter calibration is covered in the {doc}`Inverse
-Dynamics of Muscle Systems tutorial <../MuscleRecruitment/Inverse_dynamics>`.
+Detailed muscle parameter calibration is covered in the {doc}`Inverse Dynamics of Muscle Systems tutorial <../MuscleRecruitment/Inverse_dynamics>`.
 Calibration of ligaments is much the same type of process and is
-described in detail in the {doc}`Ligament tutorial, Lesson
-7 <lesson7>`.
+described in detail in the {doc}`Ligament tutorial, Lesson 7 <lesson7>`.
 
 But before we come to ligaments we must cover one last aspect of muscle
 modeling, namely General Muscles. They are the topic of the next lesson,

diff --git a/Muscle_modeling/lesson6.md b/Muscle_modeling/lesson6.md
@@ -12,10 +12,8 @@ muscles, which are confined to acting along strings.
 The solution is the AnyGeneralMuscle class. This type of muscle is
 capable of acting on *Kinematic Measures*. *Kinematic Measures* is an
 abstract class representing anything you can measure on a model, and
-there is in fact {doc}`an entire tutorial lesson devoted to the
-subject <../The_mechanical_elements/lesson4>` in the
-section on {doc}`The Mechanical
-Elements <../The_mechanical_elements/intro>`. Some
+there is in fact {doc}`an entire tutorial lesson devoted to the subject <../The_mechanical_elements/lesson4>` in the
+section on {doc}`The Mechanical Elements <../The_mechanical_elements/intro>`. Some
 examples are:
 
 - A general muscle working on a distance measure between two points
@@ -47,8 +45,8 @@ This way, the "muscle forces" computed in the general muscles will
 simply be the joint torques.
 
 The example from the preceding lessons is not well suited to play with joint
-torques, so please {download}`download a new example to start on.
-<Downloads/MuscleDemo.6.any>` This is in fact a simplified version of the simple
+torques, so please {download}`download a new example to start on. <Downloads/MuscleDemo.6.any>`
+This is in fact a simplified version of the simple
 arm example from the *Getting Started with AnyScript* tutorial, where the
 muscles have been removed. The model has two segments, an upper arm and a
 forearm, and is attached to the global reference frame at the shoulder. It has a

diff --git a/Parameter_studies_and_optimization/lesson1.md b/Parameter_studies_and_optimization/lesson1.md
@@ -14,14 +14,11 @@ Or you may be interested in knowing how the seat height and horizontal
 position influence the muscle effort and metabolism of the rider. This
 is precisely what we shall do in this tutorial. To make life a bit
 easier for you, we have prepared a bicycle model you can download and
-play around with. {download}`Please click here to download the zip file
-OptimBike.zip <Downloads/OptimBike2.zip>` and unpack it to some
+play around with. {download}`Please click here to download the zip fileOptimBike.zip <Downloads/OptimBike2.zip>` and unpack it to some
 pertinent place on your hard disk.
 
-The bicycle model is pretty much the {ref}`2D Bike
-<ammr:sphx_glr_auto_examples_Sports_plot_BikeModel2D.py>` that you may know from the
-{doc}`AnyBody Managed Model Repository
-<ammr:index>`.
+The bicycle model is pretty much the {ref}`2D Bike <ammr:sphx_glr_auto_examples_Sports_plot_BikeModel2D.py>` that you may know from the
+{doc}`AnyBody Managed Model Repository <ammr:index>`.
 
 ```{image} _static/Defining_a_parameter/bike2D.png
 ```

diff --git a/Parameter_studies_and_optimization/lesson3.md b/Parameter_studies_and_optimization/lesson3.md
@@ -213,8 +213,8 @@ and we are now ready to define the optimization process.
 
 ## Setting up the optimization study
 
-We wrap things up by creating a function, {ref}`similar to what we did in
-AnyBody <optimization-contraint>`, as well as defining the bounds and initial guess
+We wrap things up by creating a function, {ref}`similar to what we did in AnyBody <optimization-contraint>`,
+as well as defining the bounds and initial guess
 for the design variables.
 
 ```{code-block} python

diff --git a/Posture_and_movement/intro.md b/Posture_and_movement/intro.md
@@ -40,8 +40,7 @@ going to formulate a very simple problem, but the principle applies to
 much more complex models as well.
 
 Understanding this tutorial requires a-priory knowledge of the tutorial
-on {doc}`Parameter Studies and
-Optimization </Parameter_studies_and_optimization/intro>`.
+on {doc}`Parameter Studies and Optimization </Parameter_studies_and_optimization/intro>`.
 
 ## Definition of the Problem
 
@@ -77,8 +76,7 @@ So we need a simple model to play with. We are going to try to optimize
 a two-dimensional football kick. There are all sorts of reasons why a
 simple model of this task might be totally inadequate, but it will serve
 well to demonstrate the idea. Please download a model to begin on.
-{download}`Right-click the link and save the file
-Kick1.any <Downloads/Kick1.any>` in some working directory. Then open
+{download}`Right-click the link and save the fileKick1.any <Downloads/Kick1.any>` in some working directory. Then open
 it up in the AnyBody Modeling System, load it in and open a Model View
 window to have a look at the model. You should see something like this
 (except the legends):
@@ -113,8 +111,7 @@ are going to need such joint muscles for flexion and extension
 respectively for both of the two joints. The red lines below add such
 muscles with realistic joint strengths in Newton-meter. For an
 explanation of the use of the AnyGeneralMuscle class, please refer to
-the {doc}`muscle modeling
-tutorial </Muscle_modeling/intro>`.
+the {doc}`muscle modeling tutorial </Muscle_modeling/intro>`.
 
 ```AnyScriptDoc
 AnyKinEqSimpleDriver KneeDriver = {