Tutorial updates fixes (#27)

* 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

* Try with request header for linkcheck

* Add exclusion for Mathworks link in linkcheck_ignore

---------

Co-authored-by: Jacob Hilmar Adamsen <[email protected]>

Parameter_studies_and_optimization/index.md

@@ -18,5 +18,5 @@ to obtain a desired model behavior.
 Introduction <intro>
 lesson1
 lesson2
-lesson3
+lesson3/lesson3
 ```

Parameter_studies_and_optimization/lesson1.md

@@ -359,6 +359,8 @@ is that this bicycle model has a predefined ankle angle variation
 whereas a real human can compensate for a higher seat by letting the
 ankle operate in a more plantar-flexed position.
 
+### Calculating the metabolism of the muscles with integrals
+
 Before we finish this section, let us take a look at a particularly
 important feature of AnyScript mathematics: The ability to compute
 integral properties. AnyBody has a simple way of approximating the

Parameter_studies_and_optimization/lesson2.md

@@ -399,6 +399,6 @@ picture below:
 
 This completes the introduction to optimization studies.
 
-In {doc}`lesson 3 <lesson3>` we will look at how to use external (3rd. party) optimizers with
+In {doc}`lesson 3 <lesson3/lesson3>` we will look at how to use external (3rd. party) optimizers with
 AnyBody. In particular we will show how to use the Python programming language to run the
 same optimizations as we have done in this Tutorial.

Parameter_studies_and_optimization/python-optimize/BikeModel2D.main.any → Parameter_studies_and_optimization/lesson3/BikeModel2D.main.any

@@ -1,6 +1,4 @@
-#ifnpathexists "../libdef.any"
-#include "<ANYBODY_PATH_INSTALLDIR>/AMMR/libdef.any"
-#endif
+#include "libdef.any"
 
 /**2-D bicyle model.
 Although this model can be rotated in 3-D space it really is just a saggital
@@ -105,7 +103,7 @@ Main = {
     };
     AnyDesVar SaddlePos = {
       Val = Main.BikeParameters.SaddlePos;
-        Min = -0.22 /*-0.03*/;
+        Min = -0.20 /*-0.03*/;
         Max = -0.05;
     };
     AnyDesMeasure MaxAct = {
@@ -129,7 +127,7 @@ Main = {
     };
     AnyDesVar SaddlePos = {
       Val = Main.BikeParameters.SaddlePos;
-        Min = -0.22 /*-0.03*/;
+        Min = -0.20 /*-0.03*/;
         Max = -0.05;
     };
     AnyDesMeasure Metab = {