Update to new theme

Author: melund

.github/workflows/build.yaml

@@ -78,6 +78,11 @@ jobs:
         run: |
           make html O="-W"
 
+      - name: Check links
+        shell: bash -l {0}
+        run: |
+          make linkcheck
+
       - name: Deploy 🚀
         if: github.ref == 'refs/heads/master'
         uses: peaceiris/actions-gh-pages@v3

A_Getting_started/index.md

@@ -1,4 +1,4 @@
-# Getting Started
+# Getting Started - First steps
 
 The objective of this tutorial is to demonstrate some of the features of
 the AnyBody Modeling System using an existing model.

A_Getting_started/intro.md

@@ -1,33 +1,23 @@
 # Getting Started Tutorial
 
-```{rubric} The AnyBody Managed Model Repository (AMMR)
-```
-
-The AnyBody software comes along with an inbuilt model repository. This
-is the AMMR, a collection of human body models that are based on the
-latest research studies.
-
-**Most importantly, it comes with a set of demo models (eg: MoCap
-based walking model, cycling etc.) that can serve as a useful learning
-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>`".
+:::{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. 
+:::
 
-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
-```
+## Goals for this tutorial
 
 This tutorial takes the 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.
 
-This entire tutorial relies heavily on using the AMMR described above.
+This entire tutorial relies heavily on using the AnyBody Managed Model Respository (AMMR). 
+Follow the steps below to unpack a local version of the AMMR.
+
+# Setup the AMMR
 
-```{rubric} 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
@@ -39,8 +29,7 @@ Following the instructions in the Demo tab will install a copy of the AMMR in yo
 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.
 
-```{rubric} AMMR structure
-```
+# 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
@@ -61,10 +50,10 @@ A closer inspection of the Application branch reveals that it has three subfolde
 - The **Validation** folder contains models that have been used for validation purposes, typically by comparison of the model predictions
   with experimental measurements.
 
-:::{rst-class} without-title
-:::
 
-:::{seealso}
+:::{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.

A_Getting_started/lesson1.md

@@ -80,9 +80,5 @@ functions, so keyboard shortcuts have been provided:
 - If you have a scrolling wheel on your mouse, this will zoom the model
   in and out.
 
-:::{rst-class} without-title
-:::
-
-:::{seealso}
 You can now proceed to {doc}`lesson2`.
-:::
+

A_Getting_started/lesson3.md

@@ -1,7 +1,8 @@
 ---
-substitutions:
-  getting_started_8: |-
-    <img src="_static/lesson3/image3.png">
+myst:
+  substitutions:
+    getting_started_8: |-
+      <img src="_static/lesson3/image3.png">
 ---
 
 # Lesson 3: Reviewing Analysis Results

A_Getting_started_AMMR/index.md

@@ -1,21 +1,23 @@
-# Getting started: The Model Repository
+:::{figure} ammr_bodyparts.png
+:align: center
+:alt: The AnyBody Model Repository
+:figclass: margin
+
+*The AnyBody Model Repository is a unique open collection of human body parts*.
+:::
+
+# The AnyBody Model Repository
 
-The AnyBody Model Repository (AMMR), is an open library of musculoskeletal
+
+The AnyBody Managed Model Repository (AMMR), is an open library of musculoskeletal
 models and examples ready to be used with the AnyBody Modeling System.
 
-The [AMMR documentation](https://anyscript.org/ammr-doc) is hosted
+The [AMMR documentation](https://anyscript.org/ammr-doc/) is hosted
 separately, and contains a few tutorials and other usefull information. The
 [Creating a Human Model from scratch](https://anyscript.org/ammr-doc/creating_model_from_scratch.html) tutorial is
 recommended for new users.
 
-:::{figure} ammr_bodyparts.png
-:align: center
-:alt: The AnyBody Model Repository
-:figwidth: 85 %
-:width: 70 %
 
-*The AnyBody Model Repository is a unique open collection of human body parts*.
-:::
 
 ```{rubric} AMMR documentation
 ```

A_Getting_started_anyscript/index.md

@@ -1,4 +1,4 @@
-# Getting started: AnyScript Programming
+# How to write AnyScript
 
 This tutorial introduces the AnyScript modeling language, which is used
 for all modeling in AnyBody.

A_Getting_started_anyscript/intro.md

@@ -12,9 +12,4 @@ Each lesson (after lesson 1) begins with a link to a file containing the
 AnyScript code that has been introduced until that point. If you have a problem getting your to code work, simply
 download the file and start from there.
 
-:::{rst-class} without-title
-:::
-
-:::{seealso}
 Let's get started with {doc}`Lesson 1: Basic concepts <lesson1>`
-:::

A_Getting_started_anyscript/lesson1.md

@@ -124,11 +124,6 @@ Clicking the error code, e.g: ERROR(SCR.PRS11) opens a pop-up window with a comp
 ```
 
 We now assume that you have removed the errors and have loaded the model
-successfully.
+successfully. If you are up to it, let's continue onward to {doc}`Lesson 2: Segments <lesson2>`
 
-:::{rst-class} without-title
-:::
 
-:::{seealso}
-**Next lesson:** If you are up to it, let's continue onward to {doc}`Lesson 2: Segments <lesson2>`.
-:::

A_Getting_started_anyscript/lesson2.md

@@ -1,10 +1,11 @@
 ---
-substitutions:
-  Load_button_image: |-
-    <img src="_static/lesson2/image1.png">
+myst:
+  substitutions:
+    Load_button_image: |-
+      <img src="_static/lesson2/image1.png">
 
-  Zoom_button_image: |-
-     <img src="_static/lesson2/image3.png">
+    Zoom_button_image: |-
+      <img src="_static/lesson2/image3.png">
 
 ---
 
@@ -283,15 +284,10 @@ rotations as radians, hence the multiplication of the 90 degree angle by pi/180.
 Angles in AnyBody are always in radians.
 :::
 
-In the next section, we will look at how joints can be used to constrain
+In the next lesson, we will look at how joints can be used to constrain
 the movement of segments and allow them to articulate the way we desire.
 
-:::{rst-class} without-title
-:::
 
-:::{seealso}
-**Next lesson:** So if you are up to it, let's continue onward to {doc}`Lesson 3: Connecting segments by joints <lesson3>`.
-:::
 
 ```{rubric} Footnotes
 ```