Merge branch 'master-ammr-2.5' into no-leg-improvements

.gitattributes

@@ -1,4 +1,38 @@
 * text=auto
+
+# AnyBody files
+# ============
+*.any text
+*.anysurf3 binary
+*.anysurf4 binary
+
+*.md linguist-detectable
+
+# Source files
+# ============
+*.pxd    text diff=python
+*.py     text diff=python
+*.py3    text diff=python
+*.pyw    text diff=python
+*.pyx    text diff=python
+*.pyz    text diff=python
+*.pyi    text diff=python
+
+# Binary files
+# ============
+*.db     binary
+*.p      binary
+*.pkl    binary
+*.pickle binary
+*.pyc    binary export-ignore
+*.pyo    binary export-ignore
+*.pyd    binary
+
+# Jupyter notebook
+*.ipynb  text eol=lf
+
+
+# Export ignored files files
 .gitattributes export-ignore  
 .gitignore export-ignore
 .gitkeep export-ignore

CHANGELOG.md

@@ -164,9 +164,11 @@ to account for pelvis segment morphing into leg pelvis coordinate system using
 * Add an option to override the default kinematic joint limits in the MoCap
   framework
 
-
-## AMMR 2.4.4
+(ammr-2.4-changelog)=
+## AMMR 2.4.4 (2023-04-03)
 [![Zenodo link](https://zenodo.org/badge/DOI/10.5281/zenodo.7764841.svg)](https://doi.org/10.5281/zenodo.7764841)
+[![AnyBody link](https://img.shields.io/badge/Included_with_AnyBody-7.4.4-yellowgreen)](https://www.anybodytech.com/download/anybodysetup-7-4-4-8907_x64/)
+
 
 This version of AMMR adds a number fixes and tweaks to the body models which
 improves robustness of various kinematic and recruitment solvers. 
@@ -192,7 +194,6 @@ improves robustness of various kinematic and recruitment solvers.
 * Corrected small asymmetry in function for nonlinear intervertebral disc stiffness in coronal plane (affects only those who used polynomial disc stiffness).
 
 
-(ammr-2.4-changelog)=
 ## AMMR 2.4.3 (2023-01-27)
 [![Zenodo link](https://zenodo.org/badge/DOI/10.5281/zenodo.7572879.svg)](https://doi.org/10.5281/zenodo.7572879)  [![AnyBody link](https://img.shields.io/badge/Included_with_AnyBody-7.4.3-yellowgreen)](https://www.anybodytech.com/download/anybodysetup-7-4-3-8899_x64/)
 

Docs/about.md

@@ -1,4 +1,6 @@
-# The AnyBody Managed Model Repository (AMMR)
+# About the AnyBody Model Repository
+
+## Cite 
 
 The AnyBody Managed Model Repository has a DOI {{ DOI }}. This is handled by [Zenodo.org](https://zenodo.org/), which is an European Open Science platform hosted at CERN.
 You can download all archived versions of the AMMR from [Zenodo.org](https://doi.org/10.5281/zenodo.1250764).
@@ -16,11 +18,75 @@ Lund, Morten Enemark, Tørholm, Søren, et al. (2023, Jan 29). The AnyBody Manag
 :::
 
 
+## Contribute
+
+The Model Repository is the product of collaboration between AnyBody Technology,
+and many academic institutions and research projects.
+
+If you are interested in beta models/repositories you can get access to the
+development version of the AMMR. Development takes place in a semi-closed
+repository. The repository is closed to protect academic contributors who also
+often need to publish their models before release.
+
+However, access is given on request. Please [submit an issue here](https://github.com/AnyBody/ammr-doc/issues), to request access.
+
+You can also view other freely available models and resources hosted on [GitHub](https://github.com/anybody).
+
+:::{only} draft
+::::{dropdown} Release checklist
+
+1. Update `AMMR.version.any`.
+
+   - Update with the new version numbers
+
+   - Fill the `ANYBODY_HASH_BODY`. The new value can be found in `Main.HumanModel.Config.HashBodyModel`.
+
+2. Update any  AMS version number in `Docs/conf.py` (only used when building locally)
+
+3. Create new version of AMMR on Zenodo (<https://zenodo.org/record/3404750).
+
+   - Click `New version` button
+
+   - Fill the neccessary fields. Authors are those who contributed since last Release
+
+   - Note the draft DOI which zenodo reserves
+
+   - Save the draft but do **not** publish it.
+
+4. Clean up, and update `Docs/changelog.rst`
+
+   - Prof read and check that all changes are documented.
+
+   - Add Zenodo DOI url to the new release, and fill the date
+
+5. Check that the docs can build, and that the tests pass.
+
+6. Merge the branch and add a git tag.
+
+7. Upload ammr zip file to Zenodo
+
+   - Either use the AMMR zip file created by the AMS build. This  (it con or create a
+
+     **released zip file by running:**
+
+     ```
+     cd Docs
+     make release
+     mv release.zip ammr-X.Y.Z.zip
+     ```
+
+     This creates a zip file with the built documentation.
+
+   - Edit the draft Zenodo release to upload a zip file with AMMR.
+
+::::
+:::
+
+
+
+
+
+
+
 
-```{toctree}
-:maxdepth: 1
 
-changelog
-contribute
-legal
-```

Docs/bm_config/bm_constants.md

@@ -77,11 +77,11 @@ Switch off a leg
 
 
 
-::::{dropdown} `_LEG_MODEL_TLEM1_`
+::::{dropdown} `_LEG_MODEL_TLEM_`
 :animate: fade-in-slide-down
 :margin: 0 0 2 2
 
-:::{ammr:bm_constant} _LEG_MODEL_TLEM1_
+:::{ammr:bm_constant} _LEG_MODEL_TLEM_
 :value: 1
 Switch to use leg model: "TLEM 1"
 :::
@@ -95,6 +95,7 @@ Switch to use leg model: "TLEM 1"
 
 :::{ammr:bm_constant} _LEG_MODEL_TLEM1_
 :value: 1
+:deprecated:
 Switch to use leg model: "TLEM 1"
 :::
 ::::

Docs/bm_config/bm_statements.md

@@ -181,7 +181,7 @@ Parameter defining the Leg model used.
 :Example: `#define BM_LEG_MODEL _LEG_MODEL_TLEM2_`
 :Options:
   - {any}`OFF` -> Switch OFF
-  - {any}`_LEG_MODEL_TLEM1_` -> Switch to use leg model: "TLEM 1"
+  - {any}`_LEG_MODEL_TLEM_` -> Switch to use leg model: "TLEM 1"
   - {any}`_LEG_MODEL_TLEM2_` -> Switch to use leg model: "TLEM 2"
   - {any}`_LEG_MODEL_LEG_` -> Switch to use leg model: "Leg"
 

Docs/environment.yaml

@@ -4,7 +4,7 @@ channels:
 dependencies:
   - python=3.11
   - pip
-  - sphinx<6
+  - sphinx
   - pydata-sphinx-theme>=0.13.0
   - make
   - myst-parser

Docs/index.md

@@ -56,6 +56,16 @@ The AnyBody Model Repository (AMMR), is an unique open library of
 musculoskeletal models and examples ready to be used with the [AnyBody Modeling
 System][anybody modeling system]. The AnyBody Managed Model Repository consists of two parts:
 
+
+```{admonition} **First time user?**
+:class: hint dropdown margin
+
+If you are a new user check the [AnyBody Tutorials](https://anyscript.org/tutorials/) and the getting started video on AnyBody.
+
+The following {doc}`Getting Started section </getting_started>` on the AMMR provides insight into how AMMR is structured, how to
+install it and how to use it.
+```
+
 <span class="material-symbols-outlined">
 </span>
 
@@ -70,7 +80,7 @@ System][anybody modeling system]. The AnyBody Managed Model Repository consists
 The human body models which can be 
 customized and scaled to build a specific musculoskeletal model.
 +++
-{ref}`Learn more » <the-body-model>`
+{ref}`Learn more » <the-body-model>`
 :::
 
 :::{grid-item-card} {material-regular}`fitness_center;2em` Example gallery
@@ -79,7 +89,7 @@ customized and scaled to build a specific musculoskeletal model.
 
 Lots of applicaiton examples showing how the body models are used.
 +++
-{ref}`Learn more » <example-gallery>`
+{ref}`Learn more » <example-gallery>`
 :::
 
 :::{grid-item-card} {material-regular}`settings;2em` Model Configuration
@@ -88,27 +98,21 @@ Lots of applicaiton examples showing how the body models are used.
 
 Information on how to configure the body models, and enable or disable various body parts.
 +++
-{ref}`Learn more » <bm-config>`
+{ref}`Learn more » <bm-config>`
 :::
 
 ::::
 
 
 
+
+
 The models are developed in research projects at academic institutions or by
 AnyBody Technology in collaboration with academic institutions. The models are
 maintained by AnyBody Technology who ensure that various body part models can be
 used together as a full body, scalable musculoskeletal model.
 
 
-```{admonition} **First time user?**
-:class: hint dropdown
-
-If you are a new user check the [AnyBody Tutorials](https://anyscript.org/tutorials/) and the getting started video on AnyBody.
-
-The following {doc}`Getting Started section </getting_started>` on the AMMR provides insight into how AMMR is structured, how to
-install it and how to use it.
-```
 
 [anybody modeling system]: https://www.anybodytech.com/software/anybodymodelingsystem/
 
@@ -153,14 +157,15 @@ anymocap/index
 
 
 ```{toctree}
-:caption: ????????
+:caption: About
 :includehidden: true
 :hidden: true
 :maxdepth: 2
 :titlesonly: true
 
 
-
-About the model repository <about>
+changelog
+Contribute or cite <about>
+legal
 
 ```