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https://github.com/hdescobarh/learning-raven-gems
In this repository I store, for personal study purposes, solving of some RAVEN Toolbox-related tutorials and exercises.
https://github.com/hdescobarh/learning-raven-gems
Last synced: 27 days ago
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In this repository I store, for personal study purposes, solving of some RAVEN Toolbox-related tutorials and exercises.
- Host: GitHub
- URL: https://github.com/hdescobarh/learning-raven-gems
- Owner: hdescobarh
- License: gpl-3.0
- Created: 2023-08-08T00:12:38.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2023-08-25T00:14:08.000Z (over 1 year ago)
- Last Synced: 2024-10-20T15:46:08.314Z (3 months ago)
- Language: Jupyter Notebook
- Size: 61.7 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
Awesome Lists containing this project
README
# RAVEN Toolbox exercises
[](https://www.gurobi.com/downloads/gurobi-optimizer-release-notes-v10-0-2/)
[](https://github.com/SysBioChalmers/RAVEN)
[](https://www.gnu.org/licenses/gpl-3.0)
[](https://creativecommons.org/licenses/by-nc-sa/4.0/)
In this repository I store, for personal study purposes, solving of some [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN)-related tutorials and exercises.
## Set up environment
Requirements:
- Activated MATLAB installation.
- Gurobi solver (optional).
- In replace of MATLAB live editor I use Jupyter notebooks. This needs a Python environment. It is strongly recommended to use a virtual environment. In the repository root directory, there is a 'requirements.txt' file with the necessary dependencies and their correct versions.
Some other worth to mention considerations are:
### Python environment
- For working with VSCode (e.g. using the VSCode Notebook instead of the default Browser notebook), in addition to Python and Jupyter extensions, it is recommended the [MATLAB extension for Visual Studio Code](https://marketplace.visualstudio.com/items?itemName=MathWorks.language-matlab).
- The Jupyter Notebook needs the kernel for [MATLAB Integration for Jupyter](https://www.mathworks.com/products/reference-architectures/jupyter.html). The package is [jupyter-matlab-proxy](https://github.com/mathworks/jupyter-matlab-proxy).
- The jupyter-matlab-proxy has a dependency that can be very tricky to install, [jupyter_contrib_nbextensions](https://jupyter-contrib-nbextensions.readthedocs.io/en/latest/install.html). Jupyter 7 has a breaking change and jupyter_contrib_nbextensions does not work corretly with it. A workaround is to install notebook < 7.0.0. Moreover, the MATLAB kernel repository states:
MATLAB code execution is available on both JupyterLab 3 and JupyterLab 4, but other features (such as syntax highlighting) are currently only supported on JupyterLab 3. Install JupyterLab 3 using:
```MATLAB
python3 -m pip install 'jupyterlab>=3.0.0,<4.0.0a0'
```
This may also requires an specific version of the Jupyter Server:
```MATLAB
pip install -U "jupyter-server<2.0.0"
```
### Working in Windows
The MATLAB kernel, for some reason, in Windows looks for "python3" instead of "python":
```json
{
"argv": [
"python3",
"-m",
"jupyter_matlab_kernel",
"-f",
"{connection_file}"
],
"display_name": "MATLAB Kernel",
"language": "matlab",
"interrupt_mode": "message",
"env": {},
"metadata": {
"debugger": false
},
"copyright": "Copyright 2023 The MathWorks, Inc.",
"description": "Jupyter kernelspec for MATLAB Kernel. For more information, please look at https://jupyter-client.readthedocs.io/en/stable/kernels.html#kernel-specs"
}
```
A workaround to this problem is to create a "python3" alias:
```powershell
Set-Alias -Name python3 -Value python
Set-ExecutionPolicy RemoteSigned -Scope CurrentUser
```