Merge pull request #93 from EcoExtreML/add_doc_nb

Add an example notebook to run the model with global data

Author: SarahAlidoost

docs/installation_instructions.md

@@ -23,7 +23,7 @@ installed there. See [Install PyStemmusScope](#install-pystemmusscope).
 
 ## On your own machine
 
-Choose how do you want to run the model, see [Run the model](notebooks/run_model_in_notebook.ipynb).
+Choose how do you want to run the model, see [Run the model](notebooks/run_model_on_different_infra.ipynb).
 
 ## Install PyStemmusScope
 
@@ -59,7 +59,7 @@ jupyter lab
 
 JupyterLab will open automatically in your browser. Now, you can run the
 notebook
-[run_model_in_notebook.ipynb](https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing/blob/main/docs/notebooks/run_model_in_notebook.ipynb).
+[run_model_on_different_infra.ipynb](https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing/blob/main/docs/notebooks/run_model_on_different_infra.ipynb).
 
 ## Install MATLAB Runtime
 

…cs/notebooks/run_model_in_notebook.ipynb …books/run_model_on_different_infra.ipynbdocs/notebooks/run_model_in_notebook.ipynb renamed to docs/notebooks/run_model_on_different_infra.ipynb docs/notebooks/run_model_in_notebook.ipynb renamed to docs/notebooks/run_model_on_different_infra.ipynb

@@ -5,9 +5,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Running the STEMMUS_SCOPE model\n",
-    "## Which options are available?\n",
-    "This notebook shows steps to run the STEMMUS_SCOPE model, including preprocessing and postprocessing. STEMMUS_SCOPE files are located in a **private** repository https://github.com/EcoExtreML/STEMMUS_SCOPE. To clone the repository locally and access the files, make sure you have right access to the repository. Then specify the path to a config file e.g.`config_file_template.txt`, executable file `STEMMUS_SCOPE` or source code `STEMMUS_SCOPE/src` in the cells below. There are already config files for users on Snellius and CRIB, see `config_file_snellius.txt`, `config_file_crib.txt`. Choose how do you want to run the model:\n",
+    "# Running the STEMMUS_SCOPE model on a system\n",
+    "\n",
+    "This notebook shows steps to run the STEMMUS_SCOPE model, including preprocessing and postprocessing. STEMMUS_SCOPE files are located in a repository https://github.com/EcoExtreML/STEMMUS_SCOPE. Then specify the path to a config file e.g.`config_file_template.txt`, executable file `STEMMUS_SCOPE` or source code `STEMMUS_SCOPE/src` in the cells below. There are already config files for users on Snellius and CRIB, see `config_file_snellius.txt`, `config_file_crib.txt`. Depending on your system (OS, Matlab availability, etc.), there are a few ways you can run the model. Choose how do you want to run the model:\n",
     "\n",
     "\n",
     "[**Executable file**](#1-using-executable-file)\n",
@@ -229,7 +229,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Perform <echo $DISPLAY> in a terminal in the Remote Desktop (of Crib Platform), and check the output (should be similar to :1.0 ). Then execute the following line accordingly."
+    "&emsp; If you are on CRIB, to use Jupyter interface and MATLAB license manager at the same time, first perform <echo $DISPLAY> in a terminal in the Remote Desktop of Crib Platform, and check the output which should be similar to :1.0 . Then execute the following line accordingly."
    ]
   },
   {
@@ -238,6 +238,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# For CRIB users\n",
     "%env DISPLAY=:1.0"
    ]
   },
@@ -398,7 +399,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "pyss_octave",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -412,7 +413,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:50:36) [MSC v.1929 64 bit (AMD64)]"
+   "version": "3.10.13"
   },
   "vscode": {
    "interpreter": {