update text in the notebooks

Author: SarahAlidoost

docs/notebooks/run_model_on_different_infra.ipynb

@@ -5,9 +5,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Running the STEMMUS_SCOPE model with different options\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 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`. 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"
    ]
   },

docs/notebooks/run_model_with_different_dataset.ipynb

@@ -7,12 +7,10 @@
    "source": [
     "# Running the STEMMUS_SCOPE model with different dataset\n",
     "\n",
-    "This notebook shows how to run the STEMMUS_SCOPE model uisng the Executable file, including preprocessing and postprocessing. For postprocesisng, the file required_netcdf_variables.csv can be found at https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/utils/csv_to_nc/required_netcdf_variables.csv.\n",
+    "This notebook shows how to run the STEMMUS_SCOPE model uisng the `Executable` file, including preprocessing and postprocessing. For postprocesisng, the file `required_netcdf_variables.csv` can be found at https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/utils/csv_to_nc/required_netcdf_variables.csv.\n",
     "\n",
-    "## Which options are available?\n",
-    "\n",
-    "See the [Run the model with different options](./run_model_with_different_options.ipynb) for avialbale options e.g. Executable file, Matlab, Octave.\n",
-    "The STEMMUS_SCOPE executable file is located in a repository https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/run_model_on_snellius/exe/STEMMUS_SCOPE.\n",
+    "See the [Running the STEMMUS_SCOPE model on a system](./run_model_on_different_infra.ipynb) for different ways e.g. Executable file, Matlab, Octave.\n",
+    "The `STEMMUS_SCOPE` executable file is located in a repository https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/run_model_on_snellius/exe/STEMMUS_SCOPE.\n",
     "\n",
     "## Which datasets are available?\n",
     "The config file shows how to set the paths to different data needed by the model. Check the data source on Snelius and CRIB and modify the config file accordingly:\n",

docs/notebooks/run_model_with_different_dataset_on_CRIB.ipynb

@@ -8,10 +8,7 @@
     "\n",
     "This notebook shows how to run the STEMMUS_SCOPE model uisng source code, including preprocessing and postprocessing. For postprocesisng, the file required_netcdf_variables.csv can be found at https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/utils/csv_to_nc/required_netcdf_variables.csv.\n",
     "\n",
-    "## Which options are available?\n",
-    "\n",
-    "See the [Run the model with different options](./run_model_with_different_options.ipynb) for available options e.g. Executable file, Matlab, Octave.\n",
-    "The STEMMUS_SCOPE executable file is located in a repository https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/run_model_on_snellius/exe/STEMMUS_SCOPE.\n",
+    "See the [Running the STEMMUS_SCOPE model on a system](./run_model_on_different_infra.ipynb) for different ways e.g. Executable file, Matlab, Octave.\n",
     "\n",
     "## Which datasets are available?\n",
     "The config file shows how to set the paths to different data needed by the model. Check the data source on Snelius and CRIB and modify the config file accordingly:\n",
@@ -115,7 +112,7 @@
    "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."
    ]
   },
   {
@@ -132,6 +129,7 @@
     }
    ],
    "source": [
+    "# For CRIB users\n",
     "%env DISPLAY=:1.0"
    ]
   },
@@ -241,15 +239,24 @@
    "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."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "env: DISPLAY=:1.0\n"
+     ]
+    }
+   ],
    "source": [
+    "# for CRIB users\n",
     "%env DISPLAY=:1.0"
    ]
   },

mkdocs.yml

@@ -6,7 +6,7 @@ nav:
   - Getting started: index.md
   - Installation: installation_instructions.md
   - Run the model:
-      - Different ways to run the model: notebooks/run_model_with_different_options.ipynb
+      - Different ways to run the model: notebooks/run_model_on_different_infra.ipynb
       - Site and global datasets with the executable file: notebooks/run_model_with_different_dataset.ipynb
       - Site and global datasets on CRIB: notebooks/run_model_with_different_dataset_on_CRIB.ipynb