update documentation to remove reference to gempyor-simulate [skip ci]

documentation/gitbook/how-to-run/advanced-run-guides/quick-start-guide-conda.md

@@ -191,10 +191,10 @@ where:
 
 #### Non-inference run
 
-Stay in the `$DATA_PATH` folder, and run a simulation directly from forward-simulation Python package `gempyor`. To do this, call `gempyor-simulate` providing the name of the configuration file you want to run (ex. `config.yml`). An example config is provided in `flepimop_sample/config_sample_2pop_interventions.yml.`
+Stay in the `$DATA_PATH` folder, and run a simulation directly from forward-simulation Python package `gempyor`. To do this, call `flepimop simulate` providing the name of the configuration file you want to run (ex. `config.yml`). An example config is provided in `flepimop_sample/config_sample_2pop_interventions.yml.`
 
 ```
-gempyor-simulate -c config.yml
+flepimop simulate config.yml
 ```
 
 {% hint style="warning" %}

documentation/gitbook/how-to-run/advanced-run-guides/running-with-docker-locally.md

@@ -192,10 +192,10 @@ flepimop-inference-main -j 1 -n 1 -k 1 -c config.yml
 
 ### Non-inference run
 
-Stay in the `$DATA_PATH` folder, and run a simulation directly from forward-simulation Python package `gempyor,`call `gempyor-simulate` providing the name of the configuration file you want to run (ex. `config.yml` ;
+Stay in the `$DATA_PATH` folder, and run a simulation directly from forward-simulation Python package `gempyor,`call `flepimop simulate` providing the name of the configuration file you want to run (ex. `config.yml`):
 
 ```
-gempyor-simulate -c config.yml
+flepimop simulate config.yml
 ```
 
 {% hint style="warning" %}
@@ -216,7 +216,7 @@ Rscript build/local_install.R
 pip install --no-deps -e flepimop/gempyor_pkg/
 cd $DATA_PATH
 rm -rf model_output
-gempyor-simulate -c config.yml
+flepimop simulate config.yml
 </code></pre>
 
 ## Finishing up

documentation/gitbook/how-to-run/quick-start-guide.md

@@ -154,10 +154,10 @@ To get started, let's start with just running a forward simulation (non-inferenc
 
 ### Non-inference run
 
-Stay in the `PROJECT_PATH` folder, and run a simulation directly from forward-simulation Python package gempyor. Call `gempyor-simulate` providing the name of the configuration file you want to run. For example here, we use `config_sample_2pop.yml` from _flepimop\_sample_.
+Stay in the `PROJECT_PATH` folder, and run a simulation directly from forward-simulation Python package gempyor. Call `flepimop simulate` providing the name of the configuration file you want to run. For example here, we use `config_sample_2pop.yml` from _flepimop\_sample_.
 
 ```
-gempyor-simulate -c config_sample_2pop.yml
+flepimop simulate config_sample_2pop.yml
 ```
 
 This will produce a `model_output` folder, which you can look using provided post-processing functions and scripts.
@@ -173,14 +173,14 @@ cd $FLEPI_PATH
 pip install --no-deps -e flepimop/gempyor_pkg/
 cd $PROJECT_PATH
 rm -rf model_output
-gempyor-simulate -c config.yml
+flepimop simulate config.yml
 ```
 
 Note that you only have to re-run the installation steps once each time you update any of the files in the flepimop repository (either by pulling changes made by the developers and stored on Github, or by changing them yourself). If you're just running the same or different configuration file, just repeat the final steps
 
 ```
 rm -rf model_output
-gempyor-simulate -c new_config.yml
+flepimop simulate new_config.yml
 ```
 
 ### Inference run
@@ -241,7 +241,7 @@ Rscript $FLEPI_PATH/flepimop/main_scripts/inference_main.R -c config_inference_n
 
 ## 📈 Examining model output
 
-If your run is successful, you should see your output files in the model\_output folder. The structure of the files in this folder is described in the [Model Output](../gempyor/output-files.md) section. By default, all the output files are .parquet format (a compressed format which can be imported as dataframes using R's arrow package `arrow::read_parquet` or using the free desktop application [Tad ](https://www.tadviewer.com/)for quick viewing). However, you can add the option `--write-csv` to the end of the commands to run the code (e.g.,  `> gempyor-simulate -c config.yml --write-csv)` to have everything saved as .csv files instead ;
+If your run is successful, you should see your output files in the model\_output folder. The structure of the files in this folder is described in the [Model Output](../gempyor/output-files.md) section. By default, all the output files are .parquet format (a compressed format which can be imported as dataframes using R's arrow package `arrow::read_parquet` or using the free desktop application [Tad ](https://www.tadviewer.com/)for quick viewing). However, you can add the option `--write-csv` to the end of the commands to run the code (e.g.,  `> flepimop simulate --write-csv config.yml`) to have everything saved as .csv files instead ;