Replace doc_en.adoc

documentation/doc_en.adoc

 = EASEA Compiler App Documentation
 Clément Ligneul <clement.ligneul@etu.unistra.fr>
-v1.3 2021-09-12
+v2.0 13/02/2022
 :toc: left
 :toclevels: 4
 :hide-uri-scheme:
@@ -50,16 +50,15 @@ Note that if you are using macOS, plotly only works on version 10.10 or more (OS
 
 == Installation
 
-Once the dependencies are installed if you are using the development repository:
+Once the dependencies are installed, if you are using the https://git.unistra.fr/ligneul/easea-compiler-app[development repository, window=_blank]:
 
-    - clone https://git.unistra.fr/ligneul/easea-compiler-app[this repository, window=_blank]
     - run `make install` in the main directory
     - now you can run the executable in `EASEA-compiler-app/` named `easea-compiler-app`. If the executable is installed, you can also run `easea-compiler-app` from anywhere
     - run `make uninstall` in the main directory to uninstall the application
 
-If you are installing the interface from EASEA's github repository:
+If you are installing the interface from the https://github.com/EASEA/easea[EASEA github repository, window=_blank]:
 
-    - move to the `easea-interface` directory with `cd easea/easea-interface/`
+    - move to the `easea-interface/` directory with `cd easea/easea-interface/`
     - run `sudo make install`
     - you can now launch the application with the `easea-compiler-app` command from anywhere.
     - to uninstall the application run `make uninstall` from the directory `easea/easea-interface/`
@@ -80,7 +79,7 @@ In this tutorial we will compile and run the file `weierstrass.ez` from the `/ex
 . We don't use any options in this compilation so just click on the `Compile` button
 . After clicking on this button you see this :
 
-image::images/compile_weierstrass.png[compile_weierstrass image, 700, align=center]
+image::images/compile_weierstrass.png[compile_weierstrass image, 800, align=center]
 
 ==== Run
 
@@ -112,11 +111,11 @@ image::images/general_menu_batch.png[general menu batch image, 850, align=center
 
 4) At the end of these runs you should see something like this :
 
-image::images/end_run_batch.png[end run batch image, 700, align=center]
+image::images/end_run_batch.png[end run batch image, 800, align=center]
 
 5) In the `Result Plot` tab you can see the graph generated as we requested : 5 violin plots (for more informations about this graph see <<Result Plot tab>>)
 
-image::images/2d_results.png[2d results image, 700, align=center]
+image::images/2d_results.png[2d results image, 800, align=center]
 
 == Interface detailed
 
@@ -128,7 +127,7 @@ The last one is dedicated to plotting the results according to the compilation a
 
 === Compile tab
 
-image::images/empty_compile.png[empty compilation image, 700, align=center]
+image::images/empty_compile.png[empty compilation image, 800, align=center]
 
 ① Load your file
 
@@ -146,7 +145,7 @@ EASEA offers many options for compiling your `.ez` projects. If you want to see
 
 You must compile your project before running it.
 
-image::images/islands_activated.png[island activation image, 700, align=center]
+image::images/islands_activated.png[island activation image, 800, align=center]
 
 ① Size of the batch (see <<Run in batch>>)
 
@@ -220,7 +219,7 @@ image::images/general_menu.png[general menu image, 900, align=center]
 
 - [underline]#Compression# : Set the compression level
 
-- [underline]#Batch Size# : Number of runs at the same time. 
+- [underline]#Batch Size# : Number of runs at the same time. Batch size is currently limited to 500 but it is recommended to limit to 30. [red]#Caution: run a very large number of executions may cause malfunctions depending on the capabilities of the machine#
 // [red]#Don't use this option if you have compiled with options for <<Multi-objective problems>>#
 
 - [underline]#Nb Of Threads# : Number of threads to use
@@ -265,13 +264,19 @@ This menu is available after activating the remote island model
 
 image::images/island_menu.png[island menu image, 300, align=center]
 
-- [underline]#Migration Probability# : Probability to send an individual each generation
+- [underline]#Batch Type# : Type of island model (local or remote)
+
+- [underline]#Ports/machines available# : Number of ports for local executions and machines for remote executions usable
+
+- [underline]#Number of islands per run# : Number of islands per run
 
-- [underline]#IP file# : File containing all the IPs of the remote islands
+- [underline]#IP file# : File containing all the IPs of the remote islands. IP files are automatically generated in local mode
 
-- [underline]#Server Port# : Port of the server
+- [underline]#Migration Probability# : Probability to send an individual each generation
+
+- [underline]#Evaluate Immigrants# : Evaluate Immigrants
 
-- [underline]#Evaluate Immigrants# : ...
+Note that the island model execution does not produce a result plot.
 
 ==== See Results
 
@@ -303,7 +308,7 @@ In this file we have 35 generations. We choose to run a batch of 10 and print 5
 
 The first graph takes the 7 first generations, the second takes the next 7 etc...
 
-image::images/2d_results.png[2d results image, 700, align=center]
+image::images/2d_results.png[2d results image, 800, align=center]
 
 The image quality is reduced to put it in the application, we recommend using the interactive version of the graph to see the details.
 
@@ -327,13 +332,14 @@ In each graph there are 3 elements :
 
     - ③ The box plot
 
+link:./images/interactive_2d.html[Here, window=_blank] is an example of a 2D graph.
 
 
 ==== 3D plot
 
 This plot replaces the graph with the violin plots if you have compiled and run a program with the options for <<Multi-objective problems>>.
 
-image::images/3D_update.png[3d results image, 700, align=center]
+image::images/3D_update.png[3d results image, 800, align=center]
 
 ==== 3D plot interactive version
 
@@ -347,6 +353,8 @@ Right click moves the graph on the x y axis.
 
 You can reset the view with the toolbar at the top right.
 
+link:./images/interactive_3d.html[Here, window=_blank] is an example of a 3D graph.
+
 ==== Save the results graph
 
 To save the results you can click on the appropriate button :
@@ -377,7 +385,7 @@ Compilation options for multi-objective problems are :
     - `ibea`
     - `cdas`
 
-If you use one of these options do not run in batch because the results will be overwritten with each other.
+//If you use one of these options do not run in batch because the results will be overwritten with each other.
 
 == Tips