Update docs

CHANGES.md

@@ -1,6 +1,6 @@
 # v0.1.0
 
-Major changes compared to the original `MAppleT/StocaTree`:
+Major changes compared to the original `MAppleT`:
 
 * Build system and dependencies: All outdated and unmaintained dependencies have been removed or replaced
 * Modularization: The L-Py file has been splitted up into several smaller modules

README.md

@@ -1,7 +1,7 @@
 # VMAppleT
 
-Apple tree simulation library using Markov chains based on StocaTree/MAppleT:
-A [refactored and enhanced](./CHANGES.md) implementation of StocaTree. Original sources copied and modified from [openalea/incubator](https://github.com/openalea-incubator/MAppleT).
+Apple tree simulation library using Markov chains based on MAppleT:
+A [refactored and enhanced](./CHANGES.md) implementation of MAppleT. Original sources copied and modified from [openalea/incubator](https://github.com/openalea-incubator/MAppleT).
 
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jvail/vmapplet/master?urlpath=lab/tree/notebooks/simple_simulation.ipynb)
 

paper/paper.md

@@ -1,5 +1,5 @@
 ---
-title: 'VMAppleT: Apple Tree simulations based on StocaTree'
+title: 'VMappleT : A virtual modeling environment for modular functional-structural simulations of apple trees'
 tags:
   - Python
   - biology
@@ -8,27 +8,27 @@ authors:
   - name: Frédéric Boudon
     affiliation: 1
   - name: Jan Vaillant
-    affiliation: 3
+	  affiliation: 3
   - name: Evelyne Costes
-    affiliation: 2
+	  affiliation: 2
 affiliations:
- - name: CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
-   index: 1
- - name: French National Institute for Agriculture, Food, and Environment (INRAE)
-   index: 2
- - name: Independent Researcher, France
-   index: 3
+  - name: CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
+    index: 1
+  - name: French National Institute for Agriculture, Food, and Environment (INRAE)
+    index: 2
+  - name: Independent Researcher, France
+    index: 3
 date: 2 September 2023
 bibliography: paper.bib
 ---
 
 # Summary
 
-VMAppleT is a functional-structural plant model (FSPM) for apple trees based on L-Systems in Python. It is a refactored and modernized implementation of StocaTree/MAppleT [@Costes:2008] with
+VMAppleT is a functional-structural plant model (FSPM) for apple trees based on L-Systems in Python. It is a refactored and modernized implementation of MAppleT [@Costes:2008] with
 support for running simulations in Jupyter notebooks. The mechanics, theoretic foundations and the application of MappleT are extensively described in [@Costes:2008].
 VMAppleT focuses on improvements in accessibility, extensibility and customization of the model implementation to facilitate future research on apple tree FSPMs:
 
-First of all the source code of StocaTree has been refactored and modernized to support Python 3.10 and to improve its readability and usability by applying both code linting and typing.
+First of all the source code of MAppleT has been refactored and modernized to support Python 3.10 and to improve its readability and usability by applying both code linting and typing.
 The installation procedure has been simplified by removing dependencies on 3rd party libraries and replacing native dependencies with custom Python implementations. Documentation and tests
 included in the previous (MAppleT repository)[https://github.com/openalea-incubator/MAppleT] have been ported and extended wherever applicable.
 
@@ -40,11 +40,10 @@ The configuration and parameterization of a simulation has been simplified and p
 and are initialized with reasonable defaults.
 
 Supporting Jupyter notebooks by integrating Jupyter Lab including model visualization was another important goal of the reimplementation. This is particularly useful to provide users a straightforward
-access and simple examples that can even be executed and viewed via binder [@project_jupyter-proc-scipy-2018] without requiring a local installation.
-
-
+access and simple examples that can even be executed and viewed via binder [@Jupyter:2018] without requiring a local installation.
 
 # Acknowledgements
 
+This work was supported by the French National Research Agency under the Investments for the Future Program, referred as ANR-16-CONV-0004
 
 # References