Refactor README.md for improved clarity

Removed unnecessary line breaks and fixed formatting issues for better readability.

Author: ZocoLini

README.md

@@ -1,7 +1,6 @@
 # Uncertainty Quantification in Dynamic Models of Biological Systems Using Conformal Prediction
 
-This project is a transpilation of the Matlab project
-defined in this [paper](https://zenodo.org/records/13838652).
+This project is a transpilation of the Matlab project defined in this [paper](https://zenodo.org/records/13838652).
 
 ## Index
 
@@ -46,10 +45,7 @@ When running this software, there is a chance of generating an inf or NaN value.
 </ode_expr>
 ```
 
-If the value of `p1` generated by the eSS solver is 0, the model eval produces an inf value. To avoid this, when the
-evaluation of the ODE generates a non-finite value, the software will set it to 0. If you
-want to change this behavior, you can set the value you want the variable to take when an invalid value is
-generated by setting the environment variable `CUQDYN_DEF_YDOT` to the desired value.
+If the value of `p1` generated by the eSS solver is 0, the model eval produces an inf value. To avoid this, when the evaluation of the ODE generates a non-finite value, the software will set it to 0. If you want to change this behavior, you can set the value you want the variable to take when an invalid value is generated by setting the environment variable `CUQDYN_DEF_YDOT` to the desired value.
 
 ### SACESS_SEED
 
@@ -70,11 +66,7 @@ the default value.
 
 **GCC and GFortran v14 aren't supported by the project, so you need to use GCC v13 or lower.**
 
-The project has a `scripts/build.sh` script.
-`build-[variant]/` directories will be created, each one representing a variant
-off the project builded. If you call the script without arguments, it will build
-all the variants, but you can also specify the variant you want, passing it as the
-first argument. The available variants are:
+The project has a `scripts/build.sh` script. `build-[variant]/` directories will be created, each one representing a variant off the project builded. If you call the script without arguments, it will build all the variants, but you can also specify the variant you want, passing it as the first argument. The available variants are:
 
 - `serial`: Builds the project to only execute serial methods.
 - `mpi`: Builds the project to execute the sequential solver in parallel using MPI.
@@ -90,8 +82,7 @@ docker compose up
 
 ## Using the CLI
 
-After building using the `scripts/build.sh` script, you can execute this command to run the CLI
-with example config and data files like this:
+After building using the `scripts/build.sh` script, you can execute this command to run the CLI with example config and data files like this:
 
 ```bash
 mkdir output
@@ -123,19 +114,15 @@ VARIANT=serial
     -o output/
 ```
 
-After this, the file `output/cuqdyn-results.txt` contains the results of the
-algorithm but reading it as a plain text is not very useful.
-To fix this, you can run: (Needs python3 and matplotlib installed)
+After this, the file `output/cuqdyn-results.txt` contains the results of the algorithm but reading it as a plain text is not very useful. To fix this, you can run: (Needs python3 and matplotlib installed)
 
 ```bash
 python3 plot.py output/cuqdyn-results.txt
 ```
 
-Note: Be carefull when executing with `mpirun`, the number of precesses must be divisor
-of m - 1, where m is the number of rows in the input data matrix.
+Note: Be carefull when executing with `mpirun`, the number of precesses must be divisor of m - 1, where m is the number of rows in the input data matrix.
 
-This will save a graphic representation for each y(t) in different png files
-inside the directory where the results are (output folder in this example).
+This will save a graphic representation for each y(t) in different png files inside the directory where the results are (output folder in this example).
 
 To get information about all the options the cli supports, you can run the following command:
 
@@ -156,22 +143,15 @@ to get the version of the cuqdyn-c lib, sacess lib and cli you are using.
 There are three types of input files that must be provided:
 
 - **eSS Solver config xml:**
-  This file contains the configuration of the eSS solver used in the sacess library.
-  The specifications of this xml and how to build it are in
-  this [link](https://bitbucket.org/DavidPenas/sacess-library/src/main/doc/manual/DOCUMENTATION_SACESS_SOFTWARE.pdf).
+  This file contains the configuration of the eSS solver used in the sacess library. The specifications of this xml and how to build it are in this [link](https://bitbucket.org/DavidPenas/sacess-library/src/main/doc/manual/DOCUMENTATION_SACESS_SOFTWARE.pdf).
 
 - **cuqdyn config xml:**
   This file contains the configuration of the cuqdyn solver used in the cuqdyn-c library.
   - **tolerances:** rtol and atol used by the cvodes library.
   - **ode_expr:** ODE model expression or identifier.
-  - **time_scaling:** Scaling factor for time. Using lower than 1 helps cvodes speed. You may have to
-    increase the number of sacess maxevals. The sacess lb, up, and point constraints also get scaled.
-    The same for the params median written in the output file. Params that are dividing shouldn't be scaled
-    as the testing shows but they get scaled as well. This helps the solver converge faster but hasn't
-    been proved to be valid for all cases. This has been made with testing purposes, not recommended to use it.
+  - **time_scaling:** Scaling factor for time. Using lower than 1 helps cvodes speed. You may have to increase the number of sacess maxevals. The sacess lb, up, and point constraints also get scaled. The same for the params median written in the output file. Params that are dividing shouldn't be scaled as the testing shows but they get scaled as well. This helps the solver converge faster but hasn't been proved to be valid for all cases. This has been made with testing purposes, not recommended to use it.
   - **y0:** Initial conditions of the ODE.
-  - **states_transformer:** Transformations expressions or identidier applied to the different states in case of the
-    observed data being a combination of the different states.
+  - **states_transformer:** Transformations expressions or identidier applied to the different states in case of the observed data being a combination of the different states.
 
   There is an option to accelerate the process of evaluating the ODE by defining it and the states transformer inside the mevalexpr module. We will talk about this later.
 
@@ -216,8 +196,7 @@ There are three types of input files that must be provided:
   ```
 
 - **Data file:**
-  The data file containing a mtrix of observed data and the initial value
-  needed to solve the ODE. The data file should be a txt file written with the following format:
+  The data file containing a mtrix of observed data and the initial value needed to solve the ODE. The data file should be a txt file written with the following format:
 
   ```
   # The first row is gonna be used as the initial condition if y0 is not present in the config file
@@ -231,14 +210,11 @@ There are three types of input files that must be provided:
 
 ## Defining a new model
 
-Using strings and evaluate them is slow compared to compiled instructions, so, to make this
-possible, we designed a way to define the models in Rust and compile them to machine code.
+Using strings and evaluate them is slow compared to compiled instructions, so, to make this possible, we designed a way to define the models in Rust and compile them to machine code.
 
 Let's dig into it with an example of the Lotka Volterra model:
 
-First of all, we need to write some Rust code. We will be using the following file
-`modules/cuqdyn-rs/src/models.rs`. Inside, we create a new unit struct and implement
-the Model trait like this:
+First of all, we need to write some Rust code. We will be using the following file `modules/cuqdyn-rs/src/models.rs`. Inside, we create a new unit struct and implement the Model trait like this:
 
 ```Rust
 #[derive(Default)]
@@ -264,8 +240,7 @@ pub fn eval_model_fun(model: &str, ode_expr: &OdeExpr) -> Box<dyn Model> {
 }
 ```
 
-After you establish an identifier in the match at the bottom of the file, the model can be
-used indicating the identifier in the XML config file like this:
+After you establish an identifier in the match at the bottom of the file, the model can be used indicating the identifier in the XML config file like this:
 
 ```xml
 <?xml version="1.0" encoding="UTF-8" ?>