CIFASIS
diff --git a/‎.github/workflows/c-cpp.yml
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diff --git a/‎.gitignore
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diff --git a/‎.hooks/pre-commit
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diff --git a/‎CHANGELOG
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diff --git a/‎README.md
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diff --git a/‎bin/build.sh
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diff --git a/‎bin/compile.sh
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@@ -5,58 +5,77 @@ on:
   pull_request:
     branches: [ qss-solver-dev ]
 
-env:
-  MMOC_PATH: ../../..
-  MMOC_SRC: ../../../src
-  MMOC_DOC: ../../../doc
-  MMOC_LIBS: ../../../lib
-  MMOC_BUILD: ../../../build
-  MMOC_MODELS: ../../../models
-  MMOC_OUTPUT: ../../../output
-  MMOC_BIN: ../../../bin
-  MMOC_PACKAGES: ../../../packages
-  MMOC_LIBRARIES: ../../../lib
-  MMOC_ENGINE: ../../../src/engine
-  MMOC_INCLUDE: ../../../src/usr/include
-
 jobs:
   build:
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
     - uses: actions/checkout@v2
+    - name: Set environment values.
+      run: |
+        echo "MMOC_PATH=$( pwd )" >> "$GITHUB_ENV"
+        echo "MMOC_SRC=$( pwd )/src" >> "$GITHUB_ENV"
+        echo "MMOC_DOC=$( pwd )/doc" >> "$GITHUB_ENV"
+        echo "MMOC_LIBS=$( pwd )/lib" >> "$GITHUB_ENV"
+        echo "MMOC_BUILD=$( pwd )/build" >> "$GITHUB_ENV"
+        echo "MMOC_MODELS=$( pwd )/models" >> "$GITHUB_ENV"
+        echo "MMOC_OUTPUT=$( pwd )/output" >> "$GITHUB_ENV"
+        echo "MMOC_BIN=$( pwd )/bin" >> "$GITHUB_ENV"
+        echo "MMOC_PACKAGES=$( pwd )/packages" >> "$GITHUB_ENV"
+        echo "MMOC_LIBRARIES=$( pwd )/lib" >> "$GITHUB_ENV"
+        echo "MMOC_ENGINE=$( pwd )/src/engine" >> "$GITHUB_ENV"
+        echo "MMOC_INCLUDE=$( pwd )/src/usr/include" >> "$GITHUB_ENV"
+
     - name: Install deps.
       run: | 
         sudo apt-get update
         sudo apt-get install bison++
-        sudo apt-get install boost1.71
         sudo apt-get install cmake 
         sudo apt-get install g++
         sudo apt-get install gfortran
         sudo apt-get install gnuplot
         sudo apt-get install libatlas-base-dev
+        sudo apt-get install libboost1.83-dev
         sudo apt-get install libcln-dev
         sudo apt-get install libconfig-dev
         sudo apt-get install libginac-dev
         sudo apt-get install libgsl-dev
+        sudo apt-get install libmetis-dev
         sudo apt-get install libsbml5-dev
         sudo apt-get install libscotch-dev
         sudo apt-get install libsuitesparse-dev
         sudo apt-get install pkgconf
-        sudo apt-get install python
-        sudo apt-get install qt5-default
+        sudo apt-get install python3
+        sudo apt-get install qtbase5-dev
+        sudo apt-get install qtbase5-dev-tools
         sudo apt-get install rapidjson-dev
-          
-    - name: Build
+
+    - name: Install local deps.
+      working-directory: ./src/mmoc/3rd-party/flex
+      run: | 
+        sudo apt-get install ./flex-old.deb
+
+    - name: Create build folder.
       working-directory: ./src
-      run: make repo_checkout=https
+      run: |
+        mkdir -p build
+
+    - name: Configure
+      working-directory: ./src/build
+      run: |
+        cmake ..
+
+    - name: Build
+      working-directory: ./src/build
+      run: |
+        make
 
     - name: Install
-      working-directory: ./src
-      run: make install
-    
-    - name: Tests
-      working-directory: ./src
+      working-directory: ./src/build
       run: |
-        make test
+        make install
+
+    - name: Tests
+      working-directory: ./src/build
+      run: make test
@@ -9,10 +9,10 @@ models/
 
 # Generated packages.
 deploy/linux/*.deb
-deploy/windows/*.exe
-deploy/src/*.tar.gz
 
 # Local Changelog
 src/ChangeLog
 ChangeLog
-src/gui/.qmake.stash
+
+# Build folder.
+src/build/
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import subprocess
 
@@ -14,7 +14,7 @@ def apply_code_style():
                              x.endswith(b'.cpp'), files)
     for f in files:
       print("Apply code style to: " + str(f))
-      subprocess.check_output(['clang-format-7', '-i', f])
+      subprocess.check_output(['clang-format', '-i', f])
       subprocess.check_output(['git', 'add', f])
 
 def main():
 
@@ -1,5 +1,17 @@
 ## Changelog
 
+## [5.0.0] - 04-08-2025
+
+### Added
+- **New CQSS1, CQSS2 and CQSS3** development `QSS` methods that can be edited witout having to recompile the simulation engine.
+- **New Python plot script** not the default option, to enable it add `plot_data.py` as the plot command in the GUI settings.
+- **New Python environment** for the GUI that loads all the required packages.
+- **CMake build system** instead of plain make files. 
+
+### Changed
+- Changed default install path.
+- Updated/Improved all binary scripts.
+
 ## [4.5.3] - 29-01-2025
 
 ### Fixed
 
@@ -1,4 +1,4 @@
-## QSS Solver 4.5.3
+## QSS Solver 5.0.0
 
 The QSS Solver is a modeling and simulation environment for 
 continuous and hybrid systems and it's optimized for large scale model simulation.
@@ -166,58 +166,63 @@ These are generic installation instructions.
 ## Dependences
 
 In order to be able to install and compile the QSS Solver, 
-the following dependencies must be installed (**Ubuntu 22.04**): 
+the following dependencies must be installed (**Ubuntu 24.04**): 
 
 * bison++
-* libboost-dev (boost1.71 in **Ubuntu 20.04**)
 * cmake 
 * g++
-* gfortran 
+* gfortran
 * gnuplot
 * libatlas-base-dev
+* libboost1.83-dev
 * libcln-dev
 * libconfig-dev
 * libginac-dev
 * libgsl-dev
+* libmetis-dev
 * libsbml5-dev
 * libscotch-dev
 * libsuitesparse-dev
 * pkgconf
-* qtbase5-dev qt5-qmake (qt5-default in **Ubuntu 20.04**)
+* python3
+* qtbase5-dev
+* qtbase5-dev-tools
+* rapidjson-dev
+
+Additionally, `flex-old` must be installed:
+`sudo apt install ${QSS_SOLVER_ROOT}/src/mmoc/3rd-party/flex/flex-old.deb`
 
 ## Basic Installation
 
 The simplest way to compile this package is:
 
-1. `cd` to the directory containing the package's source code (**src**) and type
-		 `make` to compile the binaries and libraries.
+1. `cd` to the directory containing the package's source code (**src**) and create
+		 `build` directory to compile the binaries and libraries.
 
-2. Type `make install` to install all the binary files and the libraries.
-		 The binaries are located in the bin folder and the libraries are located
-		 in the lib folder. 
+2. `cd` to the `build` directory and run `cmake ..` to install all the binary files and the libraries.
 
-3. You can remove the program binaries and object files from the
-		 source code directory by typing `make clean`.  
+3. Type `make` to build the libraries and binary files.
 
-## Makefile options
+4. Type `make install` to install the package, the binaries are located in the bin folder and the libraries 
+		are located in the lib folder. 
 
-The makefile script accepts the following options:
+## Makefile options and targets
 
-* MODE = <Debug|Release> 	When set to Debug (default), adds the compiler's debug flags.
-	
-## Makefile targets
+* Type `make help` to check the available targets and compile options.
+
+## Changelog
 
-The makefile script accepts the following targets:
+## [5.0.0] - 04-08-2025
 
-* **qss-engine**: 		Builds the QSS solver libraries.
-* **mmo-compiler**: 	Builds the MicroModelica compiler. 	
-* **qss-solver-gui**:	Builds the graphic interface.
-* **qss-user-libs**:	Builds the user packages included in this distribution.
-* **mmo-interfaces**:	Builds the SBML-MicroModelica translator.
-* **qss-solver-doc**:	Builds the documentation for the QSS solver libraries, the MicroModelica compiler and the QSS solver GUI.
-				 
+### Added
+- **New CQSS1, CQSS2 and CQSS3** development `QSS` methods that can be edited witout having to recompile the simulation engine.
+- **New Python plot script** not the default option, to enable it add `plot_data.py` as the plot command in the GUI settings.
+- **New Python environment** for the GUI that loads all the required packages.
+- **CMake build system** instead of plain make files.
 
-## Changelog
+### Changed
+- Changed default install path.
+- Updated/Improved all binary scripts.
 
 ## [4.5.3] - 29-01-2025
 
@@ -249,17 +254,6 @@ The makefile script accepts the following targets:
 - Fixed model function includes in generated C code.
 - Window geometry changes are now saved.
 
-## [4.4.0] - 28-08-2024
-
-### Added
-- **Allow discrete Integer** definitions to be able to use them as array indexes.
-- **New MMO_CVODEMaxOder annotation** to select the max order used in `CVODE` solver.
-- **New MMO_XOutput annotation** that allows selecting state variable output (exerimental).
-
-### Changed
-- Use time variable in initial code.
-- Fixed QSS first order method recompute next time.
-
 ## Licensing
 
 Please see the file called LICENSE.
 
@@ -15,11 +15,33 @@
 #         NOTES: ---
 #        AUTHOR: Joaquin Fernandez, [email protected]
 #       PROJECT: QSS Solver
-#       VERSION: 4.5.3
+#       VERSION: 5.0.0
 #===================================================================================
 
+# Check if a parameter is provided
+if [ -z "$1" ]; then
+    echo "Usage: $0 <file>"
+    exit 1
+fi
+
 FILE=$1
 
-cd $MMOC_BUILD/$FILE
+# Check if the MMOC_BUILD environment variable is set
+if [ -z "$MMOC_BUILD" ]; then
+    echo "Error: MMOC_BUILD environment variable is not set."
+    exit 1
+fi
+
+# Change to the specified directory
+if ! cd "$MMOC_BUILD/$FILE"; then
+    echo "Error: Directory $MMOC_BUILD/$FILE does not exist."
+    exit 1
+fi
+
+# Run the make command
+if ! make -f "$FILE.makefile"; then
+    echo "Error: Make command failed."
+    exit 1
+fi
 
-make -f $FILE.makefile 
+echo "Build completed successfully."
@@ -18,25 +18,65 @@
 #         NOTES: ---
 #        AUTHOR: Joaquin Fernandez, [email protected]
 #       PROJECT: QSS Solver
-#       VERSION: 4.5.3
+#       VERSION: 5.0.0
 #===================================================================================
 
-FILE=$1
+set -e  # Exit immediately if a command exits with a non-zero status.
 
-FOLDER=$2
+# Check for required environment variables
+if [ -z "$MMOC_BUILD" ]; then
+    echo "Error: MMOC_BUILD environment variable is not set."
+    exit 1
+fi
 
-FLAGS=$3
+if [ -z "$MMOC_BIN" ]; then
+    echo "Error: MMOC_BIN environment variable is not set."
+    exit 1
+fi
 
-mkdir -p $MMOC_BUILD/$FILE
+# Check for required parameters
+if [ $# -lt 1 ]; then
+    echo "Usage: $0 <FILE> [FOLDER] [FLAGS]"
+    exit 1
+fi
 
-if [ -z $FOLDER ]; then
-	$MMOC_BIN/mmoc $FLAGS -o $MMOC_BUILD/$FILE/$FILE $FILE.mo
+FILE="$1"
+FOLDER="$2"
+FLAGS="$3"
+
+# Check if the MicroModelica file exists
+if [ -z "$FOLDER" ]; then
+    MO_FILE="$FILE.mo"
 else
-	$MMOC_BIN/mmoc $FLAGS -o $MMOC_BUILD/$FILE/$FILE $FOLDER/$FILE.mo
+    MO_FILE="$FOLDER/$FILE.mo"
+fi
+
+if [ ! -f "$MO_FILE" ]; then
+    echo "Error: MicroModelica file '$MO_FILE' does not exist."
+    exit 1
 fi
 
-cd $MMOC_BUILD/$FILE
+# Create the build directory
+BUILD_DIR="$MMOC_BUILD/$FILE"
+mkdir -p "$BUILD_DIR"
+echo "Created build directory: $BUILD_DIR"
+
+# Compile the MicroModelica file
+echo "Compiling $MO_FILE..."
+if ! "$MMOC_BIN/mmoc" $FLAGS -o "$BUILD_DIR/$FILE" "$MO_FILE"; then
+    echo "Error: Compilation failed."
+    exit 1
+fi
 
-make -f $FILE.makefile clean 
+# Change to the build directory
+cd "$BUILD_DIR"
+
+# Clean and build
+echo "Cleaning and building..."
+make -f "$FILE.makefile" clean 
+if ! make -f "$FILE.makefile"; then
+    echo "Error: Build failed."
+    exit 1
+fi
 
-make -f $FILE.makefile 
+echo "Compilation and build completed successfully."