remove warnings and clean preample files again

#Thesis_Configurations.tex#

@@ -0,0 +1,85 @@
+%------------------------------------------------------------
+\documentclass[a4paper,10pt]{report}
+\usepackage{fontspec}
+\usepackage{amsmath}
+\usepackage[hang, small, bf, margin=20pt]{caption}%, tableposition=top
+\setlength{\abovecaptionskip}{0pt}
+\usepackage{geometry}
+\geometry{ a4paper, total={170mm,257mm}, left=10mm,right=10mm, top=20mm,}
+\usepackage{graphicx}
+\usepackage{subfigure}
+\setlength{\parskip}{6pt}
+\newtheorem{theorem}{Theorem}
+\newtheorem{acknowledgement}[theorem]{Acknowledgement}
+\newtheorem{definition}[theorem]{Definition}
+%-------------------------------------------
+\usepackage{hyperref}
+\usepackage{multirow}
+\hypersetup{
+  colorlinks,
+  citecolor=blue,
+  filecolor=blue,
+  linkcolor=blue,
+  urlcolor=blue}
+\setcounter{secnumdepth}{3}
+% -------------------------------------------------------------
+%\usepackage{makecell}%###################33
+\usepackage{tabu}
+\usepackage{booktabs}% for better rules in the table
+
+\usepackage{titlesec}
+\titleformat{\chapter}[display]
+{\normalfont\huge\bfseries\centering}{\thechapter}{20pt}{\Huge}
+\newcommand{\cchapter}{\chapter}
+\titleformat{\cchapter}[display]
+{\normalfont\tiny\bfseries\centering}{\thecchapter}{12pt}{\tiny}
+% -------------------------------------------------------------
+\usepackage[dvipsnames, table]{xcolor}
+\usepackage{mathtools}
+\DeclarePairedDelimiter{\ceil}{\lceil}{\rceil}
+\usepackage{amssymb}
+\usepackage{booktabs}  % for \toprule ...
+\usepackage{collcell}
+\usepackage{pgf}
+\usepackage{setspace}
+\usepackage{tikz}
+\usetikzlibrary{shapes.geometric}
+\usetikzlibrary{arrows.meta,arrows}
+\usetikzlibrary{calc,intersections}
+\usetikzlibrary{matrix}
+\usetikzlibrary{positioning}% To get more advances positioning options
+\usetikzlibrary{patterns}
+\usepackage{polyglossia}
+\usepackage{footnote}
+\usepackage{pgfplotstable}% loads pgfplots, tikz, graphicx
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% make the tables and the figures centered automatically
+\makeatletter
+\g@addto@macro\@floatboxreset\centering
+\makeatother
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\colorlet{LightGreen}{green!25}%for figures
+\colorlet{DarkGreen}{green!90}%for figures
+\colorlet{LightBlue}{blue!40}%for figures
+\colorlet{LightPurple}{red!20}%for figures
+\colorlet{LightYellow}{yellow!30}%for figures
+\colorlet{LightBlue1}{blue!20}%for figures
+\colorlet{LightPurple1}{purple!40}%for figures
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\usepackage{listings}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\usepackage{bidipoem}
+\setmainlanguage{english}
+\setotherlanguage{arabic}
+\newfontfamily\arabicfont[Script=Arabic, Scale=1.5]{Scheherazade}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\input{listing_python_configuration.tex}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\input{pgfplot_configurations.tex}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: "master"
+%%% TeX-engine: xetex
+%%% End:

Thesis_Configurations.tex

@@ -1,12 +1,10 @@
 %------------------------------------------------------------
 \documentclass[a4paper,10pt]{report}
-\usepackage{fontspec}
-\usepackage{amsmath}
-\usepackage[hang, small, bf, margin=20pt]{caption}%, tableposition=top
-\setlength{\abovecaptionskip}{0pt}
 \usepackage{geometry}
 \geometry{ a4paper, total={170mm,257mm}, left=10mm,right=10mm, top=20mm,}
-\usepackage{makecell}%###################33
+\usepackage[hang, small, bf, margin=20pt]{caption}%, tableposition=top
+\setlength{\abovecaptionskip}{0pt}
+\usepackage{makecell}%
 \usepackage{graphicx}
 \usepackage{subfigure}
 \setlength{\parskip}{6pt}
@@ -63,17 +61,23 @@
 \colorlet{LightBlue1}{blue!20}%for figures
 \colorlet{LightPurple1}{purple!40}%for figures
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\usepackage{listings}
+\input{listing_python_configuration.tex}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\usepackage{fontspec}
+\usepackage{amsfonts}
+\usepackage{amsmath}
+\usepackage{fourier}
+\DeclareMathAlphabet{\mathcal}{OT1}{pzc}{m}{it}
+\DeclareSymbolFont{letters}{OML}{cmm}{m}{it}
 \usepackage{bidipoem}
 \setmainlanguage{english}
 \setotherlanguage{arabic}
-\newfontfamily\arabicfont[Script=Arabic, Scale=1.5]{Scheherazade}
+\newfontfamily\arabicfont[Script=Arabic]{Amiri}
+\setmainfont[Scale=0.925]{Heuristica}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\input{listing_python_configuration.tex}
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \input{pgfplot_configurations.tex}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\pdfstringdefDisableCommands{\let\uppercase\relax}%ignore warning \uppercase is not supported when a string is expanded for bookmarks.
 
 %%% Local Variables:
 %%% mode: latex