The numbering of the sections appear only in the first section - latex

Question

I'm having a problem with the numbering of the sections in latex.
I want the numbering of the chapters and sections to be as
1 first chapter
1.1 first section
1.2 second section
the problem is that the numbering of the section appears only in the first section and I have no idea why is this happening!
this is the code that I used.
\documentclass [a4paper,12pt]{report}
\usepackage{times}
\usepackage{graphicx}
\usepackage{geometry}
\usepackage[utf8]{inputenc} % for numbering of pages
\usepackage{ragged2e}
\usepackage{indentfirst}
\usepackage{setspace}
\usepackage{titlesec}
\usepackage[english]{babel}
\renewcommand\thesection{\arabic{section}} % for the chapters numbering
%margins
%1 inch from top, buttom and right side of the page and 1.5 inch from left side of the page
\geometry{
a4paper,
left=1.5in,right=1in,top=1in,bottom=1in
}
\onehalfspacing
\centering
\pagenumbering{roman}
\titleformat{\section}
{\normalfont\fontsize{16}{15}\bfseries}{\thesection}{1em}{}
\titleformat{\subsection}
{\normalfont\fontsize{14}{15}\bfseries}{\thesection}{1em}{}
\titleformat{\subsubsection}
{\normalfont\fontsize{12}{15}\bfseries}{\thesection}{1em}{}
\renewcommand{\thesection}{\thechapter.\number\numexpr\value{section}\relax}
\renewcommand{\thesubsection}{\thesection.\number\numexpr\value{subsection}\relax}
\renewcommand{\thesubsubsection}{\thesubsection.\number\numexpr\value{subsubsection}\relax}
\setcounter{secnumdepth}{3}
\setcounter{chapter}{1}% Not using chapters, but they're used in the counte
\begin{document}
% this is the table of contents of the document
\renewcommand*\contentsname{Table of Contents}
%--------------------------------------------------
\tableofcontents
\newpage
\listoffigures
\newpage
\listoftables
% this is the introduction chapter
\newpage
\pagenumbering{arabic}
\chapter*{\centering \vspace{80 mm} Chapter One: Introduction}
\addcontentsline{toc}{chapter}{\numberline{}Chapter One: Introduction}%
\newpage
\justify
\setlength{\parindent}{5 ex}
\section{Introduction}
%write introduction here
\section{Problem Definition}
%write Problem Definition here
\section{Aim and Objectives}
%write Aim and Objectives here
\section{Methodology}
%write Methodology here
\section{Project Scope}
%write Project Scope here
\section{Project Timeline}
%write Project Timeline here
\section{Conclusion}
%write Conclusion here
\end{document}
the table of contentes shows the numbring however the numbers appear only in the first section (introduction). how can I make the numbers appear in the other sections as well ?

Answer 1

for some reason the following package and code affects the numbering of the section (I have no idea why is that happening). when I removed the following code the numbering of the sections appeared in the headings also.
\usepackage{titlesec}
\titleformat{\section}
{\normalfont\fontsize{16}{15}\bfseries}{\thesection}{1em}{}
\titleformat{\subsection}
{\normalfont\fontsize{14}{15}\bfseries}{\thesection}{1em}{}
\titleformat{\subsubsection}
{\normalfont\fontsize{12}{15}\bfseries}{\thesection}{1em}{}
now I need to find another way to change the font size of the headings. I would appreciate it if any one posts a better way to chanage the font size without using titlesec package.