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\begin{frame}
\frametitle{Getting Started}

\bi
\item Administrative details
\item Additional introductions
\item Traditional project choices
\item Drasil project choices
\item Software tools
\begin{itemize}
\item Git, GitLab and GitHub (Issue Creating Exercise)
\item LaTeX
\item Make
\end{itemize}
\item Questions on suggested reading?
\item Software Engineering for Scientific Computing literature
\ei

\end{frame}

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\begin{frame}
\frametitle{Administrative Details}

\bi
\item Can everyone access GitLab?
  \href{https://gitlab.cas.mcmaster.ca/smiths/cas741}
  {https://gitlab.cas.mcmaster.ca/smiths/cas741}
\item Use folder structure given in repo (will be updating)
\item Create a GitHub account if you don't already have one
\item Add \texttt{smiths} to your GitHub repos
\item Problem statement
\begin{itemize}
\item Problem statement due Mon, Sept 21 by 11:59 pm
\item Assign the instructor an issue to review your problem
    statement
\end{itemize}
\item Issue creating exercises due Fri, Sept 18 by 1:00 pm
\item Feel free to add me to you Linked-In network
\ei

\end{frame}

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\begin{frame}
\frametitle{Administrative Details: Domain Expert}

\begin {itemize}

\item Creates issues for their partner's written deliverables
\item Asks questions during their partner's presentations
%\item Implements one module following their partner's spec

\end {itemize}

\end{frame}

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\begin{frame}

\frametitle{Administrative Details: Our Deliverables}

\begin{center}
\includegraphics[scale=0.55]{../Figures/VModelOfProcessXOut.pdf}
\end{center}
\vspace{-1.0cm}

\end{frame}

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\begin{frame}
\frametitle{Administrative Details: Presentations (Draft Deadlines)}

~\newline
\begin{tabular}{l l l}
SRS Present &amp; Week 05? &amp; Week of Sept 30?\\
POC Demo &amp; Week 06? &amp; Week of Oct 6?\\
Syst.\ VnV Present &amp; Week 07? &amp; Week of Oct 21?\\
MG + MIS Syntax Present &amp; Week 9? &amp; Week of Nov 4?\\
MIS Semantics Present &amp; Week 11? &amp; Week of Nov 18?\\
Unit VnV or Implement Present &amp; Week 12/13? &amp; Week of Nov 28?\\
\end {tabular}

\bi
%\item Very tentative dates
\item Specific schedule depends on final class registration and need
\item Informal presentations with the goal of improving everyone's written
  deliverables
\item Domain experts and secondary reviewers (and others) will ask questions
\ei

\end{frame}

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\begin{frame}
\frametitle{Administrative Details: Draft Report Deadlines}
~\newline
\begin{tabular}{l l l}
Issue Creation Exercise &amp; Week 02 &amp; Sept 18\\
Problem Statement &amp; Week 03 &amp; Sept 21\\
System Requirements Specification (SRS) &amp; Week 06? &amp; Oct 7?\\
System VnV Plan &amp; Week 08? &amp; Oct 28?\\
Module Guide (MG) + Mod Int Spec (MIS)? &amp; Week 10? &amp; Nov 25?\\
%Unit VnV Plan &amp; Week 14 &amp; Dec 3\\
Final Documentation &amp; Week 14? &amp; Dec 9?\\
\end {tabular}

\bi
\item The written deliverables will be graded based on the repo contents as of
11:59 pm of the due date
\item If you need an extension, please ask
\item Two days after each major deliverable, your GitHub issues will be due
%\item Domain expert code due 1 week after MIS deadline
\ei

\end{frame}

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\begin{frame}
\frametitle{Administrative Details: Optional Study Participation}

\bi
\item You will be contacted by Oluwaseun (Olu) Owojaiye for potential
  participation in a study
\item ``Traditional''  versus ``Generative'' for software development
\item If you participate you will be interviewed and asked to record some
  details of how you spend your development time
\item Participation is entirely voluntary
\item The course instructor will not know who has participated
\item Participation or non-Participation will not effect your grade
\item Olu will visit our class on Thursday to discuss further
\ei

\end{frame}

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\begin{frame}
\frametitle{Introductions (if necessary)}

\begin{itemize}
\item Your name
\item Degree program
\item Academic background
\item Experience with:
\begin{itemize}
\item Science (such as physics)
\item Scientific computing
\item Continuous math
\item Discrete math
\item Software engineering
\item Software development technology
\bi
\item Git
\item GitHub or GitLab
\item LaTeX
\item Make etc.
\ei
\end{itemize}
\item What do you hope to get out of this course?
\end{itemize}

\end{frame}

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\begin{frame}
\frametitle{Project Selection: Desired Qualities}
\begin{itemize}
\item Related to scientific computing
\item Simple, but not trivial
\item If feasible, select a project related to your research
\item Possibly re-implement existing software
\item Each student project needs to be unique
\item A specific physical problem
%\item Possibly a (family of) general purpose tool(s)
\item Some examples follow, the links are just places to get started
\end{itemize}
\end{frame}

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\begin{frame}
\frametitle{Project Selection: Specific Physical Problem}
\begin{itemize}
\item
  \href{https://ocw.mit.edu/courses/mathematics/18-303-linear-partial-differential-equations-fall-2006/lecture-notes/heateqni.pdf}{
    Heated
    rod}
\item \href{http://www.tech.plym.ac.uk/sme/THER204B-web/Heatran2.PDF}{Heated plate}
\item \href{https://en.wikipedia.org/wiki/Double_pendulum}{Double pendulum
    (previously done)}
\item \href{http://chrishecker.com/Rigid_Body_Dynamics}{Rigid body dynamics}
\item Column buckling
\item \href{https://en.wikipedia.org/wiki/Harmonic_oscillator}{Damped harmonic oscillator}
\item Stoichiometric calculations (chemical balance)
\item
  \href{http://www.tiem.utk.edu/~gross/bioed/bealsmodules/predator-prey.html}{Predator
    prey dynamics}
\item Imaging: filters, edge detection etc.
\item Medical Imaging
\item etc.
\end{itemize}

\end{frame}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\begin{frame}
\frametitle{Project Selection: Family of General Purpose Tools}
\begin{itemize}
\item \href{https://en.wikipedia.org/wiki/Numerical_methods_for_ordinary_differential_equations}{Solution of ODEs}
\item \href{https://en.wikibooks.org/wiki/Numerical_Methods/Solution_of_Linear_Equation_Systems}{Solution of $A x = b$}
\item \href{https://en.wikipedia.org/wiki/Linear_regression}{Regression}
\item \href{https://en.wikibooks.org/wiki/Introduction_to_Numerical_Methods/Interpolation}{Interpolation}
\item \href{https://en.wikipedia.org/wiki/Numerical_integration}{Numerical integration}
\item \href{https://en.wikipedia.org/wiki/Fast_Fourier_transform}{FFT}
\item \href{https://en.wikipedia.org/wiki/Mesh_generation}{Mesh generation}
\item \href{https://en.wikipedia.org/wiki/Finite_element_method}{Finite element method}
\item Any chapter from a standard numerical methods textbook
\item etc.
\end{itemize}
\end{frame}

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\begin{frame}
\includegraphics[width=1\textwidth]{../Figures/generate_all_the_things.jpg}
\end{frame}

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\begin{frame}

\frametitle{Knowledge Capture}

\includegraphics[width=1.0\textwidth]{../Figures/KC.jpg}

\end{frame}

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\begin{frame}

\frametitle{Drasil}
\vspace{-1cm}
\begin{center}
\includegraphics[height=20em]{../Figures/tree.png}
\end{center}
\end{frame}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\begin{frame}
\frametitle{Introduction to Drasil}
\begin{itemize}
\item Drasil uses a generative approach
\item Knowledge is captured in a Domain Specific Language (DSL)
\item Documentation (in tex and html) and code (in Java, C++, C\#, Python and
  Swift) are generated
\item Changes are propagated throughout documentation and code
\item Consistency and completeness checks
\item Reuse throughout document, between documents and between projects
\end{itemize}
\end{frame}

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\begin{frame}
\frametitle{Project Selection (Drasil): Specific Physical Problems}
\begin{itemize}
\item Set of explicit equations with the variables of interest isolated on one
  side of the equation (like
  \href{https://jacquescarette.github.io/Drasil/examples/GlassBR/srs/GlassBR_SRS.html}{GlassBR},
  or \href{https://jacquescarette.github.io/Drasil/examples/Projectile/srs/Projectile_SRS.html} {Projectile})
\item First order Initial value problem (like
  \href{https://jacquescarette.github.io/Drasil/examples/NoPCM/srs/NoPCM_SRS.html}
  {NoPCM}) 
\item Examples
\begin{itemize}
\item Cooling of a uniform temperature body over time
\item Charging or discharging of a capacitor
\item Flow into a reservoir
\item Population growth
\item Blood alcohol level over time
\item
  \href{http://ugrad.math.ubc.ca/coursedoc/math103/keshet.notes/chapter11Notes.pdf}{Some
    potential problems}
\item Worked example in a physics or chemistry textbook, using equations, like
  solving for the forces in a statically indeterminate structure
\end{itemize}
\end{itemize}
\end{frame}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\begin{frame}
\frametitle{Tool Tutorials}
\begin{itemize}
\item Best way to learn is by doing
\item Some getting started information and exercises in the
  \href{https://gitlab.cas.mcmaster.ca/smiths/cas741/tree/master/ToolTutorials}
  {ToolTutorials} folder, modified from undergrad classes
\item Tutorials for
  \href{https://gitlab.cas.mcmaster.ca/smiths/se2aa4_cs2me3/tree/master/Tutorials}
  {se 2aa4 and cs 2me3}
\item Many other resources on-line
\item Your colleagues can help too
\item
  \href{https://gitlab.cas.mcmaster.ca/smiths/cas741/-/tree/master/Tools/VM_Instructions}
  {Instructions for setting up a Virtual  Machines}
\end{itemize}
\end{frame}

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\begin{frame}
\frametitle{Git, GitLab and GitHub}
\begin{itemize}
\item Git manages changes to documents
\bi
\item Tracks changes
\item Keeps history, you can roll back
\item Useful documentation over time
\item Allows people to work simultaneously
\ei
\item Benefits for SC \cite{WilsonEtAl2016}
\bi
\item Not necessary to make a backup copy of everything, stores just enough
  information to recreate
\item Do not need to come up with names for backup copies - same file name, but
  with timestamps
\item Enforces changelog discipline
\item Facilitates identifying conflict and merging changes
\ei
\item The real bottleneck in scientific computing~\cite{Wilson2006}
\end{itemize}
\end{frame}

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\begin{frame}
\frametitle{Git Typical Usage}

First either init repo or clone (git init, git clone), then typical workflow is
\be
\item update repo (git pull)
\item create files
\item stage changes to be committed (git status, git add)
\item commit staged changes (git commit -m ``message'')
\item push to remote, if using one (git push)
\ee
\bi
\item Commit after every separate issue, and when need to stop working
\item Always include a meaningful and descriptive commit message for the log
\item If a push reveals conflicts, take appropriate action to merge
\ei
\end{frame}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\begin{frame}
\frametitle{GitLab and GitHub Issue Tracking}

\bi
\item
  \href{https://gitlab.cas.mcmaster.ca/smiths/cas741/tree/master/ToolTutorials/gitAndGitLab}
  {See brief document in course repo}
\item
  \href{https://github.com/JacquesCarette/literate-scientific-software/issues}
  {See examples}
\item Tutorials for
  \href{https://gitlab.cas.mcmaster.ca/smiths/se2aa4_cs2me3/tree/master/Tutorials/T01a-Git/slides}
  {se 2aa4 and cs 2me3}
\item \href{https://gitlab.cas.mcmaster.ca/smiths/cas741/issues} {Create an
    issue} \ei

\end{frame}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\begin{frame}
\frametitle{Issue Creating Exercise}

\bi
\item Due by Friday, Sept 18, 1:00 pm
\item Create 2 to 3 issues for case studies in Drasil repo
\item \href{https://jacquescarette.github.io/Drasil/}
  {https://jacquescarette.github.io/Drasil/}
\item Select any case study that interests you and review the SRS
\item Create issues at \href{https://github.com/JacquesCarette/Drasil/issues}
  {https://github.com/JacquesCarette/Drasil/issues}
\item Assign issues to \texttt{smiths}
\item Consider using SRS
  \href{https://gitlab.cas.mcmaster.ca/smiths/cas741/blob/master/BlankProjectTemplate/docs/SRS/SRS-Checklist.pdf}
  {checklist} (except for major revision history)
\item Additional guidance in
  \href{https://gitlab.cas.mcmaster.ca/smiths/cas741/blob/master/BlankProjectTemplate/docs/SRS/SRS.tex}
  {SRS Template}
\ei

\end{frame}

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\begin{frame}
\frametitle{LaTeX}
\begin{itemize}
\item A typesetting language
\item
  \href{https://gitlab.cas.mcmaster.ca/smiths/cas741/tree/master/ToolTutorials/LaTeX}
  {Some initial information in course repo}
\item Tutorials for
  \href{https://gitlab.cas.mcmaster.ca/smiths/se2aa4_cs2me3/tree/master/Tutorials/T02a-LaTeX}
  {se 2aa4 and cs 2me3}
\item Start from an example
\bi
\item The lectures notes
\item The Blank Project Template
\item The problem statement
\ei
\end{itemize}
\end{frame}

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\begin{frame}
\frametitle{Make}
\begin{itemize}
\item \href{https://swcarpentry.github.io/make-novice/} {Software Carpentry:
    Automation and Make}
\item The Blank Project Template
\end{itemize}
\end{frame}

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\begin{frame}
\frametitle{Suggested Reading Questions?}

\begin {itemize}

\item
  \href{https://gitlab.cas.mcmaster.ca/smiths/cas741/blob/master/ReferenceMaterial/SoftEngForScienceBook.pdf}
  {Smith2016~\cite{Smith2016}}
\item
  \href{https://gitlab.cas.mcmaster.ca/smiths/cas741/blob/master/ReferenceMaterial/SmithLaiAndKhedri2007fulltext.pdf}
  {SmithEtAl2007~\cite{SmithEtAl2007}}
\item
  \href{https://gitlab.cas.mcmaster.ca/smiths/cas741/blob/master/ReferenceMaterial/ParnasAndClements1986.pdf}
  {{ParnasAndClements1986}~\cite{ParnasAndClements1986}}
\item \href{https://github.com/smiths/swhs}{Solar Water Heating System Example}

\end{itemize}

\end{frame}

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\begin{frame}
\frametitle{SE For SC Literature}

\begin {itemize}

\item CAS 741 process is document driven, adapted
from the waterfall model~\cite{GhezziEtAl2003, VanVliet2000}
\item Many say a document driven process is not used by, nor suitable for,
scientific software.
\bi
\item Scientific developers naturally use an agile
  philosophy~\cite{AckroydEtAl2008, CarverEtAl2007, EasterbrookAndJohns2009, Segal2005}, 
\item or an amethododical process~\cite{Kelly2013}
\item or a knowledge acquisition driven process~\cite{Kelly2015}.
\ei
\item Scientists do not view rigid, process-heavy approaches,
  favourably~\cite{CarverEtAl2007}
\item Reports for each stage of development are counterproductive~\cite[p.~373]{Roache1998}
\item Up-front requirements are
impossible~\cite{CarverEtAl2007, SegalAndMorris2008}
\item \structure{What are some arguments in favour of a rational document driven
    process?}
\end{itemize}

\end{frame}

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\begin{frame}
\frametitle{Counter Arguments}

\begin {itemize}

\item Just because not used, doesn't mean docs shouldn't be
\item Documentation provides many
benefits~\cite{Parnas2010}: 
\bi
\item easier reuse of old designs
\item better communication about requirements
\item more useful design reviews
\item easier integration of separately
written modules
\item more effective code inspection
\item more effective testing
\item more efficient corrections and improvements.
\ei
\item Actually faking a rational design process
\item Too complex for up-front requirements sounds like an excuse
\bi
\item Laws of physics/science slow to change
\item Often simple design patterns
\item Think program family, not individual member
\ei
\item Debunking myth against up-front requirements~\cite{SmithEtAl2019}
\end{itemize}

\end{frame}

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\begin{frame}
\frametitle{Literature on SE applied to SCS}

\begin {itemize}

\item Highlights problems with SE
\begin{itemize}
\item
  \href{https://gitlab.cas.mcmaster.ca/smiths/cas741/blob/master/ReferenceMaterial/Miller2006.pdf}
  {Miller2006~\cite{Miller2006}}
\item
  \href{https://gitlab.cas.mcmaster.ca/smiths/cas741/blob/master/ReferenceMaterial/Hatton2007.pdf}
  {Hatton2007~\cite{Hatton2007}}
\item Sleipner A oil rig collapse~\cite[p.~38]{OliveiraAndStewart2006}
\item Patriot missile disaster~\cite[p.~36]{OliveiraAndStewart2006}
\end{itemize}
\item Highlights gap/chasm between SE and SC
\begin{itemize}
\item
  \href{https://gitlab.cas.mcmaster.ca/smiths/cas741/blob/master/ReferenceMaterial/Kelly2007.pdf}
  {Kelly2007~\cite{Kelly2007}}
\item
  \href{https://gitlab.cas.mcmaster.ca/smiths/cas741/blob/master/ReferenceMaterial/Storer2017.pdf}
  {Storer2017~\cite{Storer2017}}
\end{itemize}
\item Studies of SE applied to SC
\begin{itemize}
\item
  \href{https://gitlab.cas.mcmaster.ca/smiths/cas741/blob/master/ReferenceMaterial/CarverEtAl2007.pdf}
  {CarverEtAl2007~\cite{CarverEtAl2007}}
\item
  \href{https://gitlab.cas.mcmaster.ca/smiths/cas741/blob/master/ReferenceMaterial/Segal2005.pdf}
  {Segal2005~\cite{Segal2005}}
\end{itemize}

\end{itemize}

\end{frame}

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\begin{frame}
\frametitle{Literature on SE applied to SCS}

\begin {itemize}

\item Reproducibility
\begin{itemize}
\item
  \href{https://gitlab.cas.mcmaster.ca/smiths/cas741/blob/master/ReferenceMaterial/BaileyEtAl2016.pdf}
  {BaileyEtAl2016~\cite{BaileyEtAl2016}}
\item
  \href{https://gitlab.cas.mcmaster.ca/smiths/cas741/blob/master/ReferenceMaterial/BenureauAndRougier2017.pdf}
  {BenureauAndRougier2017~\cite{BenureauAndRougier2017}}
\end{itemize}

\item Future of SE for SC
\begin{itemize}
\item
  \href{https://gitlab.cas.mcmaster.ca/smiths/cas741/blob/master/ReferenceMaterial/JohansonAndHasselbring2018.pdf}
  {JohansonAndHasselbring2018~\cite{JohansonAndHasselbring2018}}
\item
  \href{https://gitlab.cas.mcmaster.ca/smiths/cas741/blob/master/ReferenceMaterial/Smith2018.pdf}
  {Smith2018~\cite{Smith2018}}
\end{itemize}

\end{itemize}

\end{frame}

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\begin{frame}[allowframebreaks]
\frametitle{References}

\bibliography{../../ReferenceMaterial/References}

\end{frame}

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