Added lecture for Python course.

lectures/putting_together/Makefile

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lectures/putting_together/beamerthemelumc.sty

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lectures/putting_together/bin_parser_hld.dia

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lectures/putting_together/cyrillic_1.png

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lectures/putting_together/cyrillic_2.png

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lectures/putting_together/fam_re.ps

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lectures/putting_together/logos

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lectures/putting_together/mutalyzer_disambiguation.xcf

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lectures/putting_together/mutalyzer_disambiguation_result.xcf

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lectures/putting_together/nested.png

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lectures/putting_together/putting_together.tex

+\documentclass[slidestop]{beamer}
+
+\author{Jeroen F.J. Laros}
+\title{Scientific programming using Python}
+\providecommand{\mySubTitle}{Putting everything together}
+\providecommand{\myConference}{Scientific programming using Python}
+\providecommand{\myDate}{21-09-2017}
+\providecommand{\myGroup}{}
+\providecommand{\myDepartment}{Department of Human Genetics}
+\providecommand{\myCenter}{Center for Human and Clinical Genetics}
+
+\usetheme{lumc}
+
+\begin{document}
+
+% This disables the \pause command, handy in the editing phase.
+%\renewcommand{\pause}{}
+
+% Make the title slide.
+\makeTitleSlide{\includegraphics[width=3.0cm]{python_logo}}
+
+% First page of the presentation.
+\section{Introduction}
+\makeTableOfContents
+
+
+\section{General tips}
+\subsection{Packaging}
+\begin{pframe}
+  PyPI, the Python Package Index.
+  \bigskip
+
+  Repository of software for Python.
+  \begin{itemize}
+    \item $117\!,423$ packages (september 2017).
+  \end{itemize}
+  \bigskip
+
+  \begin{lstlisting}[language=bash, caption=Software installation with
+      \lstinline{pip}.]
+    pip install tssv
+  \end{lstlisting}
+
+  Download and install the package including its dependencies.
+
+  \vfill
+  \permfoot{\url{https://pypi.python.org/pypi}}
+\end{pframe}
+
+\begin{pframe}
+  Making a package yourself is relatively easy.
+  \bigskip
+
+  Adding just a few files to your project:
+  \begin{itemize}
+    \item Installation script (a few lines): \lstinline{setup.py}.
+    \item Package metadata (optional): \lstinline{setup.cfg}.
+  \end{itemize}
+  \bigskip
+
+  Metadata contains:
+  \begin{itemize}
+    \item Name, version, description, keywords, classifiers, \ldots
+    \item List of additional files to be packaged.
+    \item Dependencies.
+  \end{itemize}
+
+  \vfill
+  \permfoot{\url{https://setuptools.readthedocs.io/en/latest/}}
+\end{pframe}
+
+\subsection{Automated tests}
+\begin{pframe}
+  Write tests for your code:
+  \begin{itemize}
+    \item Adding a feature can break functionality elsewhere.
+    \item Porting your code is easier when tests are in place.
+  \end{itemize}
+  \bigskip
+
+  \begin{lstlisting}[language=python, caption=pytest example.]
+    def inc(x):
+        return x + 1
+
+    def test_inc():
+        assert inc(8) == 9
+  \end{lstlisting}
+  \bigskip
+
+  
+
+  \vfill
+  \permfoot{\url{https://docs.pytest.org/en/latest/}}
+
+  \permfoot{\url{https://tox.readthedocs.io/en/latest/}}
+\end{pframe}
+
+\subsection{API documentation}
+\begin{pframe}
+  Have your code and its documentation in one place.
+  \bigskip
+
+  \begin{lstlisting}[language=python, caption=Docstring example.]
+    def inc(x):
+      """Increase a number by one.
+
+      :arg int x: Any number.
+
+      :returns int: x + 1
+      """
+      return x + 1
+  \end{lstlisting}
+  \bigskip
+
+  Output in \color{LUMCDonkerblauw}
+  \href{https://docs.python.org/3/library/datetime.html}{HTML}\color{black},
+  PDF, Manual pages, \ldots
+
+  \vfill
+  \permfoot{\url{http://www.sphinx-doc.org/en/stable/}}
+\end{pframe}
+
+\subsection{PEP 8}
+\begin{pframe}
+  Style guide for Python code.
+  \bigskip
+
+  Extensive set of recommendations about:
+  \begin{itemize}
+    \item Naming variables, functions, classes, \ldots
+    \item Writing comments.
+    \item Using whitespace and newlines.
+    \item Maximum line length and wrapping guidelines.
+    \item \ldots
+  \end{itemize}
+
+  \vfill
+  \permfoot{\url{https://www.python.org/dev/peps/pep-0008/}}
+\end{pframe}
+
+\subsection{Licensing}
+\begin{pframe}
+  Open Source software is software with source code that anyone can inspect,
+  modify, and enhance.
+  \bigskip
+
+  All of the tools (and Python itself) discussed here are Open Source.
+  \bigskip
+
+  Put a license on your code to enable other people to use it.
+  \begin{itemize}
+    \item Code without a license is \emph{closed}.
+    \item Well known licenses include Apache, BSD, GPL, MIT, \ldots
+    \item Do not make your own license, it will be incompatible with other
+      licenses.
+  \end{itemize}
+
+  \vfill
+  \permfoot{\url{https://opensource.org/licenses}}
+\end{pframe}
+
+\section{Example packages}
+\subsection{Mutalyzer}
+\begin{pframe}
+  A curational tool for Locus Specific Mutation Databases.
+  \bigskip
+
+  Variant nomenclature checker applying the HGVS guidelines:
+  \begin{itemize}
+    \item Is the syntax of the variant description valid?
+    \item Does the reference sequence exist?
+    \item Is the variant possible on this reference sequence?
+    \item Is this variant description the recommended one?
+  \end{itemize}
+  \bigskip
+
+  Basic effect prediction.
+  \begin{itemize}
+    \item Is the description of the transcript product as expected?
+    \item Is the predicted protein as expected?
+  \end{itemize}
+  \vfill
+
+  \permfoot{\url{https://mutalyzer.nl}}
+\end{pframe}
+
+\begin{pframe}
+  \begin{figure}[]
+    \begin{center}
+      \includegraphics[width=\textwidth]{mutalyzer_disambiguation}
+    \end{center}
+    \caption{\bt{NM\_002001.2:c.9\_10delinsTGC}.}
+  \end{figure}
+\end{pframe}
+
+\begin{pframe}
+  \begin{figure}[]
+    \begin{center}
+      \includegraphics[width=\textwidth]{mutalyzer_disambiguation_result}
+    \end{center}
+    \caption{\bt{NM\_002001.2:c.12dup}.}
+  \end{figure}
+\end{pframe}
+
+\begin{pframe}
+  Mutalyzer is free:
+  \begin{itemize}
+    \item Open source (AGPL license).
+    \item Available via GitHub.
+  \end{itemize}
+  \bigskip
+
+  Available via the web:
+  \begin{itemize}
+    \item Interactive user interface.
+    \item Batch interface:
+    \begin{itemize}
+      \item CSV, XLS, ODS.
+    \end{itemize}
+    \item Webservices (to integrate in a pipeline):
+    \begin{itemize}
+      \item SOAP.
+      \item HTTP/RPC+JSON.
+    \end{itemize}
+  \end{itemize}
+  \vfill
+
+  \permfoot{\url{https://mutalyzer.nl}}\\
+  \permfoot{\url{https://github.com/mutalyzer/mutalyzer}}
+\end{pframe}
+
+\subsection{Nested}
+\begin{pframe}
+  \begin{figure}[]
+    \begin{center}
+      \includegraphics[width=\textwidth]{nested}
+    \end{center}
+    \caption{Nested online editor.}
+  \end{figure}
+\end{pframe}
+
+\begin{pframe}
+  \begin{figure}[]
+    \begin{center}
+      \includegraphics[height=0.7\textheight]{fam_re}
+    \end{center}
+    \caption{A Cyrillic FAM file.}
+  \end{figure}
+\end{pframe}
+
+\begin{pframe}
+  \begin{figure}[]
+    \begin{center}
+      \includegraphics[height=0.3\textheight]{bin_parser_hld}
+    \end{center}
+    \caption{High level design of a general binary parser.}
+  \end{figure}
+
+  Specification separate from implementation.
+  \begin{itemize}
+    \item Specification of the basic types.
+    \item Specification of the global file structure.
+  \end{itemize}
+\end{pframe}
+
+\begin{pframe}
+  Structure: $259$ lines, types: $183$ lines.
+  \begin{lstlisting}[language=none, caption={Structure snippet.}]
+    - name: members
+      for: number_of_members
+      structure:
+        - name: surname
+        - name: forenames
+        - name: address
+          type: comment
+        - name: spouses
+          for: number_of_spouses
+          structure:
+            - name: id
+              type: int
+            - name: flags
+              type: relationship
+            - name: name
+  \end{lstlisting}
+\end{pframe}
+
+\begin{pframe}
+  Resulting output in YAML format.
+  \begin{lstlisting}[language=none, caption={Output snippet.}]
+    members:
+      - surname: 'Gambolputty'
+        forenames: 'Johann'
+        address: 'Ulm'
+        spouses:
+          - flags:
+              consanguineous: false
+              divorced: false
+              informal: false
+              separated: false
+            id: 2
+            name: ''
+  \end{lstlisting}
+\end{pframe}
+
+\begin{pframe}
+  \begin{figure}[]
+    \begin{center}
+      \includegraphics[height=0.7\textheight]{cyrillic_1}
+    \end{center}
+    \caption{Original pedigree.}
+  \end{figure}
+\end{pframe}
+
+\begin{pframe}
+  We can edit the YAML file and convert it back to FAM format.
+  \begin{lstlisting}[language=none, caption={Updating date of death field.}]
+    date_of_birth: unknown
+    date_of_death: defined
+    father_id: 0
+    flags:
+      blood: false
+      cells: false
+      committed_suicide: false
+      dna: false
+      hide_info: false
+      loop_breakpoint: false
+  \end{lstlisting}
+\end{pframe}
+
+\begin{pframe}
+  \begin{figure}[]
+    \begin{center}
+      \includegraphics[height=0.7\textheight]{cyrillic_2}
+    \end{center}
+    \caption{Edited pedigree.}
+  \end{figure}
+\end{pframe}
+
+
+% Make the acknowledgements slide.
+\makeAcknowledgementsSlide{
+  \begin{tabular}{l}
+    Guy Allard\\
+    Jonathan Vis\\
+    Mark Santcroos\\
+    Mihai Lefter\\
+  \end{tabular}
+}
+
+\end{document}

lectures/putting_together/python_logo.svg

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presentation-pics @ 0fdfa620

-Subproject commit 49bd4b899df12078e4c9e93e766960bb0d5bf951
+Subproject commit 0fdfa62033731733222d41c46513cfaa74e0aa88