Commit c3261aa9 authored by Sander Bollen's avatar Sander Bollen
Browse files

Merge branch 'master' into biopython-2018

parents 6ea54bd9 bea75ce7
......@@ -3,4 +3,7 @@
url = https://github.com/hakimel/reveal.js.git
[submodule "programming-course-assignments"]
path = programming-course-assignments
url = git@git.lumc.nl:humgen/programming-course-assignments.git
url = git@git.lumc.nl:courses/programming-course-assignments.git
[submodule ".presentation"]
path = .presentation
url = https://git.lumc.nl/j.f.j.laros/presentation.git
Subproject commit f9fe363f5209cbfe93140a077310e3fb65d72b80
......@@ -25,30 +25,30 @@ Program and Materials
- Mornings: presentations.
- Afternoons: assignments.
| Day | Time | Lesson | Teacher |
|-----------------|-------|------------------------------------ |----------|
| Tuesday, 27/11 | 9-10 | [Welcome][lesson_01], [Introduction to Python][lesson_02_01] | Mihai |
| | 10-11 | [Data types][lesson_02_02] | Mihai |
| | 11-12 | [Functions][lesson_02_03] | Mihai |
| | 12-13 | Lunch break | |
| | 13-16 | Practical session | Mihai, Sander, and Guy|
| Wednesday, 28/11 | 9-10 | Assignments review | |
| | 10-11 | [String methods, errors and exceptions][lesson_03_01] | Mihai |
| | 11-12 | [Standard library, reading and writing files][lesson_03_02] | Mihai |
| | 12-13 | Lunch break | |
| | 13-16 | Practical session | Mihai, Sander, and Mark|
| Thursday, 29/11 | 9-10 | Assignments review | |
| | 10-11 | [Object-oriented programming][lesson_oop] | Jonathan |
| | 11-12 | [Jupyter Notebook][lesson_jpn] | Mark |
| | 12-13 | [Data mangling with pandas][lesson_pandas] | Mark |
| | 12-13 | Lunch break | |
| | 13-16 | Practical session | Mihai, and Mark|
| Friday, 30/11 | 9-10 | Assignments review | |
| | 10-11 | [Data visualisation with Matplotlib][lesson_dv_01] | Guy |
| | 11-12 | [Data visualisation with Bokeh][lesson_dv_02] | Guy |
| | 12-13 | [Biopython][lesson_bp] | Sander |
| | 12-13 | Lunch break | |
| | 13-16 | Practical session | Mihai, Sander, and Guy|
| Day | Time | Lesson | Teacher |
|------------------|-------|------------------------------------ |----------|
| Tuesday, 27/11 | 9-10 | [Introduction][lesson_01_01] | Mihai |
| | 10-11 | [Data types][lesson_01_02] | Mihai |
| | 11-12 | [Flow control][lesson_01_03] | Mihai |
| | 12-13 | Lunch break | |
| | 13-16 | Practical session | Mihai, Sander, and Guy|
| Wednesday, 28/11 | 9-10 | Assignments review | |
| | 10-11 | [String methods, errors and exceptions][lesson_03_01] | Mihai |
| | 11-12 | [Standard library, reading and writing files][lesson_03_02] | Mihai |
| | 12-13 | Lunch break | |
| | 13-16 | Practical session | Mihai, Sander, and Mark|
| Thursday, 29/11 | 9-10 | Assignments review | |
| | 10-11 | [Object-oriented programming][lesson_oop] | Jonathan |
| | 11-12 | [Jupyter Notebook][lesson_jpn] | Mark |
| | 12-13 | [Data mangling with pandas][lesson_pandas] | Mark |
| | 13-14 | Lunch break | |
| | 14-16 | Practical session | Mihai, and Mark|
| Friday, 30/11 | 9-10 | Assignments review | |
| | 10-11 | [Data visualisation with Matplotlib][lesson_dv_01] | Guy |
| | 11-12 | [Data visualisation with Bokeh][lesson_dv_02] | Guy |
| | 12-13 | [Biopython][lesson_bp] | Sander |
| | 13-14 | Lunch break | |
| | 14-16 | Practical session | Mihai, Sander, and Guy|
Some of the lessons are slideshows, whereas others are just
notebooks we scroll through during class. The links above are all one-page
......@@ -67,10 +67,9 @@ Assignments
- [Visualization 2](https://classroom.github.com/a/2GAOqqBu).
[lesson_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/introduction/01_welcome.ipynb
[lesson_02_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/introduction/02_introduction_to_python_1.ipynb
[lesson_02_02]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/introduction/02_introduction_to_python_2.ipynb
[lesson_02_03]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/introduction/02_introduction_to_python_3.ipynb
[lesson_01_01]: https://git.lumc.nl/courses/programming-course/raw/master/introduction/introduction/introduction.pdf?inline=false
[lesson_01_02]: https://git.lumc.nl/courses/programming-course/raw/master/introduction/data_types/data_types.pdf?inline=false
[lesson_01_03]: https://git.lumc.nl/courses/programming-course/blob/master/introduction/flow_control/flow_control.pdf?inline=false
[lesson_03_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/more_python/03_more_python_goodness_1.ipynb
[lesson_03_02]: http://nbviewer.ipython.org/urls/git.lumc.nl/courses/programming-course/raw/master/more_python/03_more_python_goodness_2.ipynb
[lesson_oop]: https://git.lumc.nl/courses/programming-course/raw/master/oop/oop.pdf
......
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../../.presentation/Makefile
\ No newline at end of file
../../.presentation/beamerthemelumc.sty
\ No newline at end of file
\documentclass[aspectratio=1610,slidestop]{beamer}
\author{Mihai Lefter}
\title{Python Programming}
\providecommand{\mySubTitle}{Data Types}
\providecommand{\myConference}{Programming Course}
\providecommand{\myDate}{27-11-2018}
\providecommand{\myGroup}{}
\providecommand{\myDepartment}{}
\providecommand{\myCenter}{}
\usetheme{lumc}
\usepackage{minted}
\usepackage{tikz}
\usepackage[many]{tcolorbox}
\definecolor{monokaibg}{HTML}{272822}
\definecolor{emailc}{HTML}{1e90FF}
\definecolor{ipyout}{HTML}{F0FFF0}
\newenvironment{ipython}
{\begin{tcolorbox}[title=IPython,
title filled=false,
fonttitle=\scriptsize,
fontupper=\footnotesize,
enhanced,
colback=monokaibg,
drop small lifted shadow,
boxrule=0.1mm,
left=0.1cm,
arc=0mm,
colframe=black]}
{\end{tcolorbox}}
\newenvironment{terminal}
{\begin{tcolorbox}[title=terminal,
title filled=false,
fonttitle=\scriptsize,
fontupper=\footnotesize,
enhanced,
colback=monokaibg,
drop small lifted shadow,
boxrule=0.1mm,
left=0.1cm,
arc=0mm,
colframe=black]}
{\end{tcolorbox}}
\newcommand{\hrefcc}[2]{\textcolor{#1}{\href{#2}{#2}}}
\newcommand{\hrefc}[3]{\textcolor{#1}{\href{#2}{#3}}}
\newcounter{cntr}
\renewcommand{\thecntr}{\texttt{[\arabic{cntr}]}}
\newenvironment{pythonin}[1]
{\VerbatimEnvironment
\begin{minipage}[t]{0.11\linewidth}
\textcolor{green}{\texttt{{\refstepcounter{cntr}\label{#1}In \thecntr:}}}
\end{minipage}%
\begin{minipage}[t]{0.89\linewidth}%
\begin{minted}[
breaklines=true,style=monokai]{#1}}
{\end{minted}
\end{minipage}}
\newenvironment{pythonout}
{%
\addtocounter{cntr}{-1}
\begin{minipage}[t]{0.11\linewidth}
\textcolor{red}{\texttt{{\refstepcounter{cntr}\label{#1}Out\thecntr:}}}
\end{minipage}%
\color{ipyout}%
\ttfamily%
\begin{minipage}[t]{0.89\linewidth}%
}
{\end{minipage}}
\newenvironment{pythonerr}[1]
{\VerbatimEnvironment
\begin{minted}[
breaklines=true,style=monokai]{#1}}
{\end{minted}}
\begin{document}
% This disables the \pause command, handy in the editing phase.
%\renewcommand{\pause}{}
% Make the title slide.
\makeTitleSlide{\includegraphics[height=3.5cm]{../../images/Python.pdf}}
% First page of the presentation.
\section{Introduction}
\makeTableOfContents
\section{Sequence types}
\subsection{Lists}
\begin{pframe}
Mutable sequences of values.
\begin{ipython}
\begin{pythonin}{python}
l = [2, 5, 2, 3, 7]
\end{pythonin}
\\
\begin{pythonin}{python}
type(l)
\end{pythonin}
\begin{pythonout}
list
\end{pythonout}
\end{ipython}
\medskip
Lists can be heterogeneous, but we typically don't use that.
\begin{ipython}
\begin{pythonin}{python}
a = 'spezi'
\end{pythonin}
\\
\begin{pythonin}{python}
[3, 'abc', 1.3e20, [a, a, 2]]
\end{pythonin}
\begin{pythonout}
[3, 'abc', 1.3e+20, ['spezi', 'spezi', 2]]
\end{pythonout}
\end{ipython}
\end{pframe}
\subsection{Tuples}
\begin{pframe}
Immutable sequences of values.
\begin{ipython}
\begin{pythonin}{python}
t = 'white', 77, 1.5
\end{pythonin}
\\
\begin{pythonin}{python}
type(t)
\end{pythonin}
\begin{pythonout}
tuple
\end{pythonout}
\\
\begin{pythonin}{python}
color, width, scale = t
\end{pythonin}
\\
\begin{pythonin}{python}
width
\end{pythonin}
\begin{pythonout}
77
\end{pythonout}
\end{ipython}
\end{pframe}
\subsection{Strings}
\begin{pframe}
Immutable sequences of characters.
\begin{ipython}
\begin{pythonin}{python}
'a string can be written in single quotes'
\end{pythonin}
\\
\begin{pythonout}
'a string can be written in single quotes'
\end{pythonout}
\end{ipython}
Strings can also be written with double quotes, or over multiple lines with
triple-quotes.
\begin{ipython}
\begin{pythonin}{python}
"this makes it easier to use the ' character"
\end{pythonin}
\\
\begin{pythonout}
"this makes it easier to use the ' character"
\end{pythonout}
\\
\begin{pythonin}{python}
"""A multiline string.
You see? I continued after a blank line."""
\end{pythonin}
\begin{pythonout}
'A multiline string.\n\nYou see? I continued after a blank line.'
\end{pythonout}
\end{ipython}
\end{pframe}
\begin{pframe}
A common operation is formatting strings using argument substitutions.
\begin{ipython}
\begin{pythonin}{python}
'{} times {} equals {:.2f}'.format('pi', 2, 6.283185307179586)
\end{pythonin}
\\
\begin{pythonout}
'pi times 2 equals 6.28'
\end{pythonout}
\end{ipython}
Accessing arguments by position or name is more readable.
\begin{ipython}
\begin{pythonin}{python}
'{1} times {0} equals {2:.2f}'.format('pi', 2, 6.283185307179586)
\end{pythonin}
\\
\begin{pythonout}
'2 times pi equals 6.28'
\end{pythonout}
\\
\begin{pythonin}{python}
'{number} times {amount} equals {result:.2f}'.format(number='pi', amount=2, result=6.283185307179586)
\end{pythonin}
\\
\begin{pythonout}
'pi times 2 equals 6.28'