Merge changes from upstream

997104b2 · wyleung · e3d28e6a · 7894cf5c · 997104b2 · 997104b2
Commit 997104b2 authored 10 years ago by wyleung
--- a/.gitmodules
+++ b/.gitmodules
+[submodule "reveal.js"]
+	path = reveal.js
+	url = https://github.com/hakimel/reveal.js.git
--- a/welcome.ipynb
+++ b/welcome.ipynb
 {
 "metadata": {
-  "name": ""
+  "celltoolbar": "Slideshow",
+  "name": "",
+  "signature": "sha256:6c570ac428c0fbfa0115d6c05d52e3c05410cd3de42ae35e7ee7feb0f435a641"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
@@ -20,31 +22,15 @@
      "\n",
      "<br>\n",
      "\n",
-      "[Wibowo Arindrarto](mailto:w.arindrarto@lumc.nl), [Jeroen Laros](mailto:j.f.j.laros@lumc.nl), [Zuotian Tatum](mailto:z.tatum@lumc.nl), [Martijn Vermaat](mailto:m.vermaat.hg@lumc.nl)\n",
+      "[Jeroen Laros](mailto:j.f.j.laros@lumc.nl), [Department of Human Genetics, Leiden University Medical Center](http://humgen.nl)\n",
      "\n",
-      "[Department of Human Genetics, Leiden University Medical Center](http://humgen.nl)\n",
+      "[Michiel van Galen](mailto:m.van_galen@lumc.nl), [Department of Human Genetics, Leiden University Medical Center](http://humgen.nl)\n",
      "\n",
-      "License: [Creative Commons Attribution 3.0 License (CC-by)](http://creativecommons.org/licenses/by/3.0)"
-     ]
-    },
-    {
-     "cell_type": "markdown",
-     "metadata": {
-      "slideshow": {
-       "slide_type": "skip"
-      }
-     },
-     "source": [
-      "About this notebook\n",
-      "===\n",
-      "\n",
-      "This notebook is the source for a set of slides. If you want to edit them, be sure to choose *Slideshow* in the *Cell Toolbar* menu.\n",
+      "[Wai Yi Leung](mailto:w.y.leung@lumc.nl), [Sequencing Analysis Support Core, Leiden University Medical Center](http://sasc.lumc.nl)\n",
      "\n",
-      "You can use nbconvert to convert the slides to HTML and serve them:\n",
+      "[Martijn Vermaat](mailto:m.vermaat.hg@lumc.nl), [Department of Human Genetics, Leiden University Medical Center](http://humgen.nl)\n",
      "\n",
-      "    ipython nbconvert --to slides --post serve welcome.ipynb\n",
-      "\n",
-      "This will open the slides in a new browser window."
+      "License: [Creative Commons Attribution 3.0 License (CC-by)](http://creativecommons.org/licenses/by/3.0)"
     ]
    },
    {
@@ -62,7 +48,7 @@
      "* Programming as a tool to do your research.\n",
      "* Slightly focussed on bioinformatics.\n",
      "\n",
-      "**Note:** It's a pilot."
+      "**Note:** It <s>is</s> was a pilot."
     ]
    },
    {
@@ -76,16 +62,16 @@
      "Teachers\n",
      "===\n",
      "\n",
-      "* Wibowo Arindrarto<br>\n",
-      "  [w.arindrarto@lumc.nl](mailto:w.arindrarto@lumc.nl)\n",
-      "\n",
-      "\n",
      "* Jeroen Laros<br>\n",
      "  [j.f.j.laros@lumc.nl](mailto:j.f.j.laros@lumc.nl)\n",
      "\n",
      "\n",
-      "* Zuotian Tatum<br>\n",
-      "  [z.tatum@lumc.nl](mailto:z.tatum@lumc.nl)\n",
+      "* Michiel van Galen<br>\n",
+      "  [m.van_galen@lumc.nl](mailto:m.van_galen@lumc.nl)\n",
+      "\n",
+      "\n",
+      "* Wai Yi Leung<br>\n",
+      "  [w.y.leung@lumc.nl](mailto:w.y.leung@lumc.nl)\n",
      "\n",
      "\n",
      "* Martijn Vermaat<br>\n",
@@ -129,34 +115,34 @@
      "</tr>\n",
      "<tr><td>11-12</td>\n",
      "<td>Introduction to Python (3)</td>\n",
-      "<td>Zuotian</td>\n",
+      "<td>Michiel</td>\n",
      "</tr>\n",
      "<tr><td rowspan=\"3\">Tuesday</td>\n",
      "<td>09-10</td>\n",
-      "<td>Version control with Git</td>\n",
-      "<td>Zuotian</td>\n",
+      "<td>More Python (1)</td>\n",
+      "<td>Michiel</td>\n",
      "</tr>\n",
      "<tr><td>10-11</td>\n",
-      "<td>More Python (1)</td>\n",
-      "<td>Bowo</td>\n",
+      "<td>More Python (2)</td>\n",
+      "<td>Wai Yi</td>\n",
      "</tr>\n",
      "<tr><td>11-12</td>\n",
-      "<td>More Python (2)</td>\n",
+      "<td>Working with NumPy arrays</td>\n",
      "<td>Martijn</td>\n",
      "</tr>\n",
      "<tr><td rowspan=\"3\">Wednesday</td>\n",
      "<td>09-10</td>\n",
-      "<td>Working with NumPy arrays (1)</td>\n",
-      "<td>Zuotian</td>\n",
+      "<td>IPython Notebook</td>\n",
+      "<td>Michiel</td>\n",
      "</tr>\n",
      "<tr><td>10-11</td>\n",
-      "<td>Working with NumPy arrays (2)</td>\n",
-      "<td>Martijn</td>\n",
-      "</tr>\n",
-      "<tr><td>11-12</td>\n",
      "<td>Plotting with matplotlib</td>\n",
      "<td>Jeroen</td>\n",
      "</tr>\n",
+      "<tr><td>11-12</td>\n",
+      "<td>Python for data analysis</td>\n",
+      "<td>Wai Yi</td>\n",
+      "</tr>\n",
      "<tr><td rowspan=\"3\">Friday</td>\n",
      "<td>09-10</td>\n",
      "<td>Object-oriented programming</td>\n",
@@ -164,7 +150,7 @@
      "</tr>\n",
      "<tr><td>10-11</td>\n",
      "<td>Biopython (1)</td>\n",
-      "<td>Bowo</td>\n",
+      "<td>Wai Yi</td>\n",
      "</tr>\n",
      "<tr><td>11-12</td>\n",
      "<td>Biopython (2)</td>\n",
@@ -173,7 +159,7 @@
      "</tbody>\n",
      "</table>\n",
      "\n",
-      "All slides are linked as one-page documents from the course website: [humgenprojects.lumc.nl/trac/programming-course](https://humgenprojects.lumc.nl/trac/programming-course/)"
+      "All slides are linked as one-page documents from the course website: [humgenprojects.lumc.nl/trac/humgenprojects/wiki/ProgrammingCourse](https://humgenprojects.lumc.nl/trac/humgenprojects/wiki/ProgrammingCourse)"
     ]
    },
    {
@@ -190,10 +176,10 @@
      "* Linux or Mac OSX\n",
      "* Git\n",
      "* Python 2.7\n",
-      "* IPython 1.0\n",
+      "* IPython 2.1\n",
      "* NumPy, matplotlib, Biopython\n",
      "\n",
-      "Instructions on the course website: [humgenprojects.lumc.nl/trac/programming-course](https://humgenprojects.lumc.nl/trac/programming-course/)"
+      "Instructions on the course website: [humgenprojects.lumc.nl/trac/humgenprojects/wiki/ProgrammingCourse](https://humgenprojects.lumc.nl/trac/humgenprojects/wiki/ProgrammingCourse)"
     ]
    },
    {
@@ -241,32 +227,16 @@
      }
     },
     "source": [
-      "GitLab accounts\n",
+      "Getting help\n",
      "===\n",
      "\n",
-      "* Login with your LUMC username and password.\n",
-      "* Make some noise if you don't have an account\n",
-      "* We'll use this later.\n",
+      "* Ask a teacher or assistant.\n",
+      "* If it's private, mail one of the teachers.\n",
+      "* Use our etherpad:\n",
      "\n",
      "<br>\n",
      "\n",
-      "<center style=\"font-size: 300%\">[https://git.lumc.nl](https://git.lumc.nl/)</center>"
-     ]
-    },
-    {
-     "cell_type": "markdown",
-     "metadata": {
-      "slideshow": {
-       "slide_type": "slide"
-      }
-     },
-     "source": [
-      "Getting help\n",
-      "===\n",
-      "\n",
-      "* Ask a teacher or assistant.\n",
-      "* Post your question on the GitLab wall: [https://git.lumc.nl/humgen/programming-course/wall](https://git.lumc.nl/humgen/programming-course/wall)\n",
-      "* If it's private, mail one of the teachers."
+      "<center style=\"font-size: 300%\">[tinyurl.com/leidencourse](http://tinyurl.com/leidencourse)</center>"
     ]
    },
    {
@@ -289,7 +259,7 @@
      {
       "html": [
        "<style>/* Remove the vertical scrollbar added by nbconvert. */\n",
-        ".reveal {\n",
+        "html {\n",
        "  overflow-y: hidden;\n",
        "}\n",
        "\n",
@@ -302,13 +272,22 @@
        "  color: black ! important;\n",
        "  font-weight: normal ! important;\n",
        "}\n",
+        "span.title {\n",
+        "  color: black ! important;\n",
+        "}\n",
+        "span.tag {\n",
+        "  color: black ! important;\n",
+        "}\n",
+        "span.attribute {\n",
+        "  color: black ! important;\n",
+        "}\n",
        "</style>"
       ],
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 1,
       "text": [
-        "<IPython.core.display.HTML at 0x32f7210>"
+        "<IPython.core.display.HTML at 0x33caa50>"
       ]
      }
     ],

--- a/02 - Introduction to Python (1).ipynb
+++ b/02 - Introduction to Python (1).ipynb
--- a/python.ipynb
+++ b/python.ipynb
--- a/02 - Introduction to Python (3).ipynb
+++ b/02 - Introduction to Python (3).ipynb
--- a/03 - More Python goodness (1).ipynb
+++ b/03 - More Python goodness (1).ipynb
--- a/more-python.ipynb
+++ b/more-python.ipynb
--- a/INSTALL.md
+++ b/INSTALL.md
-Software installation
-=====================
-
-The following guide gets you a virtual environment with all the necessary
-packages installed.
-
-
-Linux
-----
-
-We assume Ubuntu (12.10 Quantal Quetzal or later) or Debian Linux (7.0 Wheezy
-or later), but if you manage to install everything on a different flavour
-that's also fine.
-
-You can [download Ubuntu here](http://www.ubuntu.com/) and either install it
-directly on your machine, or run it inside
-[VirtualBox](https://www.virtualbox.org/).
-
-Python version >= 2.7.3 and < 3.0 is required. This is installed by default on
-Ubuntu and Debian Linux. Note that we use Python 2, *not* Python 3.
-
-We need some system packages to be installed. For the following command, you
-need sudo rights:
-
-    sudo apt-get install -y \
-      curl python-qt4 libfreetype6-dev libpng12-dev python-cairo \
-      python-gtk2 python-gtk2-dev git gfortran
-
-From here on, everything is local for the current user.
-
-Install [virtualenv](http://www.virtualenv.org/) and
-[virtualenvwrapper](http://virtualenvwrapper.readthedocs.org/) using
-[Virtualenv Burrito](https://github.com/brainsik/virtualenv-burrito):
-
-    curl -sL https://raw.github.com/brainsik/virtualenv-burrito/master/virtualenv-burrito.sh | $SHELL
-    source ~/.venvburrito/startup.sh
-
-Automatically
-[link PyGTK/Pycairo/PyQt system packages](https://gist.github.com/martijnvermaat/6111396/)
-into our virtual environments:
-
-    curl -sL https://gist.github.com/martijnvermaat/6111396/raw/postmkvirtualenv > ~/.virtualenvs/postmkvirtualenv
-
-Create a virtual environment (named `programming-course`, but you could choose
-any name here):
-
-    mkvirtualenv programming-course
-
-Install IPython:
-
-    pip install ipython
-
-Install some of the other package we'll use:
-
-    pip install pyzmq tornado jinja2 pygments sphinx markdown nose
-    pip install numpy
-    pip install matplotlib
-    pip install biopython
-    pip install pandas==0.14.0
-    pip install openpyxl==2.0.4
-
-Define a default matplotlib backend:
-
-    mkdir -p ~/.config/matplotlib
-    echo "backend : GTKCairo" >> ~/.config/matplotlib/matplotlibrc
-
-
-Mac OSX Mountain Lion
---------------------
-
-Install
-[Xcode from the App Store](https://itunes.apple.com/us/app/xcode/id497799835?ls=1&mt=12
-Xcode from the App Store). Start Xcode and install the device support
-(Preferences -> Downloads).
-
-Install Xcode command line tools:
-
-    ruby -e "$(curl -fsSL https://raw.github.com/mxcl/homebrew/go)"
-    brew doctor
-    xcodebuild -license   # accept license
-
-Add user `bin`, and local Python to your `$PATH`:
-
-    echo 'export PATH="~/bin:/usr/local/share/python:/usr/local/bin:$PATH"' > .bash_profile
-    . .bash_profile
-
-We need some system packages:
-
-    brew install python --with-brewed-openssl
-    brew install gfortran
-
-Install [virtualenv](http://www.virtualenv.org/) and
-[virtualenvwrapper](http://virtualenvwrapper.readthedocs.org/) using
-[Virtualenv Burrito](https://github.com/brainsik/virtualenv-burrito):
-
-    curl -s https://raw.github.com/brainsik/virtualenv-burrito/master/virtualenv-burrito.sh | $SHELL
-    source .venvburrito/startup.sh
-
-Create a virtual environment (named `programming-course`, but you could choose
-any name here):
-
-    mkvirtualenv programming-course
-
-Install IPython (version 1.0):
-
-    pip install -e git+https://github.com/ipython/ipython#egg=ipython
-    # or after its 1.0 release: pip install ipython
-
-Install some of the other package we'll use:
-
-    pip install pyzmq tornado jinja2 pygments sphinx markdown nose
-    pip install numpy
-    pip install matplotlib
-    pip install biopython
-    pip install pandas==0.14.0
-    pip install openpyxl==2.0.4
-
+Software installation
+=====================
+
+The following guide gets you a virtual environment with all the necessary
+packages installed.
+
+
+Linux
+-----
+
+We assume Ubuntu (12.04 Precise Pangolin or later) or Debian Linux (7.0 Wheezy
+or later), but if you manage to install everything on a different flavour
+that's also fine.
+
+You can [download Ubuntu here](http://www.ubuntu.com/) and either install it
+directly on your machine, or run it inside
+[VirtualBox](https://www.virtualbox.org/).
+
+Python version >= 2.7.3 and < 3.0 is required. This is installed by default on
+Ubuntu and Debian Linux. Note that we use Python 2, *not* Python 3.
+
+We need some system packages to be installed. For the following command, you
+need sudo rights:
+
+    sudo apt-get install -y \
+      curl python-qt4 libfreetype6-dev libpng12-dev python-cairo \
+      python-gtk2 python-gtk2-dev git gfortran
+
+From here on, everything is local for the current user.
+
+Install [virtualenv](http://www.virtualenv.org/) and
+[virtualenvwrapper](http://virtualenvwrapper.readthedocs.org/) using
+[Virtualenv Burrito](https://github.com/brainsik/virtualenv-burrito):
+
+    curl -sL https://raw.github.com/brainsik/virtualenv-burrito/master/virtualenv-burrito.sh | $SHELL
+    source ~/.venvburrito/startup.sh
+
+Automatically
+[link PyGTK/Pycairo/PyQt system packages](https://gist.github.com/martijnvermaat/6111396/)
+into our virtual environments:
+
+    curl -sL https://gist.github.com/martijnvermaat/6111396/raw/postmkvirtualenv > ~/.virtualenvs/postmkvirtualenv
+
+Create a virtual environment (named `programming-course`, but you could choose
+any name here):
+
+    mkvirtualenv programming-course
+
+Install Python packages:
+
+    pip install -r requirements.txt
+
+Define a default matplotlib backend:
+
+    mkdir -p ~/.config/matplotlib
+    echo "backend : GTKCairo" >> ~/.config/matplotlib/matplotlibrc
+
+
+Mac OSX Mountain Lion
+---------------------
+
+Install
+[Xcode from the App Store](https://itunes.apple.com/us/app/xcode/id497799835?ls=1&mt=12
+Xcode from the App Store). Start Xcode and install the device support
+(Preferences -> Downloads).
+
+Install Xcode command line tools:
+
+    ruby -e "$(curl -fsSL https://raw.github.com/mxcl/homebrew/go)"
+    brew doctor
+    xcodebuild -license   # accept license
+
+Add user `bin`, and local Python to your `$PATH`:
+
+    echo 'export PATH="~/bin:/usr/local/share/python:/usr/local/bin:$PATH"' > .bash_profile
+    . .bash_profile
+
+We need some system packages:
+
+    brew install python --with-brewed-openssl
+    brew install gfortran
+
+Install [virtualenv](http://www.virtualenv.org/) and
+[virtualenvwrapper](http://virtualenvwrapper.readthedocs.org/) using
+[Virtualenv Burrito](https://github.com/brainsik/virtualenv-burrito):
+
+    curl -sL https://raw.github.com/brainsik/virtualenv-burrito/master/virtualenv-burrito.sh | $SHELL
+    source .venvburrito/startup.sh
+
+Create a virtual environment (named `programming-course`, but you could choose
+any name here):
+
+    mkvirtualenv programming-course
+
+Install Python packages:
+
+    pip install -r requirements.txt
--- a/README.md
+++ b/README.md
 Programming course
 ==================

-This repository contains material for the first installment (August 2013) of
-a programming course for scientists organised by the department of Human
+This repository contains material for the second installment (July 2014) of a
+programming course for scientists organised by the department of Human
 Genetics of the Leiden University Medical Center.

 The course is targeted at PhD students, Postdocs, or anyone willing to learn
@@ -23,35 +23,55 @@ Software installation
 See the instructions in `INSTALL.md`.


-Slides
------
+Materials
+---------

-The top-level directory contains slides for the following lessons.
+The top-level directory contains materials for the following lessons:

-1. [Welcome](http://nbviewer.ipython.org/urls/raw.github.com/LUMC/programming-course/master/welcome.ipynb)
-2. [Introduction to Python](http://nbviewer.ipython.org/urls/raw.github.com/LUMC/programming-course/master/python.ipynb)
-3. [Version control with Git](http://nbviewer.ipython.org/urls/raw.github.com/LUMC/programming-course/master/git.ipynb)
-4. [More Python Goodness](http://nbviewer.ipython.org/urls/raw.github.com/LUMC/programming-course/master/more-python.ipynb)
-5. [Working with NumPy arrays](http://nbviewer.ipython.org/urls/raw.github.com/LUMC/programming-course/master/numpy.ipynb)
-6. [Plotting with matplotlib](http://nbviewer.ipython.org/urls/raw.github.com/LUMC/programming-course/master/matplotlib.ipynb)
-7. [Object-oriented programming](http://nbviewer.ipython.org/urls/raw.github.com/LUMC/programming-course/master/classes.ipynb)
-8. [A sip of Biopython](http://nbviewer.ipython.org/urls/raw.github.com/LUMC/programming-course/master/biopython.ipynb)
+1. Welcome (slides) [view](http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/welcome.ipynb)
+2. Introduction to Python (slides) [view](http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/python.ipynb)
+3. More Python Goodness (notebook) [view](http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/more-python.ipynb)
+4. Working with NumPy arrays (slides) [view](http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/numpy.ipynb)
+5. Plotting with matplotlib (slides) [view](http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/matplotlib.ipynb)
+6. Object-oriented programming (slides) [view](http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/classes.ipynb)
+7. A sip of Biopython (notebook) [view](http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/biopython.ipynb)

-Note: These links are to one-page renderings on [IPython Notebook Viewer](http://nbviewer.ipython.org/), see below how to get the real slideshows.
+As indicated, some of the lessons are slideshows, whereas others are just
+notebooks we scroll through during class. The links above are all one-page
+static renderings on [IPython Notebook Viewer](http://nbviewer.ipython.org/).

+We also have a
+[repository with material for the assignments](https://git.lumc.nl/humgen/programming-course-assignments).

-Editing the slides
------------------

-The slides are simple IPython notebooks, you can edit them by starting a
-notebook server:
+Notebooks
+---------
+
+We apply some custom styling to the notebooks (e.g., body width, font), which
+is loaded in the last cell. This loads `styles/notebook.css` and
+`styles/notebook.js`.
+
+A variant `styles/notebook.css.small` is provided that is more suitable for
+use on low-resolution displays. To use it, manually change the reference to
+this file in the bottom cell, and rerun it.
+
+
+Slideshows
+----------
+
+The sources for the slideshows are also IPython notebooks and you can edit
+them by starting a notebook server:

    ipython notebook

 Choose *Slideshow* in the *Cell Toolbar* menu.

 Some aditional information on editing slides in the Notebook can be found
-here in [this presentation](http://www.slideviper.oquanta.info/tutorial/slideshow_tutorial_slides.html).
+here in
+[this presentation](http://www.slideviper.oquanta.info/tutorial/slideshow_tutorial_slides.html).
+
+We also apply some custom styling to the slideshows, which is loaded in the
+last cell.


 Live rendering of the slides
@@ -72,12 +92,17 @@ think it's usually not a good idea to rely on internet connectivity for your
 slides, so you can also place a copy of reveal.js on your local computer and
 specify the location like this:

-    --RevealHelpTransformer.url_prefix=reveal.js
+    --reveal-prefix reveal.js
+
+This would look for the reveal.js library in the `reveal.js` directory. A Git
+submodule is already setup for this, so you can just do:

-This would look for the reveal.js library in the reveal.js directory. You can
-download reveal.js by cloning its GitHub repository:
+    git submodule init
+    git submodule update

-    git clone https://github.com/hakimel/reveal.js.git
+(Unfortunately, there are other online dependencies such Font Awesome, so
+without an internet connection, not everything will look ok, but it will
+work.)

 Also, if you just want to compile the slides to HTML without serving them to
 your browser, leave out the `--post serve` argument.
--- a/exercises.ipynb
+++ b/exercises.ipynb
--- a/git.ipynb
+++ b/git.ipynb
--- a/requirements.txt
+++ b/requirements.txt
-ipython==2.1.0
-pyzmq==14.3.1
-tornado==3.2.2
+Cython==0.20.2
 Jinja2==2.7.3
+Markdown==2.4.1
 Pygments==1.6
 Sphinx==1.2.2
-Markdown==2.4.1
+biopython==1.64
+ipython==2.1.0
+matplotlib==1.3.1
 nose==1.3.3
 numpy==1.8.1
-matplotlib==1.3.1
-biopython==1.64
-pandas==0.14.0
 openpyxl==1.8.6
-seaborn==0.3.1
+pandas==0.14.0
+pyzmq==14.3.1
+scikit-learn==0.14.1
 scipy==0.14.0
+seaborn==0.3.1
+tornado==3.2.2
--- a/reveal.js @ 131c0068
+++ b/reveal.js @ 131c0068
+Subproject commit 131c00689a4c7a18e5c991fc8102347e4594b5d4
--- a/sequencer.ipynb
+++ b/sequencer.ipynb
--- a/sequencer_old.py
+++ b/sequencer_old.py
--- a/styles/custom.css
+++ b/styles/custom.css