Restructuring

Moved notebooks to toplevel dir for easier opening. Created subdirs for
data and images. Harmonized all notebook opening slides.

README.md

@@ -7,3 +7,77 @@ Genetics of the Leiden University Medical Center.
 
 See the [Trac Wiki](https://humgenprojects.lumc.nl/trac/programming-course)
 for more information.
+
+
+Introduction to Python
+======================
+
+Slides are created as an IPython Notebook (IPython 1.0) and exported to
+reveal.js.
+
+
+Installation in a virtual environment
+-------------------------------------
+
+Required IPython version is 1.0 and you can install it from source in a
+virtual environment like this (on Debian Wheezy):
+
+    mkvirtualenv --no-site-packages programming-course
+
+We need IPython 1.0 which is not yet released, so we get it from GitHub:
+
+    pip install -e git+https://github.com/ipython/ipython#egg=ipython
+
+If IPython 1.0 is released, you can just do this:
+
+    pip install ipython
+
+Some additional packages:
+
+    pip install pyzmq tornado jinja2 pygments sphinx markdown
+    pip install numpy
+
+For matplotlib, we need some development and system packages:
+
+    sudo aptitude install libfreetype6-dev libpng12-dev python-cairo \
+      python-gtk2 python-gtk2-dev
+    mkdir -p $VIRTUAL_ENV/lib/python2.7/dist-packages
+    ln -s /usr/lib/python2.7/dist-packages/{glib,gobject,gtk-2.0*,pygtk.pth} \
+      $VIRTUAL_ENV/lib/python2.7/dist-packages/
+    ln -s /usr/lib/pymodules/python2.7/cairo \
+      $VIRTUAL_ENV/lib/python2.7/dist-packages/
+
+    pip install matplotlib
+    echo "backend : GTKCairo" >> ~/.matplotlib/matplotlibrc
+
+If you want the IPython qtconsole to work, I found the following snippet to
+take PyQT from system packages:
+
+    https://gist.github.com/jlesquembre/2042882
+
+We might want to use the same approach for the PyGTK/PyCAIRO stuff above.
+
+
+Editing the slides
+------------------
+
+    ipython notebook python-intro.ipynb
+
+Some aditional information on editing slides in the Notebook can be found
+here:
+
+http://www.slideviper.oquanta.info/tutorial/slideshow_tutorial_slides.html
+
+
+Exporting the slides
+--------------------
+
+This will create a set of slides to be viewed in a browser:
+
+    ipython nbconvert --FilesWriter.build_directory= --format reveal \
+      python-intro.ipynb
+
+As a reference for students, you could also create a full HTML dump:
+
+    ipython nbconvert --FilesWriter.build_directory= --format full_html \
+      python-intro.ipynb

version-control-git/version-control-git.ipynb → git-slides.ipynb

@@ -15,26 +15,18 @@
       }
      },
      "source": [
-      "\n",
-      "<span style=\"font-size: 200%; color: darkblue;\">Version Control with Git</span>\n",
+      "<span style=\"font-size: 200%\">Version control with Git</span>\n",
       "===\n",
       "\n",
-      "<br><br>\n",
-      "\n",
-      "Martijn Vermaat<br>\n",
-      "[m.vermaat.hg@lumc.nl](mailto:m.vermaat.hg@lumc.nl)\n",
+      "<br>\n",
       "\n",
-      "Zuotian Tatum<br>\n",
-      "[z.tatum@lumc.nl](mailto:z.tatum@lumc.nl)\n",
+      "[Zuotian Tatum](mailto:z.tatum@lumc.nl), [Martijn Vermaat](mailto:m.vermaat.hg@lumc.nl)\n",
       "\n",
+      "[Department of Human Genetics, Leiden University Medical Center](http://humgen.nl)\n",
       "\n",
-      "Department of Human Genetics, Leiden University Medical Center<br>\n",
-      "[humgen.nl](http://humgen.nl)\n",
+      "License: [Creative Commons Attribution 3.0 License (CC-by)](http://creativecommons.org/licenses/by/3.0)\n",
       "\n",
-      "Sources:\n",
-      "http://git-scm.com/\n",
-      "https://teach.github.com/\n",
-      "http://try.github.io/"
+      "Sources: [Git homepage](http://git-scm.com/), [GitHub Teaching](https://teach.github.com/), [Try Git](http://try.github.io/)"
      ]
     },
     {
@@ -106,7 +98,7 @@
       "Local VCS\n",
       "---\n",
       "\n",
-      "<img src=\"files/local_vcs.png\">"
+      "<img src=\"files/images/local_vcs.png\">"
      ]
     },
     {
@@ -122,7 +114,7 @@
       "\n",
       "Centralized VCS\n",
       "---\n",
-      "<img src=\"files/centralized_vcs.png\">"
+      "<img src=\"files/images/centralized_vcs.png\">"
      ]
     },
     {
@@ -138,7 +130,7 @@
       "\n",
       "Distributed VCS\n",
       "---\n",
-      "<img src=\"files/distributed_vcs.png\">"
+      "<img src=\"files/images/distributed_vcs.png\">"
      ]
     },
     {
@@ -216,7 +208,7 @@
       "Git\n",
       "===\n",
       "\n",
-      "To itialize a Git repository\n",
+      "To initialize a Git repository\n",
       "---"
      ]
     },
@@ -654,7 +646,7 @@
       }
      },
      "source": [
-      "Github and Gitlab\n",
+      "GitHub and Gitlab\n",
       "===\n",
       "\n",
       "TODO."

python-intro/README

-Introduction to Python
-======================
-
-Slides are created as an IPython Notebook (IPython 1.0) and exported to
-reveal.js.
-
-
-Installation in a virtual environment
--------------------------------------
-
-Required IPython version is 1.0 and you can install it from source in a
-virtual environment like this (on Debian Wheezy):
-
-    mkvirtualenv --no-site-packages programming-course
-
-We need IPython 1.0 which is not yet released, so we get it from GitHub:
-
-    pip install -e git+https://github.com/ipython/ipython#egg=ipython
-
-If IPython 1.0 is released, you can just do this:
-
-    pip install ipython
-
-Some additional packages:
-
-    pip install pyzmq tornado jinja2 pygments sphinx markdown
-    pip install numpy
-
-For matplotlib, we need some development and system packages:
-
-    sudo aptitude install libfreetype6-dev libpng12-dev python-cairo \
-      python-gtk2 python-gtk2-dev
-    mkdir -p $VIRTUAL_ENV/lib/python2.7/dist-packages
-    ln -s /usr/lib/python2.7/dist-packages/{glib,gobject,gtk-2.0*,pygtk.pth} \
-      $VIRTUAL_ENV/lib/python2.7/dist-packages/
-    ln -s /usr/lib/pymodules/python2.7/cairo \
-      $VIRTUAL_ENV/lib/python2.7/dist-packages/
-
-    pip install matplotlib
-    echo "backend : GTKCairo" >> ~/.matplotlib/matplotlibrc
-
-If you want the IPython qtconsole to work, I found the following snippet to
-take PyQT from system packages:
-
-    https://gist.github.com/jlesquembre/2042882
-
-We might want to use the same approach for the PyGTK/PyCAIRO stuff above.
-
-
-Editing the slides
-------------------
-
-    ipython notebook python-intro.ipynb
-
-Some aditional information on editing slides in the Notebook can be found
-here:
-
-http://www.slideviper.oquanta.info/tutorial/slideshow_tutorial_slides.html
-
-
-Exporting the slides
---------------------
-
-This will create a set of slides to be viewed in a browser:
-
-    ipython nbconvert --FilesWriter.build_directory= --format reveal \
-      python-intro.ipynb
-
-As a reference for students, you could also create a full HTML dump:
-
-    ipython nbconvert --FilesWriter.build_directory= --format full_html \
-      python-intro.ipynb

python-intro/python-intro.ipynb → python-slides.ipynb

@@ -7,31 +7,24 @@
  "worksheets": [
   {
    "cells": [
-    {
-     "cell_type": "heading",
-     "level": 1,
-     "metadata": {
-      "slideshow": {
-       "slide_type": "slide"
-      }
-     },
-     "source": [
-      "<a><span style=\"font-size: 200%\">Introduction to NumPy</span></a>"
-     ]
-    },
     {
      "cell_type": "markdown",
      "metadata": {
       "slideshow": {
-       "slide_type": "-"
+       "slide_type": "slide"
       }
      },
      "source": [
-      "Martijn Vermaat<br>\n",
-      "[m.vermaat.hg@lumc.nl](mailto:m.vermaat.hg@lumc.nl)\n",
+      "<span style=\"font-size: 200%\">Introduction to Python</span>\n",
+      "===\n",
+      "\n",
+      "<br>\n",
+      "\n",
+      "[Martijn Vermaat](mailto:m.vermaat.hg@lumc.nl)\n",
+      "\n",
+      "[Department of Human Genetics, Leiden University Medical Center](http://humgen.nl)\n",
       "\n",
-      "Department of Human Genetics, Leiden University Medical Center<br>\n",
-      "[humgen.nl](http://humgen.nl)\n",
+      "Based on: [Python Scientific Lecture Notes](http://scipy-lectures.github.io/)\n",
       "\n",
       "License: [Creative Commons Attribution 3.0 License (CC-by)](http://creativecommons.org/licenses/by/3.0)"
      ]
@@ -3027,7 +3020,7 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "for line in open('short_file.txt'):\n",
+      "for line in open('data/short_file.txt'):\n",
       "    print line"
      ],
      "language": "python",