Merge remote-tracking branch 'course/master'

01 - Welcome.ipynb

@@ -2,7 +2,7 @@
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   "celltoolbar": "Slideshow",
   "name": "",
-  "signature": "sha256:6c570ac428c0fbfa0115d6c05d52e3c05410cd3de42ae35e7ee7feb0f435a641"
+  "signature": "sha256:a016c0815699df8dae5155425df47f34e59e2aac64d4fa7f4edaa9c43a33ad3f"
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  "nbformat": 3,
  "nbformat_minor": 0,
@@ -259,8 +259,8 @@
       {
        "html": [
         "<style>/* Remove the vertical scrollbar added by nbconvert. */\n",
-        "html {\n",
-        "  overflow-y: hidden;\n",
+        ".reveal {\n",
+        "  overflow: hidden;\n",
         "}\n",
         "\n",
         "/* Workaround some highlight.js bugs in language autodetection. */\n",
@@ -287,7 +287,7 @@
        "output_type": "pyout",
        "prompt_number": 1,
        "text": [
-        "<IPython.core.display.HTML at 0x33caa50>"
+        "<IPython.core.display.HTML at 0x1f71a50>"
        ]
       }
      ],

02 - Introduction to Python (1).ipynb

@@ -2,7 +2,7 @@
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   "name": "",
-  "signature": "sha256:06632e3aab84ba95070db9bd6588d5a6fa8e7440ebe85cac2ce1a3c91911db47"
+  "signature": "sha256:48b5e4d61de5dfa8cebfe8fe0c78f8587586ee15c8ea50fe5c1d67f8ea5caa4a"
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  "nbformat": 3,
  "nbformat_minor": 0,
@@ -893,8 +893,8 @@
       {
        "html": [
         "<style>/* Remove the vertical scrollbar added by nbconvert. */\n",
-        "html {\n",
-        "  overflow-y: hidden;\n",
+        ".reveal {\n",
+        "  overflow: hidden;\n",
         "}\n",
         "\n",
         "/* Workaround some highlight.js bugs in language autodetection. */\n",
@@ -919,13 +919,13 @@
        ],
        "metadata": {},
        "output_type": "pyout",
-       "prompt_number": 25,
+       "prompt_number": 1,
        "text": [
-        "<IPython.core.display.HTML at 0x7f39d4043c90>"
+        "<IPython.core.display.HTML at 0x3463a50>"
        ]
       }
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-     "prompt_number": 25
+     "prompt_number": 1
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    ],
    "metadata": {}

02 - Introduction to Python (2).ipynb

@@ -2,7 +2,7 @@
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   "name": "",
-  "signature": "sha256:57d29de0d77287096e49247676a76ea06e3730e1e5f819ecfc6b4b3f6d85e4e9"
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  "nbformat_minor": 0,
@@ -1842,8 +1842,8 @@
       {
        "html": [
         "<style>/* Remove the vertical scrollbar added by nbconvert. */\n",
-        "html {\n",
-        "  overflow-y: hidden;\n",
+        ".reveal {\n",
+        "  overflow: hidden;\n",
         "}\n",
         "\n",
         "/* Workaround some highlight.js bugs in language autodetection. */\n",
@@ -1868,13 +1868,13 @@
        ],
        "metadata": {},
        "output_type": "pyout",
-       "prompt_number": 60,
+       "prompt_number": 1,
        "text": [
-        "<IPython.core.display.HTML at 0x24f0cd0>"
+        "<IPython.core.display.HTML at 0x1873a50>"
        ]
       }
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-     "prompt_number": 60
+     "prompt_number": 1
     }
    ],
    "metadata": {}

02 - Introduction to Python (3).ipynb

@@ -2,7 +2,7 @@
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   "name": "",
-  "signature": "sha256:74676c0cad25c0954fa4f8352dda1c9010bd747de1752b4ccc667d9132427fdd"
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  "nbformat_minor": 0,
@@ -851,8 +851,8 @@
       {
        "html": [
         "<style>/* Remove the vertical scrollbar added by nbconvert. */\n",
-        "html {\n",
-        "  overflow-y: hidden;\n",
+        ".reveal {\n",
+        "  overflow: hidden;\n",
         "}\n",
         "\n",
         "/* Workaround some highlight.js bugs in language autodetection. */\n",
@@ -877,13 +877,13 @@
        ],
        "metadata": {},
        "output_type": "pyout",
-       "prompt_number": 24,
+       "prompt_number": 1,
        "text": [
-        "<IPython.core.display.HTML at 0x1965a50>"
+        "<IPython.core.display.HTML at 0x2e0ea50>"
        ]
       }
      ],
-     "prompt_number": 24
+     "prompt_number": 1
     }
    ],
    "metadata": {}

03 - More Python goodness (1).ipynb

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   "name": "",
-  "signature": "sha256:70bfb8ad86899454fd23b5db2e3184de272ec729cf9cdc477127a1e7d7f0f60b"
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  "nbformat_minor": 0,
@@ -33,7 +33,12 @@
       "3. [String methods](#stringmethods)\n",
       "4. [Comments and docstrings](#docstrings)\n",
       "5. [Detour: PEP8 and other PEPs](#peps)\n",
-      "6. [Errors and exceptions](#exceptions)"
+      "6. [Errors and exceptions](#exceptions)\n",
+      "7. Working with modules\n",
+      "8. Examples from the standard library\n",
+      "9. Reading and writing files\n",
+      "10. Assignment: Finding the most common 7-mer in a FASTA file\n",
+      "11. Further reading"
      ]
     },
     {

03 - More Python goodness (2).ipynb

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  "metadata": {
   "name": "",
-  "signature": "sha256:449f59d356a6f72e179ef39e58da7265eae4ecb8253da3c52cc6b41277fe2909"
+  "signature": "sha256:0892ec60b3a9f342f46559142d68b8c002cd1f86043508cf29b9fb892b41d031"
  },
  "nbformat": 3,
  "nbformat_minor": 0,
@@ -28,6 +28,12 @@
      "source": [
       "## Table of contents\n",
       "\n",
+      "1. Working with scripts\n",
+      "2. The standard library\n",
+      "3. String methods\n",
+      "4. Comments and docstrings\n",
+      "5. Detour: PEP8 and other PEPs\n",
+      "6. Errors and exceptions\n",
       "7. [Working with modules](#modules)\n",
       "8. [Examples from the standard library](#stdlib-examples)\n",
       "9. [Reading and writing files](#io)\n",

INSTALL.md

@@ -23,8 +23,8 @@ 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
+      curl gfortran git libblas-dev libfreetype6-dev liblapack-dev
+      libpng12-dev python-cairo python-gtk2 python-gtk2-dev python-qt4
 
 From here on, everything is local for the current user.
 

README.md

@@ -28,13 +28,26 @@ Materials
 
 The top-level directory contains materials for the following lessons:
 
-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)
+1. Welcome ([slides][lesson_01])
+2. Introduction to Python ([slides 1][lesson_02_01], [slides 2][lesson_02_02],
+   [slides 3][lesson_02_03])
+3. More Python Goodness ([notebook 1][lesson_03_01], [notebook 2][lesson_03_02])
+4. Working with NumPy arrays
+5. IPython Notebook ([notebook][lesson_05])
+6. Plotting with matplotlib
+7. Python for data analysis
+8. Object-oriented programming
+9. A sip of Biopython ([notebook 1][lesson_09_01], [notebook 2][lesson_09_02])
+
+[lesson_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/01%20-%20Welcome.ipynb
+[lesson_02_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/02%20-%20Introduction%20to%20Python%20(1).ipynb
+[lesson_02_02]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/02%20-%20Introduction%20to%20Python%20(2).ipynb
+[lesson_02_03]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/02%20-%20Introduction%20to%20Python%20(3).ipynb
+[lesson_03_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/03%20-%20More%20Python%20goodness%20(1).ipynb
+[lesson_03_02]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/03%20-%20More%20Python%20goodness%20(2).ipynb
+[lesson_05]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/05%20-%20IPython%20Notebook.ipynb
+[lesson_09_01]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/09%20-%20A%20sip%20of%20Biopython%20(1).ipynb
+[lesson_09_02]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/09%20-%20A%20sip%20of%20Biopython%20(2).ipynb
 
 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

styles/custom.css

 /* Remove the vertical scrollbar added by nbconvert. */
-html {
-  overflow-y: hidden;
+.reveal {
+  overflow: hidden;
 }
 
 /* Workaround some highlight.js bugs in language autodetection. */