From 9d2bf3642b2391381672a0d8c7db835683a7d719 Mon Sep 17 00:00:00 2001
From: mlefter <m.lefter@lumc.nl>
Date: Fri, 15 Sep 2017 14:23:15 +0200
Subject: [PATCH] Moved into a special folder the 2014 course session
materials.
---
.../2014_july/01 - Welcome.ipynb | 0
.../02 - Introduction to Python (1).ipynb | 0
.../02 - Introduction to Python (2).ipynb | 0
.../02 - Introduction to Python (3).ipynb | 0
.../03 - More Python goodness (1).ipynb | 0
.../03 - More Python goodness (2).ipynb | 0
.../04 - Working with NumPy arrays.ipynb | 0
.../2014_july/05 - IPython Notebook.ipynb | 0
.../06 - Plotting with matplotlib.ipynb | 0
.../2014_july/07 - Painting Pandas.ipynb | 0
.../08 - Object-oriented programming.ipynb | 0
.../09 - A sip of Biopython (1).ipynb | 0
.../09 - A sip of Biopython (2).ipynb | 0
.../2014_july/INSTALL.md | 0
past_sessions/2014_july/README.md | 132 ++++++++++++++++++
.../2014_july/person.py | 0
.../More_goodness_progression.ipynb | 0
.../2014_july/solutions}/matplotlib.ipynb | 0
.../solutions}/more_python_seq_toolbox.py | 0
.../2014_july/solutions}/notebook.ipynb | 0
.../2014_july/solutions}/numpy.ipynb | 0
.../solutions}/python_01_bottles_of_beer.py | 0
.../solutions}/python_02_repeat_structure.py | 0
.../solutions}/python_03_combining_lists.py | 0
.../solutions}/python_04_dictionaries.py | 0
.../solutions}/python_05_kmer_counting.py | 0
.../python_08_scientific_calculator.py | 0
reveal.js | 2 +-
28 files changed, 133 insertions(+), 1 deletion(-)
rename 01 - Welcome.ipynb => past_sessions/2014_july/01 - Welcome.ipynb (100%)
rename 02 - Introduction to Python (1).ipynb => past_sessions/2014_july/02 - Introduction to Python (1).ipynb (100%)
rename 02 - Introduction to Python (2).ipynb => past_sessions/2014_july/02 - Introduction to Python (2).ipynb (100%)
rename 02 - Introduction to Python (3).ipynb => past_sessions/2014_july/02 - Introduction to Python (3).ipynb (100%)
rename 03 - More Python goodness (1).ipynb => past_sessions/2014_july/03 - More Python goodness (1).ipynb (100%)
rename 03 - More Python goodness (2).ipynb => past_sessions/2014_july/03 - More Python goodness (2).ipynb (100%)
rename 04 - Working with NumPy arrays.ipynb => past_sessions/2014_july/04 - Working with NumPy arrays.ipynb (100%)
rename 05 - IPython Notebook.ipynb => past_sessions/2014_july/05 - IPython Notebook.ipynb (100%)
rename 06 - Plotting with matplotlib.ipynb => past_sessions/2014_july/06 - Plotting with matplotlib.ipynb (100%)
rename 07 - Painting Pandas.ipynb => past_sessions/2014_july/07 - Painting Pandas.ipynb (100%)
rename 08 - Object-oriented programming.ipynb => past_sessions/2014_july/08 - Object-oriented programming.ipynb (100%)
rename 09 - A sip of Biopython (1).ipynb => past_sessions/2014_july/09 - A sip of Biopython (1).ipynb (100%)
rename 09 - A sip of Biopython (2).ipynb => past_sessions/2014_july/09 - A sip of Biopython (2).ipynb (100%)
rename INSTALL.md => past_sessions/2014_july/INSTALL.md (100%)
create mode 100644 past_sessions/2014_july/README.md
rename person.py => past_sessions/2014_july/person.py (100%)
rename {solutions => past_sessions/2014_july/solutions}/More_goodness_progression.ipynb (100%)
rename {solutions => past_sessions/2014_july/solutions}/matplotlib.ipynb (100%)
rename {solutions => past_sessions/2014_july/solutions}/more_python_seq_toolbox.py (100%)
rename {solutions => past_sessions/2014_july/solutions}/notebook.ipynb (100%)
rename {solutions => past_sessions/2014_july/solutions}/numpy.ipynb (100%)
rename {solutions => past_sessions/2014_july/solutions}/python_01_bottles_of_beer.py (100%)
rename {solutions => past_sessions/2014_july/solutions}/python_02_repeat_structure.py (100%)
rename {solutions => past_sessions/2014_july/solutions}/python_03_combining_lists.py (100%)
rename {solutions => past_sessions/2014_july/solutions}/python_04_dictionaries.py (100%)
rename {solutions => past_sessions/2014_july/solutions}/python_05_kmer_counting.py (100%)
rename {solutions => past_sessions/2014_july/solutions}/python_08_scientific_calculator.py (100%)
diff --git a/01 - Welcome.ipynb b/past_sessions/2014_july/01 - Welcome.ipynb
similarity index 100%
rename from 01 - Welcome.ipynb
rename to past_sessions/2014_july/01 - Welcome.ipynb
diff --git a/02 - Introduction to Python (1).ipynb b/past_sessions/2014_july/02 - Introduction to Python (1).ipynb
similarity index 100%
rename from 02 - Introduction to Python (1).ipynb
rename to past_sessions/2014_july/02 - Introduction to Python (1).ipynb
diff --git a/02 - Introduction to Python (2).ipynb b/past_sessions/2014_july/02 - Introduction to Python (2).ipynb
similarity index 100%
rename from 02 - Introduction to Python (2).ipynb
rename to past_sessions/2014_july/02 - Introduction to Python (2).ipynb
diff --git a/02 - Introduction to Python (3).ipynb b/past_sessions/2014_july/02 - Introduction to Python (3).ipynb
similarity index 100%
rename from 02 - Introduction to Python (3).ipynb
rename to past_sessions/2014_july/02 - Introduction to Python (3).ipynb
diff --git a/03 - More Python goodness (1).ipynb b/past_sessions/2014_july/03 - More Python goodness (1).ipynb
similarity index 100%
rename from 03 - More Python goodness (1).ipynb
rename to past_sessions/2014_july/03 - More Python goodness (1).ipynb
diff --git a/03 - More Python goodness (2).ipynb b/past_sessions/2014_july/03 - More Python goodness (2).ipynb
similarity index 100%
rename from 03 - More Python goodness (2).ipynb
rename to past_sessions/2014_july/03 - More Python goodness (2).ipynb
diff --git a/04 - Working with NumPy arrays.ipynb b/past_sessions/2014_july/04 - Working with NumPy arrays.ipynb
similarity index 100%
rename from 04 - Working with NumPy arrays.ipynb
rename to past_sessions/2014_july/04 - Working with NumPy arrays.ipynb
diff --git a/05 - IPython Notebook.ipynb b/past_sessions/2014_july/05 - IPython Notebook.ipynb
similarity index 100%
rename from 05 - IPython Notebook.ipynb
rename to past_sessions/2014_july/05 - IPython Notebook.ipynb
diff --git a/06 - Plotting with matplotlib.ipynb b/past_sessions/2014_july/06 - Plotting with matplotlib.ipynb
similarity index 100%
rename from 06 - Plotting with matplotlib.ipynb
rename to past_sessions/2014_july/06 - Plotting with matplotlib.ipynb
diff --git a/07 - Painting Pandas.ipynb b/past_sessions/2014_july/07 - Painting Pandas.ipynb
similarity index 100%
rename from 07 - Painting Pandas.ipynb
rename to past_sessions/2014_july/07 - Painting Pandas.ipynb
diff --git a/08 - Object-oriented programming.ipynb b/past_sessions/2014_july/08 - Object-oriented programming.ipynb
similarity index 100%
rename from 08 - Object-oriented programming.ipynb
rename to past_sessions/2014_july/08 - Object-oriented programming.ipynb
diff --git a/09 - A sip of Biopython (1).ipynb b/past_sessions/2014_july/09 - A sip of Biopython (1).ipynb
similarity index 100%
rename from 09 - A sip of Biopython (1).ipynb
rename to past_sessions/2014_july/09 - A sip of Biopython (1).ipynb
diff --git a/09 - A sip of Biopython (2).ipynb b/past_sessions/2014_july/09 - A sip of Biopython (2).ipynb
similarity index 100%
rename from 09 - A sip of Biopython (2).ipynb
rename to past_sessions/2014_july/09 - A sip of Biopython (2).ipynb
diff --git a/INSTALL.md b/past_sessions/2014_july/INSTALL.md
similarity index 100%
rename from INSTALL.md
rename to past_sessions/2014_july/INSTALL.md
diff --git a/past_sessions/2014_july/README.md b/past_sessions/2014_july/README.md
new file mode 100644
index 0000000..75c9c3e
--- /dev/null
+++ b/past_sessions/2014_july/README.md
@@ -0,0 +1,132 @@
+Programming course
+==================
+
+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
+how to program in Python. Students are assumed to have some experience with
+programming, but not necessarily in Python, and the UNIX shell.
+
+The program consists of four mornings with lessons and some assignments to
+be done in your own time (i.e., during the afternoons).
+
+See the
+[Trac Wiki](https://humgenprojects.lumc.nl/trac/humgenprojects/wiki/ProgrammingCourse)
+for more information.
+
+Software installation
+---------------------
+
+See the instructions in `INSTALL.md`.
+
+
+Materials
+---------
+
+The top-level directory contains materials for the following lessons:
+
+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 ([slides][lesson_04])
+5. IPython Notebook ([notebook][lesson_05])
+6. Plotting with matplotlib ([notebook][lesson_06])
+7. Painting Pandas ([slides][lesson_07])
+8. Object-oriented programming ([slides][lesson_08])
+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/courses/programming-course/raw/master/past_sessions/2014_july/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_04]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/04%20-%20Working%20with%20NumPy%20arrays.ipynb
+[lesson_05]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/05%20-%20IPython%20Notebook.ipynb
+[lesson_06]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/06%20-%20Plotting%20with%20matplotlib.ipynb
+[lesson_07]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/07%20-%20Painting%20Pandas.ipynb
+[lesson_08]: http://nbviewer.ipython.org/urls/git.lumc.nl/humgen/programming-course/raw/master/08%20-%20Object-oriented%20programming.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
+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).
+
+
+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).
+
+We also apply some custom styling to the slideshows, which is loaded in the
+last cell.
+
+
+Live rendering of the slides
+----------------------------
+
+You can use nbconvert to convert the slides to HTML and serve them. For
+example:
+
+ ipython nbconvert --to slides --post serve numpy.ipynb
+
+This will open the slides in a new browser window. If you don't want that, add
+this argument:
+
+ --ServePostProcessor.open_in_browser=False
+
+To serve on another IP address than the default 127.0.0.1, use the `ip`
+configuration of the serve postprocessing. For example, to listen on all IP
+addresses:
+
+ --ServePostProcessor.ip=0.0.0.0
+
+Changing the port can be done similarly with `port`.
+
+By default, the reveal.js library is loaded over the internet from a CDN. I
+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:
+
+ --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:
+
+ git submodule init
+ git submodule update
+
+(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.
diff --git a/person.py b/past_sessions/2014_july/person.py
similarity index 100%
rename from person.py
rename to past_sessions/2014_july/person.py
diff --git a/solutions/More_goodness_progression.ipynb b/past_sessions/2014_july/solutions/More_goodness_progression.ipynb
similarity index 100%
rename from solutions/More_goodness_progression.ipynb
rename to past_sessions/2014_july/solutions/More_goodness_progression.ipynb
diff --git a/solutions/matplotlib.ipynb b/past_sessions/2014_july/solutions/matplotlib.ipynb
similarity index 100%
rename from solutions/matplotlib.ipynb
rename to past_sessions/2014_july/solutions/matplotlib.ipynb
diff --git a/solutions/more_python_seq_toolbox.py b/past_sessions/2014_july/solutions/more_python_seq_toolbox.py
similarity index 100%
rename from solutions/more_python_seq_toolbox.py
rename to past_sessions/2014_july/solutions/more_python_seq_toolbox.py
diff --git a/solutions/notebook.ipynb b/past_sessions/2014_july/solutions/notebook.ipynb
similarity index 100%
rename from solutions/notebook.ipynb
rename to past_sessions/2014_july/solutions/notebook.ipynb
diff --git a/solutions/numpy.ipynb b/past_sessions/2014_july/solutions/numpy.ipynb
similarity index 100%
rename from solutions/numpy.ipynb
rename to past_sessions/2014_july/solutions/numpy.ipynb
diff --git a/solutions/python_01_bottles_of_beer.py b/past_sessions/2014_july/solutions/python_01_bottles_of_beer.py
similarity index 100%
rename from solutions/python_01_bottles_of_beer.py
rename to past_sessions/2014_july/solutions/python_01_bottles_of_beer.py
diff --git a/solutions/python_02_repeat_structure.py b/past_sessions/2014_july/solutions/python_02_repeat_structure.py
similarity index 100%
rename from solutions/python_02_repeat_structure.py
rename to past_sessions/2014_july/solutions/python_02_repeat_structure.py
diff --git a/solutions/python_03_combining_lists.py b/past_sessions/2014_july/solutions/python_03_combining_lists.py
similarity index 100%
rename from solutions/python_03_combining_lists.py
rename to past_sessions/2014_july/solutions/python_03_combining_lists.py
diff --git a/solutions/python_04_dictionaries.py b/past_sessions/2014_july/solutions/python_04_dictionaries.py
similarity index 100%
rename from solutions/python_04_dictionaries.py
rename to past_sessions/2014_july/solutions/python_04_dictionaries.py
diff --git a/solutions/python_05_kmer_counting.py b/past_sessions/2014_july/solutions/python_05_kmer_counting.py
similarity index 100%
rename from solutions/python_05_kmer_counting.py
rename to past_sessions/2014_july/solutions/python_05_kmer_counting.py
diff --git a/solutions/python_08_scientific_calculator.py b/past_sessions/2014_july/solutions/python_08_scientific_calculator.py
similarity index 100%
rename from solutions/python_08_scientific_calculator.py
rename to past_sessions/2014_july/solutions/python_08_scientific_calculator.py
diff --git a/reveal.js b/reveal.js
index 131c006..43eada7 160000
--- a/reveal.js
+++ b/reveal.js
@@ -1 +1 @@
-Subproject commit 131c00689a4c7a18e5c991fc8102347e4594b5d4
+Subproject commit 43eada79901830702bd40dce857831aef8e76759
--
GitLab