I’m wondering if it’s possible to populate sys.argv (or some other structure) with command line arguments in a jupyter/ipython notebook, similar to how it’s done through a python script.
I would like to use an IPython notebook as a way to interactively analyze some genome charts I am making with Biopython’s GenomeDiagram module. While there is extensive documentation on how to use matplotlib to get graphs inline in IPython notebook, GenomeDiagram uses the ReportLab toolkit which I don’t think is supported for inline graphing in IPython.
I am using IPython with --pylab=inline and would sometimes like to quickly switch to the interactive, zoomable matplotlib GUI for viewing plots (the one that pops up when you plot something in a terminal Python console). How could I do that? Preferably without leaving or restarting my notebook.
I’m trying to set a good environnement for doing some scientific stuff with python. To do so, I installed Jupyter & miniconda.
Environment: Python 2.7, Matplotlib 1.3, IPython notebook 1.1, Linux, and Chrome. The code is in one single input cell, using --pylab=inline.
In the answers to how to dynamically update a plot in a loop in ipython notebook (within one cell), an example is given of how to dynamically update a plot inside a Jupyter notebook within a Python loop. However, this works by destroying and re-creating the plot on every iteration, and a comment in one of the threads notes that this situation can be improved by using the new-ish %matplotlib nbagg magic, which provides an interactive figure embedded in the notebook, rather than a static image.
As I know, %debug magic can do debug within one cell.
How do I execute a bash command from Ipython/Jupyter notebook passing the value of a python variable as an argument like in this example:
I would like to include image in a jupyter notebook.
IPython Notebook comes with nbconvert, which can export notebooks to other formats. But how do I convert text in the opposite direction? I ask because I already have materials, and a good workflow, in a different format, but I would like to take advantage of Notebook’s interactive environment.