added ArrayPloter and plotepiscan into Biotite

[ferrervi]

I am willing to generalize ArrayPlotter as much as possible but It was not immediately clear to me how to do that . Comments and help are very appreciated.
thanks

[padix-key]

Hi, thank you for contributing your work! I will probably need a few days for a proper review, but here are some initial comments:

• Your commits also include the Jupyter notebook checkpoint files (the ipynb_checkpints ones). Could you remove them? This can be done with git rm and giving the directory names (with additional -r option).
• The signalarray.py content is quite specific to the actual application you provide. Therefore, I would not put it into sequence.graphics, but put its functions directly into plotepiscan.py.

[ferrervi]

Hi, I incorporated your suggestions and updated the PR. Thank you.
🙂

[padix-key]

Thanks. I am on vacation for a week in a few days, so maybe I will not be able to review your contribution before it.

[padix-key]

For now I would mainly request only some style changes, for which I made suggestions. Please check if the line length is still OK after accepting the suggestions. Furthermore I would propose that you add pandas to environment.yml, so that your example can be run in the automatic build of the documentation. In addition you might also add yourself to CONTRIB.rst, if you like! I might bring up some additional points, as soon as I had time to execute you example.

[padix-key]

Hi, sorry for the delay, but finally I found time to finish the review. It looks mostly fine to me, there are mainly some small typos and docstring changes I would like to request.

[padix-key]

Fix rendering

Suggested change

	#

[padix-key]

But the following lines call set_color:

biotite/src/biotite/sequence/graphics/alignment.py

Lines 1003 to 1004 in b86594b

	if color is not None or cmap is not None:
	symbol_plotter.set_color(color=color, cmap=cmap)

I tested setting the color parameter in plot_alignment_array() in your example and it would lead to:

AttributeError: 'ArrayPlotter' object has no attribute 'set_color'

[padix-key]

Hi, thanks for implementing the suggestions. The final plot has still some issue with its colorbar. If you cannot reproduce it, I will have a look on on it.

[ferrervi]

I fixed the rendering of the final plot. It should be displaying correctly now. Thank you.

[padix-key]

Looks good to me. I would merge this PR as soon as the tests pass, if you are ready.