fjossinet/rna-science-toolbox

A platform to do RNA science

Hi there 👋

My name is Fabrice Jossinet. I'm biologist, bioinformatician & assistant professor at the University of Strasbourg, France.

I'm creating visual tools to explore and study 2D and 3D architectures of RNA molecules.

Languages used: Java, Kotlin, JavaFX, Python.

Some screenshots of my current highly active project RNArtist:

rna-science-toolbox's Issues

python 3 compatibility for print statements in fabfile.py

Hello,

I am using python 3.7.10:

python --version
Python 3.7.10

When I attempt to run "fab python" in the top level directory, I get the following error:

Traceback (most recent call last):
File "/Users/patrickheenan/opt/anaconda3/envs/assemble2/lib/python3.7/site-packages/fabric/main.py", line 673, in main
    docstring, callables, default = load_fabfile(fabfile)
File "/Users/patrickheenan/opt/anaconda3/envs/assemble2/lib/python3.7/site-packages/fabric/main.py", line 174, in load_fabfile
    imported = importer(os.path.splitext(fabfile)[0])
File "/Users/patrickheenan/scratch/RNA-Science-Toolbox/fabfile.py", line 40
    print "You need to install the following Python packages:"

SyntaxError: Missing parentheses in call to 'print'. 
Did you mean print("You need to install the following Python packages:")?

Per the error messages, the problem appears to be a few missing parenthesis. I've attached a "fabfile.py.zip" which runs properly, as well as a screenshot of the diff. If you include these changes, running "fab python" will work for python 3.7.10.

fabfile.py.zip

Improving installation instructions

Hi Fabrice,

Great work on packaging everything in a virtual box, way to go!

Just wanted to point out that if you do vagrant ssh and then pyrna_tests.py (as suggested in the README) the command will not be found and even when one locates pyrna_tests.py and runs it directly the script won't be able to import PyRNA modules because it won't be able to find pyrna.db etc. Same with running server.py.

You might want to update Readme and play with PYTHONPATH or maybe there is another solution.

Anton