I am starting a project using Python to track, archive, assign and manage bioinformatics bugs. This software will be able to be integrated into project management software or stand alone.

  • How do you currently track bugs/assign bioinformatics bugs using freely available bioinformatics software/websites?
  • What are features that you like/dislike? What are features that you would like to see in a bioinformatics bug tracker?

I am a Biology student with basic/core Python skills.

  • $\begingroup$ Thanks for posting this question! Unfortunately, this question is unlikely to be answered by a single best response. This type of question is probably better suited to biostars.org $\endgroup$
    – winni2k
    May 17 at 7:33

Use IPython and activate the trace in the Python debugger as follows

%pdb 1 


%pdb on

to turn this off %pdb 0 or %pdf off

I do recommend using a formal IDE such as PyCharm or Visual Studio Code. The professional version of PyCharm is highly rated and within that use breakpoints . In Python3.7 there is supposed to be breakpoint() so you may not need an IDE, i.e. you set the breakpoint in your code using breakpoint(). In older versions of Python you can import this function via, import pdb; pdb.set_trace()

Finally check out PDB++ which is found here

Its important to note that experienced programmers often debug by simply inserting print() throughout their code and don't bother with an IDE


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