pairwise-alignment working directory is algorithms. When trying to import iab.algorithms, need to change back to project root about an-introduction-to-applied-bioinformatics

[gregcaporaso]

@2grep, you shouldn't need to do this if either installing with pip (recommended - see note here), or if the iab module is in your $PYTHONPATH. Either of those are preferred over directly editing the search path. I'll close this for now - if those options aren't working, please re-open and we can go from there.

Thanks for the input!

[2grep]

I see. I cloned it as

cd ~
git clone https://github.com/2grep/An-Introduction-To-Applied-Bioinformatics

so the correct $PYTHONPATH entry would be

/Users/2grep/An-Introduction-To-Applied-Bioinformatics

but I thought I was supposed to be going to the directory (which does exist)

/Users/2grep/An-Introduction-To-Applied-Bioinformatics/iab/

To be consistent with the project, the better git command would be

cd ~
git clone https://github.com/2grep/An-Introduction-To-Applied-Bioinformatics iab

so the correct $PYTHONPATH entry is

/Users/2grep/iab/

[gregcaporaso]

@2grep, either of those should work fine. It doesn't matter what you call the top-level directory, though it's typically named the same as the project (so in this case /Users/2grep/An-Introduction-To-Applied-Bioinformatics).