Re: [Biopython] [PATCH] Use https:// instead of git:// in examples
Markus Piotrowski <[email protected]>
| Newsgroups | gmane.comp.python.bio.general |
|---|---|
| Message-ID | <[email protected]> |
Am 04.10.2019 um 11:28 schrieb Adam Sjøgren: > > Speaking of stumbling blocks: I cloned the biopython repo to try and > make a small change (the .fetch() thing we talked about earlier). > > What I would usually do is to use "PYTHONPATH=path/to/checkout/of/library python" > while experimenting/developing, but this failed with a warning and an > error about something that couldn't be linked¹. > > How do you do development - do you make your changes and go through > "python setup.py install" before trying them out? > > > Best regards, > > Adam > > > ¹ The warning: > > /home/adsj/work/biopython/Bio/__init__.py:128: BiopythonWarning: You may be importing Biopython from inside the source tree. This is bad practice and might lead to downstream issues. In particular, you might encounter ImportErrors due to missing compiled C extensions. We recommend that you try running your code from outside the source tree. If you are outside the source tree then you have a setup.py file in an unexpected directory: /home/adsj/work/biopython. > format(_parent_dir), BiopythonWarning) The warning is mostly intended for end user who didn't properly installed their Biopython. As a developer you need to get used to it... > > The error: > > ... > from Bio.SeqIO import write > File "/home/adsj/work/biopython/Bio/SeqIO/__init__.py", line 390, in <module> > from Bio.Align import MultipleSeqAlignment > File "/home/adsj/work/biopython/Bio/Align/__init__.py", line 22, in <module> > from Bio.Align import _aligners > ImportError: cannot import name '_aligners' > Actually, the top-level import of _aligners, which should be a compiled C extension, is indeed a pain. We have this since a few versions and it makes testing of many modules, which actually do not use _aligners, more complicated. To get rid of it you need to compile Biopython. Best, Markus _______________________________________________ Biopython mailing list - [email protected] https://mailman.open-bio.org/mailman/listinfo/biopython