On Thu, Mar 1, 2012 at 8:14 AM, Mic <micta...@gmail.com> wrote: > Hello, > Is it possible to use PyPy with: > * BioPython > * Pysam > * Matplotlib > * etc > > If not than it might be good idea to get a support for it with help of > Google Summer of Code, because PyPy getting faster and faster.
Most of Biopython is working under PyPy (ignoring the C extensions, much like our situation under Jython). This was mentioned in the release notice for Bioython 1.59 - early adopters may be able to find other problems that we're not aware of from the unit tests: http://news.open-bio.org/news/2012/02/biopython-1-59-released/ I doubt there is enough work here alone to make a GSoC project. I'm not sure about pysam under PyPy - but I would be interested to know, because here interfacing with the samtools C code is the essence of pysam. My impression from the PyPy mailing lists calling external C libraries from PyPy is that this is another area of active work. For matplotlib, you would need NumPy under PyPy. That is an area of active work for the PyPy team who are currently trying to re-implement a pure-python version of NumPy which they are calling NumPyPy (originally it was called micronumpy) sufficient for other libraries using just the Python numpy API to run. A problem with this is many Python libraries also use the NumPy C API (e.g. bits of Biopython). See for example: http://morepypy.blogspot.com/2012/01/numpypy-status-update.html http://technicaldiscovery.blogspot.com/2011/10/thoughts-on-porting-numpy-to-pypy.html I suggest reading the PyPy and NumPy mailing list archives for more about this. Peter ------------------------------------------------------------------------------ Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ _______________________________________________ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
