FAQs and Known Issues

Q: My program does not terminate (i.e. it does not crash but runs forever) when I use pypet in multiprocessing mode in combination with matplotlib and savefig!?

A: Matplotlib uses numpy for linear algebra operations, these operations are often necessary when plotting. So, to solve the issues take a look at the next question.

Q: My program does not terminate (i.e. it does not crash but runs forever) when I use pypet in multiprocessing mode in combination with numpy and linalg.inv or some similar function!?

A: Numpy uses openBLAS (http://www.openblas.net/) to solve linear algebra operations. Yet, there are many issues with openBLAS and multiprocessing. To resolve this set the environment variable OPENBLAS_NUM_THREADS=1.

Q: GitPython does not work. If I specify my repository git_repository='./myrepo', pypet crashes with an AttributeError: ‘Repo’ object has no attribute ‘index’. What should I do?

A: You probably have an older version of GitPython (likely 0.1.7), install a newer one. If pip install GitPython still downloads the old version, try pip install --pre GitPython or if you simply want to upgrade use pip install --upgrade --pre GitPython.

Q: I am still using the old tree structure how can I update my hdf5files to the new one?

A: See Migrating from Old Tree-Structure to the New One

Q: If I create and environment in an IPython console everything becomes gibberish!?

A: Pypet will redirect STDOUT and STDERROR to files. Unfortunately, this messes with the IPython console. To avoid this simply disable logging of these two streams setting the log_stdout to False: env = Environment( ..., log_stdout=False, ...).

Q: Why can I no longer decide on the search strategy and what happened to v_check_uniqueness?

A: Both of them have been removed because they lead to inconsistencies. The child nodes of a particular group are not ordered, so tree traversal happens arbitrary. Thus, if you search for two nodes with the same name and same depth in the tree, the search result also becomes arbitrary. Thus, pypet will now always check if your search yields a unique result up to a particular depth. Accordingly, v_check_uniqueness is rendered obsolete. Likewise is depth first search because this automatic checking only works with breadth first tree traversal. Sorry for any inconvenience caused by this API change.