vk doesnot work on mac

[andreyurch]

tests-MBP:TEST testaccount$ vk Traceback (most recent call last): File "/usr/local/bin/vk", line 5, in from pkg_resources import load_entry_point File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/init.py", line 3095, in @_call_aside File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/init.py", line 3081, in _call_aside f(*args, **kwargs) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/init.py", line 3108, in _initialize_master_working_set working_set = WorkingSet._build_master() File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/init.py", line 660, in _build_master return cls._build_from_requirements(requires) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/init.py", line 673, in _build_from_requirements dists = ws.resolve(reqs, Environment()) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources/init.py", line 851, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (scipy 0.13.0b1 (/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python), Requirement.parse('scipy>=0.13.3'), set(['yahmm']))

[danielecook]

Hi Andrey - It looks like you have a pretty old version of scipy (0.13.0?)

Can you try:

pip install scipy --upgrade

And give it another go?

[andreyurch]

Hi Daniel, The version is OK: import scipy

scipy.version '1.0.0'

Probably some problems with system environment which can see only the old version?

Thank you!

[danielecook]

Can you send me the output of:

pip freeze

?

[andreyurch]

Please:

pip freeze args==0.1.0 awesome-slugify==1.6.5 backports.functools-lru-cache==1.4 biopython==1.70 certifi==2017.11.5 chardet==3.0.4 clint==0.5.1 cycler==0.10.0 Cython==0.27.3 cyvcf2==0.8.3 decorator==4.1.2 docopt==0.6.2 idna==2.6 intervaltree==2.1.0 Jinja2==2.10 MarkupSafe==1.0 matplotlib==2.1.0 networkx==1.11 numpy==1.13.3 pyparsing==2.2.0 python-dateutil==2.6.1 pytz==2017.3 regex==2017.11.9 requests==2.18.4 scipy==1.0.0 six==1.11.0 sortedcontainers==1.5.7 subprocess32==3.2.7 tabulate==0.8.1 Unidecode==0.4.21 urllib3==1.22 VCF-kit==0.1.6 yahmm==1.1.2

[danielecook]

The issue here is that newer versions of scipy are not compatible with yahmm unfortunately. Until I find time to find an appropriate alternative for yahmm - i'm afraid users will have to downgrade yahmm.