Issue with SourceTracker2 installation

[lizdasa]

Hello,

I am trying to install sourcetracker in a cluster computer and I am getting an error after I test if my installation was successful.

What I did:

conda create -n sourcetracker2 -c biocore python=3.5 numpy scipy scikit-bio biom-format h5py hdf5 seaborn conda activate sourcetracker2 conda install -c bioconda sourcetracker sourcetracker2 gibbs --help ****after this I get the following error:

Traceback (most recent call last): File "/storage/home/hcoda1/6/ldavila3/.conda/envs/sourcetracker2/bin/sourcetracker2", line 6, in from sourcetracker._cli import cli File "/storage/home/hcoda1/6/ldavila3/.conda/envs/sourcetracker2/lib/python3.5/site-packages/sourcetracker/_cli/init.py", line 19, in import_module('sourcetracker._cli.gibbs') File "/storage/home/hcoda1/6/ldavila3/.conda/envs/sourcetracker2/lib/python3.5/importlib/init.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "/storage/home/hcoda1/6/ldavila3/.conda/envs/sourcetracker2/lib/python3.5/site-packages/sourcetracker/_cli/gibbs.py", line 23, in from sourcetracker._sourcetracker import ( File "/storage/home/hcoda1/6/ldavila3/.conda/envs/sourcetracker2/lib/python3.5/site-packages/sourcetracker/_sourcetracker.py", line 15, in from skbio.stats import subsample_counts File "/storage/home/hcoda1/6/ldavila3/.conda/envs/sourcetracker2/lib/python3.5/site-packages/skbio/init.py", line 13, in import skbio.io # noqa File "/storage/home/hcoda1/6/ldavila3/.conda/envs/sourcetracker2/lib/python3.5/site-packages/skbio/io/init.py", line 238, in import_module('skbio.io.format.lsmat') File "/storage/home/hcoda1/6/ldavila3/.conda/envs/sourcetracker2/lib/python3.5/importlib/init.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "/storage/home/hcoda1/6/ldavila3/.conda/envs/sourcetracker2/lib/python3.5/site-packages/skbio/io/format/lsmat.py", line 77, in from skbio.stats.distance import DissimilarityMatrix, DistanceMatrix File "/storage/home/hcoda1/6/ldavila3/.conda/envs/sourcetracker2/lib/python3.5/site-packages/skbio/stats/distance/init.py", line 192, in from ._base import (DissimilarityMatrixError, DistanceMatrixError, File "/storage/home/hcoda1/6/ldavila3/.conda/envs/sourcetracker2/lib/python3.5/site-packages/skbio/stats/distance/_base.py", line 13, in from IPython.core.pylabtools import print_figure File "/storage/home/hcoda1/6/ldavila3/.conda/envs/sourcetracker2/lib/python3.5/site-packages/IPython/init.py", line 55, in from .terminal.embed import embed File "/storage/home/hcoda1/6/ldavila3/.conda/envs/sourcetracker2/lib/python3.5/site-packages/IPython/terminal/embed.py", line 16, in from IPython.terminal.interactiveshell import TerminalInteractiveShell File "/storage/home/hcoda1/6/ldavila3/.conda/envs/sourcetracker2/lib/python3.5/site-packages/IPython/terminal/interactiveshell.py", line 32, in from .debugger import TerminalPdb, Pdb File "/storage/home/hcoda1/6/ldavila3/.conda/envs/sourcetracker2/lib/python3.5/site-packages/IPython/terminal/debugger.py", line 6, in from IPython.core.completer import IPCompleter File "/storage/home/hcoda1/6/ldavila3/.conda/envs/sourcetracker2/lib/python3.5/site-packages/IPython/core/completer.py", line 146, in import jedi File "/storage/home/hcoda1/6/ldavila3/.conda/envs/sourcetracker2/lib/python3.5/site-packages/jedi/init.py", line 41, in from jedi.api import Script, Interpreter, set_debug_function, \ File "/storage/home/hcoda1/6/ldavila3/.conda/envs/sourcetracker2/lib/python3.5/site-packages/jedi/api/init.py", line 15, in import parso File "/storage/home/hcoda1/6/ldavila3/.conda/envs/sourcetracker2/lib/python3.5/site-packages/parso/init.py", line 41, in from parso.parser import ParserSyntaxError File "/storage/home/hcoda1/6/ldavila3/.conda/envs/sourcetracker2/lib/python3.5/site-packages/parso/parser.py", line 113 node_map: Dict[str, type] = {} ^ SyntaxError: invalid syntax

I'll appreciate any help!

[celinecuinat]

Hi Lizdasa, I am getting the same error, did you manage to solve this issue? Thanks for any help!

[claireewilliams]

@celinecuinat I ran into a different error and used python=3.6 instead of 3.5 because it appears there are some compatibility issues between the packages. Not sure if that would solve your error, but thought I'd mention it!

[mavmac97]

I'm also having similar issues and would be interested if anyone has answers!

[tuttigiuperterra]

I'm having the exact same problem! Does anyone know how to solution it?

[tuttigiuperterra]

I used python=3.6 and solutioned the previous problem but now I get this new one:

Traceback (most recent call last): File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/bin/sourcetracker2", line 6, in from sourcetracker._cli import cli File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.6/site-packages/sourcetracker/_cli/init.py", line 19, in import_module('sourcetracker._cli.gibbs') File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.6/importlib/init.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.6/site-packages/sourcetracker/_cli/gibbs.py", line 27, in from ipyparallel import Client File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.6/site-packages/ipyparallel/init.py", line 17, in from .serialize import * File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.6/site-packages/ipyparallel/serialize/init.py", line 5, in from .serialize import ( File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.6/site-packages/ipyparallel/serialize/serialize.py", line 26, in from jupyter_client.session import MAX_ITEMS, MAX_BYTES File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.6/site-packages/jupyter_client/init.py", line 11, in from .manager import AsyncKernelManager # noqa File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.6/site-packages/jupyter_client/manager.py", line 32, in from .provisioning import KernelProvisionerBase File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.6/site-packages/jupyter_client/provisioning/init.py", line 1, in from .factory import KernelProvisionerFactory # noqa File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.6/site-packages/jupyter_client/provisioning/factory.py", line 19, in from .provisioner_base import KernelProvisionerBase File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.6/site-packages/jupyter_client/provisioning/provisioner_base.py", line 17, in from ..connect import KernelConnectionInfo ImportError: cannot import name 'KernelConnectionInfo'

[tuttigiuperterra]

When installing from git (pip uninstall sourcetracker && pip install git+https://github.com/biota/sourcetracker2.git) the same command works!!!

[YimHCLab]

I encountered the same problem using Python 3.5.6 after running this:

sourcetracker2 gibbs --help

Traceback (most recent call last): File "/srv/scratch/z3520673/bin/miniconda3/envs/st2/bin/sourcetracker2", line 5, in from sourcetracker._cli.gibbs import gibbs File "/srv/scratch/z3520673/bin/miniconda3/envs/st2/lib/python3.5/site-packages/sourcetracker/init.py", line 11, in from ._sourcetracker import gibbs File "/srv/scratch/z3520673/bin/miniconda3/envs/st2/lib/python3.5/site-packages/sourcetracker/_sourcetracker.py", line 17, in from skbio.stats import subsample_counts File "/srv/scratch/z3520673/bin/miniconda3/envs/st2/lib/python3.5/site-packages/skbio/init.py", line 13, in import skbio.io # noqa File "/srv/scratch/z3520673/bin/miniconda3/envs/st2/lib/python3.5/site-packages/skbio/io/init.py", line 238, in import_module('skbio.io.format.lsmat') File "/srv/scratch/z3520673/bin/miniconda3/envs/st2/lib/python3.5/importlib/init.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "/srv/scratch/z3520673/bin/miniconda3/envs/st2/lib/python3.5/site-packages/skbio/io/format/lsmat.py", line 77, in from skbio.stats.distance import DissimilarityMatrix, DistanceMatrix File "/srv/scratch/z3520673/bin/miniconda3/envs/st2/lib/python3.5/site-packages/skbio/stats/distance/init.py", line 192, in from ._base import (DissimilarityMatrixError, DistanceMatrixError, File "/srv/scratch/z3520673/bin/miniconda3/envs/st2/lib/python3.5/site-packages/skbio/stats/distance/_base.py", line 13, in from IPython.core.pylabtools import print_figure File "/srv/scratch/z3520673/bin/miniconda3/envs/st2/lib/python3.5/site-packages/IPython/init.py", line 55, in from .terminal.embed import embed File "/srv/scratch/z3520673/bin/miniconda3/envs/st2/lib/python3.5/site-packages/IPython/terminal/embed.py", line 16, in from IPython.terminal.interactiveshell import TerminalInteractiveShell File "/srv/scratch/z3520673/bin/miniconda3/envs/st2/lib/python3.5/site-packages/IPython/terminal/interactiveshell.py", line 32, in from .debugger import TerminalPdb, Pdb File "/srv/scratch/z3520673/bin/miniconda3/envs/st2/lib/python3.5/site-packages/IPython/terminal/debugger.py", line 6, in from IPython.core.completer import IPCompleter File "/srv/scratch/z3520673/bin/miniconda3/envs/st2/lib/python3.5/site-packages/IPython/core/completer.py", line 146, in import jedi File "/srv/scratch/z3520673/bin/miniconda3/envs/st2/lib/python3.5/site-packages/jedi/init.py", line 41, in from jedi.api import Script, Interpreter, set_debug_function, \ File "/srv/scratch/z3520673/bin/miniconda3/envs/st2/lib/python3.5/site-packages/jedi/api/init.py", line 15, in import parso File "/srv/scratch/z3520673/bin/miniconda3/envs/st2/lib/python3.5/site-packages/parso/init.py", line 41, in from parso.parser import ParserSyntaxError File "/srv/scratch/z3520673/bin/miniconda3/envs/st2/lib/python3.5/site-packages/parso/parser.py", line 113 node_map: Dict[str, type] = {} ^ SyntaxError: invalid syntax

Any solution?

[wasade]

Hi @lizdasa, unfortunately this repository is no longer maintained. I have a reasonably functional fork though that should be installable with: pip install https://github.com/wasade/sourcetracker2/archive/be_sparse.zip