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