ModuleNotFoundError: No module named 'batchglm.xarray_sparse'

[SNRNS]

Hi,

For some reason when I do:

from diffxpy.api import test

I get:

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-3-fb760d550d91> in <module>
----> 1 from diffxpy.api import test

~/Documents/Postdoc/DanaPeer/6.Science/1.Software/batchglm/diffxpy-master/diffxpy/api/__init__.py in <module>
      2 from ..log_cfg import logger, unconfigure_logging, enable_logging
      3 
----> 4 from . import test
      5 from . import enrich
      6 from . import stats

~/Documents/Postdoc/DanaPeer/6.Science/1.Software/batchglm/diffxpy-master/diffxpy/api/test.py in <module>
----> 1 from diffxpy.testing import lrt, wald, t_test, rank_test, two_sample, pairwise, \
      2     versus_rest, partition, continuous_1d
      3 from diffxpy.testing import design_matrix, coef_names

~/Documents/Postdoc/DanaPeer/6.Science/1.Software/batchglm/diffxpy-master/diffxpy/testing/__init__.py in <module>
----> 1 from .tests import lrt, wald, t_test, rank_test, two_sample, pairwise, \
      2     versus_rest, partition, continuous_1d
      3 from .utils import design_matrix, coef_names

~/Documents/Postdoc/DanaPeer/6.Science/1.Software/batchglm/diffxpy-master/diffxpy/testing/tests.py in <module>
     10 
     11 from batchglm import data as data_utils
---> 12 from batchglm.xarray_sparse import SparseXArrayDataSet
     13 from diffxpy import pkg_constants
     14 from diffxpy.models.batch_bfgs.optim import Estim_BFGS

ModuleNotFoundError: No module named 'batchglm.xarray_sparse'

However, xarray_sparse is under batchglm. Also, other models under batchglm like utils, are loaded correctly.

Any idea of why this may be happening?

Thanks,
Alejandro

[davidsebfischer]

Hi @alejandro-jimenezsanchez, are you on batchglm master branch, installed from a github clone, and diffxpy dev branch, also from a clone?

[SNRNS]

Hi @davidsebfischer

I cloned both master branches.

I set up the directory like:

.
+-- batchglm
|   +-- batchglm-master
|   +-- diffxpy-master

[davidsebfischer]

Switching diffxpy to dev and reinstalling diffxpy should fix it. Sorry about this conflict, I ll fix this soon.

[SNRNS]

So I installed batchglm-master, then when I tried to install diffxpy-dev I got the following error:

ERROR: Could not find a version that satisfies the requirement batchglm>=0.6.0 (from diffxpy==0+unknown) (from versions: 0.4.1)
ERROR: No matching distribution found for batchglm>=0.6.0 (from diffxpy==0+unknown)

Setup directory is:

.
+-- batchglm
|    +-- batchglm-master
|    +-- diffxpy-dev

I am using conda environment for this:

     active environment : diffxpy
    active env location : /Users/jimeneza/miniconda3/envs/diffxpy
            shell level : 2
       user config file : /Users/jimeneza/.condarc
 populated config files : 
          conda version : 4.7.5
    conda-build version : not installed
         python version : 3.7.3.final.0
       virtual packages : 
       base environment : /Users/jimeneza/miniconda3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/jimeneza/miniconda3/pkgs
                          /Users/jimeneza/.conda/pkgs
       envs directories : /Users/jimeneza/miniconda3/envs
                          /Users/jimeneza/.conda/envs
               platform : osx-64
             user-agent : conda/4.7.5 requests/2.21.0 CPython/3.7.3 Darwin/18.6.0 OSX/10.14.5
                UID:GID : 2059644158:9696963
             netrc file : None
           offline mode : False

@davidsebfischer, any idea of how to solve this issue?

Thanks,
A

[davidsebfischer]

All versions should be sorted now, the necessary version to run all new code are on the dev and master branch and pypi for both packages.

[Nero-Rome]

I am still getting errors when trying to import diffxpy. Both diffxpy and batchglm are from the master branch. The error reads: ModuleNotFoundError: No module named 'batchglm.data'. No idea how to fix this. Any help is appreciated!

[davidsebfischer]

If you want to use our newer code which is not yet fully benchmarked, you could try this branch: batchglm from dev and diffxpy from #218

[TomasDemeter]

any update on this issue? Thanks!

[MariaRosariaNucera]

I am still getting errors when trying to import diffxpy. Both diffxpy and batchglm are from the master branch. The error reads: ModuleNotFoundError: No module named 'batchglm.data'. No idea how to fix this. Any help is appreciated!

same, any solution?