Error while installing diffxpy

[aditisk]

Hi,

I followed the steps in the installation but I am still getting an error when I try to import diffxpy. Any help in fixing this is appreciated. Thank you.

Traceback

AttributeError                            Traceback (most recent call last)
<ipython-input-3-67d78b0a15d8> in <module>()
      1 
----> 2 import diffxpy.api as de

~/Downloads/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

~/Downloads/diffxpy-master/diffxpy/api/test.py in <module>()
----> 1 from diffxpy.testing.base import two_sample
      2 from diffxpy.testing.base import lrt
      3 from diffxpy.testing.base import wald
      4 from diffxpy.testing.base import t_test
      5 from diffxpy.testing.base import wilcoxon

~/Downloads/diffxpy-master/diffxpy/testing/base.py in <module>()
     14 
     15 import batchglm.data as data_utils
---> 16 from batchglm.models.glm_nb import Model as GeneralizedLinearModel
     17 
     18 from ..stats import stats

~/Downloads/batchglm-master/batchglm/models/glm_nb/__init__.py in <module>()
----> 1 from .model import Model, Model_XArray
      2 from .external import InputData
      3 from .simulator import Simulator
      4 from .estimator import AbstractEstimator, EstimatorStoreXArray

~/Downloads/batchglm-master/batchglm/models/glm_nb/model.py in <module>()
      7 import numpy as np
      8 
----> 9 from .external import InputData
     10 from .external import _Model_GLM, _Model_XArray_GLM, MODEL_PARAMS, _model_from_params
     11 

~/Downloads/batchglm-master/batchglm/models/glm_nb/external.py in <module>()
----> 1 from batchglm.models.base_glm import _Estimator_GLM, _EstimatorStore_XArray_GLM, ESTIMATOR_PARAMS
      2 from batchglm.models.base_glm import InputData, INPUT_DATA_PARAMS
      3 from batchglm.models.base_glm import _Model_GLM, _Model_XArray_GLM, MODEL_PARAMS, _model_from_params
      4 from batchglm.models.base_glm import _Simulator_GLM
      5 from batchglm.models.base_glm import closedform_glm_mean, closedform_glm_var

~/Downloads/batchglm-master/batchglm/models/base_glm/__init__.py in <module>()
----> 1 from .estimator import _Estimator_GLM, _EstimatorStore_XArray_GLM, ESTIMATOR_PARAMS
      2 from .input import InputData, INPUT_DATA_PARAMS
      3 from .model import _Model_GLM, _Model_XArray_GLM, MODEL_PARAMS, _model_from_params
      4 from .simulator import _Simulator_GLM
      5 from .utils import parse_design

~/Downloads/batchglm-master/batchglm/models/base_glm/estimator.py in <module>()
      6     anndata = None
      7 
----> 8 from .model import MODEL_PARAMS
      9 from .external import _Estimator_Base, _EstimatorStore_XArray_Base
     10 

~/Downloads/batchglm-master/batchglm/models/base_glm/model.py in <module>()
      8 import xarray as xr
      9 
---> 10 from .input import InputData, INPUT_DATA_PARAMS
     11 from .external import _Model_Base, _Model_XArray_Base
     12 

~/Downloads/batchglm-master/batchglm/models/base_glm/input.py in <module>()
      9 import pandas as pd
     10 
---> 11 from .utils import parse_constraints, parse_design
     12 from .external import _InputData_Base, INPUT_DATA_PARAMS
     13 

~/Downloads/batchglm-master/batchglm/models/base_glm/utils.py in <module>()
     11 import patsy
     12 
---> 13 from .external import groupwise_solve_lm
     14 from .external import weighted_mean, weighted_variance
     15 

~/Downloads/batchglm-master/batchglm/models/base_glm/external.py in <module>()
----> 1 from batchglm.models.base import _Estimator_Base, _EstimatorStore_XArray_Base
      2 from batchglm.models.base import _InputData_Base
      3 from batchglm.models.base import _Model_Base, _Model_XArray_Base
      4 from batchglm.models.base import _Simulator_Base
      5 from batchglm.models.base import INPUT_DATA_PARAMS

~/Downloads/batchglm-master/batchglm/models/base/__init__.py in <module>()
----> 1 from .input import _InputData_Base, INPUT_DATA_PARAMS
      2 from .estimator import _Estimator_Base, _EstimatorStore_XArray_Base
      3 from .model import _Model_Base, _Model_XArray_Base
      4 from .simulator import _Simulator_Base

~/Downloads/batchglm-master/batchglm/models/base/input.py in <module>()
     10     anndata = None
     11 
---> 12 from .external import pkg_constants, data_utils
     13 
     14 logger = logging.getLogger(__name__)

~/Downloads/batchglm-master/batchglm/models/base/external.py in <module>()
----> 1 import batchglm.pkg_constants as pkg_constants
      2 import batchglm.data as data_utils

~/Downloads/batchglm-master/batchglm/pkg_constants.py in <module>()
      2 import multiprocessing
      3 
----> 4 import tensorflow as tf
      5 
      6 TF_NUM_THREADS = int(os.environ.get('TF_NUM_THREADS', 0))

/anaconda3/lib/python3.6/site-packages/tensorflow/__init__.py in <module>()
     22 
     23 # pylint: disable=g-bad-import-order
---> 24 from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
     25 
     26 try:

/anaconda3/lib/python3.6/site-packages/tensorflow/python/__init__.py in <module>()
     53     parent_package_str='tensorflow.python',
     54     child_package_str=(
---> 55         'tensorflow_estimator.python.estimator'))
     56 del component_api_helper
     57 

/anaconda3/lib/python3.6/site-packages/tensorflow/python/tools/component_api_helper.py in package_hook(parent_package_str, child_package_str, error_msg)
     54   parent_pkg = importlib.import_module(parent_package_str)
     55   try:
---> 56     child_pkg = importlib.import_module(child_package_str)
     57   except ImportError:
     58     if error_msg:

/anaconda3/lib/python3.6/importlib/__init__.py in import_module(name, package)
    124                 break
    125             level += 1
--> 126     return _bootstrap._gcd_import(name[level:], package, level)
    127 
    128 

/anaconda3/lib/python3.6/site-packages/tensorflow_estimator/python/estimator/__init__.py in <module>()
     23 from __future__ import print_function
     24 
---> 25 import tensorflow_estimator.python.estimator.estimator_lib

/anaconda3/lib/python3.6/site-packages/tensorflow_estimator/python/estimator/estimator_lib.py in <module>()
     20 
     21 # pylint: disable=unused-import,line-too-long,wildcard-import
---> 22 from tensorflow_estimator.python.estimator.canned.baseline import BaselineClassifier
     23 from tensorflow_estimator.python.estimator.canned.baseline import BaselineEstimator
     24 from tensorflow_estimator.python.estimator.canned.baseline import BaselineRegressor

/anaconda3/lib/python3.6/site-packages/tensorflow_estimator/python/estimator/canned/baseline.py in <module>()
     62 from tensorflow.python.training import training_util
     63 from tensorflow.python.util.tf_export import estimator_export
---> 64 from tensorflow_estimator.python.estimator import estimator
     65 from tensorflow_estimator.python.estimator.canned import head as head_lib
     66 from tensorflow_estimator.python.estimator.canned import optimizers

/anaconda3/lib/python3.6/site-packages/tensorflow_estimator/__init__.py in <module>()
      6 from __future__ import print_function as _print_function
      7 
----> 8 from tensorflow_estimator._api.v1 import estimator
      9 _names_with_underscore = []
     10 __all__ = [_s for _s in dir() if not _s.startswith('_')]

/anaconda3/lib/python3.6/site-packages/tensorflow_estimator/_api/v1/estimator/__init__.py in <module>()
      6 from __future__ import print_function as _print_function
      7 
----> 8 from tensorflow_estimator._api.v1.estimator import experimental
      9 from tensorflow_estimator._api.v1.estimator import export
     10 from tensorflow_estimator._api.v1.estimator import inputs

/anaconda3/lib/python3.6/site-packages/tensorflow_estimator/_api/v1/estimator/experimental/__init__.py in <module>()
      6 from __future__ import print_function as _print_function
      7 
----> 8 from tensorflow_estimator.python.estimator.canned.dnn import dnn_logit_fn_builder
      9 from tensorflow_estimator.python.estimator.canned.linear import LinearSDCA
     10 from tensorflow_estimator.python.estimator.canned.linear import linear_logit_fn_builder

/anaconda3/lib/python3.6/site-packages/tensorflow_estimator/python/estimator/canned/dnn.py in <module>()
     38 from tensorflow_estimator.python.estimator.canned import head as head_lib
     39 from tensorflow_estimator.python.estimator.canned import optimizers
---> 40 from tensorflow_estimator.python.estimator.head import head_utils
     41 from tensorflow_estimator.python.estimator.head import regression_head
     42 

/anaconda3/lib/python3.6/site-packages/tensorflow_estimator/python/estimator/head/head_utils.py in <module>()
     21 from tensorflow.core.framework import summary_pb2
     22 from tensorflow.python.saved_model import signature_constants
---> 23 from tensorflow_estimator.python.estimator.head import binary_class_head
     24 from tensorflow_estimator.python.estimator.head import multi_class_head
     25 

/anaconda3/lib/python3.6/site-packages/tensorflow_estimator/python/estimator/head/binary_class_head.py in <module>()
     22 from tensorflow.python.framework import ops
     23 from tensorflow.python.keras import metrics
---> 24 from tensorflow.python.keras.utils import metrics_utils
     25 from tensorflow.python.ops import array_ops
     26 from tensorflow.python.ops import control_flow_ops

/anaconda3/lib/python3.6/site-packages/tensorflow/python/keras/utils/metrics_utils.py in <module>()
     29 from tensorflow.python.framework import ops
     30 from tensorflow.python.keras.utils.generic_utils import to_list
---> 31 from tensorflow.python.keras.utils.losses_utils import squeeze_or_expand_dimensions
     32 from tensorflow.python.ops import array_ops
     33 from tensorflow.python.ops import check_ops

/anaconda3/lib/python3.6/site-packages/tensorflow/python/keras/utils/losses_utils.py in <module>()
    142 
    143 def _reduce_weighted_loss(
--> 144     weighted_losses, reduction=losses_impl.ReductionV2.SUM_OVER_BATCH_SIZE):
    145   """Reduces the individual weighted loss measurements."""
    146   if reduction == losses_impl.ReductionV2.NONE:

AttributeError: module 'tensorflow.python.ops.losses.losses_impl' has no attribute 'ReductionV2'

[Hoeze]

Hi, I'd recommend to install diffxpy via pip install diffxpy.

@davidsebfischer I'm not up to date to your batchglm changes, maybe the documentation should be changed to recommend pip? Otherwise there will be a lot of questions like this one...

[davidsebfischer]

Hi @aditisk, I am on this, I am still doing changes to the backend which are necessary for this to run smoothly, I hope to push this in the next couple of days.

[aditisk]

@davidsebfischer and @Hoeze thanks for your response. @davidsebfischer how can I know when this is ready to use ? Could you please comment here or is there somewhere that I can check for updates ?

Thanks.

[davidsebfischer]

Hi @aditisk, sorry for the delay! The installation from pypi should work smoothly now.

[aditisk]

@davidsebfischer I think the installation worked. Thanks for the update. However, as mentioned in #127 I am unable to look at the tutorials to test the installation. Could you please look into why the tutorial links are down ? Thanks a lot.