'Simulator' object has no attribute 'np_clip_param' when following diffxpy tutorial

[davidhbrann]

I tried to run the diffxpy tutorial here, but ran into the following issue. I also had the same issue when trying the numpy backend of the Simulator.

from batchglm.api.models.tf1.glm_nb import Simulator

sim = Simulator(num_observations=200, num_features=100)
sim.generate_sample_description(num_batches=0, num_conditions=2)
sim.generate_params(
    rand_fn_loc=lambda shape: np.random.uniform(-0.1, 0.1, shape),
    rand_fn_scale=lambda shape: np.random.uniform(0.1, 2, shape)
)
sim.generate_data()

Here's the traceback:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-15-cdb736ba0fd1> in <module>
      7     rand_fn_scale=lambda shape: np.random.uniform(0.1, 2, shape)
      8 )
----> 9 sim.generate_data()

~/source/batchglm/batchglm/models/glm_nb/simulator.py in generate_data(self)
     47         """
     48         data_matrix = np.random.negative_binomial(
---> 49             n=self.phi,
     50             p=1 - self.mu / (self.phi + self.mu),
     51             size=None

~/source/batchglm/batchglm/models/glm_nb/model.py in phi(self)
     52     @property
     53     def phi(self) -> np.ndarray:
---> 54         return self.scale

~/source/batchglm/batchglm/models/base_glm/model.py in scale(self)
    109     @property
    110     def scale(self):
--> 111         return self.inverse_link_scale(self.eta_scale)
    112
    113     @abc.abstractmethod

~/source/batchglm/batchglm/models/base_glm/model.py in eta_scale(self)
    100     def eta_scale(self) -> np.ndarray:
    101         eta = np.matmul(self.design_scale, self.b)
--> 102         eta = self.np_clip_param(eta, "eta_scale")
    103         return eta
    104

AttributeError: 'Simulator' object has no attribute 'np_clip_param'

Here's the versions I'm using:

[('tensorflow', '1.15.0'),
 ('tensorflow_probability', '0.8.0'),
 ('anndata', <Version('0.7.1')>),
 ('seaborn', '0.10.0'),
 ('logging', '0.5.1.2'),
 ('numpy', '1.18.1'),
 ('pandas', '1.0.0'),
 ('scipy', '1.4.1'),
 ('diffxpy.api', 'v0.7.3+15.g00f8a83')]

[davidsebfischer]

Hi @dhb2128, thanks for the issue! Can you try installing diffxpy and batchglm from dev? The issue should be resolved there now.

[davidhbrann]

Sorry, I didn't see your response on the diffxpy issue. That fixed my problem, thanks!