ValueError: assignment destination is read-only

[SalvatoreRa]

Hi,

I am trying just to replicate the tutorial:

https://nbviewer.org/github/theislab/diffxpy_tutorials/blob/master/diffxpy_tutorials/test/introduction_differential_testing.ipynb

import anndata
import matplotlib.pyplot as plt
import seaborn as sns
import logging
import numpy as np
import pandas as pd
import scipy.stats
import diffxpy.api as de

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()

data = anndata.AnnData(
    X=sim.x,
    var=pd.DataFrame(index=["gene" + str(i) for i in range(sim.x.shape[1])]),
    obs=sim.sample_description
)

test = de.test.wald(
    data=data,
    formula_loc="~ 1 + condition",
    factor_loc_totest="condition"
)

and I got this error:

ValueError                                Traceback (most recent call last)
<ipython-input-6-046dde1595dc> in <module>
      2     data=data,
      3     formula_loc="~ 1 + condition",
----> 4     factor_loc_totest="condition"
      5 )

~/anaconda3/lib/python3.7/site-packages/diffxpy/testing/tests.py in wald(data, factor_loc_totest, coef_to_test, formula_loc, formula_scale, as_numeric, init_a, init_b, gene_names, sample_description, dmat_loc, dmat_scale, constraints_loc, constraints_scale, noise_model, size_factors, batch_size, backend, train_args, training_strategy, quick_scale, dtype, **kwargs)
    734         quick_scale=quick_scale,
    735         dtype=dtype,
--> 736         **kwargs,
    737     )
    738 

~/anaconda3/lib/python3.7/site-packages/diffxpy/testing/tests.py in _fit(noise_model, data, design_loc, design_scale, design_loc_names, design_scale_names, constraints_loc, constraints_scale, init_model, init_a, init_b, gene_names, size_factors, batch_size, backend, training_strategy, quick_scale, train_args, close_session, dtype)
    242     estim.train_sequence(
    243         training_strategy=training_strategy,
--> 244         **train_args
    245     )
    246 

~/anaconda3/lib/python3.7/site-packages/batchglm/models/base/estimator.py in train_sequence(self, training_strategy, **kwargs)
    122                         (x, str(d[x]), str(kwargs[x]))
    123                     )
--> 124             self.train(**d, **kwargs)
    125             logger.debug("Training sequence #%d complete", idx + 1)
    126 

~/anaconda3/lib/python3.7/site-packages/batchglm/train/numpy/base_glm/estimator.py in train(self, max_steps, method_b, update_b_freq, ftol_b, lr_b, max_iter_b, nproc, **kwargs)
    110                         lr=lr_b,
    111                         max_iter=max_iter_b,
--> 112                         nproc=nproc
    113                     )
    114                     # Perform trial update.

~/anaconda3/lib/python3.7/site-packages/batchglm/train/numpy/base_glm/estimator.py in b_step(self, idx_update, method, ftol, lr, max_iter, nproc)
    349                 ftol=ftol,
    350                 max_iter=max_iter,
--> 351                 nproc=nproc
    352             )
    353 

~/anaconda3/lib/python3.7/site-packages/batchglm/train/numpy/base_glm/estimator.py in _b_step_loop(self, idx_update, method, max_iter, ftol, nproc)
    479                 )
    480                 pool.close()
--> 481             delta_theta[0, idx_update] = np.array([x[0] for x in results])
    482             sys.stdout.write('\r')
    483             sys.stdout.flush()

ValueError: assignment destination is read-only