AttributeError: 'NoneType' object has no attribute 'split'

[VivianQM]

Hi,

I am trying to run Harmonypy on an anndata object. It gave me the error below.

AttributeError                            Traceback (most recent call last)
Cell In[198], line 1
----> 1 sc.external.pp.harmony_integrate(xenium_breast_htma_breast, key = 'patient')

File ~/anaconda3/lib/python3.10/site-packages/scanpy/external/pp/_harmony_integrate.py:82, in harmony_integrate(adata, key, basis, adjusted_basis, **kwargs)
     79 except ImportError:
     80     raise ImportError("\nplease install harmonypy:\n\n\tpip install harmonypy")
---> 82 harmony_out = harmonypy.run_harmony(adata.obsm[basis], adata.obs, key, **kwargs)
     84 adata.obsm[adjusted_basis] = harmony_out.Z_corr.T

File ~/anaconda3/lib/python3.10/site-packages/harmonypy/harmony.py:124, in run_harmony(data_mat, meta_data, vars_use, theta, lamb, sigma, nclust, tau, block_size, max_iter_harmony, max_iter_kmeans, epsilon_cluster, epsilon_harmony, plot_convergence, verbose, reference_values, cluster_prior, random_state)
    120 phi_moe = np.vstack((np.repeat(1, N), phi))
    122 np.random.seed(random_state)
--> 124 ho = Harmony(
    125     data_mat, phi, phi_moe, Pr_b, sigma, theta, max_iter_harmony, max_iter_kmeans,
    126     epsilon_cluster, epsilon_harmony, nclust, block_size, lamb_mat, verbose
    127 )
    129 return ho

File ~/anaconda3/lib/python3.10/site-packages/harmonypy/harmony.py:172, in Harmony.__init__(self, Z, Phi, Phi_moe, Pr_b, sigma, theta, max_iter_harmony, max_iter_kmeans, epsilon_kmeans, epsilon_harmony, K, block_size, lamb, verbose)
    169 self.kmeans_rounds  = []
    171 self.allocate_buffers()
--> 172 self.init_cluster()
    173 self.harmonize(self.max_iter_harmony, self.verbose)

File ~/anaconda3/lib/python3.10/site-packages/harmonypy/harmony.py:191, in Harmony.init_cluster(self)
    188 logger.info("Computing initial centroids with sklearn.KMeans...")
    189 model = KMeans(n_clusters=self.K, init='k-means++',
    190                n_init=10, max_iter=25)
--> 191 model.fit(self.Z_cos.T)
    192 km_centroids, km_labels = model.cluster_centers_, model.labels_
    193 logger.info("sklearn.KMeans initialization complete.")

File ~/anaconda3/lib/python3.10/site-packages/sklearn/cluster/_kmeans.py:1468, in KMeans.fit(self, X, y, sample_weight)
   1465     print("Initialization complete")
   1467 # run a k-means once
-> 1468 labels, inertia, centers, n_iter_ = kmeans_single(
   1469     X,
   1470     sample_weight,
   1471     centers_init,
   1472     max_iter=self.max_iter,
   1473     verbose=self.verbose,
   1474     tol=self._tol,
   1475     n_threads=self._n_threads,
   1476 )
   1478 # determine if these results are the best so far
   1479 # we chose a new run if it has a better inertia and the clustering is
   1480 # different from the best so far (it's possible that the inertia is
   1481 # slightly better even if the clustering is the same with potentially
   1482 # permuted labels, due to rounding errors)
   1483 if best_inertia is None or (
   1484     inertia < best_inertia
   1485     and not _is_same_clustering(labels, best_labels, self.n_clusters)
   1486 ):

File ~/anaconda3/lib/python3.10/site-packages/sklearn/cluster/_kmeans.py:679, in _kmeans_single_lloyd(X, sample_weight, centers_init, max_iter, verbose, tol, n_threads)
    675 strict_convergence = False
    677 # Threadpoolctl context to limit the number of threads in second level of
    678 # nested parallelism (i.e. BLAS) to avoid oversubscription.
--> 679 with threadpool_limits(limits=1, user_api="blas"):
    680     for i in range(max_iter):
    681         lloyd_iter(
    682             X,
    683             sample_weight,
   (...)
    689             n_threads,
    690         )

File ~/anaconda3/lib/python3.10/site-packages/sklearn/utils/fixes.py:139, in threadpool_limits(limits, user_api)
    137     return controller.limit(limits=limits, user_api=user_api)
    138 else:
--> 139     return threadpoolctl.threadpool_limits(limits=limits, user_api=user_api)

File ~/anaconda3/lib/python3.10/site-packages/threadpoolctl.py:171, in threadpool_limits.__init__(self, limits, user_api)
    167 def __init__(self, limits=None, user_api=None):
    168     self._limits, self._user_api, self._prefixes = \
    169         self._check_params(limits, user_api)
--> 171     self._original_info = self._set_threadpool_limits()

File ~/anaconda3/lib/python3.10/site-packages/threadpoolctl.py:268, in threadpool_limits._set_threadpool_limits(self)
    265 if self._limits is None:
    266     return None
--> 268 modules = _ThreadpoolInfo(prefixes=self._prefixes,
    269                           user_api=self._user_api)
    270 for module in modules:
    271     # self._limits is a dict {key: num_threads} where key is either
    272     # a prefix or a user_api. If a module matches both, the limit
    273     # corresponding to the prefix is chosed.
    274     if module.prefix in self._limits:

File ~/anaconda3/lib/python3.10/site-packages/threadpoolctl.py:340, in _ThreadpoolInfo.__init__(self, user_api, prefixes, modules)
    337     self.user_api = [] if user_api is None else user_api
    339     self.modules = []
--> 340     self._load_modules()
    341     self._warn_if_incompatible_openmp()
    342 else:

File ~/anaconda3/lib/python3.10/site-packages/threadpoolctl.py:371, in _ThreadpoolInfo._load_modules(self)
    369 """Loop through loaded libraries and store supported ones"""
    370 if sys.platform == "darwin":
--> 371     self._find_modules_with_dyld()
    372 elif sys.platform == "win32":
    373     self._find_modules_with_enum_process_module_ex()

File ~/anaconda3/lib/python3.10/site-packages/threadpoolctl.py:428, in _ThreadpoolInfo._find_modules_with_dyld(self)
    425 filepath = filepath.decode("utf-8")
    427 # Store the module if it is supported and selected
--> 428 self._make_module_from_path(filepath)

File ~/anaconda3/lib/python3.10/site-packages/threadpoolctl.py:515, in _ThreadpoolInfo._make_module_from_path(self, filepath)
    513 if prefix in self.prefixes or user_api in self.user_api:
    514     module_class = globals()[module_class]
--> 515     module = module_class(filepath, prefix, user_api, internal_api)
    516     self.modules.append(module)

File ~/anaconda3/lib/python3.10/site-packages/threadpoolctl.py:606, in _Module.__init__(self, filepath, prefix, user_api, internal_api)
    604 self.internal_api = internal_api
    605 self._dynlib = ctypes.CDLL(filepath, mode=_RTLD_NOLOAD)
--> 606 self.version = self.get_version()
    607 self.num_threads = self.get_num_threads()
    608 self._get_extra_info()

File ~/anaconda3/lib/python3.10/site-packages/threadpoolctl.py:646, in _OpenBLASModule.get_version(self)
    643 get_config = getattr(self._dynlib, "openblas_get_config",
    644                      lambda: None)
    645 get_config.restype = ctypes.c_char_p
--> 646 config = get_config().split()
    647 if config[0] == b"OpenBLAS":
    648     return config[1].decode("utf-8")

AttributeError: 'NoneType' object has no attribute 'split'

I tried the method in the closed issue. Didn't work for me. Any help is greatly appreciated!! Thanks.

[slowkow]

Hi @VivianQM , thanks for reporting an issue.

Here is a post from stackoverflow that looks like it might be related to your error:

https://stackoverflow.com/questions/74569163/lazyppredict-attributeerror-nonetype-object-has-no-attribute-split

When reporting issues with software, it is good practice to share your operating system version, python version, and all package versions.

I have an inkling that your system might not have OpenBLAS installed, so that might be why you're seeing this error message:

File ~/anaconda3/lib/python3.10/site-packages/threadpoolctl.py:646, in _OpenBLASModule.get_version(self)
643 get_config = getattr(self._dynlib, "openblas_get_config",
644 lambda: None)
645 get_config.restype = ctypes.c_char_p
--> 646 config = get_config().split()
647 if config[0] == b"OpenBLAS":
648 return config[1].decode("utf-8")

AttributeError: 'NoneType' object has no attribute 'split'

If you use a search engine to find issues related to this error, you might find posts by others who have resolved this issue. Please consider sharing your solution here in this thread, if you find one.

[VivianQM]

Hi @slowkow,
Thanks for the quick reply!
I am using Jupyter Notebook on a Mac. Please let me know if you need certain package versions.
I installed OpenBLAS and the error remains. I also searched around but found nothing that could solve the problem. Any suggestions are appreciated!

Thanks again,
V

[slowkow]

I found another related post:

https://stackoverflow.com/questions/71352354/sklearn-kmeans-is-not-working-as-i-only-get-nonetype-object-has-no-attribute

Does the error go away if you do this?

pip install threadpoolctl

You can check what version you have installed with this (on my machine I have 3.2.0):

python -c 'import threadpoolctl as t; print(t.__version__)'

[VivianQM]

That worked! Thank you so much

[slowkow]

Great, thanks for sharing that it works. I hope others will find this solution in the future.

My conclusion is that an outdated version of the threadpoolctl Python package is the culprit of this issue.