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hi,thanks for developing this useful method!
I was trying to run the desc_2.1.1_paul tutorial,but i got the AttributeError: can't set attribute, i don't know where the wrong exist.
my desc_2.1.1 env
anndata 0.9.2
scanpy 1.9.6
python 3.8.18
PIL 10.2.0
absl NA
asttokens NA
astunparse 1.6.3
backcall 0.2.0
certifi 2023.11.17
charset_normalizer 3.3.2
comm 0.2.1
cycler 0.12.1
cython_runtime NA
dab0eaeee8bfae79490a0d4f23f5ad820bb199d8 NA
dateutil 2.8.2
debugpy 1.8.0
decorator 5.1.1
desc 2.1.1
executing 2.0.1
flatbuffers 23.5.26
gast NA
get_annotations NA
google NA
h5py 3.10.0
idna 3.6
igraph 0.10.8
importlib_resources NA
ipykernel 6.29.0
jedi 0.19.1
joblib 1.3.2
keras 2.13.1
kiwisolver 1.4.5
llvmlite 0.41.1
louvain 0.8.1
matplotlib 3.7.4
matplotlib_inline 0.1.6
mpl_toolkits NA
natsort 8.4.0
numba 0.58.1
numexpr 2.8.6
numpy 1.24.3
opt_einsum v3.3.0
packaging 23.2
pandas 2.0.3
parso 0.8.3
pexpect 4.9.0
pickleshare 0.7.5
pkg_resources NA
platformdirs 4.1.0
prompt_toolkit 3.0.43
psutil 5.9.8
ptyprocess 0.7.0
pure_eval 0.2.2
pydev_ipython NA
pydevconsole NA
pydevd 2.9.5
pydevd_file_utils NA
pydevd_plugins NA
pydevd_tracing NA
pygments 2.17.2
pynndescent 0.5.11
pyparsing 3.1.1
pytz 2023.3.post1
requests 2.31.0
scipy 1.10.1
session_info 1.0.0
setuptools 68.2.2
six 1.16.0
sklearn 1.3.2
stack_data 0.6.3
tensorboard 2.13.0
tensorflow 2.13.1
termcolor NA
texttable 1.7.0
threadpoolctl 3.2.0
tornado 6.4
tqdm 4.66.1
traitlets 5.14.1
typing_extensions NA
umap 0.5.5
urllib3 2.1.0
wcwidth 0.2.13
wrapt 1.16.0
zipp NA
zmq 25.1.2
IPython 8.12.3
jupyter_client 8.6.0
jupyter_core 5.7.1
the question appeared when i ran the code adata=desc.train(adata, dims=[adata.shape[1],64,32], tol=0.005, n_neighbors=10, batch_size=256, louvain_resolution=[0.8,1.0], save_dir=str(save_dir), do_tsne=True, learning_rate=200, # the parameter of tsne use_GPU=False, num_Cores=1, #for reproducible, only use 1 cpu num_Cores_tsne=4, save_encoder_weights=False, save_encoder_step=3,# save_encoder_weights is False, this parameter is not used use_ae_weights=False, do_umap=False)
some warnings appreared
Start to process resolution= 0.8
The number of cpu in your computer is 96 You must install pydot (pip install pydot) and install graphviz (see instructions at https://graphviz.gitlab.io/download/) for plot_model to work.(i'm confused)
use_ae_weights=False, the program will rerun autoencoder
Pretraining the 1th layer...
learning rate = 0.1
2024-01-26 11:29:54.242148: E tensorflow/compiler/xla/stream_executor/cuda/cuda_driver.cc:268] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected
2024-01-26 11:29:54.242179: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:168] retrieving CUDA diagnostic information for host: bgi-algo
2024-01-26 11:29:54.242184: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:175] hostname: bgi-algo
2024-01-26 11:29:54.242362: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:199] libcuda reported version is: 535.86.10
2024-01-26 11:29:54.242380: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:203] kernel reported version is: 535.86.10
2024-01-26 11:29:54.242383: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:309] kernel version seems to match DSO: 535.86.10
Epoch 1/50
11/11 [==============================] - 1s 34ms/step - loss: 0.9599
........
........
11/11 [==============================] - 0s 9ms/step - loss: 0.2231
Epoch 5/5
11/11 [==============================] - 0s 9ms/step - loss: 0.2146
delta_label 0.004395604395604396 < tol 0.005
Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. model.compile_metrics will be empty until you train or evaluate the model.
raised the error likeAttributeError: can't set attribute
File /DATA/User/luowei/software/anaconda3/envs/DESC/lib/python3.8/site-packages/pandas/core/base.py:178, in NoNewAttributesMixin.setattr(self, key, value)
172 if getattr(self, "__frozen", False) and not (
173 key == "_cache"
174 or key in type(self).dict
175 or getattr(self, key, None) is not None
176 ):
177 raise AttributeError(f"You cannot add any new attribute '{key}'")
--> 178 object.setattr(self, key, value)
hi,thanks for developing this useful method!
I was trying to run the desc_2.1.1_paul tutorial,but i got the AttributeError: can't set attribute, i don't know where the wrong exist.
anndata 0.9.2
scanpy 1.9.6
python 3.8.18
PIL 10.2.0
absl NA
asttokens NA
astunparse 1.6.3
backcall 0.2.0
certifi 2023.11.17
charset_normalizer 3.3.2
comm 0.2.1
cycler 0.12.1
cython_runtime NA
dab0eaeee8bfae79490a0d4f23f5ad820bb199d8 NA
dateutil 2.8.2
debugpy 1.8.0
decorator 5.1.1
desc 2.1.1
executing 2.0.1
flatbuffers 23.5.26
gast NA
get_annotations NA
google NA
h5py 3.10.0
idna 3.6
igraph 0.10.8
importlib_resources NA
ipykernel 6.29.0
jedi 0.19.1
joblib 1.3.2
keras 2.13.1
kiwisolver 1.4.5
llvmlite 0.41.1
louvain 0.8.1
matplotlib 3.7.4
matplotlib_inline 0.1.6
mpl_toolkits NA
natsort 8.4.0
numba 0.58.1
numexpr 2.8.6
numpy 1.24.3
opt_einsum v3.3.0
packaging 23.2
pandas 2.0.3
parso 0.8.3
pexpect 4.9.0
pickleshare 0.7.5
pkg_resources NA
platformdirs 4.1.0
prompt_toolkit 3.0.43
psutil 5.9.8
ptyprocess 0.7.0
pure_eval 0.2.2
pydev_ipython NA
pydevconsole NA
pydevd 2.9.5
pydevd_file_utils NA
pydevd_plugins NA
pydevd_tracing NA
pygments 2.17.2
pynndescent 0.5.11
pyparsing 3.1.1
pytz 2023.3.post1
requests 2.31.0
scipy 1.10.1
session_info 1.0.0
setuptools 68.2.2
six 1.16.0
sklearn 1.3.2
stack_data 0.6.3
tensorboard 2.13.0
tensorflow 2.13.1
termcolor NA
texttable 1.7.0
threadpoolctl 3.2.0
tornado 6.4
tqdm 4.66.1
traitlets 5.14.1
typing_extensions NA
umap 0.5.5
urllib3 2.1.0
wcwidth 0.2.13
wrapt 1.16.0
zipp NA
zmq 25.1.2
IPython 8.12.3
jupyter_client 8.6.0
jupyter_core 5.7.1
Python 3.8.18 (default, Sep 11 2023, 13:40:15) [GCC 11.2.0]
Linux-6.2.0-34-generic-x86_64-with-glibc2.17
Session information updated at 2024-01-26 10:23
the question appeared when i ran the code
adata=desc.train(adata, dims=[adata.shape[1],64,32], tol=0.005, n_neighbors=10, batch_size=256, louvain_resolution=[0.8,1.0], save_dir=str(save_dir), do_tsne=True, learning_rate=200, # the parameter of tsne use_GPU=False, num_Cores=1, #for reproducible, only use 1 cpu num_Cores_tsne=4, save_encoder_weights=False, save_encoder_step=3,# save_encoder_weights is False, this parameter is not used use_ae_weights=False, do_umap=False)
some warnings appreared
Start to process resolution= 0.8
The number of cpu in your computer is 96
You must install pydot (
pip install pydot
) and install graphviz (see instructions at https://graphviz.gitlab.io/download/) for plot_model to work.(i'm confused)use_ae_weights=False, the program will rerun autoencoder
Pretraining the 1th layer...
learning rate = 0.1
2024-01-26 11:29:54.242148: E tensorflow/compiler/xla/stream_executor/cuda/cuda_driver.cc:268] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected
2024-01-26 11:29:54.242179: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:168] retrieving CUDA diagnostic information for host: bgi-algo
2024-01-26 11:29:54.242184: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:175] hostname: bgi-algo
2024-01-26 11:29:54.242362: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:199] libcuda reported version is: 535.86.10
2024-01-26 11:29:54.242380: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:203] kernel reported version is: 535.86.10
2024-01-26 11:29:54.242383: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:309] kernel version seems to match DSO: 535.86.10
Epoch 1/50
11/11 [==============================] - 1s 34ms/step - loss: 0.9599
........
........
11/11 [==============================] - 0s 9ms/step - loss: 0.2231
Epoch 5/5
11/11 [==============================] - 0s 9ms/step - loss: 0.2146
delta_label 0.004395604395604396 < tol 0.005
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built.
model.compile_metrics
will be empty until you train or evaluate the model.raised the error like
AttributeError: can't set attribute
File /DATA/User/luowei/software/anaconda3/envs/DESC/lib/python3.8/site-packages/pandas/core/base.py:178, in NoNewAttributesMixin.setattr(self, key, value)
172 if getattr(self, "__frozen", False) and not (
173 key == "_cache"
174 or key in type(self).dict
175 or getattr(self, key, None) is not None
176 ):
177 raise AttributeError(f"You cannot add any new attribute '{key}'")
--> 178 object.setattr(self, key, value)
File /DATA/User/luowei/software/anaconda3/envs/DESC/lib/python3.8/site-packages/pandas/core/accessor.py:99, in PandasDelegate._add_delegate_accessors.._create_delegator_property.._setter(self, new_values)
98 def _setter(self, new_values):
---> 99 return self._delegate_property_set(name, new_values)
File /DATA/User/luowei/software/anaconda3/envs/DESC/lib/python3.8/site-packages/pandas/core/arrays/categorical.py:2460, in CategoricalAccessor._delegate_property_set(self, name, new_values)
2459 def _delegate_property_set(self, name, new_values):
-> 2460 return setattr(self._parent, name, new_values)
is there anyone can help me?
thanks a lot!!!
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