Closed m-fayer closed 11 months ago
Please try installing the latest version by specifying the targeted version number.
pip install stereopy==0.13.0b1
This command gave output with some errors below:
...
Successfully built stereopy
Installing collected packages: tornado, requests, lxml, fastcluster, distinctipy, joypy, stereopy
Attempting uninstall: tornado
Found existing installation: tornado 6.3.3
Uninstalling tornado-6.3.3:
Successfully uninstalled tornado-6.3.3
Attempting uninstall: requests
Found existing installation: requests 2.31.0
Uninstalling requests-2.31.0:
Successfully uninstalled requests-2.31.0
Attempting uninstall: stereopy
Found existing installation: stereopy 0.12.1
Uninstalling stereopy-0.12.1:
Successfully uninstalled stereopy-0.12.1
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
jupyter-client 8.3.0 requires tornado>=6.2, but you have tornado 6.1 which is incompatible.
jupyter-server 2.7.2 requires tornado>=6.2.0, but you have tornado 6.1 which is incompatible.
jupyterlab 4.0.5 requires tornado>=6.2.0, but you have tornado 6.1 which is incompatible.
jupyterlab-server 2.24.0 requires requests>=2.28, but you have requests 2.26.0 which is incompatible.
notebook 7.0.2 requires tornado>=6.2.0, but you have tornado 6.1 which is incompatible.
Successfully installed distinctipy-1.2.2 fastcluster-1.2.6 joypy-0.2.6 lxml-4.9.3 requests-2.26.0 stereopy-0.13.0b1 tornado-6.1
But the import command worked. Thanks!
Hi, after the installation, I tried some commands in the tutorial. For the "data_dir=" line, I used the downloaded demo data: data_dir = 'Demo_3D_Drosophila/3D_AnnData_0.8.0'
. The files inside are:
-a---- 1/06/2023 4:26 PM 30096216 0.h5ad
-a---- 1/06/2023 4:25 PM 33928248 1.h5ad
-a---- 1/06/2023 4:24 PM 62371088 10.h5ad
-a---- 1/06/2023 4:24 PM 75232060 11.h5ad
-a---- 1/06/2023 4:25 PM 58477648 12.h5ad
-a---- 1/06/2023 4:24 PM 63967060 13.h5ad
-a---- 1/06/2023 4:24 PM 74081548 14.h5ad
-a---- 4/07/2023 4:47 PM 66953940 15.h5ad
-a---- 1/06/2023 4:25 PM 36824980 2.h5ad
-a---- 1/06/2023 4:25 PM 44668232 3.h5ad
-a---- 1/06/2023 4:25 PM 45767372 4.h5ad
-a---- 1/06/2023 4:25 PM 49402992 5.h5ad
-a---- 1/06/2023 4:26 PM 55391352 6.h5ad
-a---- 1/06/2023 4:25 PM 76786828 7.h5ad
-a---- 1/06/2023 4:25 PM 77017488 8.h5ad
-a---- 1/06/2023 4:25 PM 75554284 9.h5ad
Everything looks good, until I reached the lines:
# add all samples into MSData
for sample in data_list:
ms_data += st.io.read_h5ad(file_path=sample, bin_type='bins', bin_size=1)
Some errors came out:
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
File ~\AppData\Local\miniconda3\envs\stm\lib\site-packages\anndata\_io\utils.py:156, in report_read_key_on_error.<locals>.func_wrapper(elem, *args, **kwargs)
155 try:
--> 156 return func(elem, *args, **kwargs)
157 except Exception as e:
File ~\AppData\Local\miniconda3\envs\stm\lib\site-packages\anndata\_io\h5ad.py:532, in read_group(group)
531 if encoding_type:
--> 532 EncodingVersions[encoding_type].check(
533 group.name, group.attrs["encoding-version"]
534 )
535 if encoding_type in {None, "raw"}:
File ~\AppData\Local\miniconda3\envs\stm\lib\enum.py:387, in EnumMeta.__getitem__(cls, name)
386 def __getitem__(cls, name):
--> 387 return cls._member_map_[name]
KeyError: 'dict'
During handling of the above exception, another exception occurred:
AnnDataReadError Traceback (most recent call last)
Cell In[9], line 2
1 for sample in data_list:
----> 2 ms_data += st.io.read_h5ad(file_path=sample, bin_type='bins', bin_size=1)
File ~\AppData\Local\miniconda3\envs\stm\lib\site-packages\stereo\io\reader.py:634, in read_h5ad(file_path, anndata, flavor, bin_type, bin_size, **kwargs)
632 if file_path is not None and anndata is not None:
633 raise Exception("'file_path' and 'anndata' only can input one of them")
--> 634 return AnnBasedStereoExpData(h5ad_file_path=file_path, based_ann_data=anndata, bin_type=bin_type, bin_size=bin_size, **kwargs)
635 else:
636 raise ValueError("Invalid value for 'flavor'")
File ~\AppData\Local\miniconda3\envs\stm\lib\site-packages\stereo\core\stereo_exp_data.py:601, in AnnBasedStereoExpData.__init__(self, h5ad_file_path, based_ann_data, bin_type, bin_size, *args, **kwargs)
599 self._ann_data = based_ann_data
600 else:
--> 601 self._ann_data = anndata.read_h5ad(h5ad_file_path)
602 self._genes = AnnBasedGene(self._ann_data, self._genes.gene_name)
603 self._cells = AnnBasedCell(self._ann_data, self._cells.cell_name)
File ~\AppData\Local\miniconda3\envs\stm\lib\site-packages\anndata\_io\h5ad.py:426, in read_h5ad(filename, backed, as_sparse, as_sparse_fmt, chunk_size)
424 d[k] = read_dataframe(f[k])
425 else: # Base case
--> 426 d[k] = read_attribute(f[k])
428 d["raw"] = _read_raw(f, as_sparse, rdasp)
430 X_dset = f.get("X", None)
File ~\AppData\Local\miniconda3\envs\stm\lib\functools.py:875, in singledispatch.<locals>.wrapper(*args, **kw)
871 if not args:
872 raise TypeError(f'{funcname} requires at least '
873 '1 positional argument')
--> 875 return dispatch(args[0].__class__)(*args, **kw)
File ~\AppData\Local\miniconda3\envs\stm\lib\site-packages\anndata\_io\utils.py:162, in report_read_key_on_error.<locals>.func_wrapper(elem, *args, **kwargs)
160 else:
161 parent = _get_parent(elem)
--> 162 raise AnnDataReadError(
163 f"Above error raised while reading key {elem.name!r} of "
164 f"type {type(elem)} from {parent}."
165 )
AnnDataReadError: Above error raised while reading key '/layers' of type <class 'h5py._hl.group.Group'> from /.
How can I fix it? Thanks.
@m-fayer
Hi!! Download the demo data: Demo_3D_Drosophila/3D_AnnData_0.7.5
to use, because the version of anndata
depended by stereopy is 0.7.5 which is not compatible with anndata
0.8.0 and higher.
It worked. Thank you so much.
Hi, I am trying the latest multi sample function.
When running command
from stereo.core.ms_pipeline import slice_generator
it showed error:
From the output of command
help(st.core)
, there is no content "ms_pipeline", but there is "st_pipeline":But
from stereo.core.st_pipeline import slice_generator
also gave error:I installed using PyPi way in the instructions. Using command "conda list", I noticed stereopy version is 0.12.1, not the 0.13.0b1 shown in the page. So it looks the error is because I failed to install the latest version? How can I fix it? I tried the Development way in installation instructions but failed. Thanks.