Installation issue

[zhenlyu]

Hi,
I tried creating an environment using the commands below but encountered errors. Could you please help me resolve them?

conda create -n scgpt python=3.10 -y
conda activate scgpt
pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118
pip install scgpt
pip install wandb

[rank: 0] Global seed set to 0
/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_csv from `anndata` is deprecated. Import anndata.io.read_csv instead.
  warnings.warn(msg, FutureWarning)
/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_loom from `anndata` is deprecated. Import anndata.io.read_loom instead.
  warnings.warn(msg, FutureWarning)
/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/site-packages/anndata/utils.py:429: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.
  warnings.warn(msg, FutureWarning)
Traceback (most recent call last):
  File "/cluster/pixstor/joshitr-lab/zl7w2/scGPT/examples/finetune_integration.py", line 16, in <module>
    import scvi
  File "/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/site-packages/scvi/__init__.py", line 10, in <module>
    from . import autotune, data, model, external, utils
  File "/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/site-packages/scvi/autotune/__init__.py", line 1, in <module>
    from ._manager import TuneAnalysis, TunerManager
  File "/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/site-packages/scvi/autotune/_manager.py", line 21, in <module>
    from scvi.data._constants import _SETUP_ARGS_KEY, _SETUP_METHOD_NAME
  File "/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/site-packages/scvi/data/__init__.py", line 25, in <module>
    from ._manager import AnnDataManager, AnnDataManagerValidationCheck
  File "/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/site-packages/scvi/data/_manager.py", line 22, in <module>
    from ._utils import (
  File "/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/site-packages/scvi/data/_utils.py", line 13, in <module>
    from anndata._core.sparse_dataset import SparseDataset
ImportError: cannot import name 'SparseDataset' from 'anndata._core.sparse_dataset' (/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/site-packages/anndata/_core/sparse_dataset.py)

[zhenlyu]

I tried pip install anndata==0.10.8 which resolved the previous issue. However, I encountered a new error. Should I downgrade NumPy to version 1.19.5 to address this?

### Starting at: Fri Jan  3 10:35:57 CST 2025 ###
[rank: 0] Global seed set to 0
/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/site-packages/scgpt/model/model.py:21: UserWarning: flash_attn is not installed
  warnings.warn("flash_attn is not installed")
/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/site-packages/scgpt/model/multiomic_model.py:19: UserWarning: flash_attn is not installed
  warnings.warn("flash_attn is not installed")
wandb: Using wandb-core as the SDK backend.  Please refer to https://wandb.me/wandb-core for more information.
/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/site-packages/wandb/sdk/wandb_init.py:202: PydanticDeprecatedSince20: The `copy` method is deprecated; use `model_copy` instead. See the docstring of `BaseModel.copy` for details about how to handle `include` and `exclude`. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.10/migration/
  settings = self._wl.settings.copy()
wandb: Currently logged in as: tang27abu (zl7w2). Use `wandb login --relogin` to force relogin
wandb: Tracking run with wandb version 0.19.1
wandb: Run data is saved locally in /cluster/pixstor/joshitr-lab/zl7w2/scGPT/examples/wandb/run-20250103_103607-5d74gpgz
wandb: Run `wandb offline` to turn off syncing.
wandb: Syncing run drawn-waterfall-15
wandb: ⭐️ View project at https://wandb.ai/zl7w2/scGPT
wandb: 🚀 View run at https://wandb.ai/zl7w2/scGPT/runs/5d74gpgz
{'seed': 42, 'dataset_name': 'PBMC_10K', 'do_train': True, 'load_model': 'save/scGPT_bc', 'mask_ratio': 0.4, 'epochs': 30, 'n_bins': 51, 'GEPC': True, 'ecs_thres': 0.8, 'dab_weight': 1.0, 'lr': 0.0001, 'batch_size': 64, 'layer_size': 128, 'nlayers': 4, 'nhead': 4, 'dropout': 0.2, 'schedule_ratio': 0.9, 'save_eval_interval': 5, 'log_interval': 100, 'fast_transformer': True, 'pre_norm': False, 'amp': True}
save to save/dev_PBMC_10K-Jan03-10-36
�[34mINFO    �[0m File data/gene_info_pbmc.csv already downloaded                        
�[34mINFO    �[0m File data/pbmc_metadata.pickle already downloaded                      
�[34mINFO    �[0m File data/pbmc8k/filtered_gene_bc_matrices.tar.gz already downloaded   
�[34mINFO    �[0m Extracting tar file                                                    
�[34mINFO    �[0m Removing extracted data at data/pbmc8k/filtered_gene_bc_matrices       
�[34mINFO    �[0m File data/pbmc4k/filtered_gene_bc_matrices.tar.gz already downloaded   
�[34mINFO    �[0m Extracting tar file                                                    
�[34mINFO    �[0m Removing extracted data at data/pbmc4k/filtered_gene_bc_matrices       
/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/site-packages/scvi/data/_built_in_data/_pbmc.py:76: FutureWarning: Use anndata.concat instead of AnnData.concatenate, AnnData.concatenate is deprecated and will be removed in the future. See the tutorial for concat at: https://anndata.readthedocs.io/en/latest/concatenation.html
  adata = pbmc8k.concatenate(pbmc4k)
/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/site-packages/scvi/data/_built_in_data/_pbmc.py:81: FutureWarning: In the future `np.str` will be defined as the corresponding NumPy scalar.
  barcodes_metadata = pbmc_metadata["barcodes"].index.values.ravel().astype(np.str)
Traceback (most recent call last):
  File "/cluster/pixstor/joshitr-lab/zl7w2/scGPT/examples/finetune_integration.py", line 115, in <module>
    adata = scvi.data.pbmc_dataset()  # 11990 × 3346
  File "/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/site-packages/scvi/data/_datasets.py", line 57, in pbmc_dataset
    return _load_pbmc_dataset(
  File "/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/site-packages/scvi/data/_built_in_data/_pbmc.py", line 81, in _load_pbmc_dataset
    barcodes_metadata = pbmc_metadata["barcodes"].index.values.ravel().astype(np.str)
  File "/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/site-packages/numpy/__init__.py", line 324, in __getattr__
    raise AttributeError(__former_attrs__[attr])
AttributeError: module 'numpy' has no attribute 'str'.
`np.str` was a deprecated alias for the builtin `str`. To avoid this error in existing code, use `str` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.str_` here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
    https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations. Did you mean: 'std'?
Traceback (most recent call last):
  File "/cluster/pixstor/joshitr-lab/zl7w2/scGPT/examples/finetune_integration.py", line 115, in <module>
    adata = scvi.data.pbmc_dataset()  # 11990 × 3346
  File "/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/site-packages/scvi/data/_datasets.py", line 57, in pbmc_dataset
    return _load_pbmc_dataset(
  File "/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/site-packages/scvi/data/_built_in_data/_pbmc.py", line 81, in _load_pbmc_dataset
    barcodes_metadata = pbmc_metadata["barcodes"].index.values.ravel().astype(np.str)
  File "/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/site-packages/numpy/__init__.py", line 324, in __getattr__
    raise AttributeError(__former_attrs__[attr])
AttributeError: module 'numpy' has no attribute 'str'.
`np.str` was a deprecated alias for the builtin `str`. To avoid this error in existing code, use `str` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.str_` here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
    https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations. Did you mean: 'std'?
�[1;34mwandb�[0m: 🚀 View run �[33mdrawn-waterfall-15�[0m at: �[34mhttps://wandb.ai/zl7w2/scGPT/runs/5d74gpgz�[0m
�[1;34mwandb�[0m: Find logs at: �[1;35m../../../../../cluster/pixstor/joshitr-lab/zl7w2/scGPT/examples/wandb/run-20250103_103607-5d74gpgz/logs�[0m
/mnt/pixstor/dbllab/zl7w2/miniconda3/envs/scgpt/lib/python3.10/tempfile.py:869: ResourceWarning: Implicitly cleaning up <TemporaryDirectory '/tmp/tmp8sgyo74m'>
  _warnings.warn(warn_message, ResourceWarning)