The install of pixi from conda have error, the conda version is 1.7.7, I have try

[yudalang3]

Please make sure these conditions are met

• I have checked that this issue has not already been reported.
• I have confirmed this bug exists on the latest version of omicverse.
• (optional) I have confirmed this bug exists on the main branch of omicverse.

What happened?

my pixi toml is:

$ cat pixi.toml
[workspace]
authors = ["yudalang3 <dalangyusci@gmail.com>"]
name = "Wnt_activation_env"
platforms = ["linux-64"]
version = "0.1.0"

#channels = [
#  "conda-forge",
#  "bioconda",
#  "https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main",
#  "https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free"
#]

channels = [
  "https://mirror.nju.edu.cn/anaconda/cloud/conda-forge/",
  "https://mirror.nju.edu.cn/anaconda/cloud/bioconda/",
  "https://mirror.nju.edu.cn/anaconda/pkgs/main/",
  "https://mirror.nju.edu.cn/anaconda/pkgs/free/"
]

[dependencies]
pixi-pycharm = ">=0.0.9,<0.0.10"
omicverse = ">=1.7.7,<2"
pandas-stubs = "==2.3.2.250926"
notebook = ">=7.4.7,<8"
huggingface_hub = "==0.19.4"
transformers = "==4.37.2"

[tasks]

for

huggingface_hub = "==0.19.4"
transformers = "==4.37.2"

I try to fix the previous version of the huggingface_hub and transformers , It can run

But

$ pixi run python test1.py
Error processing line 1 of /opt/BioInfo/xxx_env/.pixi/envs/default/lib/python3.11/site-packages/distutils-precedence.pth:

  Traceback (most recent call last):
    File "<frozen site>", line 195, in addpackage
    File "<string>", line 1, in <module>
  ModuleNotFoundError: No module named '_distutils_hack'

Remainder of file ignored
/opt/BioInfo/xxx_env/.pixi/envs/default/lib/python3.11/site-packages/torch/cuda/__init__.py:58: FutureWarning: The pynvml package is deprecated. Please install nvidia-ml-py instead. If you did not install pynvml directly, please report this to the maintainers of the package that installed pynvml for you.
  import pynvml  # type: ignore[import]
🔬 Starting plot initialization...
🧬 Detecting CUDA devices…
🚫 No CUDA devices found

   ____            _     _    __
  / __ \____ ___  (_)___| |  / /__  _____________
 / / / / __ `__ \/ / ___/ | / / _ \/ ___/ ___/ _ \
/ /_/ / / / / / / / /__ | |/ /  __/ /  (__  )  __/
\____/_/ /_/ /_/_/\___/ |___/\___/_/  /____/\___/

🔖 Version: 1.7.7   📚 Tutorials: https://omicverse.readthedocs.io/
✅ plot_set complete.

I have CUDA device!

Now I thank it work, while, hope author to fix.

Minimal code sample

import scanpy as sc
import omicverse as ov
import matplotlib.pyplot as plt
ov.plot_set()

Error output

/opt/BioInfo/xxx_env/.pixi/envs/default/lib/python3.11/site-packages/torch/cuda/__init__.py:61: FutureWarning: The pynvml package is deprecated. Please install nvidia-ml-py instead. If you did not install pynvml directly, please report this to the maintainers of the package that installed pynvml for you.
  import pynvml  # type: ignore[import]


ImportError: cannot import name 'HfFolder' from 'huggingface_hub' (/opt/BioInfo/Wnt_activation_env/.pixi/envs/default/lib/python3.11/site-packages/huggingface_hub/__init__.py)

Versions

Details

🔬 Starting plot initialization...
🧬 Detecting CUDA devices…
🚫 No CUDA devices found

   ____            _     _    __
  / __ \____ ___  (_)___| |  / /__  _____________
 / / / / __ `__ \/ / ___/ | / / _ \/ ___/ ___/ _ \
/ /_/ / / / / / / / /__ | |/ /  __/ /  (__  )  __/
\____/_/ /_/ /_/_/\___/ |___/\___/_/  /____/\___/

🔖 Version: 1.7.7   📚 Tutorials: https://omicverse.readthedocs.io/
✅ plot_set complete.

[yudalang3]

I'm studying this tutorial: https://github.com/Starlitnightly/omicverse/blob/master/omicverse_guide/docs/Tutorials-bulk/t_wgcna.ipynb

The warning that appears afterward doesn't seem to affect my subsequent processing.

If the author has time, they could look into fixing it.

我在学习这个教程 https://github.com/Starlitnightly/omicverse/blob/master/omicverse_guide/docs/Tutorials-bulk/t_wgcna.ipynb
这个警告后面似乎不影响我后续的处理。
如果作者有空的话，可以处理一下。

[yudalang3]

也升级一下这个依赖的matplotlib吧：$ pixi run python -c "import matplotlib-inline; print(matplotlib-inline.version)"
WARN Encountered ambiguous version specifier 3.10.7, could be 3.10.7.* but assuming you meant ==3.10.7. In the future this will result in an error.
Error: × failed to solve requirements of environment 'default' for platform 'linux-64'
├─▶ × failed to solve the environment
│
╰─▶ Cannot solve the request because of: matplotlib ==3.10.7 cannot be installed because there are no viable options:
└─ matplotlib 3.10.7 would require
└─ python >=3.10,<3.11.0a0, for which no candidates were found.
The following packages are incompatible
├─ omicverse >=1.7.7,<2 can be installed with any of the following options:
│ └─ omicverse 1.7.7 | 1.7.7 would require
│ └─ matplotlib-base <3.7, which can be installed with any of the following options:
│ └─ matplotlib-base 3.6.1
└─ matplotlib ==3.10.7 cannot be installed because there are no viable options:
└─ matplotlib 3.10.7 | 3.10.7 | 3.10.7 | 3.10.7 would require
└─ matplotlib-base >=3.10.7,<3.10.8.0a0, which cannot be installed because there are no viable options:
├─ matplotlib-base 3.10.7, which conflicts with the versions reported above.
├─ matplotlib-base 3.10.7, which conflicts with the versions reported above.
├─ matplotlib-base 3.10.7, which conflicts with the versions reported above.
├─ matplotlib-base 3.10.7, which conflicts with the versions reported above.
└─ matplotlib-base 3.10.7 would require
└─ python >=3.10,<3.11.0a0, for which no candidates were found.

这里的 matplotlib-base 3.6.1 也太老了，conda的版本

[yudalang3]

我自己解决了这个问题，最好还是从PyPi上来下载 omicVerse这个工具。
我用pixi， 我在PyCharm的Gateway远程来使用
下面分析我的toml配置文件：

要注意：要从pypi上安装，这个比较方便，conda有些依赖解析不到位。
作者如果上传到conda上，最好fix各个版本

$ cat pixi.toml
[workspace]
authors = ["yudalang3 <dalangyusci@gmail.com>"]
name = "scvi_test"
platforms = ["linux-64"]
version = "0.1.0"

channels = [
  "https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/",
  "https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/",
  "https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/",
  "https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/",
  "nvidia"
]

[dependencies]
python = "3.11.*"
pixi-pycharm = ">=0.0.9,<0.0.10"
notebook = ">=7.4.7,<8"

[pypi-dependencies]
omicverse = "==1.7.8"
torch-geometric = "*"
torch = "*"


[pypi-options]
index-url = "https://pypi.tuna.tsinghua.edu.cn/simple"
extra-index-urls = [
    "https://mirrors.aliyun.com/pypi/simple/",
    "https://pypi.mirrors.ustc.edu.cn/simple"
]