Dalang Yu

 我相信我找到出错的原因了。我看了 netEmbedding/netClustering/netVisual_embedding的源代码，我发现netVisual_embedding这里，少了一个if else。 I believe I have found the reason for the mistake. I watched netEmbedding/netClustering/netVisual_embedding source code, I found netVisual_embedding here, less an if the else. 

I also think, not to change is the better solution. Such thing aslo happen in base R.

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...

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...

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 "] 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/",...

I can not agree with more, becase annother package doing this job is appropriate. If you must do this, I recommand therJavaEnv package. And I really , recommand to install...

Yes, it is a great progress, any managers could handle this ?

@jordibc @ArnaudBelcour @idoerg @fransua Can you hearing me ? There enhancement is very important.

I also give PR for this issue, the solution is equal and modify some annotations and configuration. see #793

This will be a novel feature to allow the DAG data structure, besides the tree structure. In fact I implement the JAVA tree code is like this. see https://github.com/yudalang3/eGPS2.1 https://github.com/yudalang3/eGPS2.1/blob/main/ydl.lab.utils/src/main/java/evoltree/struct/ArrayBasedNode.java...