semvec/pypi-packages huggingface dataset:
vines-infer-sdk 0.0.2
Vines Python 训练项目 SDK （供内部使用）
License: MIT

# Vines Python 训练项目 SDK （供内部使用）

这个项目希望解决的问题，将开发一个新的训练项目中的很多重复性工作进行统一封装：

1. 每次开一个新训练项目都需要起 HTTP Server
2. 里面有可能会用到很多通用能力，比如上传、下载文件、以及一些基础方法等，这些都应该封装好。
3. 错误日志推送逻辑
4. 运行时日志逻辑
5. api 入参、出参统一格式封装
6. 统一的日志格式、日志收集

## 安装

```shell
pip install vines-infer-sdk
```

## 使用示例

### 作为 conductor 客户端

详情见 `exampels/example_conductor.py` 文件中的内容。

### 使用 flask http server

从 `lib.server` 引入 `create_server` 方法，初始化 flask app，参数：

- sentry_dsn: sentry dsn, 如果配置，会自动收集异常推送到 sentry
- log_redis_queue_url: 如果配置，在调用 request.logger 方法的时候，会自动推送到消息队列，从而给前端展示。

打印日志的方法：直接使用 `request.logger` 实例的方法。

详情见 `exampels/example_server.py` 文件中的内容。
excellxgene 2.9.6
Web application for exploration of large scale scRNA-seq datasets, upgraded to enable end-to-end interactive analysis.
License: MIT

<img src="./cellxgene-logo.png" width="300">

# Exploratory CellxGene (ExCellxGene)


## V2.9.6
The latest stable version is V2.9.6. The current version of exCellxgene relies on anndata==0.7.8, so might crash with anndata objects generated with anndata==0.8.0 or above. Until we fix this bug, we recommend users to follow the installation instruction below. The key part is installing exCellxgene, then upgrading the anndata version to 0.8.0 in the "cxg" conda environment.

### Installation

1. Install miniconda if conda not available already:

```
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O ~/miniconda.sh
bash ~/miniconda.sh -b -p $HOME/miniconda
```

2. Create and activate a new environment:

```
conda create -n cxg python=3.8
conda activate cxg
```

3. Install excellxgene with pip:
```
pip install excellxgene
pip install anndata==0.8.0
```

If your operating system is CentOS, then you may run into issues installing dependencies that require up-to-date `gcc` or `g++` compilers. Please install with the following and try reinstalling `excellxgene` with pip:
```
conda install -c conda-forge gcc cxx-compiler
```

4. Download the git repository to get the example datasets (assumes git is available, if not install it with conda install -c anaconda git)
```
git clone https://github.com/czbiohub/excellxgene
cd excellxgene
```
Datasets are stored in `example-dataset`

5. Launch excellxgene with:
```
excellxgene launch example-dataset
```


This should launch an excellxgene session with all the datasets in example-datasets/ loaded in.

If you're running excellxgene remotely, please launch with:
```
excellxgene launch example-datasets --host 0.0.0.0
```

### Preprint on how to do manual cell-type annotation using interactive tools: 
https://www.biorxiv.org/content/10.1101/2023.07.11.548639v1

### Tutorial slides highligting some use cases:
https://cellxgene.cziscience.com/docs/05__Annotate%20and%20Analyze%20Your%20Data/5_8__Multimodal%20Annotations

More tutorial slides for multi-omics datasets (RNA, ATAC, CITE-seq, spatial transcriptomics) are coming soon (Q1/Q2 2024).