semvec/pypi-packages huggingface dataset:
treasmo 1.1.1
Transcription regulation analysis toolkit for single-cell multi-omics data

# TREASMO
[![License](https://img.shields.io/github/license/ChaozhongLiu/DyberPet.svg)](LICENSE)
![Python Version](https://img.shields.io/badge/python-3.x-blue.svg)
![TREASMO Version](https://img.shields.io/badge/TREASMO-v1.1.1-green.svg)  
[![Documentation Status](https://readthedocs.org/projects/treasmo/badge/?version=latest)](https://treasmo.readthedocs.io/en/latest/?badge=latest)


**TREASMO** is a Transcription regulation analysis toolkit for single-cell multi-omics data. It quantifies the single-cell level gene-peak correlation strength, based on which a series of analysis and visualization functions are built to help researchers understand their multi-omics data.  

![](./Supplementary_Materials/Fig1.png)

## Installation
TREASMO is written in Python and is available from PyPI. Note that Python version should be 3.x.

### Install from PyPI
Please run the following command. Creating new environment using conda is recommended.
```
pip3 install treasmo

# For all the functions, please also install leidenalg and minisom
pip3 install leidenalg
pip3 install minisom
```
If the above method failed, please try create a new environment using conda first then re-install the three packages above.  
  
If things still doesn't work, try the method below.

### Use the package locally
If there is conflicts with other packages or something unexpected happened, try download the package and use it locally in a new conda environment.
```
# Create a new conda environment
conda create -n treasmo numpy=1.22
conda activate treasmo

# Setting up kernels for Jupyter Notebook if needed
conda install ipykernel
ipython kernel install --user --name=treasmo

# Install dependencies
conda install -c conda-forge scanpy python-igraph leidenalg
conda install -c conda-forge libpysal
conda install -c conda-forge hdf5plugin
conda install -c conda-forge muon
conda install -c conda-forge fa2
conda install -c conda-forge louvain

# Option 1 to install minisom
git clone https://github.com/JustGlowing/minisom.git
cd minisom
python setup.py install

# Option 2 to install minisom
pip3 install minisom

# install Homer if needed
```
  

  
## Quick start
- To test whether the package is working without error and go through important functions in TREASMO:
  - Download the toy example data via [Google Drive](https://drive.google.com/drive/folders/1pQY_Xj22KtizxYmxDzHekFFcGNMNCWa_?usp=sharing)
  - Follow this [Jupyter Notebook tutorial](example/quick_start.ipynb)  to get familiar with the package

- To prepare your own single-cell multiome data for TREASMO, see refer to Notebook [here](replication/1_Data_preprocessing.ipynb).


## Manuscript-related information
- For supplementary materials, please check the ``Supplementary_Materials`` folder
- For manuscript results replication, please check the ``replication`` folder
mpzinke 0.8.4
Python libraries for MPZinke.
Requires Python: >=3.11

# Python
Python libraries for MPZinke.

## Modules

### `DownloadIterator`
An object that takes a request to download large amounts of data and can run a function for each chunk.

#### Alternatives & Justification
`requests` allows for downloading large amounts of data, but when downloading a large amount of data, memory usage can be a factor. As such, writing to a file may be required. The DownloadIterator object wraps the request to allow for iterative download and processing of data.

Additionally, the request timeout specifies the amount of time for the server to respond, not the amount of time spent downloading the response. DownloadIterator provides a way to specify a maximum amount of time downloading a file.

#### Usage
[Usage can be found here](./Examples/DownloadIterator.py)
**Notably, `stream` must be set to `True`.**


### `Generic`
A class that can be called or inherited to make a function, method or class generic.

#### Alternatives & Justification
`typing.Generic` is a built-in class for generics. It however lacks the ability to be inherited from nor to store the generic's type. EG, if `MyGenericClass` inherits from `typing.Generic`, there is no way in `MyGenericClass[int]` to know the type of int once the class is instantiated.

Further more, `typing.Generic` cannot be applied to functions. As such, the `mpzinke.Generic` stores the type in a `.__args__` attribute like `list` and `Dict`.

#### Usage
[Usage can be found here]()


### `is_json(string: str) -> bool:`
`is_json` checks when a string is JSON parsable.

#### Alternatives & Justification
`json.loads` is the core of the `is_json` function. However to know if a string can be safely parsed, one must wrap it with a try-catch block. This does that automatically.

#### Usage
[Usage can be found here](./Examples/is_json.py)

#### Possible Future Enhancements
1. Add optional function to execute if string is successfully parsed.


### `Server`
`Server` is a class that wraps a Flask server to provide for easier server setup, error handling, authorization, and route addition. Additionally, it uses the doc strings of functions' passed to routes to document all endpoints.

#### Alternatives & Justification
Flask servers offer great API's for adding routes, but are limited in that a route only take 1 function for all METHODS. 

#### Usage
[Usage can be found here](./Examples/Generic.py)

#### Possible Future Enhancements
1. Add optional function to execute if string is successfully parsed.



A Flask server class for simple routing by HTTP method.




## Build Commands
FROM: https://packaging.python.org/en/latest/tutorials/packaging-projects/

- `python3 -m pip install --upgrade build`
- `python3 -m pip install --upgrade twine`
- `python3 -m build`
- `python3 -m twine upload --repository testpypi dist/*`
	- username: `__token__`
	- password: `<API KEY>`

`python3 -m pip install --index-url https://test.pypi.org/simple/ --no-deps python_server_MPZinke`
lavos 0.1.0
Lavos: A Pythonic Cron Expression Serializer with Fluent Syntax.
Requires Python: >=3.11,<4.0

# Lavos: A Pythonic Cron Expression Serializer with Fluent Syntax

Lavos is an innovative Python library that simplifies working with cron expressions. It replaces the cryptic syntax of traditional cron expressions with a fluent, human-readable API. Lavos allows you to define cron schedules for your tasks intuitively, making schedule management in Python applications easier than ever.

## Features
- **Fluent Syntax**: Enjoy a fluent and expressive syntax for defining cron schedules, making your code more readable and maintainable.
- **AWS Cron Support**: Compatible with traditional Unix and AWS cron expressions, providing versatility for different environments.
- **Syntax Sugars**: Includes convenient syntax sugars for common scheduling patterns, allowing for more concise code.

## Installation

Install Lavos using pip:

```bash
pip install lavos
```

## Usage

Lavos offers a range of functionalities for scheduling tasks. Below are examples demonstrating its versatility:

### Basic Usage

```python
from lavos import Lavos, MON, JAN, FEB, MAR, WEEKDAYS

cron = Lavos()
```


- **Every 5 Minutes**:
  ```python
  # Cron: */5 * * * *
  cron.every(5).minutes
  ```
- **Every Hour**:
  ```python
  # Cron: 0 * * * *
  cron.every(1).hours
  ```
- **Daily at Specific Time**:
  ```python
  # Cron: 0 14 * * *
  cron.at("14:00").daily
  ```
- **Specific Weekday at Time**:
  ```python
  # Cron: 0 12 * * 5
  cron.at("12:00").on(THU)
  ```
- **First Day of Every Month**:
  ```python
  # Cron: 0 0 1 * *
  cron.on(1).monthly
  ```
- **Specific Days of Specific Months**:
  ```python
  # Cron: 0 0 15 1,2 *
  cron.on(15).of(JAN, FEB)
  ```
- **Every Weekday at Multiple Times**:
  ```python
  # Cron: 0 9,17 * * 1-5
  cron.at("09:00", "17:00").on(WEEKDAYS)
  ```
- **First Day of Spring**:
  ```python
  # Cron: 0 0 20 3 *
  cron.on(20).of(MAR).annually()
  ```

### Using AWS Format

You can also create schedules using the AWS cron format:

```python
cron = Lavos(format="aws")

# Every 5 minutes in AWS format
# */5 * * * ? *
cron.every(5).minutes

# Every weekday at 09:00 in AWS format
# 0 9 * * ? *
cron.at("09:00").on(WEEKDAYS)
```

## Advanced Features

## Contributing

We welcome contributions to Lavos! Whether it's adding new features, improving documentation, or fixing bugs, your input is valuable.

## License

Lavos is released under MIT. See the LICENSE file for more details.