semvec/pypi-packages huggingface dataset:
pylich 0.4.0
A super simple Python utility to check for dead links in a website
Requires Python: <4.0,>=3.9

# PyLich

![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/georgeholt1/pylich/unit_tests.yml)
![PyPI - Version](https://img.shields.io/pypi/v/pylich)
![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pylich)
![GitHub License](https://img.shields.io/github/license/georgeholt1/pylich)

A super simple Python utility to check for dead links in a website.

## Installation

PyLich is available on [PyPI](https://pypi.org/project/pylich/) and can be installed using [pip](https://pip.pypa.io/en/stable/):

```bash
pip install pylich
```

## Usage

Simply provide the URL of the sitemap and `pylich` will crawl through links in the pages and check their status. `pylich` can be used as a command line tool or as a Python package.

### Command Line

```bash
pylich https://www.example.com/sitemap.xml
```

The command will exit with a status code of 1 if any dead links are found and 0 otherwise.

#### Options

| Flag | Arguments | Description |
| --- | --- | --- |
| `-v` | N/A | Verbose mode. Print progress to the console as well as a summary of the dead links at the end. |
| `-i` | List of integer HTTP response codes | Ignore links with the specified HTTP response codes. |
| `--failed-is-dead` | N/A | Treat any failed HTTP request as a dead link, regardless of the HTTP status code. |

```bash
pylich https://www.example.com/sitemap.xml -v -i 404 500
```

### Python Package

PyLich can also be used as a Python package. 

```python
from pylich import LinkChecker
checker = LinkChecker(
    "https://www.example.com/sitemap.xml",
    verbose=True,
    ignored_status_codes=[404, 500]
)
urls = checker.get_sitemap_urls()
broken_links = checker.check_links(urls)
checker.print_dead_links()
```

## Contributing

Pull requests are welcome.

Package and dependency management is done using [Poetry](https://python-poetry.org/). To install the dependencies and the package in development mode, run:

```bash
poetry install
```

To run the tests, run:

```bash
pytest
```

Pre-commit hooks are available to run code formatting and linting. To install the hooks, run:

```bash
pre-commit install
```
Bering 0.1.2
Bering: Transfer Learning of Cell Segmentation and Annotation for Spatial Omics

|PyPI| |Docs| |downloads|

Bering - Spatial Segmentation and Cell Annotation in Python
================================================

**Bering** is a deep learning algorithm for simultaneous molecular annotation and cell segmentation in single-cell spatial transcriptomics data. 
It builds on top of `torch_geometric`_ and `scanpy`_, from which it inherits modularity and scalability.
It provides versatile models that leverages the spatial coordinates of the data, as well as pre-trained models across spatial technologies and tissues.

Visit our `documentation`_ for installation, tutorials, examples and more.

Bering's key applications
--------------------------
- Identify background and real signals in noisy spatial transcriptomics data.
- Identify cell annotations for transcripts on single-cell spatial data.
- Efficiently cell segmentation with cell annotations.
- Build and fine-tune pre-trained model on new data using transfer learning.

Installation
------------
Install Bering via PyPI by running::

    pip install Bering

or via Conda as::

    conda install -c conda-forge Bering

Manuscript
----------
Please refer to our manuscript `Jin, Zhang et al. (2023)`_ for more details.

Contact
-----------------------
We are happy about any feedback! If you have any questions, please feel free to contact kangjin@fas.harvard.edu, zuobai.zhang@mila.quebec.
Find more research in `Shu_Jian_Lab`_.

.. |PyPI| image:: https://img.shields.io/pypi/v/Bering
    :target: https://pypi.org/project/Bering/
    :alt: PyPI

.. |Docs| image:: https://img.shields.io/readthedocs/bering
    :target: https://bering.readthedocs.io/en/latest/
    :alt: Documentation

.. |downloads| image:: https://img.shields.io/pepy/dt/Bering
    :target: https://www.pepy.tech/projects/Bering
    :alt: Downloads

.. _Jin, Zhang et al. (2023): https://www.biorxiv.org/content/10.1101/2023.09.19.558548v1
.. _scanpy: https://scanpy.readthedocs.io/en/stable/
.. _torch_geometric: https://pytorch-geometric.readthedocs.io/en/latest/
.. _documentation: https://bering.readthedocs.io/en/latest/
.. _Shu_Jian_Lab: https://www.jianshulab.org/team
sims-slack-bot 0.1.0
A simple Slack bot for sending messages to channels and users
Requires Python: >=3.6

# Slack DM Bot

A simple Python bot for sending direct messages to users on Slack.

## Installation

1. Install the required package:
```bash
pip install sims-slack-bot
```

## Configuration

1. Load the config file I'll send to y'all through slack. That config file contains the bot token and also the users ID so you can be found by the bot. The file format is as follows (JSON):
```json
{
    "slack_token": "xoxb-your-bot-token",
    "users": {
        "username1": "U12345678",
        "username2": "U87654321"
    }
}
```

## Usage

```python
from sims_slack_bot import EnhancedSlackBot

# Initialize the bot with your config file
bot = EnhancedSlackBot('config.json')

# Send a DM using username from config
bot.send_dm(
    user_name="username1",
    message="Hello! This is a test message",
    emoji=":robot_face:"  # Optional, defaults to :robot_face:
)
```

## send_dm() Method Details

The `send_dm()` method allows you to send direct messages to Slack users in two ways:

### Parameters

- `user_name` (str): The username as defined in your config file
- `message` (str): The message content to send
- `emoji` (str, optional): Custom emoji to appear before the message. Defaults to ":robot_face:"
- `email` (str, optional): User's Slack email address (alternative to username)

### Features

- Messages are automatically formatted with timestamp and emoji
- Can identify users either by configured username or email address
- Provides error handling for invalid users or failed message delivery
- Prints confirmation when message is successfully sent

### Example Output Format

Your message will be formatted as:
```
🤖 *Bot Message* (2024-01-14 15:30:45)
Your message text here
```

## Error Handling

The method will raise a ValueError if:
- The specified username is not found in the config file
- The provided email doesn't correspond to a valid Slack user