semvec/pypi-packages huggingface dataset:
summer-ai 0.0.3
ai cli tool
License: MIT
Requires Python: >=3.10

# Python Project

## Usage

```sh
venv/bin/python main.py

curl localhost:7869/api/generate -d '{
	"model": "llama3.1",
	"prompt": "hi",
	"stream": false
}'
```

## Environment

| key             | type   | default                 | description                             |
| --------------- | ------ | ----------------------- | --------------------------------------- |
| HOST            | string | "http://localhost:7869" | base url to the Ollama server           |
| MODEL           | string | "llama3.2"              | default model to use                    |
| KEEP_ALIVE_MINS | int    | 20                      | max time to keep unused model in memory |
JupyterClearCheck 0.2.1
A Python CLI to check that a Jupyter Notebook's Outputs' have been cleared.
License: MIT
Requires Python: >=3.9

# JupyterClearCheck

![Build Status](https://github.com/guru-desh/JupyterClearCheck/actions/workflows/ci.yml/badge.svg) ![License](https://img.shields.io/github/license/guru-desh/JupyterClearCheck) ![PyPI version](https://img.shields.io/pypi/v/JupyterClearCheck)

A Python CLI to check that a Jupyter Notebook's Outputs' have been cleared.

## Why does this exist?

During the development of a Jupyter Notebook, it is common to run cells multiple times. Every time a cell is run, its output is stored in the `.ipynb` file format. Because the outputs are saved, this can cause merge conflicts in version control systems like Git when multiple people are working on the same notebook.

`nbconvert` can be used to clear the outputs of a notebook, but to our knowledge, there was no package to check if the outputs have been cleared. This package aims to fill that gap. 

This package can be used in a CI/CD pipeline to ensure that the outputs of a notebook have been cleared before merging a pull request reducing merge conflicts on the outputs of a notebook.

## Installation

This package is available on PyPI and can be installed using pip.

```bash
pip install JupyterClearCheck
```

## Usage

You can run the command via `jupyterclearcheck` or `python -m jupyterclearcheck`.

```bash
$ jupyterclearcheck --help

usage: jupyterclearcheck [-h] --notebook NOTEBOOK

Check a Jupyter Notebook for output cells.

options:
  -h, --help           show this help message and exit
  --notebook NOTEBOOK  Path to the Jupyter Notebook file
```

The notebook parameter is required and should be the path to the Jupyter Notebook file.

## Contributing

We welcome contributions! Thank you in advance for your help. Feel free to submit a pull request or open an issue.

### Getting Started for Development

We use Python 3.9 and PDM for dependency management. To get started, install Python 3.9 and then install PDM using pip.

```bash
pip install pdm
```

Once this step is done, PDM can be used to run commands related to the development of this package.

- Install dependencies: `pdm install`
- Run linting and formatting: `pdm run lint_and_format`
- Checking linting, formatting, and type annotations: `pdm run check`
- Run tests: `pdm run test`
- Build package: `pdm build`

#### Running CI pipeline locally

The CI pipeline can be run locally using the following scripts:

- Windows: `./build_and_test.sh`
- Linux/MacOS: `./build_and_test.cmd.`

## Future Work

- [ ] Add shellcheck to lint bash scripts currently in use
- [ ] Add pre-commit hook
- [ ] Add markdown lint
- [ ] Publish on conda-forge
pyTwoBit 0.1.0
A fast reader for local or remote UCSC twobit sequence files.
License: MIT

# pyTwoBit

Package for fetching sequence from twobit files from local paths or URLs. 

## Usage

To fetch sequence for a genomic region create a TwoBit object with either a local file path or url.  Sequence
is fetched with the `fetch` function which takes chromosome name, start, and end coordinates.
The UCSC coordinate convention is used (0 start, half-open).


Local file

```python

from pytwobit import TwoBit

twobit = TwoBit('test.2bit')
seq = twobit.fetch("chr1", 50, 57)  # -> "CTATCTA"


```

Remote file

```python

from pytwobit import TwoBit

twobit = TwoBit("https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit")
seq = twobit.fetch("chr1", 120565294, 120565335)  # -> "TATGAACTTTTGTTCGTTGGTgctcagtcctagaccctttt"

```