semvec/pypi-packages huggingface dataset:
geoslurp 3.1.0
Python postgreSQL-PostGIS client for managing earth science datasets
Requires Python: >=3.8

# Download and manage datasets in a PostGreSQL database with the PostGIS

[![Build and Publish](https://github.com/strawpants/geoslurp/actions/workflows/python-publish.yml/badge.svg)](https://github.com/strawpants/geoslurp/actions/workflows/python-publish.yml)
[![PyPI version](https://badge.fury.io/py/geoslurp.svg)](https://badge.fury.io/py/geoslurp)
[![Documentation Status](https://readthedocs.org/projects/geoslurp/badge/?version=latest)](https://geoslurp.wobbly.earth/latest/?badge=latest)
The idea is that this tool contains script to download (i.e. **slurp**) commonly used datasets and to register them in a postgresql+postgis database. This database can then be queried allowing the retrieval of the relevant data or datafiles. 

The main documentation lives at [geoslurp.wobbly.earth](https://geoslurp.wobbly.earth)

## Workings

The geoslurp module itself is a pure python module, which acts as a client. For this to work one needs to [set up a running PostGreSQL database](https://github.com/strawpants/docker-geoslurp).

![Image of geoslurp clients versus database server](docs/source/_static/geoslurp_network.svg)

## Change log V3
* Use python entry points to register datasets, views and functions (removes registration of user plugin directories)
* Move documentation to [https://readthedocs.org](https://geoslurp.wobbly.earth)
* Change github actions to pusblish and then release
* Work with SQAlchemy 2
* more (see commit messages)

## TODO's
* Move remaining 'orphaned' datasets to suitable python packages modules or include in the main package
* Improve this README
mstr-rest-requests 0.15.0
Easily make requests of the MicroStrategy REST API
Requires Python: <4,>=3.9

# mstr-rest-requests

A extension to the excellent `requests` `Session` object, to enable more straightforward interaction with MicroStrategy's REST API.

![Python package](https://github.com/paulbailey/mstr-rest-requests/workflows/Python%20package/badge.svg)

## Usage

### Installation

Simply install the package however you normally install them, for example:

`pip install mstr-rest-requests`

### Examples

#### Authentication

Here's how to get an authenticated session (currently only standard and anonymous authentication are supported):

```
from mstr.requests import MSTRRESTSession

session = MSTRRESTSession(base_url='https://demo.microstrategy.com/MicroStrategyLibrary/api/')
session.login(username='dave', password='hellodave')
session.has_session()
# returns True
```

#### Session handling

Several convenience methods are implemented to make dealing with Session objects easier.

`def has_session(self)`

Will return a boolean as to whether the session contains an authentication tokem.

`def destroy_auth_token(self)`

Removes the auth token from the session

`def json(self)`

Returns a JSON representation of the session that can be reconstituted with:

`update_from_json(self, data)`

where `data` is either a dict or a string containing JSON data.

#### HTTP requests

The MSTRRESTSession adds two parameters to all request methods:

`include_auth=True, project_id=None`

so you can specify a `project_id` on any request by adding the parameter.

#### Convenience methods for API calls

TODO
newmap 0.2
Newmap: tools for genome and methylome mappability
Requires Python: >=3.9

# Newmap

## Introduction

Newmap is a software package that efficiently identifies uniquely mappable
regions of any genome. It accomplishes this task by outputting read lengths at
every position that are unique to that genome. From the range of unique read
lengths produced, the single-read mappability and the multi-read mappability
for a specific read length can be generated.

Newmap can search for unique k-mer/read lengths on specific values, or entire
continuous ranges using a binary search method allowing for finding the
minimum possible unique k-mer/read length.

Newmap requires a CPU that supports the AVX2 instruction set.

OpenMP is required for parallel processing.

## Documentation
The latest for Newmap is available on [Read the Docs](https://newmap.readthedocs.io).

All commands have a `--help` option to provide additional usage information.

## Quick start

### Installation

#### Python Package Index (PyPI)
```python
pip install newmap
```

#### Bioconda
```bash
conda install newmap
```

### Usage

#### 1. Create an index for a genome
```bash
newmap index genome.fa
```
By default this will create a `genome.awfmi` file in the current directory.

#### 2. Find the minimum unique k-mer lengths for the genome using the index
Searching the entire genome, using 20 threads, printing status information, and
searching lengths ranging from 20 to 200 bp:
```bash
newmap search --verbose --num-threads=20 --search-range=20:200 --output-directory=unique_lengths genome.fa
```
This will create `*.unique.uint8` files (one for each sequence ID) in the `unique_lengths` directory.

#### 3. Convert the unique lengths to mappability tracks
To output single-read and multi-read mappability for a 24 bp read length:
```bash
newmap track --single-read=24.bed --multi-read=24.wig 24 unique_lengths/*.unique.uint8
```
For both single-read and multi-read mappability, this will generate a single
file that contains the mappability for all sequences listed in the
`unique_lengths` directory.
The resulting BED file will be the single read mappability, and the WIG file
will be the multi-read mappability.


Credits
-------
Newmap is a reimplementation of the output of Umap. Umap was developed by Mehran Karimzadeh.
The repository for that implmemention is found at [https://www.github.com/hoffmangroup/umap](https://www.github.com/hoffmangroup/umap).
Umap in turn was originally developed by Anshul Kundaje and was written in MATLAB.
The original repository is available [https://sites.google.com/site/anshulkundaje/projects/mappability](https://sites.google.com/site/anshulkundaje/projects/mappability).

This project uses the excellent [AvxWindowFMIndex
library](https://github.com/TravisWheelerLab/AvxWindowFmIndex). Read their
published article here
([https://doi.org/10.1186/s13015-021-00204-6](https://doi.org/10.1186/s13015-021-00204--6))