semvec/pypi-packages huggingface dataset:
genome-grist 0.11.7
tools to support genome and metagenome analysis
Requires Python: >=3.12

# genome-grist README

<!-- CTB: this is /README.md in dib-lab/genome-grist -->

<a href="https://pypi.org/project/genome-grist/"><img alt="PyPI" src="https://badge.fury.io/py/genome-grist.svg"></a>
<img alt="License: 3-Clause BSD" src="https://img.shields.io/badge/License-BSD%203--Clause-blue.svg">

genome-grist analyzes the strain composition of microbial metagenomes
using
[minimum metagenome covers](https://dib-lab.github.io/2020-paper-sourmash-gather/)
and produces a variety of compositional and taxonomic summaries.

Check out the
[quick start!](https://dib-lab.github.io/genome-grist/quickstart/) And
please also see
[the rest of the docs](https://dib-lab.github.io/genome-grist/) for
more information!

## Example: the strain composition of a gut microbiome (iHMP)

This figure was autogenerated by genome-grist.

![an example image made with genome-grist](doc/gather-vs-mapping.png)

---

[CTB](https://twitter.com/ctitusbrown/) 01/22
get-some-ncbi-genomes 0.3.3
download one or more NCBI genomes by accession
Requires Python: >=3.11

# get-some-ncbi-genomes

## Installation

```
pip install get-some-ncbi-genomes
```

## Usage

Download one or more NCBI genomes, given accession.

Build a CSV file containing download info:
```
get-some-ncbi-genomes GCA_002440745.1 --csv xyz.csv
```

Download the genome files directly:
```
get-some-ncbi-genomes --output-dir genomes/ --download-genomes GCA_002440745.1
```

Use the sourmash plugin to download genome files and make an info.csv:
```
sourmash scripts get-genomes GCA_002440745.1
```

## Support

We suggest filing issues in [the main sourmash issue tracker](https://github.com/dib-lab/sourmash/issues) as that receives more attention!

## Dev docs

`get-some-ncbi-genomes` is developed at https://github.com/ctb/get-some-ncbi-genomes/

### Testing

Run:
```
pytest tests
```

### Generating a release

Bump version number in `pyproject.toml` and push.

Make a new release on github.

Then pull, and:

```
python -m build
```

followed by `twine upload dist/...`.
processflow 1.0.1
A Python package for creating process flow diagrams
Requires Python: >=3.9

# ProcessFlow

A Python package for creating process flow diagrams and BPMN-style workflow visualizations.

## Features

- Create process maps with pools and lanes
- Add various elements: start/end events, tasks, gateways, etc.
- Connect elements with labeled connections
- Export to PNG, SVG, and other formats
- Export to BPMN XML and Draw.io formats
- Customizable themes and styling

## Installation

```bash
pip install processflow
```

## Quick Start

```python
import processflow

# Create a process map
with processflow.ProcessMap(title="Order Processing") as pm:
    # Add a lane
    lane = pm.add_lane("Customer Service")
    
    # Add elements
    start = lane.add_element("Receive Order", processflow.EventType.START)
    task = lane.add_element("Process Order", processflow.ActivityType.TASK)
    end = lane.add_element("Order Complete", processflow.EventType.END)
    
    # Connect elements
    start.connect(task)
    task.connect(end)

# Draw and save
pm.draw()
pm.save("process_diagram.png")
```

## Documentation

For detailed documentation and examples, visit the project repository.

## License

MIT License