semvec/pypi-packages huggingface dataset:
aa-wanderer 0.1.5
AA wanderer
Requires Python: >=3.10

# aa-wanderer

[Alliance Auth](https://gitlab.com/allianceauth/allianceauth) application linking your auth with a [wanderer](https://wanderer.ltd/) instance.

**Currently, in active development. Use at your own risks**

Big shoutout to A-A-Ron for his work on [allianceauth-multiverse](https://github.com/Solar-Helix-Independent-Transport/allianceauth-discord-multiverse) without which I wouldn't have been able to have multiple services.

## Planned features
- [ ] Wanderer ACL management through the auth
- [ ] Automated pings when a marked system is connected to the home hole

## Usage
Currently, I recommend keeping a normal wanderer access list on your map that you configure yourself.
You can add your corporation/alliance on this access list to make sure that all mains can easily open your map.
It also allows you to add another group if needed during a joint op. \
The application will create another access list that will be fully managed and shouldn't be manually edited.
The only thing you can change on that access list is moving some characters to admin or manager to keep an overview.
But even these admin/manager characters will be removed from the access list if they lose access to the service.

## Installation

### Step 1 - Check prerequisites

1. aa-wanderer is a plugin for Alliance Auth. If you don't have Alliance Auth running already, please install it first before proceeding. (see the official [AA installation guide](https://allianceauth.readthedocs.io/en/latest/installation/auth/allianceauth/) for details)
2. You need to have a map with administrator access on wanderer to recover the map API key that will be used to create a new access list.

### Step 2 - Install app

Make sure you are in the virtual environment (venv) of your Alliance Auth installation. Then install the newest release from PyPI:

```bash
pip install aa-wanderer
```

### Step 3 - Configure Auth settings

Configure your Auth settings (`local.py`) as follows:

- Add `'wanderer'` to `INSTALLED_APPS`
- Add below lines to your settings file:

```python
CELERYBEAT_SCHEDULE['wanderer_cleanup_access_lists'] = {
    'task': 'wanderer.tasks.cleanup_all_access_lists',
    'schedule': crontab(minute='0', hour='*/1'),
}
```

### Step 4 - Finalize App installation

Run migrations & copy static files

```bash
python manage.py migrate
python manage.py collectstatic --noinput
```

Restart your supervisor services for Auth.


### Commands

The following commands can be used when running the module:

| Name                    | Description                                                                              |
|-------------------------|------------------------------------------------------------------------------------------|
| `wanderer_cleanup_acls` | Will execute the cleanup command on all your managed maps and update their access lists. |
py251112app 0.2.0
Development flow as Paleofuturistic Python
Requires Python: >=3.12

# py251112app

Development flow as Paleofuturistic Python

## Usage

Legacy: `pip install py251112app`

Preferred: `uv add py251112app`

## Developing further

> Development flow as [Paleofuturistic Python](https://github.com/schubergphilis/paleofuturistic_python)

Prerequisite: [uv](https://docs.astral.sh/uv/)

### Setup

- Clone this repository.
- Download additional dependencies: `uv sync --all-extras --dev`
- Optional: validate the setup with `uv run python -m unittest`

### Workflow

- Download dependencies (if you need any): `uv add some_lib_you_need`
- Develop (optional, tinker: `uvx --with-editable . ptpython`)
- QA:
    - Format: `uv run ruff format`
    - Lint: `uv run ruff check`
    - Type check: `uv run mypy`
    - Test: `uv run python -m unittest`
- Build (to validate it works): `uv build`
- Review documentation updates: `uvx --with mkdocstrings[python] mkdocs serve`
- Make a pull request.
AmpliGone 2.0.2
AmpliGone is a tool which accurately removes primer sequences from FastQ NGS reads in an amplicon sequencing experiment
Requires Python: >=3.10

[![CodeFactor](https://www.codefactor.io/repository/github/rivm-bioinformatics/ampligone/badge)](https://www.codefactor.io/repository/github/rivm-bioinformatics/ampligone)
![GitHub release (latest by date including pre-releases)](https://img.shields.io/github/v/release/RIVM-bioinformatics/AmpliGone?include_prereleases)
![GitHub](https://img.shields.io/github/license/RIVM-bioinformatics/AmpliGone)  
[![Build and release](https://github.com/RIVM-bioinformatics/AmpliGone/actions/workflows/release.yml/badge.svg)](https://github.com/RIVM-bioinformatics/AmpliGone/actions/workflows/release.yml)
![GitHub deployments](https://img.shields.io/github/deployments/RIVM-bioinformatics/AmpliGone/github-pages?label=Documentation%20deployment)  
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/ampligone/README.html)


# AmpliGone

AmpliGone is a tool which accurately finds and removes primer sequences from NGS reads in an amplicon experiment.

In contrast to a lot of other primer-removal tools, AmpliGone does not actively look for primer sequences within the NGS reads. Instead, reads are trimmed based on primer sequence coordinates in relation to a given reference sequence.
Additionally, AmpliGone is able to compensate for, and therefore properly clean, reads that start or end outside of a primer-region as this is a common occurrence in amplicon-based sequencing data.

AmpliGone is build and tested with Nanopore and Illumina data (fastq) in mind and supports 'end-to-end', 'end-to-mid' and 'fragmented' amplicons to be cleaned.  
Please see [this page](https://rivm-bioinformatics.github.io/AmpliGone/latest/amplicon-types/) to learn more about this terminology.

## Installation instructions

AmpliGone can be installed easily with [conda](https://anaconda.org/bioconda/ampligone) or [pip](https://pypi.org/project/AmpliGone/).
Installation through conda is recommended.

### Installation with conda

```bash
conda install -c bioconda ampligone
```

### Installation with pip

```bash
pip install AmpliGone
```

Please see the [documentation](https://rivm-bioinformatics.github.io/AmpliGone/) for more information as well as extended [installation instructions](https://rivm-bioinformatics.github.io/AmpliGone/latest/installation/) and [usage instructions](https://rivm-bioinformatics.github.io/AmpliGone/latest/user-guide/).

AmpliGone is freely available under the [AGPLv3 license](https://www.gnu.org/licenses/agpl-3.0.en.html).

If you use AmpliGone in your work, please cite us as follows:
> Zwagemaker, F., Hajji, K., Raaijmakers, G., Schmitz, D., Kroneman, A. AmpliGone [Computer software]. https://doi.org/10.5281/zenodo.7684307