semvec/pypi-packages huggingface dataset:
fabrial 0.2.8
Fabrial lets you create sequences to automate lab experiments.
Requires Python: >=3.13

## Fabrial

Fabrial runs user-built sequences. It was originally designed to control lab instruments, but it can be extended through plugins to do much more.

## Installation

> The easiest way to install and manage Python executables is with [`uv tool`](https://docs.astral.sh/uv/guides/tools/). See [`uv`](https://docs.astral.sh/uv/)'s documentation for using this command. Otherwise, I highly recommend using a [virtual environment](https://docs.python.org/3/library/venv.html).

Install fabrial with
```
pip install fabrial
```
and run it with
```
fabrial
```

### Application Shortcut

If you'd like Fabrial to have an application shortcut (i.e. the Start Menu on Windows or a `.desktop` file on Linux), run

```
pip install fabrial[shortcut]
```

instead. Then, inside virtual environment Fabrial is installed in, enter the Python shell and run

```
>>> import fabrial
>>> fabrial.create_application_shortcut()
```

## Usage

Drag and drop sequence actions from the left into the sequence builder on the right. Then, select a directory to record data it, press the start button, and voilà! You've got a running sequence. Each action has its own parameters you can customize from the sequence builder, as well as a description of what the action does.

## Plugins

Fabrial does very little on its own, but it can be extended through plugins that add new sequence actions.

Fabrial plugins on [PyPi](https://pypi.org/) are generally prefixed with `fabrial-`. If you install a local plugin with `pip`, Fabrial will recognize it automatically. Global plugins can be installed through the settings menu. Note that if a plugin is installed in both the current environment and in the **`plugins`** folder, the latter plugin is ignored.

If no plugin exists for your use case, you can also [write your own](./doc/plugin_guide/plugin_guide.md)!

## Error Log
Fabrial logs any errors it encounters in **`HOME/.fabrial/lastrun.log`**. This error log is wiped at startup, so if Fabrial encounters an error, please consider reporting before starting restarting the application!

## Icons Attribution

Fabrial's [internal](./fabrial/assets/icons/internal/) icons come from the [Fugue Icon Set](https://p.yusukekamiyamane.com/) by [Yusuke Kamiyamane](https://p.yusukekamiyamane.com/about/), which is licensed under [CC BY 3.0](https://creativecommons.org/licenses/by/3.0/).
movierender 0.2.1
A package for rendering images and overlay data to video; designed for microscopy data.
Requires Python: >=3.9
Keywords: microscopy, movie, render

# Movie Render
This package renders movies from configuration files referencing microscopy data.

## Table of contents
* [Documentation](#documentation)
* [Setup](#setup)
* [Features](#features)
* [Status](#status)
* [Contact](#contact)
* [License](#license)


## Documentation
See documentation [here](docs/main.md)

## Setup
`pip install movierender`
    
### Libraries used
* [FileOps](https://github.com/fabio-echegaray/fileops) (sister project for data loading)
* [Matplotlib](https://github.com/matplotlib/matplotlib)

The package also uses other libraries.
For a complete list, check the dependencies variable of the pyproject.toml file.


## Features
### Ability to write configuration files for volume export and movie rendering
This feature helps to programmatically render different versions of the data.
For example, it is possible to export the data in volumetric formats using either OpenVDB or the VTK library. 
Similarly, it can render the data in a movie format using each channel separately, or in a composite image.
For more details, see the documentation of the [FileOps project](https://github.com/fabio-echegaray/fileops) where the syntax of configuration files is specified.
I'm currently working on the declarative grammar of this feature to make it consistent.


### To-do list for development in the future:
* Keep writting test functions (maybe generate a repository of image files to test against?).
* Write examples of file export.
* Improve exporting volumetric files and the related syntax in the configuration files.

## Status
Project is active writing and _in progress_.

## Contact
Created by [@fabioechegaray](https://twitter.com/fabioechegaray)
* [fabio.echegaray@gmail.com](mailto:fabio.echegaray@gmail.com)
* [GitHub](https://github.com/fabio-echegaray)
Feel free to contact me!

## License
    Movie-Render
    Copyright (C) 2021-2025  Fabio Echegaray

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU Affero General Public License as
    published by the Free Software Foundation, either version 3 of the
    License, or (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU Affero General Public License for more details.

    You should have received a copy of the GNU Affero General Public License
    along with this program.  If not, see <https://www.gnu.org/licenses/>.
vbl-aquarium 1.2.0
Collection of Pydantic models describing data objects passed between Virtual Brain Lab projects.
Requires Python: >=3.8
Keywords: neuroscience, pydantic, virtualbrainlab

# Virtual Brain Lab Aquarium

![PyPI - Version](https://img.shields.io/pypi/v/vbl-aquarium)
[![Build Models](https://github.com/VirtualBrainLab/vbl-aquarium/actions/workflows/build-models.yml/badge.svg)](https://github.com/VirtualBrainLab/vbl-aquarium/actions/workflows/build-models.yml)
[![Static Analysis](https://github.com/VirtualBrainLab/vbl-aquarium/actions/workflows/static-analysis.yml/badge.svg)](https://github.com/VirtualBrainLab/vbl-aquarium/actions/workflows/static-analysis.yml)
[![Pydantic v2](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/pydantic/pydantic/main/docs/badge/v2.json)](https://pydantic.dev)
[![Hatch project](https://img.shields.io/badge/%F0%9F%A5%9A-Hatch-4051b5.svg)](https://github.com/pypa/hatch)
[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
[![Checked with pyright](https://microsoft.github.io/pyright/img/pyright_badge.svg)](https://microsoft.github.io/pyright/)

Collection of Pydantic models describing data objects passed between Virtual
Brain Lab projects.

Corresponding JSON schema and C# files are generated automatically and are
located in the `models` directory.

## Usage

For C# structs or JSON schemas, copy or reference whatever models you need from
the `models` directory.

To use the Pydantic models directly in Python, install the package with

```bash
pip install vbl-aquarium
```

Then import the models with

```python
from vbl_aquarium.models.module_name import ModelName
```

replacing `.module_name` and `ModelName` with the desired model.

## Further Documentation

For more information regarding updating models and each model's specification,
see the VBL
Aquarium [documentation](https://aquarium.virtualbrainlab.org).