Metadata-Version: 2.1
Name: fsl-pipe
Version: 0.6.0
Summary: Declative pipelines based on Filetrees
Home-page: https://git.fmrib.ox.ac.uk/ndcn0236/fsl-pipe
Author: Michiel Cottaar
Author-email: michiel.cottaar@ndcn.ox.ac.uk
Project-URL: Bug Tracker, https://git.fmrib.ox.ac.uk/ndcn0236/fsl-pipe/-/issues
Project-URL: Documentation, https://open.win.ox.ac.uk/pages/ndcn0236/fsl-pipe
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.6
Description-Content-Type: text/markdown
License-File: LICENSE

[![Documentation](https://img.shields.io/badge/Documentation-pipe--tree-blue)](https://open.win.ox.ac.uk/pages/ndcn0236/fsl-pipe)
[![File-tree Documentation](https://img.shields.io/badge/Documentation-file--tree-blue)](https://open.win.ox.ac.uk/pages/ndcn0236/file-tree)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6577070.svg)](https://doi.org/10.5281/zenodo.6577070)
[![Pipeline status](https://git.fmrib.ox.ac.uk/ndcn0236/fsl-pipe/badges/main/pipeline.svg)](https://git.fmrib.ox.ac.uk/ndcn0236/fsl-pipe/-/pipelines/latest)
[![Coverage report](https://git.fmrib.ox.ac.uk/ndcn0236/fsl-pipe/badges/main/coverage.svg)](https://open.win.ox.ac.uk/pages/ndcn0236/fsl-pipe/htmlcov)

Declative pipelines based on Filetrees

# Installation
```shell
pip install fsl-pipe
```

Any bug reports and feature requests are very welcome (see [issue tracker](https://git.fmrib.ox.ac.uk/ndcn0236/fsl-pipe/-/issues)).

# Setting up local test environment
First clone the repository:
```shell
git clone https://git.fmrib.ox.ac.uk/ndcn0236/fsl-pipe.git
```

Then, we install the package in an interactive manner:
```shell
cd fsl-pipe
pip install -e .
```

## Running tests
Tests are run using the [pytest](https://docs.pytest.org) framework. After installation (`pip install pytest`) they can be run from the project root as:
```shell
pytest src/tests
```

## Compiling documentation
The documentation is build using [sphinx](https://www.sphinx-doc.org/en/master/). After installation (`pip install sphinx`) run:
```shell
cd doc
sphinx-build source build
open build/index.html
```

## Contributing
[Merge requests](https://git.fmrib.ox.ac.uk/ndcn0236/fsl-pipe/-/merge_requests) with any bug fixes or documentation updates are always welcome. 

For new features, please raise an [issue](https://git.fmrib.ox.ac.uk/ndcn0236/fsl-pipe/-/issues) to allow for discussion before you spend the time implementing them.

## Releasing new versions
- Run `bump2version` (install using `pip install bump2version`)
- Push to gitlab (including tags in the push)
- After the continuous integration (CI) succeeds, manually run the job to upload fsl-pipe to pypi (see [here](https://git.fmrib.ox.ac.uk/ndcn0236/fsl-pipe/-/pipelines/latest))
- Upload code on conda-forge using their automated release detection.
