Metadata-Version: 2.1
Name: osl
Version: 0.1.1
Summary: OHBA Software Library
Home-page: UNKNOWN
Author: OHBA Analysis Group
License: MIT
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Requires-Dist: numpy
Requires-Dist: scipy
Requires-Dist: matplotlib
Requires-Dist: mne (>=1.0.0)
Requires-Dist: sklearn
Requires-Dist: fslpy
Requires-Dist: sails
Requires-Dist: tabulate
Requires-Dist: pyyaml (>=5.1)
Requires-Dist: neurokit2
Requires-Dist: jinja2
Requires-Dist: glmtools
Requires-Dist: numba
Requires-Dist: nilearn
Requires-Dist: dask
Requires-Dist: distributed
Requires-Dist: parse
Requires-Dist: opencv-python
Requires-Dist: pythreejs
Provides-Extra: dev
Requires-Dist: setuptools (>=41.0.1) ; extra == 'dev'
Requires-Dist: pytest ; extra == 'dev'
Requires-Dist: pytest-cov ; extra == 'dev'
Requires-Dist: coverage ; extra == 'dev'
Requires-Dist: flake8 ; extra == 'dev'
Provides-Extra: doc
Requires-Dist: sphinx (==4.0.2) ; extra == 'doc'
Requires-Dist: numpydoc ; extra == 'doc'
Requires-Dist: sphinx-gallery ; extra == 'doc'
Requires-Dist: pydata-sphinx-theme ; extra == 'doc'
Provides-Extra: full
Requires-Dist: setuptools (>=41.0.1) ; extra == 'full'
Requires-Dist: pytest ; extra == 'full'
Requires-Dist: pytest-cov ; extra == 'full'
Requires-Dist: coverage ; extra == 'full'
Requires-Dist: flake8 ; extra == 'full'
Requires-Dist: sphinx (==4.0.2) ; extra == 'full'
Requires-Dist: numpydoc ; extra == 'full'
Requires-Dist: sphinx-gallery ; extra == 'full'
Requires-Dist: pydata-sphinx-theme ; extra == 'full'

OHBA Software Library (OSL) in Python
=====================================
Python version of https://github.com/OHBA-analysis/osl-core.

Installation
------------
The recommended installation depends on your operating system. If you are installing on a Mac or Linux machine, we recommend:
```
git clone https://github.com/OHBA-analysis/oslpy.git
cd oslpy
conda env create -f envs/linux.yml
conda activate osl
pip install -e .
```
Here, the `-e` indicates we have installed in 'editable mode'. This means if we execute `git pull` or make any local modifications these changes will be reflected when we import the package.

If you use the OHBA workstation (hbaws) with TigerVNC, we recommend:
```
git clone https://github.com/OHBA-analysis/oslpy.git
cd oslpy
conda env create -f envs/hbaws-vnc.yml
conda activate osl
pip install -e .
```

On remote servers without displays specific package versions are required (related to source reconstruction visualisation). The following can be used to install on machines without a display:
```
git clone https://github.com/OHBA-analysis/oslpy.git
cd oslpy
conda env create -f envs/headless-server.yml
conda activate osl
pip install -e .
```

If you use the BMRC server, we recommend:
```
git clone https://github.com/OHBA-analysis/oslpy.git
cd oslpy
conda env create -f envs/bmrc.yml
conda activate osl
pip install -e .
```

If you use the OHBA workstation (hbaws) via the terminal only, we recommend:
```
git clone https://github.com/OHBA-analysis/oslpy.git
cd oslpy
conda env create -f envs/hbaws-no-display.yml
conda activate osl-nd
pip install -e .
```

For Developers
--------------
Run tests:
```
cd osl
pytest tests
```
or to run a specific test:
```
cd osl/tests
pytest test_file_handling.py
```

Build documentation:
```
python setup.py build_sphinx
```
Compiled docs can be found in `doc/build/html/index.html`.


