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Merge pull request #58 from BrainLesion/45-we-need-readthedocs
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45 we need readthedocs
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MarcelRosier authored Apr 8, 2024
2 parents 7fe8fa4 + 4608437 commit 760f5e7
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22 changes: 5 additions & 17 deletions .readthedocs.yaml
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# .readthedocs.yaml
# Read the Docs configuration file
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details

# Required
version: 2

# Set the version of Python and other tools you might need
build:
os: ubuntu-22.04
os: "ubuntu-22.04"
tools:
python: "3.10"
jobs:
post_create_environment:
# Install poetry
# https://python-poetry.org/docs/#installing-manually
- pip install poetry
# Tell poetry to not use a virtual environment
- poetry config virtualenvs.create false
post_install:
# Install dependencies with 'docs' dependency group
# https://python-poetry.org/docs/managing-dependencies/#dependency-groups
- poetry install --with docs
# VIRTUAL_ENV needs to be set manually for now.
# See https://github.com/readthedocs/readthedocs.org/pull/11152/
- VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs

# Build documentation in the docs/ directory with Sphinx
sphinx:
configuration: docs/source/conf.py
# If using Sphinx, optionally build your docs in additional formats such as PDF
# formats:
# - pdf

# Optionally declare the Python requirements required to build your docs
configuration: docs/source/conf.py
10 changes: 7 additions & 3 deletions README.md
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[![PyPI version preprocessing](https://badge.fury.io/py/eReg.svg)](https://pypi.python.org/pypi/eReg/)
[![Documentation Status](https://readthedocs.org/projects/ereg/badge/?version=latest)](http://ereg.readthedocs.io/?badge=latest)
[![tests](https://github.com/BrainLesion/eReg/actions/workflows/tests.yml/badge.svg)](https://github.com/BrainLesion/eReg/actions/workflows/tests.yml)

# eReg - A Simple Registration Tool
**eReg** is a robust, fast and user-friendly registration tool that can be used in clinical environments without the need for virtualization or containerization technologies. It supports most platforms across various hardware configurations.

## Need

Because of security concerns, users in clinical environments do not have access to virtualization and containerization technologies such as Docker and Singularity. This becomes a problem, because most research code (especially for image registration) is built around the need to have access to these technologies. Alternatively, some tools only work on a Linux environment, or they need specific hardware resources (such as a DL accelerator card), which are not always available in clinical settings.

**eReg** is a simple registration tool that can be used in clinical environments without the need for virtualization or containerization technologies. It supports most platforms across various hardware configurations.


## Installation

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```
### Pythonic Interface
The `ereg` package provides two Python interfaces, an object-oriented interface, as well as convenience functions.
The `ereg` package provides two Python interfaces, an object-oriented interface, as well as convenience functions. A [Jupyter notebook tutorial](https://github.com/BrainLesion/tutorials/tree/main/eReg) is available to illustrate usage of the Python API.
#### Object-Oriented Interface
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4 changes: 2 additions & 2 deletions docs/source/conf.py
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# -- Project information -----------------------------------------------------

project = "panoptica"
project = "eReg"
copyright = "2023, florian kofler et al."
author = "Florian Kofler et al."

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autodoc_default_options = {
"members": True,
"undoc-members": True,
"private-members": True,
"private-members": False,
"show-inheritance": True,
}
14 changes: 14 additions & 0 deletions docs/source/ereg.rst
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eReg
======================


ereg.registration
--------------------------------------------

.. automodule:: ereg.registration


ereg.functional
--------------------------------------------

.. automodule:: ereg.functional
14 changes: 14 additions & 0 deletions docs/source/ereg.utils.rst
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eReg utils
======================


ereg.metrics
--------------------------------------------

.. automodule:: ereg.utils.metrics


ereg.io
--------------------------------------------

.. automodule:: ereg.utils.io
21 changes: 4 additions & 17 deletions docs/source/index.rst
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.. panoptica documentation master file, created by
sphinx-quickstart on Tue Nov 21 12:02:41 2023.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.

Welcome to panoptica's documentation!
Welcome to eReg's documentation!
=====================================

.. include:: ../../README.md
Expand All @@ -24,22 +20,13 @@ Indices and tables

.. toctree::
:maxdepth: 2
:caption: Panoptica:

panoptica.rst



.. toctree::
:maxdepth: 2
:caption: Metrics:

panoptica.metrics.rst
:caption: eReg:

ereg.rst


.. toctree::
:maxdepth: 2
:caption: Utils:

panoptica.utils.rst
ereg.utils.rst
22 changes: 0 additions & 22 deletions docs/source/panoptica.metrics.rst

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32 changes: 0 additions & 32 deletions docs/source/panoptica.rst

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23 changes: 0 additions & 23 deletions docs/source/panoptica.utils.rst

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16 changes: 8 additions & 8 deletions pyproject.toml
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Expand Up @@ -37,11 +37,11 @@ pytest-mock = "^3.6.0"
register = "ereg.cli.run:main"
ereg = "ereg.cli.run:main"

# [tool.poetry.group.docs]
# optional = true

# [tool.poetry.group.docs.dependencies]
# Sphinx = ">=7.0.0"
# sphinx-copybutton = ">=0.5.2"
# sphinx-rtd-theme = ">=1.3.0"
# myst-parser = ">=2.0.0"
[tool.poetry.group.docs]
optional = true

[tool.poetry.group.docs.dependencies]
Sphinx = ">=7.0.0"
sphinx-copybutton = ">=0.5.2"
sphinx-rtd-theme = ">=1.3.0"
myst-parser = ">=2.0.0"

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