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fepegar merged 1 commit into from
Jul 13, 2025
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Remove references to Read the Docs #1348

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27 changes: 0 additions & 27 deletions .readthedocs.yml
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63 changes: 31 additions & 32 deletions README.md
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@@ -1,6 +1,6 @@
<!-- markdownlint-disable -->
<p align="center">
<a href="http://torchio.rtfd.io/">
<a href="https://torchio-project.github.io/torchio/">
<img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/source/favicon_io/for_readme_2000x462.png" alt="TorchIO logo">
</a>
</p>
Expand Down Expand Up @@ -39,8 +39,8 @@ at [OpenAI](https://openai.com/) ([link](https://jack-clark.net/2020/03/17/)).
<a href="https://github.com/TorchIO-project/torchio/actions/workflows/tests.yml">
<img src="https://github.com/TorchIO-project/torchio/actions/workflows/tests.yml/badge.svg" alt="Tests status">
</a>
<a href="https://torchio.rtfd.io/?badge=latest">
<img src="https://img.shields.io/readthedocs/torchio?label=Docs&logo=Read%20the%20Docs" alt="Documentation status">
<a href="https://github.com/TorchIO-project/torchio/actions/workflows/docs.yml">
<img src="https://github.com/TorchIO-project/torchio/actions/workflows/docs.yml/badge.svg" alt="Documentation status">
</a>
<a href="https://app.codecov.io/github/TorchIO-project/torchio">
<img src="https://codecov.io/gh/TorchIO-project/torchio/branch/main/graphs/badge.svg" alt="Coverage status">
Expand Down Expand Up @@ -94,13 +94,13 @@ at [OpenAI](https://openai.com/) ([link](https://jack-clark.net/2020/03/17/)).
---

<p align="center">
<a href="https://torchio.readthedocs.io/transforms/augmentation.html">
<a href="https://torchio-project.github.io/torchio/transforms/augmentation.html">
<img style="width: 600px; overflow: hidden;" src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/fpg_progressive.gif" alt="Progressive artifacts">
</a>
</p>

<p align="center">
<a href="https://torchio.readthedocs.io/transforms/augmentation.html">
<a href="https://torchio-project.github.io/torchio/transforms/augmentation.html">
<img style="width: 360px; height: 360px; overflow: hidden;" src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/augmentation.gif" alt="Augmentation">
</a>
</p>
Expand All @@ -111,93 +111,93 @@ at [OpenAI](https://openai.com/) ([link](https://jack-clark.net/2020/03/17/)).
<tr>
<td align="center">Original</td>
<td align="center">
<a href="http://torchio.rtfd.io/transforms/augmentation.html#randomblur">Random blur</a>
<a href="https://torchio-project.github.io/torchio/transforms/augmentation.html#randomblur">Random blur</a>
</td>
</tr>
<tr>
<td align="center"><img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/1_Lambda_mri.png" alt="Original"></td>
<td align="center">
<a href="http://torchio.rtfd.io/transforms/augmentation.html#randomblur">
<a href="https://torchio-project.github.io/torchio/transforms/augmentation.html#randomblur">
<img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/2_RandomBlur_mri.gif" alt="Random blur">
</a>
</td>
</tr>
<tr>
<td align="center">
<a href="http://torchio.rtfd.io/transforms/augmentation.html#randomflip">Random flip</a>
<a href="https://torchio-project.github.io/torchio/transforms/augmentation.html#randomflip">Random flip</a>
</td>
<td align="center">
<a href="http://torchio.rtfd.io/transforms/augmentation.html#randomnoise">Random noise</a>
<a href="https://torchio-project.github.io/torchio/transforms/augmentation.html#randomnoise">Random noise</a>
</td>
</tr>
<tr>
<td align="center">
<a href="http://torchio.rtfd.io/transforms/augmentation.html#randomflip">
<a href="https://torchio-project.github.io/torchio/transforms/augmentation.html#randomflip">
<img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/3_RandomFlip_mri.gif" alt="Random flip">
</a>
</td>
<td align="center">
<a href="http://torchio.rtfd.io/transforms/augmentation.html#randomnoise">
<a href="https://torchio-project.github.io/torchio/transforms/augmentation.html#randomnoise">
<img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/4_Compose_mri.gif" alt="Random noise">
</a>
</td>
</tr>
<tr>
<td align="center">
<a href="http://torchio.rtfd.io/transforms/augmentation.html#randomaffine">Random affine transformation</a>
<a href="https://torchio-project.github.io/torchio/transforms/augmentation.html#randomaffine">Random affine transformation</a>
</td>
<td align="center">
<a href="http://torchio.rtfd.io/transforms/augmentation.html#randomelasticdeformation">Random elastic transformation</a>
<a href="https://torchio-project.github.io/torchio/transforms/augmentation.html#randomelasticdeformation">Random elastic transformation</a>
</td>
</tr>
<tr>
<td align="center">
<a href="http://torchio.rtfd.io/transforms/augmentation.html#randomaffine">
<a href="https://torchio-project.github.io/torchio/transforms/augmentation.html#randomaffine">
<img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/5_RandomAffine_mri.gif" alt="Random affine transformation">
</a>
</td>
<td align="center">
<a href="http://torchio.rtfd.io/transforms/augmentation.html#randomelasticdeformation">
<a href="https://torchio-project.github.io/torchio/transforms/augmentation.html#randomelasticdeformation">
<img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/6_RandomElasticDeformation_mri.gif" alt="Random elastic transformation">
</a>
</td>
</tr>
<tr>
<td align="center">
<a href="http://torchio.rtfd.io/transforms/augmentation.html#randombiasfield">Random bias field artifact</a>
<a href="https://torchio-project.github.io/torchio/transforms/augmentation.html#randombiasfield">Random bias field artifact</a>
</td>
<td align="center">
<a href="http://torchio.rtfd.io/transforms/augmentation.html#randommotion">Random motion artifact</a>
<a href="https://torchio-project.github.io/torchio/transforms/augmentation.html#randommotion">Random motion artifact</a>
</td>
</tr>
<tr>
<td align="center">
<a href="http://torchio.rtfd.io/transforms/augmentation.html#randombiasfield">
<a href="https://torchio-project.github.io/torchio/transforms/augmentation.html#randombiasfield">
<img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/7_RandomBiasField_mri.gif" alt="Random bias field artifact">
</a>
</td>
<td align="center">
<a href="http://torchio.rtfd.io/transforms/augmentation.html#randommotion">
<a href="https://torchio-project.github.io/torchio/transforms/augmentation.html#randommotion">
<img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/8_RandomMotion_mri.gif" alt="Random motion artifact">
</a>
</td>
</tr>
<tr>
<td align="center">
<a href="http://torchio.rtfd.io/transforms/augmentation.html#randomspike">Random spike artifact</a>
<a href="https://torchio-project.github.io/torchio/transforms/augmentation.html#randomspike">Random spike artifact</a>
</td>
<td align="center">
<a href="http://torchio.rtfd.io/transforms/augmentation.html#randomghosting">Random ghosting artifact</a>
<a href="https://torchio-project.github.io/torchio/transforms/augmentation.html#randomghosting">Random ghosting artifact</a>
</td>
</tr>
<tr>
<td align="center">
<a href="http://torchio.rtfd.io/transforms/augmentation.html#randomspike">
<a href="https://torchio-project.github.io/torchio/transforms/augmentation.html#randomspike">
<img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/9_RandomSpike_mri.gif" alt="Random spike artifact">
</a>
</td>
<td align="center">
<a href="http://torchio.rtfd.io/transforms/augmentation.html#randomghosting">
<a href="https://torchio-project.github.io/torchio/transforms/augmentation.html#randomghosting">
<img src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/gifs_readme/10_RandomGhosting_mri.gif" alt="Random ghosting artifact">
</a>
</td>
Expand All @@ -207,13 +207,13 @@ at [OpenAI](https://openai.com/) ([link](https://jack-clark.net/2020/03/17/)).
---

<p align="center">
<a href="https://torchio.readthedocs.io/patches/patch_training.html#queue">
<a href="https://torchio-project.github.io/torchio/patches/patch_training.html#queue">
<img style="width: 640px; height: 360px; overflow: hidden;" src="https://raw.githubusercontent.com/TorchIO-project/torchio/main/docs/images/queue.gif" alt="Queue">
</a>
</p>

([Queue](https://torchio.readthedocs.io/patches/patch_training.html#queue)
for [patch-based training](https://torchio.readthedocs.io/patches/index.html))
([Queue](https://torchio-project.github.io/torchio/patches/patch_training.html#queue)
for [patch-based training](https://torchio-project.github.io/torchio/patches/index.html))

<!-- markdownlint-restore -->

Expand Down Expand Up @@ -265,20 +265,19 @@ This project is supported by the following institutions:

## Getting started

See [Getting started](https://torchio.readthedocs.io/quickstart.html) for
[installation](https://torchio.readthedocs.io/quickstart.html#installation)
See [Getting started](https://torchio-project.github.io/torchio/quickstart.html) for
[installation](https://torchio-project.github.io/torchio/quickstart.html#installation)
instructions
and a [Hello, World!](https://torchio.readthedocs.io/quickstart.html#hello-world)
and a [Hello, World!](https://torchio-project.github.io/torchio/quickstart.html#hello-world)
example.

Longer usage examples can be found in the
[tutorials](https://github.com/TorchIO-project/torchio/blob/main/tutorials/README.md).

All the documentation is hosted on
[Read the Docs](http://torchio.rtfd.io/).
Read the [documentation](https://torchio-project.github.io/torchio/) for more information.

Please
[open a new issue](https://github.com/TorchIO-project/torchio/issues/new/choose)
[create an issue](https://github.com/TorchIO-project/torchio/issues/new/choose)
if you think something is missing.

## Contributors
Expand Down
4 changes: 2 additions & 2 deletions docs/source/README.rst
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Expand Up @@ -81,8 +81,8 @@ If you found a bug or have a feature request, please open an issue:
:target: https://github.com/TorchIO-project/torchio/blob/main/tutorials/README.md
:alt: Google Colab notebooks

.. |Docs-status| image:: https://img.shields.io/readthedocs/torchio?label=Docs&logo=Read%20the%20Docs
:target: https://torchio.rtfd.io/?badge=latest
.. |Docs-status| image:: https://github.com/TorchIO-project/torchio/actions/workflows/docs.yml/badge.svg
:target: https://github.com/TorchIO-project/torchio/actions/workflows/docs.yml
:alt: Documentation status

.. |Tests-status| image:: https://github.com/TorchIO-project/torchio/actions/workflows/tests.yml/badge.svg
Expand Down
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Expand Up @@ -43,14 +43,6 @@ bump-python:
new_version_string = f"{old_version.major}.{old_version.minor + 1}"
python_version_path.write_text(new_version_string + "\n")

docs_config_path = Path(".readthedocs.yml")
docs_config = docs_config_path.read_text()
docs_config = docs_config.replace(
f'python: "{old_version_string}"',
f'python: "{new_version_string}"',
)
docs_config_path.write_text(docs_config)

tests_workflow_path = Path(".github/workflows/tests.yml")
tests_workflow = tests_workflow_path.read_text()
tests_workflow = tests_workflow.replace(
Expand Down
4 changes: 2 additions & 2 deletions pyproject.toml
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Expand Up @@ -58,10 +58,10 @@ tiotr = "torchio.cli.apply_transform:app"
torchio-transform = "torchio.cli.apply_transform:app"

[project.urls]
Homepage = "http://torchio.rtfd.io"
Homepage = "https://torchio-project.github.io/torchio"
Source = "https://github.com/TorchIO-project/torchio"
"Issue tracker" = "https://github.com/TorchIO-project/torchio/issues"
Documentation = "http://torchio.rtfd.io"
Documentation = "https://torchio-project.github.io/torchio"
"Release notes" = "https://github.com/TorchIO-project/torchio/releases"

[dependency-groups]
Expand Down
4 changes: 2 additions & 2 deletions src/torchio/data/image.py
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Expand Up @@ -121,8 +121,8 @@ class Image(dict):
>>> image = tio.ScalarImage('t1.npy', reader=numpy_reader)

.. _lazy loaders: https://en.wikipedia.org/wiki/Lazy_loading
.. _preprocessing: https://torchio.readthedocs.io/transforms/preprocessing.html#intensity
.. _augmentation: https://torchio.readthedocs.io/transforms/augmentation.html#intensity
.. _preprocessing: https://torchio-project.github.io/torchio/transforms/preprocessing.html#intensity
.. _augmentation: https://torchio-project.github.io/torchio/transforms/augmentation.html#intensity
.. _NiBabel docs: https://nipy.org/nibabel/image_orientation.html
.. _NiBabel docs on coordinates: https://nipy.org/nibabel/coordinate_systems.html#the-affine-matrix-as-a-transformation-between-spaces
.. _3D Slicer wiki: https://www.slicer.org/wiki/Coordinate_systems
Expand Down
2 changes: 1 addition & 1 deletion src/torchio/transforms/data_parser.py
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Expand Up @@ -75,7 +75,7 @@ def get_subject(self):
'If the input is a dictionary, a value for "include" must'
' be specified when instantiating the transform. See the'
' docs for Transform:'
' https://torchio.readthedocs.io/transforms/transforms.html#torchio.transforms.Transform'
' https://torchio-project.github.io/torchio/transforms/transforms.html#torchio.transforms.Transform'
)
raise RuntimeError(message)
subject = self._get_subject_from_dict(
Expand Down
2 changes: 1 addition & 1 deletion src/torchio/transforms/preprocessing/spatial/crop_or_pad.py
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Expand Up @@ -59,7 +59,7 @@ class CropOrPad(SpatialTransform):

.. warning:: If :attr:`target_shape` is ``None``, subjects in the dataset
will probably have different shapes. This is probably fine if you are
using `patch-based training <https://torchio.readthedocs.io/patches/index.html>`_.
using `patch-based training <https://torchio-project.github.io/torchio/patches/index.html>`_.
If you are using full volumes for training and a batch size larger than
one, an error will be raised by the :class:`~torch.utils.data.DataLoader`
while trying to collate the batches.
Expand Down
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