Remove references to Read the Docs (#1348)

Author: fepegar

.readthedocs.yml

@@ -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>
@@ -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">
@@ -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>
@@ -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>
@@ -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 -->
 
@@ -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

README.md

@@ -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

docs/source/README.rst

@@ -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(

justfile

@@ -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]

pyproject.toml

@@ -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

src/torchio/data/image.py

@@ -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(

src/torchio/transforms/data_parser.py

@@ -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.