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@@ -94,13 +94,13 @@ at [OpenAI](https://openai.com/) ([link](https://jack-clark.net/2020/03/17/)).
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@@ -111,93 +111,93 @@ at [OpenAI](https://openai.com/) ([link](https://jack-clark.net/2020/03/17/)).
- +
-([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)) @@ -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 diff --git a/docs/source/README.rst b/docs/source/README.rst index ac1c0db2a..7b29462d8 100644 --- a/docs/source/README.rst +++ b/docs/source/README.rst @@ -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 diff --git a/justfile b/justfile index 0e160d8d5..90d3541c2 100644 --- a/justfile +++ b/justfile @@ -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( diff --git a/pyproject.toml b/pyproject.toml index 5c36185cd..c3550acc0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -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] diff --git a/src/torchio/data/image.py b/src/torchio/data/image.py index f3959bf06..f682335db 100644 --- a/src/torchio/data/image.py +++ b/src/torchio/data/image.py @@ -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 diff --git a/src/torchio/transforms/data_parser.py b/src/torchio/transforms/data_parser.py index 3a125d2ed..bfe3fb9b5 100644 --- a/src/torchio/transforms/data_parser.py +++ b/src/torchio/transforms/data_parser.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( diff --git a/src/torchio/transforms/preprocessing/spatial/crop_or_pad.py b/src/torchio/transforms/preprocessing/spatial/crop_or_pad.py index 24dab4554..62be39fbe 100644 --- a/src/torchio/transforms/preprocessing/spatial/crop_or_pad.py +++ b/src/torchio/transforms/preprocessing/spatial/crop_or_pad.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
