Merge branch 'main' into 1222-fix-memory-leak

TorchIO-project · Jan 27, 2025 · 3c1a7ff · 3c1a7ff
2 parents f8335ef + c7f3b82
commit 3c1a7ff
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diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -824,6 +824,15 @@
       "contributions": [
         "code"
       ]
+    },
+    {
+      "login": "sravan953",
+      "name": "Keerthi Sravan Ravi",
+      "avatar_url": "https://avatars.githubusercontent.com/u/6049061?v=4",
+      "profile": "https://github.com/sravan953",
+      "contributions": [
+        "bug"
+      ]
     }
   ],
   "contributorsPerLine": 7,

diff --git a/.bumpversion.cfg b/.bumpversion.cfg
diff --git a/.github/workflows/code_quality.yml b/.github/workflows/code_quality.yml
@@ -30,7 +30,7 @@ jobs:
           fetch-depth: 0
 
       - name: Install the latest version of uv
-        uses: astral-sh/setup-uv@v3
+        uses: astral-sh/setup-uv@v5
         with:
           enable-cache: true
           cache-dependency-glob: "pyproject.toml"

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -1,52 +1,55 @@
-# Adapted from https://packaging.python.org/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
-
 name: Publish
 
 on: push
 
-# https://github.com/fepegar/torchio/actions/runs/6076955855/job/17283217522?pr=1103
-permissions:
-  id-token: write
-
 jobs:
-  Build-and-publish:
-    name: Build and publish if needed
+  build:
+    name: Build the package
     runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@v4
 
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: "3.12"
-
-    - name: Install pypa/build
-      run: >-
-        python -m
-        pip install
-        build
-        --user
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
 
     - name: Build a binary wheel and a source tarball
-      run: >-
-        python -m
-        build
-        --sdist
-        --wheel
-        --outdir dist/
-        .
-
-    - name: Publish package to TestPyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        repository-url: https://test.pypi.org/legacy/
-        verbose: true
-        skip-existing: true
-
-    # Publish only tagged commits
-    - name: Publish package to PyPI, if tagged
-      if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@release/v1
+      run: uv build
+
+    - name: Upload dist directory
+      uses: actions/upload-artifact@v4
       with:
-        verbose: true
+        name: dist
+        path: dist
+
+  publish:
+    name: Publish the package
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Print ref
+        run: echo ${{ github.ref }}
+
+      - name: Download all workflow run artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist
+
+      - name: Publish package to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          skip-existing: true
+
+      - name: Install uv if commit is tagged
+        if: startsWith(github.ref, 'refs/tags')
+        uses: astral-sh/setup-uv@v5
+
+      - name: Publish package to PyPI if commit is tagged
+        # Publish only tagged commits
+        if: startsWith(github.ref, 'refs/tags')
+        run: uv publish --verbose
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -22,7 +22,6 @@ jobs:
           windows-latest,
         ]
         python: [
-          '3.8',
           '3.9',
           '3.10',
           '3.11',
@@ -41,7 +40,7 @@ jobs:
           fetch-depth: 0
 
       - name: Install the latest version of uv
-        uses: astral-sh/setup-uv@v3
+        uses: astral-sh/setup-uv@v5
         with:
           enable-cache: true
           cache-dependency-glob: "pyproject.toml"
@@ -73,7 +72,7 @@ jobs:
 
       - name: Upload coverage reports to Codecov
         if: ${{ matrix.os == 'ubuntu-latest' && matrix.python == '3.12' }}
-        uses: codecov/codecov-action@v4.6.0
+        uses: codecov/codecov-action@v5.3.1
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
@@ -90,7 +89,7 @@ jobs:
           fetch-depth: 0
 
       - name: Install the latest version of uv
-        uses: astral-sh/setup-uv@v3
+        uses: astral-sh/setup-uv@v5
         with:
           enable-cache: true
           cache-dependency-glob: "pyproject.toml"

diff --git a/.gitignore b/.gitignore
@@ -64,6 +64,8 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/build/
+docs/source/sg_execution_times.rst
 
 # PyBuilder
 target/
@@ -110,3 +112,6 @@ ENV/
 *DS_Store
 .pylintrc
 auto_examples
+
+# uv
+uv.lock
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -17,7 +17,7 @@ repos:
       - id: trailing-whitespace        # Trims trailing whitespace
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.0
+    rev: v0.9.3
     hooks:
       - id: ruff
       - id: ruff-format
@@ -34,10 +34,10 @@ repos:
       - id: rst-inline-touching-normal        # detect mistake of inline code touching normal text in rst
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.18.0
+    rev: v3.19.1
     hooks:
       - id: pyupgrade
-        args: ['--py38-plus', '--keep-runtime-typing']
+        args: ['--py39-plus', '--keep-runtime-typing']
 
   - repo: https://github.com/PyCQA/doc8
     rev: v1.1.2

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -8,6 +8,7 @@ version: 2
 # Don't publish the docs if there are any warnings, as they might be relevant
 # https://github.com/readthedocs/readthedocs.org/issues/6837#issuecomment-607229633
 sphinx:
+  configuration: docs/source/conf.py
   fail_on_warning: true
 
 # Formats of the documentation to be built
@@ -19,10 +20,8 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.12"
-
-python:
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - doc
+  jobs:
+    install:
+      - pip install .
+      - pip install dependency-groups
+      - pip-install-dependency-groups doc
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -9,10 +9,10 @@ helps, and credit will always be given.
 
 You can contribute in many ways:
 
-Types of Contributions
+Types of contributions
 ----------------------
 
-Report Bugs
+Report bugs
 ~~~~~~~~~~~
 
 Report bugs
@@ -24,26 +24,26 @@ If you are reporting a bug, please include:
 * Any details about your local setup that might be helpful in troubleshooting.
 * Detailed steps to reproduce the bug.
 
-Fix Bugs
+Fix bugs
 ~~~~~~~~
 
 Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
 wanted" is open to whoever wants to implement it.
 
-Implement Features
+Implement features
 ~~~~~~~~~~~~~~~~~~
 
 Look through the GitHub issues for features. Anything tagged with "enhancement"
 and "help wanted" is open to whoever wants to implement it.
 
-Write Documentation
+Write documentation
 ~~~~~~~~~~~~~~~~~~~
 
 TorchIO could always use more documentation, whether as part of the
 official TorchIO docs, in docstrings, or even on the web in blog posts,
 articles, and such.
 
-Submit Feedback
+Submit feedback
 ~~~~~~~~~~~~~~~
 
 The best way to send feedback is to file an issue at https://github.com/fepegar/torchio/issues.
@@ -55,7 +55,7 @@ If you are proposing a feature:
 * Remember that this is a volunteer-driven project, and that contributions
   are welcome :)
 
-Get Started!
+Get started!
 ------------
 
 Ready to contribute? Here's how to set up ``torchio`` for local development.
@@ -80,12 +80,12 @@ already be implemented.
 4) Install your local copy into a virtual environment
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-If you use ``conda``, this is how you can set up your fork for local development::
+`uv <https://docs.astral.sh/uv/>`_ is recommended for development.
+You can use `just <https://just.systems/>`_ to set up the development environment.
+This will 1) install ``uv`` if not found and 2) install ``torchio`` and all its
+dependencies::
 
-    conda create --name torchioenv python --yes
-    conda activate torchioenv
-    pip install --editable ".[all]"
-    pre-commit install
+    just setup
 
 5) Create a branch for local development using the issue number
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -102,7 +102,7 @@ Now you can make your changes locally.
 When you're done making changes, check that your changes pass the tests
 using ``pytest``::
 
-    pytest -x
+    uv run pytest -x
 
 7) Commit your changes and push your branch to GitHub
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -130,6 +130,11 @@ time you modify them and reload them in the browser::
 
     make livehtml
 
+If you prefer to activate your environment manually or not use ``uv``,
+add ``PREFIX=""`` to the command::
+
+    make html PREFIX=""
+
 9) Submit a pull request on GitHub
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

diff --git a/README.md b/README.md
@@ -408,7 +408,8 @@ Thanks goes to all these people ([emoji key](https://allcontributors.org/docs/en
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/marius-sm"><img src="https://avatars.githubusercontent.com/u/40166021?v=4?s=100" width="100px;" alt="marius-sm"/><br /><sub><b>marius-sm</b></sub></a><br /><a href="#ideas-marius-sm" title="Ideas, Planning, & Feedback">🤔</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/haarisr"><img src="https://avatars.githubusercontent.com/u/122410226?v=4?s=100" width="100px;" alt="haarisr"/><br /><sub><b>haarisr</b></sub></a><br /><a href="https://github.com/fepegar/torchio/commits?author=haarisr" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/c-winder"><img src="https://avatars.githubusercontent.com/u/50587864?v=4?s=100" width="100px;" alt="Chris Winder"/><br /><sub><b>Chris Winder</b></sub></a><br /><a href="https://github.com/fepegar/torchio/issues?q=author%3Ac-winder" title="Bug reports">🐛</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://www.linkedin.com/in/ricky-walsh/"><img src="https://avatars.githubusercontent.com/u/70853488?v=4?s=100" width="100px;" alt="Ricky Walsh"/><br /><sub><b>Ricky Walsh</b></sub></a><br /> <a href="https://github.com/fepegar/torchio/commits?author=rickymwalsh" title="Code">💻</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://www.linkedin.com/in/ricky-walsh/"><img src="https://avatars.githubusercontent.com/u/70853488?v=4?s=100" width="100px;" alt="Ricky Walsh"/><br /><sub><b>Ricky Walsh</b></sub></a><br /><a href="https://github.com/fepegar/torchio/commits?author=rickymwalsh" title="Code">💻</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/sravan953"><img src="https://avatars.githubusercontent.com/u/6049061?v=4?s=100" width="100px;" alt="Keerthi Sravan Ravi"/><br /><sub><b>Keerthi Sravan Ravi</b></sub></a><br /><a href="https://github.com/fepegar/torchio/issues?q=author%3Asravan953" title="Bug reports">🐛</a></td>
     </tr>
   </tbody>
 </table>

diff --git a/docs/Makefile b/docs/Makefile
@@ -2,21 +2,23 @@
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-SOURCEDIR     = source
-BUILDDIR      = build
+SPHINXOPTS    	=
+SPHINXBUILD   	= sphinx-build
+SPHINXAUTOBUILD	= sphinx-autobuild
+SOURCEDIR     	= source
+BUILDDIR      	= build
+PREFIX			= uv run
 
 # Put it first so that "make" without argument is like "make help".
 help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(PREFIX) $(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 .PHONY: help Makefile
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(PREFIX) $(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 livehtml:
-	sphinx-autobuild "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(PREFIX) $(SPHINXAUTOBUILD) "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/examples/plot_3d_to_2d.py b/docs/examples/plot_3d_to_2d.py
@@ -36,7 +36,7 @@ def plot_batch(sampler):
     loader = tio.SubjectsLoader(queue, batch_size=16)
     batch = tio.utils.get_first_item(loader)
 
-    fig, axes = plt.subplots(4, 4, figsize=(12, 10))
+    _, axes = plt.subplots(4, 4, figsize=(12, 10))
     for ax, im in zip(axes.flatten(), batch['t1']['data']):
         ax.imshow(im.squeeze(), cmap='gray')
     plt.suptitle(sampler.__class__.__name__)

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -12,7 +12,6 @@
 import os
 import sys
 from datetime import date
-from typing import List
 
 sys.path.insert(0, os.path.abspath('../../src'))
 import torchio  # noqa: E402
@@ -83,7 +82,7 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns: List[str] = []
+exclude_patterns: list[str] = []
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'friendly'