Merge branch 'main' into add-smokeshow-coverage

Author: fepegar

.all-contributorsrc

@@ -24,7 +24,8 @@
         "ideas",
         "review",
         "code",
-        "question"
+        "question",
+        "bug"
       ]
     },
     {
@@ -647,7 +648,8 @@
       "avatar_url": "https://avatars.githubusercontent.com/u/56117447?v=4",
       "profile": "https://github.com/mueller-franzes",
       "contributions": [
-        "code"
+        "code",
+        "bug"
       ]
     },
     {
@@ -684,7 +686,8 @@
       "avatar_url": "https://avatars.githubusercontent.com/u/70891565?v=4",
       "profile": "https://github.com/nicoloesch",
       "contributions": [
-        "code"
+        "code",
+        "bug"
       ]
     },
     {
@@ -722,6 +725,69 @@
       "contributions": [
         "bug"
       ]
+    },
+    {
+      "login": "blakedewey",
+      "name": "Blake Dewey",
+      "avatar_url": "https://avatars.githubusercontent.com/u/4713571?v=4",
+      "profile": "https://github.com/blakedewey",
+      "contributions": [
+        "doc"
+      ]
+    },
+    {
+      "login": "haughty-yeon",
+      "name": "Doyeon Kim",
+      "avatar_url": "https://avatars.githubusercontent.com/u/84639487?v=4",
+      "profile": "https://github.com/haughty-yeon",
+      "contributions": [
+        "bug"
+      ]
+    },
+    {
+      "login": "KonoMaxi",
+      "name": "KonoMaxi",
+      "avatar_url": "https://avatars.githubusercontent.com/u/13138999?v=4",
+      "profile": "https://github.com/KonoMaxi",
+      "contributions": [
+        "bug"
+      ]
+    },
+    {
+      "login": "lchauvin",
+      "name": "Laurent Chauvin",
+      "avatar_url": "https://avatars.githubusercontent.com/u/1707237?v=4",
+      "profile": "http://www.etsmtl.ca",
+      "contributions": [
+        "bug"
+      ]
+    },
+    {
+      "login": "ChristianHinge",
+      "name": "Christian Hinge",
+      "avatar_url": "https://avatars.githubusercontent.com/u/17361630?v=4",
+      "profile": "http://christianhinge.com",
+      "contributions": [
+        "bug"
+      ]
+    },
+    {
+      "login": "zzz123xyz",
+      "name": "zzz123xyz",
+      "avatar_url": "https://avatars.githubusercontent.com/u/2671968?v=4",
+      "profile": "https://github.com/zzz123xyz",
+      "contributions": [
+        "bug"
+      ]
+    },
+    {
+      "login": "AminAlam",
+      "name": "Amin Alam",
+      "avatar_url": "https://avatars.githubusercontent.com/u/50844047?v=4",
+      "profile": "http://aminalam.info",
+      "contributions": [
+        "doc"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.18.92
+current_version = 0.19.6
 commit = True
 tag = True
 

.github/workflows/code_quality.yml

@@ -16,12 +16,12 @@ jobs:
 
     steps:
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -37,12 +37,12 @@ jobs:
 
     steps:
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -58,12 +58,12 @@ jobs:
 
     steps:
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -79,12 +79,12 @@ jobs:
 
     steps:
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/publish.yml

@@ -4,16 +4,20 @@ 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
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python 3.11
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: "3.11"
 
@@ -38,9 +42,9 @@ jobs:
       with:
         user: __token__
         password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-        repository_url: https://test.pypi.org/legacy/
+        repository-url: https://test.pypi.org/legacy/
         verbose: true
-        skip_existing: true
+        skip-existing: true
 
     # Publish only tagged commits
     - name: Publish package to PyPI, if tagged

.github/workflows/tests.yml

@@ -14,19 +14,17 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
-        exclude:
-          - os: macos-latest
-            python-version: '3.7'
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        exclude:  # run only latest Python on Windows and macOS
           - os: macos-latest
             python-version: '3.8'
           - os: macos-latest
             python-version: '3.9'
+          - os: macos-latest
+            python-version: '3.10'
           - os: macos-latest
             python-version: '3.11'
 
-          - os: windows-latest
-            python-version: '3.7'
           - os: windows-latest
             python-version: '3.8'
           - os: windows-latest
@@ -43,22 +41,30 @@ jobs:
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Install tox
         run: pip install tox
 
+      # Run all tests on schedule, but only non-slow tests on push
       - name: Run unit tests
-        run: tox -e py
+        run: |
+          if [ "${{ github.event_name }}" == "schedule" ]; then
+            tox -e py
+          else
+            tox -e py -- -m "not slow"
+          fi
+        shell: bash  # so it doesn't fail on Windows
 
       - name: Upload coverage reports to Codecov
+        if: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12' }}
         run: |
           OS_LOWERCASE=$(echo $RUNNER_OS | tr '[:upper:]' '[:lower:]')
           curl -Os https://uploader.codecov.io/latest/${OS_LOWERCASE}/codecov
@@ -68,15 +74,17 @@ jobs:
   cli:
     name: CLI smoke tests
     runs-on: ubuntu-latest
+    env:
+      PYTHON_VERSION: '3.12'
 
     steps:
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: ${{ env.PYTHON_VERSION }}
 
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: check-ast                  # Simply check whether the files parse as valid python
       - id: check-case-conflict        # Check for files that would conflict in case-insensitive filesystems
@@ -21,12 +21,12 @@ repos:
         exclude: setup.cfg
 
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 24.4.2
     hooks:
     - id: black
 
   - repo: https://github.com/pycqa/flake8
-    rev: 6.0.0
+    rev: 7.0.0
     hooks:
       - id: flake8
         additional_dependencies: [
@@ -55,13 +55,13 @@ repos:
       - id: rst-inline-touching-normal        # detect mistake of inline code touching normal text in rst
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.6.0
+    rev: v3.15.2
     hooks:
       - id: pyupgrade
-        args: ['--py37-plus', '--keep-runtime-typing']
+        args: ['--py38-plus', '--keep-runtime-typing']
 
   - repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v2.3.0
+    rev: v2.5.0
     hooks:
     - id: setup-cfg-fmt
       args: ['--include-version-classifiers']
@@ -72,7 +72,7 @@ repos:
     - id: doc8
 
   - repo: https://github.com/PyCQA/docformatter
-    rev: v1.7.2
+    rev: v1.7.5
     hooks:
     - id: docformatter
 

.readthedocs.yml

@@ -15,6 +15,11 @@ formats:
   - htmlzip
   - pdf
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
 python:
   install:
     - method: pip

README.md

@@ -298,7 +298,7 @@ Thanks goes to all these people ([emoji key](https://allcontributors.org/docs/en
   <tbody>
     <tr>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/fepegar"><img src="https://avatars1.githubusercontent.com/u/12688084?v=4?s=100" width="100px;" alt="Fernando Pérez-García"/><br /><sub><b>Fernando Pérez-García</b></sub></a><br /><a href="https://github.com/fepegar/torchio/commits?author=fepegar" title="Code">💻</a> <a href="https://github.com/fepegar/torchio/commits?author=fepegar" title="Documentation">📖</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/romainVala"><img src="https://avatars1.githubusercontent.com/u/5611962?v=4?s=100" width="100px;" alt="valabregue"/><br /><sub><b>valabregue</b></sub></a><br /><a href="#ideas-romainVala" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/fepegar/torchio/pulls?q=is%3Apr+reviewed-by%3AromainVala" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/fepegar/torchio/commits?author=romainVala" title="Code">💻</a> <a href="#question-romainVala" title="Answering Questions">💬</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/romainVala"><img src="https://avatars1.githubusercontent.com/u/5611962?v=4?s=100" width="100px;" alt="valabregue"/><br /><sub><b>valabregue</b></sub></a><br /><a href="#ideas-romainVala" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/fepegar/torchio/pulls?q=is%3Apr+reviewed-by%3AromainVala" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/fepegar/torchio/commits?author=romainVala" title="Code">💻</a> <a href="#question-romainVala" title="Answering Questions">💬</a> <a href="https://github.com/fepegar/torchio/issues?q=author%3AromainVala" title="Bug reports">🐛</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/GFabien"><img src="https://avatars1.githubusercontent.com/u/39873986?v=4?s=100" width="100px;" alt="GFabien"/><br /><sub><b>GFabien</b></sub></a><br /><a href="https://github.com/fepegar/torchio/commits?author=GFabien" title="Code">💻</a> <a href="https://github.com/fepegar/torchio/pulls?q=is%3Apr+reviewed-by%3AGFabien" title="Reviewed Pull Requests">👀</a> <a href="#ideas-GFabien" title="Ideas, Planning, & Feedback">🤔</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/GReguig"><img src="https://avatars1.githubusercontent.com/u/11228281?v=4?s=100" width="100px;" alt="G.Reguig"/><br /><sub><b>G.Reguig</b></sub></a><br /><a href="https://github.com/fepegar/torchio/commits?author=GReguig" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/nwschurink"><img src="https://avatars3.githubusercontent.com/u/12720130?v=4?s=100" width="100px;" alt="Niels Schurink"/><br /><sub><b>Niels Schurink</b></sub></a><br /><a href="https://github.com/fepegar/torchio/commits?author=nwschurink" title="Code">💻</a></td>
@@ -383,18 +383,27 @@ Thanks goes to all these people ([emoji key](https://allcontributors.org/docs/en
       <td align="center" valign="top" width="14.28%"><a href="https://yanivresearch.info/"><img src="https://avatars.githubusercontent.com/u/338645?v=4?s=100" width="100px;" alt="Ziv Yaniv"/><br /><sub><b>Ziv Yaniv</b></sub></a><br /><a href="https://github.com/fepegar/torchio/commits?author=zivy" title="Documentation">📖</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/LucaLumetti"><img src="https://avatars.githubusercontent.com/u/7543386?v=4?s=100" width="100px;" alt="Luca Lumetti"/><br /><sub><b>Luca Lumetti</b></sub></a><br /><a href="https://github.com/fepegar/torchio/commits?author=LucaLumetti" title="Code">💻</a> <a href="https://github.com/fepegar/torchio/commits?author=LucaLumetti" title="Documentation">📖</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/chagelo"><img src="https://avatars.githubusercontent.com/u/49865033?v=4?s=100" width="100px;" alt="chagelo"/><br /><sub><b>chagelo</b></sub></a><br /><a href="https://github.com/fepegar/torchio/issues?q=author%3Achagelo" title="Bug reports">🐛</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/mueller-franzes"><img src="https://avatars.githubusercontent.com/u/56117447?v=4?s=100" width="100px;" alt="mueller-franzes"/><br /><sub><b>mueller-franzes</b></sub></a><br /><a href="https://github.com/fepegar/torchio/commits?author=mueller-franzes" title="Code">💻</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/mueller-franzes"><img src="https://avatars.githubusercontent.com/u/56117447?v=4?s=100" width="100px;" alt="mueller-franzes"/><br /><sub><b>mueller-franzes</b></sub></a><br /><a href="https://github.com/fepegar/torchio/commits?author=mueller-franzes" title="Code">💻</a> <a href="https://github.com/fepegar/torchio/issues?q=author%3Amueller-franzes" title="Bug reports">🐛</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/wahabk"><img src="https://avatars.githubusercontent.com/u/43846328?v=4?s=100" width="100px;" alt="Abdelwahab Kawafi"/><br /><sub><b>Abdelwahab Kawafi</b></sub></a><br /><a href="https://github.com/fepegar/torchio/issues?q=author%3Awahabk" title="Bug reports">🐛</a></td>
     </tr>
     <tr>
       <td align="center" valign="top" width="14.28%"><a href="http://arthurmasson.xyz"><img src="https://avatars.githubusercontent.com/u/1814799?v=4?s=100" width="100px;" alt="Arthur Masson"/><br /><sub><b>Arthur Masson</b></sub></a><br /><a href="https://github.com/fepegar/torchio/issues?q=author%3Aarthursw" title="Bug reports">🐛</a> <a href="https://github.com/fepegar/torchio/commits?author=arthursw" title="Documentation">📖</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/hsyang1222"><img src="https://avatars.githubusercontent.com/u/79962117?v=4?s=100" width="100px;" alt="양현식"/><br /><sub><b>양현식</b></sub></a><br /><a href="https://github.com/fepegar/torchio/commits?author=hsyang1222" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/nicoloesch"><img src="https://avatars.githubusercontent.com/u/70891565?v=4?s=100" width="100px;" alt="nicoloesch"/><br /><sub><b>nicoloesch</b></sub></a><br /><a href="https://github.com/fepegar/torchio/commits?author=nicoloesch" title="Code">💻</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/nicoloesch"><img src="https://avatars.githubusercontent.com/u/70891565?v=4?s=100" width="100px;" alt="nicoloesch"/><br /><sub><b>nicoloesch</b></sub></a><br /><a href="https://github.com/fepegar/torchio/commits?author=nicoloesch" title="Code">💻</a> <a href="https://github.com/fepegar/torchio/issues?q=author%3Anicoloesch" title="Bug reports">🐛</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/vedal"><img src="https://avatars.githubusercontent.com/u/22004000?v=4?s=100" width="100px;" alt="Amund Vedal"/><br /><sub><b>Amund Vedal</b></sub></a><br /><a href="https://github.com/fepegar/torchio/commits?author=vedal" title="Documentation">📖</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/alabamagan"><img src="https://avatars.githubusercontent.com/u/11690091?v=4?s=100" width="100px;" alt="Alabamagan"/><br /><sub><b>Alabamagan</b></sub></a><br /><a href="https://github.com/fepegar/torchio/issues?q=author%3Aalabamagan" title="Bug reports">🐛</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/sbdoherty"><img src="https://avatars.githubusercontent.com/u/46537211?v=4?s=100" width="100px;" alt="sbdoherty"/><br /><sub><b>sbdoherty</b></sub></a><br /><a href="https://github.com/fepegar/torchio/commits?author=sbdoherty" title="Documentation">📖</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/Zhack47"><img src="https://avatars.githubusercontent.com/u/54006084?v=4?s=100" width="100px;" alt="Zhack47"/><br /><sub><b>Zhack47</b></sub></a><br /><a href="https://github.com/fepegar/torchio/issues?q=author%3AZhack47" title="Bug reports">🐛</a></td>
     </tr>
+    <tr>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/blakedewey"><img src="https://avatars.githubusercontent.com/u/4713571?v=4?s=100" width="100px;" alt="Blake Dewey"/><br /><sub><b>Blake Dewey</b></sub></a><br /><a href="https://github.com/fepegar/torchio/commits?author=blakedewey" title="Documentation">📖</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/haughty-yeon"><img src="https://avatars.githubusercontent.com/u/84639487?v=4?s=100" width="100px;" alt="Doyeon Kim"/><br /><sub><b>Doyeon Kim</b></sub></a><br /><a href="https://github.com/fepegar/torchio/issues?q=author%3Ahaughty-yeon" title="Bug reports">🐛</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/KonoMaxi"><img src="https://avatars.githubusercontent.com/u/13138999?v=4?s=100" width="100px;" alt="KonoMaxi"/><br /><sub><b>KonoMaxi</b></sub></a><br /><a href="https://github.com/fepegar/torchio/issues?q=author%3AKonoMaxi" title="Bug reports">🐛</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="http://www.etsmtl.ca"><img src="https://avatars.githubusercontent.com/u/1707237?v=4?s=100" width="100px;" alt="Laurent Chauvin"/><br /><sub><b>Laurent Chauvin</b></sub></a><br /><a href="https://github.com/fepegar/torchio/issues?q=author%3Alchauvin" title="Bug reports">🐛</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="http://christianhinge.com"><img src="https://avatars.githubusercontent.com/u/17361630?v=4?s=100" width="100px;" alt="Christian Hinge"/><br /><sub><b>Christian Hinge</b></sub></a><br /><a href="https://github.com/fepegar/torchio/issues?q=author%3AChristianHinge" title="Bug reports">🐛</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/zzz123xyz"><img src="https://avatars.githubusercontent.com/u/2671968?v=4?s=100" width="100px;" alt="zzz123xyz"/><br /><sub><b>zzz123xyz</b></sub></a><br /><a href="https://github.com/fepegar/torchio/issues?q=author%3Azzz123xyz" title="Bug reports">🐛</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="http://aminalam.info"><img src="https://avatars.githubusercontent.com/u/50844047?v=4?s=100" width="100px;" alt="Amin Alam"/><br /><sub><b>Amin Alam</b></sub></a><br /><a href="https://github.com/fepegar/torchio/commits?author=AminAlam" title="Documentation">📖</a></td>
+    </tr>
   </tbody>
 </table>
 

docs/examples/plot_3d_to_2d.py

@@ -5,6 +5,7 @@
 In this example, volumes are padded, scaled, rotated and sometimes flipped.
 Then, 2D slices are extracted.
 """
+
 import matplotlib.pyplot as plt
 import torch
 import torchio as tio

docs/examples/plot_colin27.py

@@ -4,6 +4,7 @@
 
 Use :meth:`torchio.Subject.plot` to plot the images within a subject.
 """
+
 import torchio as tio
 
 tio.datasets.Colin27().plot()