pyAFQ 2.1__tar.gz → 3.1__tar.gz

pyafq-3.1/.codespellrc

@@ -0,0 +1,3 @@
+[codespell]
+skip = [setup.cfg] 
+ignore-words-list = Reson, DNE, ACI, FPT, sagital, saggital, abd, Joo, Mapp, Commun, vor, Claus, coo

{pyafq-2.1 → pyafq-3.1}/.github/workflows/docbuild.yml

@@ -3,7 +3,7 @@ name: Documentation build
 on: [push, pull_request]
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
 permissions:
@@ -14,11 +14,17 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
 
     steps:
     - name: Checkout repo
       uses: actions/checkout@v1
+
+    - name: Increase swap space
+      uses: actionhippie/swap-space@v1
+      with:
+        size: 16G
+
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v1
       with:
@@ -27,13 +33,16 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install .[all]
-        sudo apt-get install -y xvfb
+        sudo apt-get install -y \
+              libgl1 \
+              libglx-mesa0 \
+              libegl1 \
+              libgl1-mesa-dri \
+              libvulkan1 \
+              mesa-vulkan-drivers \
+              vulkan-tools
     - name: Build docs
-      env:
-        XVFB: 1
-        DISPLAY: :99
       run: |
-        Xvfb :99 -screen 0 1280x1024x24 &
         cd docs
         make html
     - name: Upload docs

{pyafq-2.1 → pyafq-3.1}/.github/workflows/docker_pyafq.yml

@@ -2,6 +2,10 @@ name: Build and Push pyAFQ Docker Image
 
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ubuntu-latest

{pyafq-2.1 → pyafq-3.1}/.github/workflows/docker_pyafq_cuda12.yml

@@ -2,6 +2,10 @@ name: Build and Push pyAFQ CUDA12 Image
 
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     runs-on: ubuntu-latest

{pyafq-2.1 → pyafq-3.1}/.github/workflows/nightly_anisotropic_test.yml

@@ -1,4 +1,4 @@
-name: Nightly test suite
+name: Nightly Anisotropic test suite
 
 on:
   schedule:
@@ -11,11 +11,15 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
 
     steps:
     - name: Checkout repo
       uses: actions/checkout@v1
+    - name: Increase swap space
+      uses: actionhippie/swap-space@v1
+      with:
+        size: 16G
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v1
       with:
@@ -23,7 +27,7 @@ jobs:
     - name: Install
       run: |
         python -m pip install --upgrade pip
-        pip install .[dev,fury,afqbrowser,plot]
+        pip install .[dev,fury,afqbrowser,plot,nn]
     - name: Lint
       run: |
         flake8 --ignore N802,N806,W503 --select W504 `find . -name \*.py | grep -v setup.py | grep -v version.py | grep -v __init__.py | grep -v /docs/`

{pyafq-2.1 → pyafq-3.1}/.github/workflows/nightly_basic_test.yml

@@ -1,4 +1,4 @@
-name: Nightly test suite
+name: Nightly Basic test suite
 
 on:
   schedule:
@@ -11,11 +11,15 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
 
     steps:
     - name: Checkout repo
       uses: actions/checkout@v1
+    - name: Increase swap space
+      uses: actionhippie/swap-space@v1
+      with:
+        size: 16G
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v1
       with:
@@ -23,7 +27,7 @@ jobs:
     - name: Install
       run: |
         python -m pip install --upgrade pip
-        pip install .[dev,fury,afqbrowser,plot]
+        pip install .[dev,fury,afqbrowser,plot,nn]
     - name: Lint
       run: |
         flake8 --ignore N802,N806,W503 --select W504 `find . -name \*.py | grep -v setup.py | grep -v version.py | grep -v __init__.py | grep -v /docs/`

{pyafq-2.1 → pyafq-3.1}/.github/workflows/nightly_custom_test.yml

@@ -1,4 +1,4 @@
-name: Nightly test suite
+name: Nightly Custom test suite
 
 on:
   schedule:
@@ -11,11 +11,15 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
 
     steps:
     - name: Checkout repo
       uses: actions/checkout@v1
+    - name: Increase swap space
+      uses: actionhippie/swap-space@v1
+      with:
+        size: 16G
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v1
       with:
@@ -23,11 +27,18 @@ jobs:
     - name: Install
       run: |
         python -m pip install --upgrade pip
-        pip install .[dev,fury,afqbrowser]
+        pip install .[dev,fury,afqbrowser,nn]
+        sudo apt-get install -y \
+              libgl1 \
+              libglx-mesa0 \
+              libegl1 \
+              libgl1-mesa-dri \
+              libvulkan1 \
+              mesa-vulkan-drivers \
+              vulkan-tools
     - name: Lint
       run: |
         flake8 --ignore N802,N806,W503 --select W504 `find . -name \*.py | grep -v setup.py | grep -v version.py | grep -v __init__.py | grep -v /docs/`
     - name: Test
       run: |
-        export TEST_WITH_XVFB=true
         cd && mkdir for_test && cd for_test && pytest --pyargs AFQ --cov-report term-missing --cov=AFQ -m "nightly_custom" --durations=0

{pyafq-2.1 → pyafq-3.1}/.github/workflows/nightly_reco80_test.yml

@@ -1,4 +1,4 @@
-name: Nightly test suite
+name: Nightly Recobundles80 test suite
 
 on:
   schedule:
@@ -11,11 +11,15 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
 
     steps:
     - name: Checkout repo
       uses: actions/checkout@v1
+    - name: Increase swap space
+      uses: actionhippie/swap-space@v1
+      with:
+        size: 32G
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v1
       with:
@@ -23,7 +27,7 @@ jobs:
     - name: Install
       run: |
         python -m pip install --upgrade pip
-        pip install .[dev,fury,afqbrowser,plot]
+        pip install .[dev,fury,afqbrowser,plot,nn]
     - name: Lint
       run: |
         flake8 --ignore N802,N806,W503 --select W504 `find . -name \*.py | grep -v setup.py | grep -v version.py | grep -v __init__.py | grep -v /docs/`

{pyafq-2.1 → pyafq-3.1}/.github/workflows/nightly_reco_test.yml

@@ -1,4 +1,4 @@
-name: Nightly test suite
+name: Nightly Recobundles test suite
 
 on:
   schedule:
@@ -11,11 +11,15 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
 
     steps:
     - name: Checkout repo
       uses: actions/checkout@v1
+    - name: Increase swap space
+      uses: actionhippie/swap-space@v1
+      with:
+        size: 16G
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v1
       with:
@@ -23,7 +27,7 @@ jobs:
     - name: Install
       run: |
         python -m pip install --upgrade pip
-        pip install .[dev,fury,afqbrowser,plot]
+        pip install .[dev,fury,afqbrowser,plot,nn]
     - name: Lint
       run: |
         flake8 --ignore N802,N806,W503 --select W504 `find . -name \*.py | grep -v setup.py | grep -v version.py | grep -v __init__.py | grep -v /docs/`

{pyafq-2.1 → pyafq-3.1}/.github/workflows/nightly_test.yml

@@ -1,4 +1,4 @@
-name: Nightly test suite
+name: Nightly Other Datasets test suite
 
 on:
   schedule:
@@ -11,11 +11,15 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
 
     steps:
     - name: Checkout repo
       uses: actions/checkout@v1
+    - name: Increase swap space
+      uses: actionhippie/swap-space@v1
+      with:
+        size: 16G
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v1
       with:
@@ -23,7 +27,7 @@ jobs:
     - name: Install
       run: |
         python -m pip install --upgrade pip
-        pip install .[dev,fury,afqbrowser,plot]
+        pip install .[dev,fury,afqbrowser,plot,nn]
     - name: Lint
       run: |
         flake8 --ignore N802,N806,W503 --select W504 `find . -name \*.py | grep -v setup.py | grep -v version.py | grep -v __init__.py | grep -v /docs/`

pyafq-3.1/.github/workflows/publish-to-test-pypi.yml

@@ -0,0 +1,94 @@
+name: Publish to TestPyPI and PyPI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "*"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build-sdist:
+    name: Build sdist
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+      - name: Build sdist
+        run: pipx run build
+      - uses: actions/upload-artifact@v6
+        with:
+          name: source-dist
+          path: ./dist/*
+  test-sdist:
+    name: Test sdist
+    needs: [build-sdist]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v7
+        with:
+          name: source-dist
+          path: ./dist
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Install sdist without optional dependencies
+        run: pip install dist/*.tar.gz
+      - run: python -c 'import AFQ; print(AFQ.__version__)'
+      - name: Install pytest
+        run: pip install pytest
+      - name: Run tests
+        run: pytest -v --pyargs AFQ -m "not nightly and not nightly_basic and not nightly_custom and not nightly_anisotropic and not nightly_slr and not nightly_reco and not nightly_reco80" --durations=0
+
+  pre-publish:
+    runs-on: ubuntu-latest
+    needs: [test-sdist]
+    steps:
+      - uses: actions/download-artifact@v7
+        with:
+          path: dist/
+          pattern: '*-dist'
+          merge-multiple: true
+      - run: ls -lR dist/
+      - run: pipx run twine check dist/*
+
+  test-pypi-publish:
+    runs-on: ubuntu-latest
+    needs: [pre-publish]
+    steps:
+      - uses: actions/download-artifact@v7
+        with:
+          path: dist/
+          pattern: '*-dist'
+          merge-multiple: true
+      - run: ls -lR dist/
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          repository-url: https://test.pypi.org/legacy/
+          verbose: true
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    environment: "Package deployment"
+    needs: [pre-publish]
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+    steps:
+      - uses: actions/download-artifact@v7
+        with:
+          path: dist/
+          pattern: '*-dist'
+          merge-multiple: true
+      - run: ls -lR dist/
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

{pyafq-2.1 → pyafq-3.1}/.github/workflows/test.yml

@@ -3,7 +3,7 @@ name: Test suite
 on: [push, pull_request]
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
 jobs:
@@ -13,7 +13,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
         nibabel-pre: [true, false]
 
     steps:
@@ -36,7 +36,7 @@ jobs:
         python -m pip check
     - name: Lint
       run: |
-        flake8 --ignore N802,N806,W503 --select W504 `find . -name \*.py | grep -v setup.py | grep -v version.py | grep -v __init__.py | grep -v /docs/`
+        ruff check .
     - name: Test
       run: |
-        cd && mkdir for_test && cd for_test && pytest --pyargs AFQ --cov-report term-missing --cov=AFQ -m "not nightly and not nightly_basic and not nightly_custom and not nightly_anisotropic and not nightly_slr and not nightly_pft and not nightly_reco and not nightly_reco80" --durations=0
+        cd && mkdir for_test && cd for_test && pytest --pyargs AFQ --cov-report term-missing --cov=AFQ -m "not nightly and not nightly_basic and not nightly_custom and not nightly_anisotropic and not nightly_slr and not nightly_reco and not nightly_reco80" --durations=0

{pyafq-2.1 → pyafq-3.1}/.maintenance/update_zenodo.py

@@ -7,81 +7,80 @@ For the full LICENSE and terms of use, see
 https://github.com/nipreps/dmriprep/blob/master/LICENSE
 
 """
-import sys
+
+import json
 import shutil
+import subprocess as sp
+import sys
 from pathlib import Path
-import json
+
 from rapidfuzz import fuzz, process
-import subprocess as sp
 
 # These ORCIDs should go last
-CREATORS_LAST = ['Yeatman, Jason', 'Rokem, Ariel']
+CREATORS_LAST = ["Yeatman, Jason", "Rokem, Ariel"]
 # for entries not found in line-contributions
-MISSING_ENTRIES = [
-]
+MISSING_ENTRIES = []
 
-if __name__ == '__main__':
-    contrib_file = Path('line-contributors.txt')
+if __name__ == "__main__":
+    contrib_file = Path("line-contributors.txt")
     lines = []
     if contrib_file.exists():
-        print('WARNING: Reusing existing line-contributors.txt file.',
-              file=sys.stderr)
+        print("WARNING: Reusing existing line-contributors.txt file.", file=sys.stderr)
         lines = contrib_file.read_text().splitlines()
 
-    git_line_summary_path = shutil.which('git-summary')
+    git_line_summary_path = shutil.which("git-summary")
     if not lines and git_line_summary_path:
         print("Running git-line-summary on the repo")
         lines = sp.check_output([git_line_summary_path]).decode().splitlines()
-        contrib_file.write_text('\n'.join(lines))
+        contrib_file.write_text("\n".join(lines))
 
     if not lines:
         raise RuntimeError(
             """Could not find line-contributors from git repository.%s"""
             % """git-line-summary not found, please install git-extras. """
-            * (git_line_summary_path is None))
+            * (git_line_summary_path is None)
+        )
 
-    data = [' '.join(line.strip().split()[1:-1]) for line in lines if '%'
-            in line]
+    data = [" ".join(line.strip().split()[1:-1]) for line in lines if "%" in line]
 
     # load zenodo from master
-    zenodo_file = Path('.zenodo.json')
+    zenodo_file = Path(".zenodo.json")
     zenodo = json.loads(zenodo_file.read_text())
-    zen_names = [' '.join(val['name'].split(',')[::-1]).strip()
-                 for val in zenodo['creators']]
+    zen_names = [
+        " ".join(val["name"].split(",")[::-1]).strip() for val in zenodo["creators"]
+    ]
     total_names = len(zen_names) + len(MISSING_ENTRIES)
 
     name_matches = []
     position = 1
     for ele in data:
-        match = process.extractOne(ele, zen_names,
-                                   scorer=fuzz.token_sort_ratio,
-                                   score_cutoff=80)
+        match = process.extractOne(
+            ele, zen_names, scorer=fuzz.token_sort_ratio, score_cutoff=80
+        )
 
         if match:
-            val = zenodo['creators'][zen_names.index(match[0])]
+            val = zenodo["creators"][zen_names.index(match[0])]
         else:
             # skip unmatched names
             print("No entry to sort:", ele)
             continue
 
         if val not in name_matches:
-            if val['name'] not in CREATORS_LAST:
-                val['position'] = position
+            if val["name"] not in CREATORS_LAST:
+                val["position"] = position
                 position += 1
             else:
-                val['position'] = total_names + \
-                    CREATORS_LAST.index(val['name'])
+                val["position"] = total_names + CREATORS_LAST.index(val["name"])
             name_matches.append(val)
 
     for missing in MISSING_ENTRIES:
-        missing['position'] = position
+        missing["position"] = position
         position += 1
         name_matches.append(missing)
 
-    zenodo['creators'] = sorted(name_matches, key=lambda k: k['position'])
+    zenodo["creators"] = sorted(name_matches, key=lambda k: k["position"])
     # Remove position
-    for creator in zenodo['creators']:
-        del creator['position']
+    for creator in zenodo["creators"]:
+        del creator["position"]
 
-    zenodo_file.write_text('%s\n' % json.dumps(zenodo, indent=2,
-                           sort_keys=True))
+    zenodo_file.write_text("%s\n" % json.dumps(zenodo, indent=2, sort_keys=True))

pyafq-3.1/.pre-commit-config.yaml

@@ -0,0 +1,18 @@
+default_language_version:
+  python: python3
+
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.10
+    hooks:
+      # Run the linter
+      - id: ruff
+        args: [ --fix, --config, pyproject.toml ]
+      # Run the formatter
+      - id: ruff-format
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli