chore: Update dependencies, transition to tox-uv

.github/workflows/build-test-publish.yml

@@ -49,18 +49,32 @@ jobs:
       AFNI_IMSAVE_WARNINGS: NO
       AFNI_TTATLAS_DATASET: /opt/afni/atlases
       AFNI_PLUGINPATH: /opt/afni/plugins
+      MARKS: ${{ matrix.marks }}
+      DEPENDS: ${{ matrix.dependencies }}
     strategy:
-      max-parallel: 6
+      fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
-        marks: ["not slow"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        dependencies:  ["latest", "pre"]
+        marks: ["fast"]
         include:
           - python-version: "3.9"
-            marks: "slow and not veryslow"
+            dependencies: "min"
+            marks: "fast"
+          - python-version: "3.9"
+            dependencies: "latest"
+            marks: "slow"
           - python-version: "3.12"
+            dependencies: "latest"
             marks: "veryslow"
+        exclude:
+          - python-version: "3.9"
+            dependencies: "pre"
+          - python-version: "3.10"
+            dependencies: "pre"
 
     steps:
+    - uses: actions/checkout@v4
     - uses: actions/cache@v4
       with:
         path: /var/lib/apt
@@ -89,11 +103,15 @@ jobs:
           curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries && \
           tcsh @update.afni.binaries -package linux_ubuntu_16_64 -bindir ${AFNI_HOME}
         fi
+        ls -l ${AFNI_HOME}
+        echo "PATH=${AFNI_HOME}:$PATH" | tee -a $GITHUB_ENV
 
     - name: Git settings (pacify DataLad)
       run: |
         git config --global user.name 'NiPreps Bot'
         git config --global user.email '[email protected]'
+    - name: Install the latest version of uv
+      uses: astral-sh/setup-uv@v4
     - name: Set up Python ${{ matrix.python-version }}
       uses: conda-incubator/setup-miniconda@v3
       with:
@@ -110,22 +128,14 @@ jobs:
           ~/conda_pkgs_dir
           /home/runner/.cache/pip
         key: python-${{ matrix.python-version }}-${{ env.CACHE_NUM }}
-        restore-keys: |
-          python-${{ matrix.python-version }}-${{ env.CACHE_NUM }}
     - name: Install DataLad
       run: |
-        conda install git-annex=*=alldep* pip
-        pip install datalad datalad-osf
+        conda install git-annex=*=alldep*
+        uv tool install datalad --with=datalad-next --with=datalad-osf
+        uv tool install datalad-osf --with=datalad-next
     - name: Install fsl and ANTs
       run: |
         conda install fsl-fugue fsl-topup ants
-    - uses: actions/checkout@v4
-    - name: Install dependencies
-      timeout-minutes: 5
-      run: |
-        pip install .[tests]
-
-
     - uses: actions/cache@v4
       with:
         path: ~/.cache/templateflow
@@ -134,7 +144,7 @@ jobs:
           tf-cache-
     - name: Get TemplateFlow's required objects
       run: |
-        python tools/cache_templateflow.py
+        uv run tools/cache_templateflow.py
 
     - uses: actions/cache@v4
       with:
@@ -198,18 +208,16 @@ jobs:
         mkdir -p $( dirname $FS_LICENSE )
         echo "b2VzdGViYW5Ac3RhbmZvcmQuZWR1CjMwNzU2CiAqQ1MzYkJ5VXMxdTVNCiBGU2kvUGJsejJxR1V3Cg==" | base64 -d > $FS_LICENSE
 
-    - name: Run pytest with coverage
+    - name: Install tox
       run: |
-        export PATH=${AFNI_HOME}:$PATH
-        export FSLDIR=${CONDA_PREFIX}
-        pytest -v --cov sdcflows --cov-report xml:cov.xml --doctest-modules -n auto sdcflows \
-          --durations=20 --durations-min=10 -m "$MARKS"
-      env:
-        MARKS: ${{ matrix.marks }}
+        uv tool install tox --with=tox-uv --with=tox-gh-actions
+    - name: Show tox config
+      run: tox c
+    - name: Run tox
+      run: tox -v --exit-and-dump-after 1200
 
-    - uses: codecov/codecov-action@v4
+    - uses: codecov/codecov-action@v5
       with:
-        file: cov.xml
         token: ${{ secrets.CODECOV_TOKEN }}
       if: ${{ always() }}
 

pyproject.toml

@@ -17,23 +17,24 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
 ]
 license = "Apache-2.0"
 requires-python = ">=3.9"
 dependencies = [
+    "acres >= 0.2.0",
     "attrs >= 20.1.0",
-    "nibabel >=3.1.0",
-    "nipype >=1.8.5,<2.0",
-    "traits <6.4",
+    "nibabel >= 3.0",
+    "nipype >= 1.8.5",
     "migas >= 0.4.0",
     "niworkflows >= 1.7.0",
-    "nitransforms >= 23.0.1",
-    "numpy >= 1.21.0",
+    "nitransforms >= 24.1.0",
+    "numpy >= 1.22",
     "pybids >= 0.16.4",
     "scikit-image >= 0.18",
     "scipy >= 1.8.1",
-    "templateflow",
-    "toml",
+    "templateflow >= 23.1",
+    "toml >= 0.10",
 ]
 dynamic = ["version"]
 
@@ -49,22 +50,13 @@ doc = [
     "importlib_resources",
     "ipykernel",
     "ipython",
-    "matplotlib >= 2.2.0",
     "nbsphinx",
-    "nibabel",
-    "nipype >= 1.5.1",
-    "niworkflows >= 1.10.0",
-    "numpy",
-    "packaging",
     "pandoc",
     "pydot >= 1.2.3",
     "pydotplus",
-    "scipy",
     "sphinx >= 7.2.2",
     "sphinx-argparse",
     "sphinxcontrib-apidoc",
-    "templateflow",
-    "traits < 6.4"
 ]
 
 mem = [
@@ -79,11 +71,11 @@ dev = [
 ]
 
 test = [
-    "coverage",
-    "pytest",
-    "pytest-cov",
+    "coverage[toml] >=5.2.1",
+    "pytest >= 6",
+    "pytest-cov >= 2.11",
     "pytest-env",
-    "pytest-xdist"
+    "pytest-xdist >= 2.5",
 ]
 
 # Aliases
@@ -159,8 +151,22 @@ per-file-ignores = [
 ]
 
 [tool.pytest.ini_options]
+minversion = "6"
+testpaths = ["sdcflows"]
+log_cli_level = "INFO"
+xfail_strict = true
 norecursedirs = [".git"]
-addopts = "-svx --doctest-modules --strict-markers"
+addopts = [
+  "-svx",
+  "-ra",
+  "--strict-config",
+  "--strict-markers",
+  "--doctest-modules",
+  # Config pytest-cov
+  "--cov=sdcflows",
+  "--cov-report=xml",
+  "--cov-config=pyproject.toml",
+]
 doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS"
 env = "PYTHONHASHSEED=0"
 filterwarnings = ["ignore::DeprecationWarning"]
@@ -173,7 +179,6 @@ markers = [
 
 [tool.coverage.run]
 branch = true
-concurrency = 'multiprocessing'
 omit = [
     '*/tests/*',
     '*/__init__.py',

sdcflows/data/__init__.py

@@ -10,173 +10,6 @@
 
 .. autoclass:: Loader
 """
-from __future__ import annotations
+from acres import Loader
 
-import atexit
-import os
-from contextlib import AbstractContextManager, ExitStack
-from functools import cached_property
-from pathlib import Path
-from types import ModuleType
-from typing import Union
-
-try:
-    from functools import cache
-except ImportError:  # PY38
-    from functools import lru_cache as cache
-
-try:  # Prefer backport to leave consistency to dependency spec
-    from importlib_resources import as_file, files
-except ImportError:
-    from importlib.resources import as_file, files  # type: ignore
-
-try:  # Prefer stdlib so Sphinx can link to authoritative documentation
-    from importlib.resources.abc import Traversable
-except ImportError:
-    from importlib_resources.abc import Traversable
-
-__all__ = ["load"]
-
-
-class Loader:
-    """A loader for package files relative to a module
-
-    This class wraps :mod:`importlib.resources` to provide a getter
-    function with an interpreter-lifetime scope. For typical packages
-    it simply passes through filesystem paths as :class:`~pathlib.Path`
-    objects. For zipped distributions, it will unpack the files into
-    a temporary directory that is cleaned up on interpreter exit.
-
-    This loader accepts a fully-qualified module name or a module
-    object.
-
-    Expected usage::
-
-        '''Data package
-
-        .. autofunction:: load_data
-
-        .. automethod:: load_data.readable
-
-        .. automethod:: load_data.as_path
-
-        .. automethod:: load_data.cached
-        '''
-
-        from sdcflows.data import Loader
-
-        load_data = Loader(__package__)
-
-    :class:`~Loader` objects implement the :func:`callable` interface
-    and generate a docstring, and are intended to be treated and documented
-    as functions.
-
-    For greater flexibility and improved readability over the ``importlib.resources``
-    interface, explicit methods are provided to access resources.
-
-    +---------------+----------------+------------------+
-    | On-filesystem | Lifetime       | Method           |
-    +---------------+----------------+------------------+
-    | `True`        | Interpreter    | :meth:`cached`   |
-    +---------------+----------------+------------------+
-    | `True`        | `with` context | :meth:`as_path`  |
-    +---------------+----------------+------------------+
-    | `False`       | n/a            | :meth:`readable` |
-    +---------------+----------------+------------------+
-
-    It is also possible to use ``Loader`` directly::
-
-        from sdcflows.data import Loader
-
-        Loader(other_package).readable('data/resource.ext').read_text()
-
-        with Loader(other_package).as_path('data') as pkgdata:
-            # Call function that requires full Path implementation
-            func(pkgdata)
-
-        # contrast to
-
-        from importlib_resources import files, as_file
-
-        files(other_package).joinpath('data/resource.ext').read_text()
-
-        with as_file(files(other_package) / 'data') as pkgdata:
-            func(pkgdata)
-
-    .. automethod:: readable
-
-    .. automethod:: as_path
-
-    .. automethod:: cached
-    """
-
-    def __init__(self, anchor: Union[str, ModuleType]):
-        self._anchor = anchor
-        self.files = files(anchor)
-        self.exit_stack = ExitStack()
-        atexit.register(self.exit_stack.close)
-        # Allow class to have a different docstring from instances
-        self.__doc__ = self._doc
-
-    @cached_property
-    def _doc(self):
-        """Construct docstring for instances
-
-        Lists the public top-level paths inside the location, where
-        non-public means has a `.` or `_` prefix or is a 'tests'
-        directory.
-        """
-        top_level = sorted(
-            os.path.relpath(p, self.files) + "/"[: p.is_dir()]
-            for p in self.files.iterdir()
-            if p.name[0] not in (".", "_") and p.name != "tests"
-        )
-        doclines = [
-            f"Load package files relative to ``{self._anchor}``.",
-            "",
-            "This package contains the following (top-level) files/directories:",
-            "",
-            *(f"* ``{path}``" for path in top_level),
-        ]
-
-        return "\n".join(doclines)
-
-    def readable(self, *segments) -> Traversable:
-        """Provide read access to a resource through a Path-like interface.
-
-        This file may or may not exist on the filesystem, and may be
-        efficiently used for read operations, including directory traversal.
-
-        This result is not cached or copied to the filesystem in cases where
-        that would be necessary.
-        """
-        return self.files.joinpath(*segments)
-
-    def as_path(self, *segments) -> AbstractContextManager[Path]:
-        """Ensure data is available as a :class:`~pathlib.Path`.
-
-        This method generates a context manager that yields a Path when
-        entered.
-
-        This result is not cached, and any temporary files that are created
-        are deleted when the context is exited.
-        """
-        return as_file(self.files.joinpath(*segments))
-
-    @cache
-    def cached(self, *segments) -> Path:
-        """Ensure data is available as a :class:`~pathlib.Path`.
-
-        Any temporary files that are created remain available throughout
-        the duration of the program, and are deleted when Python exits.
-
-        Results are cached so that multiple calls do not unpack the same
-        data multiple times, but the cache is sensitive to the specific
-        argument(s) passed.
-        """
-        return self.exit_stack.enter_context(as_file(self.files.joinpath(*segments)))
-
-    __call__ = cached
-
-
-load = Loader(__package__)
+load = Loader(__spec__.name)