Merge tag '1.11.0'

1.11.0 (July 31, 2024)

New minor release to start the 1.11.x series.

The major changes include:
- a deprecation to T1w-only based template processing
- addition of a new dependency ``acres`` for accessing package data

However, this is still backwards compatible with the 1.10.x series.

* MAINT: Depend on acres for data access
* ENH: Add PrepareDerivative/SaveDerivative interfaces (#885)
* ENH: Make template dimensions support T2w as well (#879)
* ENH: Modify FSSource to output T2 (#868)
* FIX: Set cal_max in the NIfTI header for visualization after ``IntensityClip`` (#878)
* FIX: Remove accidental MRIQC dependency, allow app config to be passed to workflow plugin (#876)
* TEST: Fix plugin invocation, use an initializer that can be verified (#880)

CHANGES.rst

@@ -1,3 +1,22 @@
+1.11.0 (July 31, 2024)
+======================
+New minor release to start the 1.11.x series.
+
+The major changes include:
+- a deprecation to T1w-only based template processing
+- addition of a new dependency ``acres`` for accessing package data
+
+However, this is still backwards compatible with the 1.10.x series.
+
+* MAINT: Depend on acres for data access
+* ENH: Add PrepareDerivative/SaveDerivative interfaces (#885)
+* ENH: Make template dimensions support T2w as well (#879)
+* ENH: Modify FSSource to output T2 (#868)
+* FIX: Set cal_max in the NIfTI header for visualization after ``IntensityClip`` (#878)
+* FIX: Remove accidental MRIQC dependency, allow app config to be passed to workflow plugin (#876)
+* TEST: Fix plugin invocation, use an initializer that can be verified (#880)
+
+
 1.10.2 (June 10, 2024)
 ======================
 Bug-fix release in the 1.10.x series

docs/requirements.txt

@@ -1,3 +1,4 @@
+acres
 attrs
 furo
 importlib_resources

niworkflows/__init__.py

@@ -3,8 +3,9 @@
 """NeuroImaging Workflows (NIWorkflows) is a selection of image processing workflows."""
 import logging
 
+from acres import Loader
+
 from .__about__ import __packagename__, __copyright__, __credits__
-from .data import Loader
 try:
     from ._version import __version__
 except ImportError:  # pragma: no cover

niworkflows/data/__init__.py

@@ -7,176 +7,8 @@
 .. automethod:: load.as_path
 
 .. automethod:: load.cached
-
-.. autoclass:: Loader
 """
-from __future__ import annotations
-
-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 niworkflows.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 niworkflows.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
 
+from acres import Loader
 
 load = Loader(__package__)

niworkflows/interfaces/tests/data/__init__.py

@@ -2,6 +2,6 @@
 
 .. autofunction:: load_test_data
 """
-from ....data import Loader
+from acres import Loader
 
 load_test_data = Loader(__package__)

niworkflows/tests/data/__init__.py

@@ -2,6 +2,6 @@
 
 .. autofunction:: load_test_data
 """
-from ...data import Loader
+from acres import Loader
 
 load_test_data = Loader(__package__)

pyproject.toml

@@ -24,6 +24,7 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Image Recognition",
 ]
 dependencies = [
+    "acres",
     "attrs",
     "importlib_resources >= 5.7; python_version < '3.11'",
     "jinja2",