Merge pull request #109 from templateflow/mnt/py312

MNT: Python 3.12 support, drop Python 3.7 and pkg_resources

.circleci/config.yml

@@ -25,7 +25,7 @@ jobs:
             source /tmp/venv/bin/activate
             pip install -U pip
             pip install -r /tmp/src/templateflow/requirements.txt
-            pip install "datalad ~= 0.11.8"
+            pip install datalad
             pip install "setuptools>=45" "setuptools_scm >= 6.2" nipreps-versions build twine codecov
 
       - run:

.github/workflows/pythonpackage.yml

@@ -62,12 +62,12 @@ jobs:
     needs: build
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
         mode: ['wheel']
         include:
-          - {python-version: '3.9', mode: 'repo'}
-          - {python-version: '3.9', mode: 'sdist'}
-          - {python-version: '3.9', mode: 'editable'}
+          - {python-version: '3.11', mode: 'repo'}
+          - {python-version: '3.11', mode: 'sdist'}
+          - {python-version: '3.11', mode: 'editable'}
 
     env:
       TEMPLATEFLOW_HOME: /tmp/home

requirements.txt

@@ -1,4 +1,5 @@
 pybids>=0.15.2
+importlib_resources >= 5.7; python_version < '3.11'
 requests
 tqdm
 pytest

setup.cfg

@@ -4,10 +4,11 @@ classifiers =
     Intended Audience :: Science/Research
     Topic :: Scientific/Engineering :: Image Recognition
     License :: OSI Approved :: Apache Software License
-    Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
 description = TemplateFlow Python Client - TemplateFlow is the Zone of neuroimaging templates.
 license = Apache-2.0
 license_file = LICENSE
@@ -24,13 +25,14 @@ project_urls =
     Source Code = https://github.com/templateflow/python-client
 
 [options]
-python_requires = >= 3.7
+python_requires = >= 3.8
 setup_requires =
     setuptools >= 45
     setuptools_scm >= 6.2
     wheel
 install_requires =
     pybids >= 0.15.2
+    importlib_resources >= 5.7; python_version < '3.11'
     requests
     tqdm
 test_requires =

templateflow/__init__.py

@@ -6,14 +6,13 @@
 try:
     from ._version import __version__
 except ModuleNotFoundError:
-    from pkg_resources import get_distribution, DistributionNotFound
-
+    from importlib.metadata import version, PackageNotFoundError
     try:
-        __version__ = get_distribution(__packagename__).version
-    except DistributionNotFound:
-        __version__ = "unknown"
-    del get_distribution
-    del DistributionNotFound
+        __version__ = version(__packagename__)
+    except PackageNotFoundError:
+        __version__ = "0+unknown"
+    del version
+    del PackageNotFoundError
 
 import os
 from . import api

templateflow/_loader.py

@@ -0,0 +1,171 @@
+"""Resource loader module
+
+.. 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  # pragma: no cover
+    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:  # pragma: no cover
+    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:  # pragma: no cover
+    from importlib_resources.abc import Traversable
+
+__all__ = ["Loader"]
+
+
+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 templateflow._loader 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 templateflow._loader 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

templateflow/conf/__init__.py

@@ -5,6 +5,9 @@
 from pathlib import Path
 from contextlib import suppress
 from functools import wraps
+from .._loader import Loader
+
+load_data = Loader(__package__)
 
 TF_DEFAULT_HOME = Path.home() / ".cache" / "templateflow"
 TF_HOME = Path(getenv("TEMPLATEFLOW_HOME", str(TF_DEFAULT_HOME)))

templateflow/conf/_s3.py

@@ -1,16 +1,15 @@
 """Tooling to handle S3 downloads."""
 from pathlib import Path
 from tempfile import mkstemp
-from pkg_resources import resource_filename
+
+from . import load_data
 
 TF_SKEL_URL = (
     "https://raw.githubusercontent.com/templateflow/python-client/"
     "{release}/templateflow/conf/templateflow-skel.{ext}"
 ).format
-TF_SKEL_PATH = Path(resource_filename("templateflow", "conf/templateflow-skel.zip"))
-TF_SKEL_MD5 = Path(
-    resource_filename("templateflow", "conf/templateflow-skel.md5")
-).read_text()
+TF_SKEL_PATH = load_data("templateflow-skel.zip")
+TF_SKEL_MD5 = load_data.readable("templateflow-skel.md5").read_text()
 
 
 def update(dest, local=True, overwrite=True, silent=False):

templateflow/conf/bids.py

@@ -1,8 +1,9 @@
 """Extending pyBIDS for querying TemplateFlow."""
-from pkg_resources import resource_filename
 from bids.layout import BIDSLayout, add_config_paths
 
-add_config_paths(templateflow=resource_filename("templateflow", "conf/config.json"))
+from . import load_data
+
+add_config_paths(templateflow=load_data("config.json"))
 
 
 class Layout(BIDSLayout):

templateflow/tests/test_version.py

@@ -1,7 +1,7 @@
 """Test _version.py."""
 import sys
 from collections import namedtuple
-from pkg_resources import DistributionNotFound
+from importlib.metadata import PackageNotFoundError
 from importlib import reload
 import templateflow
 
@@ -18,14 +18,13 @@ class _version:
 
 
 def test_version_scm1(monkeypatch):
-    """Retrieve the version via pkg_resources."""
+    """Retrieve the version via importlib.metadata."""
     monkeypatch.setitem(sys.modules, "templateflow._version", None)
 
-    def _dist(name):
-        Distribution = namedtuple("Distribution", ["name", "version"])
-        return Distribution(name, "success")
+    def _ver(name):
+        return "success"
 
-    monkeypatch.setattr("pkg_resources.get_distribution", _dist)
+    monkeypatch.setattr("importlib.metadata.version", _ver)
     reload(templateflow)
     assert templateflow.__version__ == "success"
 
@@ -35,8 +34,8 @@ def test_version_scm2(monkeypatch):
     monkeypatch.setitem(sys.modules, "templateflow._version", None)
 
     def _raise(name):
-        raise DistributionNotFound("No get_distribution mock")
+        raise PackageNotFoundError("No get_distribution mock")
 
-    monkeypatch.setattr("pkg_resources.get_distribution", _raise)
+    monkeypatch.setattr("importlib.metadata.version", _raise)
     reload(templateflow)
-    assert templateflow.__version__ == "unknown"
+    assert templateflow.__version__ == "0+unknown"