scverse-misc 0.0.2__tar.gz → 0.0.3__tar.gz

{scverse_misc-0.0.2 → scverse_misc-0.0.3}/.pre-commit-config.yaml

@@ -7,16 +7,16 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.4.6
+    rev: v2.4.10
     hooks:
       - id: biome-format
         exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.16.2
+    rev: v2.21.0
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.5
+    rev: v0.15.9
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]

scverse_misc-0.0.3/CHANGELOG.md

@@ -0,0 +1,30 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog][],
+and this project adheres to [Semantic Versioning][].
+
+[keep a changelog]: https://keepachangelog.com/en/1.1.0/
+[semantic versioning]: https://semver.org/spec/v2.0.0.html
+
+## [0.0.3]
+
+## Added
+
+- A `deprecated` decorator wrapping `warnings.deprecated` that additionally modifies the
+  docstring to include a deprecation notice.
+
+## [0.0.2]
+
+## Removed
+
+- The Pandas utility functions
+
+## [0.0.1]
+
+- Initial release
+
+[0.0.3]: https://github.com/scverse/scverse-misc/compare/v0.0.2...v0.0.3
+[0.0.2]: https://github.com/scverse/scverse-misc/compare/v0.0.1...v0.0.2
+[0.0.1]: https://github.com/scverse/scverse-misc/releases/tag/v0.0.1

{scverse_misc-0.0.2 → scverse_misc-0.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scverse-misc
-Version: 0.0.2
+Version: 0.0.3
 Summary: Miscellaneous utility code used by scverse packages
 Project-URL: Documentation, https://scverse-misc.readthedocs.io/
 Project-URL: Homepage, https://github.com/scverse/scverse-misc
@@ -38,13 +38,14 @@ License: BSD 3-Clause License
         OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 License-File: LICENSE
 Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3.14
-Requires-Python: >=3.11
-Requires-Dist: pandas>=1
+Requires-Python: >=3.10
 Requires-Dist: session-info2
+Requires-Dist: typing-extensions; python_version < '3.13'
 Description-Content-Type: text/markdown
 
 # scverse-misc
@@ -101,7 +102,7 @@ If you found a bug, please use the [issue tracker][].
 [scverse discourse]: https://discourse.scverse.org/
 [issue tracker]: https://github.com/scverse/scverse-misc/issues
 [tests]: https://github.com/scverse/scverse-misc/actions/workflows/test.yaml
-[codecov]: https://codecov.io/gh/bioFAM/mofaflex
+[codecov]: https://codecov.io/gh/scverse/scverse-misc
 [documentation]: https://scverse-misc.readthedocs.io
 [changelog]: https://scverse-misc.readthedocs.io/en/latest/changelog.html
 [api documentation]: https://scverse-misc.readthedocs.io/latest/api.html

{scverse_misc-0.0.2 → scverse_misc-0.0.3}/README.md

@@ -52,7 +52,7 @@ If you found a bug, please use the [issue tracker][].
 [scverse discourse]: https://discourse.scverse.org/
 [issue tracker]: https://github.com/scverse/scverse-misc/issues
 [tests]: https://github.com/scverse/scverse-misc/actions/workflows/test.yaml
-[codecov]: https://codecov.io/gh/bioFAM/mofaflex
+[codecov]: https://codecov.io/gh/scverse/scverse-misc
 [documentation]: https://scverse-misc.readthedocs.io
 [changelog]: https://scverse-misc.readthedocs.io/en/latest/changelog.html
 [api documentation]: https://scverse-misc.readthedocs.io/latest/api.html

{scverse_misc-0.0.2 → scverse_misc-0.0.3}/docs/api.md

@@ -20,3 +20,12 @@ Types used by the former:
 
     ExtensionNamespace
 ```
+
+## Deprecations
+``` {eval-rst}
+.. autosummary::
+   :toctree: generated
+
+   deprecated
+   Deprecation
+```

{scverse_misc-0.0.2 → scverse_misc-0.0.3}/pyproject.toml

@@ -13,9 +13,10 @@ maintainers = [
 authors = [
   { name = "Ilia Kats" },
 ]
-requires-python = ">=3.11"
+requires-python = ">=3.10"
 classifiers = [
   "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
@@ -23,9 +24,9 @@ classifiers = [
 ]
 dynamic = [ "version" ]
 dependencies = [
-  "pandas>=1",
   # for debug logging (referenced from the issue template)
   "session-info2",
+  "typing-extensions; python_version<'3.13'",
 ]
 # https://docs.pypi.org/project_metadata/#project-urls
 urls.Documentation = "https://scverse-misc.readthedocs.io/"
@@ -64,7 +65,7 @@ envs.docs.scripts.clean = "git clean -fdX -- {args:docs}"
 envs.hatch-test.dependency-groups = [ "dev", "test" ]
 envs.hatch-test.matrix = [
   # Test the lowest and highest supported Python versions with normal deps
-  { deps = [ "stable" ], python = [ "3.11", "3.14" ] },
+  { deps = [ "stable" ], python = [ "3.10", "3.14" ] },
   # Test the newest supported Python version also with pre-release deps
   { deps = [ "pre" ], python = [ "3.14" ] },
 ]

{scverse_misc-0.0.2 → scverse_misc-0.0.3}/src/scverse_misc/__init__.py

@@ -1,2 +1,3 @@
+from ._deprecated import Deprecation, deprecated
 from ._extensions import ExtensionNamespace, make_register_namespace_decorator
 from ._version import __version__, __version_tuple__

scverse_misc-0.0.3/src/scverse_misc/_deprecated.py

@@ -0,0 +1,79 @@
+from __future__ import annotations
+
+import sys
+from inspect import getdoc
+from typing import TYPE_CHECKING, TypeVar
+
+if sys.version_info >= (3, 11):
+    from typing import LiteralString
+else:
+    from typing_extensions import LiteralString
+
+if sys.version_info >= (3, 13):
+    from warnings import deprecated as _deprecated
+else:
+    from typing_extensions import deprecated as _deprecated
+
+if TYPE_CHECKING:
+    from collections.abc import Callable
+
+    F = TypeVar("F", bound=Callable)
+
+
+class Deprecation(str):
+    """Utility class storing information on deprecated functionality.
+
+    Args:
+        version_deprecated: The version of the package where the functionality was deprecated.
+        msg: The deprecation message.
+    """
+
+    def __new__(cls, version_deprecated: LiteralString, msg: LiteralString = "") -> LiteralString:
+        obj = super().__new__(cls, msg)
+        obj.version_deprecated = version_deprecated
+        return obj
+
+
+def _deprecated_at(msg: Deprecation, *, category=FutureWarning, stacklevel=1) -> Callable[[F], F]:
+    """Decorator to indicate that a class, function, or overload is deprecated.
+
+    Wraps :func:`warnings.deprecated` and additionally modifies the docstring to include a deprecation notice.
+
+    Args:
+        msg: The deprecation message.
+        category: The category of the warning that will be emitted at runtime.
+        stacklevel: The stack level of the warning.
+
+    Examples:
+        >>> @deprecated(Deprecation("0.2", "Use bar() instead."))
+        ... def foo(baz):
+        ...     pass
+    """
+
+    def decorate(func: F) -> F:
+        kind = "function" if func.__name__ == func.__qualname__ else "method"
+        warnmsg = f"The {kind} {func.__name__} is deprecated and will be removed in the future."
+
+        doc = getdoc(func)
+        docmsg = f".. version-deprecated:: {msg.version_deprecated}"
+        if len(msg) is not None:
+            docmsg += f"\n   {msg}"
+            warnmsg += f" {msg}"
+
+        if doc is None:
+            doc = docmsg
+        else:
+            lines = doc.splitlines()
+            body = "\n".join(lines[1:])
+            doc = f"{lines[0]}\n\n{docmsg}\n{body}"
+        func.__doc__ = doc
+
+        return _deprecated(warnmsg, category=category, stacklevel=stacklevel)(func)
+
+    return decorate
+
+
+if TYPE_CHECKING:
+    deprecated = _deprecated
+else:
+    deprecated = _deprecated_at

scverse_misc-0.0.3/src/scverse_misc/_version.py

@@ -0,0 +1,24 @@
+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '0.0.3'
+__version_tuple__ = version_tuple = (0, 0, 3)
+
+__commit_id__ = commit_id = None

scverse_misc-0.0.3/tests/test_deprecation_decorator.py

@@ -0,0 +1,54 @@
+import pytest
+
+from scverse_misc import Deprecation, deprecated
+
+
+@pytest.fixture(params=[None, "Test message."])
+def msg(request: pytest.FixtureRequest):
+    return request.param
+
+
+@pytest.fixture(
+    params=[
+        None,
+        "Test function",
+        """Test function
+
+    This is a test.
+
+    Parameters
+    ----------
+    foo
+        bar
+    bar
+        baz
+""",
+    ]
+)
+def docstring(request):
+    return request.param
+
+
+@pytest.fixture
+def deprecated_func(msg, docstring):
+    def func(foo, bar):
+        return 42
+
+    func.__doc__ = docstring
+    return deprecated(Deprecation("foo", msg))(func)
+
+
+def test_deprecation_decorator(deprecated_func, docstring, msg):
+    with pytest.warns(FutureWarning, match="deprecated"):
+        assert deprecated_func(1, 2) == 42
+
+    lines = deprecated_func.__doc__.expandtabs().splitlines()
+    if docstring is None:
+        assert lines[0].startswith(".. version-deprecated::")
+    else:
+        lines_orig = docstring.expandtabs().splitlines()
+        assert lines[0] == lines_orig[0]
+        assert len(lines[1].strip()) == 0
+        assert lines[2].startswith(".. version-deprecated")
+        if msg is not None:
+            assert lines[3] == f"   {msg}"

scverse_misc-0.0.2/CHANGELOG.md

@@ -1,15 +0,0 @@
-# Changelog
-
-All notable changes to this project will be documented in this file.
-
-The format is based on [Keep a Changelog][],
-and this project adheres to [Semantic Versioning][].
-
-[keep a changelog]: https://keepachangelog.com/en/1.0.0/
-[semantic versioning]: https://semver.org/spec/v2.0.0.html
-
-## [Unreleased]
-
-### Added
-
-- Basic tool, preprocessing and plotting functions

scverse_misc-0.0.2/src/scverse_misc/_version.py

@@ -1,34 +0,0 @@
-# file generated by setuptools-scm
-# don't change, don't track in version control
-
-__all__ = [
-    "__version__",
-    "__version_tuple__",
-    "version",
-    "version_tuple",
-    "__commit_id__",
-    "commit_id",
-]
-
-TYPE_CHECKING = False
-if TYPE_CHECKING:
-    from typing import Tuple
-    from typing import Union
-
-    VERSION_TUPLE = Tuple[Union[int, str], ...]
-    COMMIT_ID = Union[str, None]
-else:
-    VERSION_TUPLE = object
-    COMMIT_ID = object
-
-version: str
-__version__: str
-__version_tuple__: VERSION_TUPLE
-version_tuple: VERSION_TUPLE
-commit_id: COMMIT_ID
-__commit_id__: COMMIT_ID
-
-__version__ = version = '0.0.2'
-__version_tuple__ = version_tuple = (0, 0, 2)
-
-__commit_id__ = commit_id = None