code cleanup to prep for release

Author: nsheff

.github/workflows/run-pytest.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.10", "3.13"]
+        python-version: ["3.10", "3.14"]
         os: [ubuntu-latest]
 
     steps:

changelog.md

@@ -7,12 +7,19 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ### Changed
 - Migrated packaging from setup.py/setup.cfg to pyproject.toml with hatchling backend
 - Replaced black with ruff for linting and formatting
-- Added .pre-commit-config.yaml with ruff
-- Updated GitHub Actions workflows to latest versions (checkout@v4, setup-python@v5)
+- Updated GitHub Actions workflows to latest versions (checkout@v6, setup-python@v6)
 - Updated publish workflow to use `python -m build` instead of `setup.py sdist`
 - Modernized type hints: replaced `Optional`/`Union` with PEP 604 `X | None` / `X | Y` syntax
 - Converted remaining Sphinx-style docstrings to Google style
 - Dropped Python 3.9 support (minimum is now 3.10)
+- Added Python 3.14 support
+
+### Fixed
+- Deduplicated `mkabs` in `file_locking.py` — `ThreeLocker` now uses the canonical version from `paths.py` which handles None, URLs, and file-as-reldir
+- Deduplicated `_create_lock` in `file_locking.py` — consolidated to single implementation in `files.py`
+- Fixed `tarfile.extractall()` deprecation warning for Python 3.12+ (added `filter="data"`)
+- Fixed typo "assiated" → "associated" in `cli_tools.py`
+- Re-exported `uniqify` function that was accidentally dropped during explicit-exports migration
 
 ### Removed
 - Deprecated `asciify_dict()` function (was a Python 2 no-op)

pyproject.toml

@@ -18,6 +18,7 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
 dependencies = []
@@ -41,4 +42,7 @@ line-length = 100
 
 [tool.ruff.lint]
 select = ["E", "F", "I", "W"]
-ignore = ["E501", "F403", "F405"]
+ignore = ["E501"]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/*" = ["F403", "F405"]

tests/test_packaging.py

@@ -20,6 +20,7 @@
         ("is_collection_like", isfunction),
         ("merge_dicts", isfunction),
         ("powerset", isfunction),
+        ("uniqify", isfunction),
         # environment
         ("TmpEnv", isclass),
         # file_locking

ubiquerg/__init__.py

@@ -11,7 +11,7 @@
     convert_value,
     query_yes_no,
 )
-from .collection import deep_update, is_collection_like, merge_dicts, powerset
+from .collection import deep_update, is_collection_like, merge_dicts, powerset, uniqify
 from .environment import TmpEnv
 from .file_locking import (
     READ,
@@ -70,6 +70,7 @@
     "size",
     "ThreeLocker",
     "TmpEnv",
+    "uniqify",
     "untar",
     "VersionInHelpParser",
     "wait_for_lock",

ubiquerg/cli_tools.py

@@ -46,7 +46,7 @@ def subparsers(self) -> _SubParsersAction:
         return subs[0]
 
     def top_level_args(self) -> list[Any]:
-        """Get actions not assiated with any subparser.
+        """Get actions not associated with any subparser.
 
         Help and version are also excluded.
 

ubiquerg/file_locking.py

@@ -1,11 +1,11 @@
-import errno
 import glob
 import logging
 import os
 from contextlib import contextmanager
 from signal import SIGINT, SIGTERM, signal
 
-from .files import create_file_racefree, wait_for_lock
+from .files import _create_lock, create_file_racefree, wait_for_lock
+from .paths import mkabs
 
 PID = os.getpid()
 READ = f"read-{PID}"
@@ -290,32 +290,6 @@ def ensure_write_access(lock_path, strict_ro_locks=False):
             return True
 
 
-def _create_lock(lock_path, filepath, wait_max) -> None:
-    # _LOGGER.debug(f"Creating lock for {filepath} at {lock_path}")
-    _LOGGER.debug(f"Creating lock at {os.path.basename(lock_path)}")
-    try:
-        create_file_racefree(lock_path)
-    except FileNotFoundError:
-        parent_dir = os.path.dirname(filepath)
-        os.makedirs(parent_dir)
-        _create_lock(lock_path, filepath, wait_max)
-    except Exception as e:
-        if e.errno == errno.EEXIST:
-            # Rare case: file already exists;
-            # the lock has been created in the split second since the
-            # last lock existence check,
-            # wait for the lock file to be gone, but no longer than
-            # `wait_max`.
-            _LOGGER.info(
-                "The lock has been created in the split second since the "
-                "last lock existence check. Waiting"
-            )
-            wait_for_lock(lock_path, wait_max)
-            _create_lock(lock_path, filepath, wait_max)
-        else:
-            raise e
-
-
 def _remove_lock(lock_path) -> bool:
     """Remove lock.
 
@@ -345,32 +319,6 @@ def make_all_lock_paths(filepath):
     return lock_paths
 
 
-def mkabs(path, reldir=None):
-    """Make sure a path is absolute.
-
-    If not already absolute, it's made absolute relative to a given directory.
-    Also expands ~ and environment variables for kicks.
-
-    Args:
-        path: Path to make absolute
-        reldir: Relative directory to make path absolute from if it's not already absolute
-
-    Returns:
-        str: Absolute path
-    """
-
-    def xpand(path):
-        return os.path.expandvars(os.path.expanduser(path))
-
-    if os.path.isabs(xpand(path)):
-        return xpand(path)
-
-    if not reldir:
-        return os.path.abspath(xpand(path))
-
-    return os.path.join(xpand(reldir), xpand(path))
-
-
 # class OneLocker(object):
 # def lock(self, type=READ):
 #     if not self.filepath:

ubiquerg/files.py

@@ -111,7 +111,10 @@ def untar(src: str, dst: str) -> None:
         dst: path to output folder
     """
     with topen(src) as tf:
-        tf.extractall(path=dst)
+        if sys.version_info >= (3, 12):
+            tf.extractall(path=dst, filter="data")
+        else:
+            tf.extractall(path=dst)
 
 
 def get_file_mod_time(pth: str) -> float: