Merge branch 'main' into subloops

.github/workflows/ci.yml

@@ -30,26 +30,17 @@ jobs:
       fail-fast: false
       matrix:
         platform: [macos-latest, windows-latest, "ubuntu-latest"]
-        python-version: ["3.9", "3.10", "3.11"]
-        include:
-          - python-version: "3.7"
-            platform: "ubuntu-latest"
-          - python-version: "3.8"
-            platform: "ubuntu-latest"
-          - python-version: "3.8"
-            platform: "windows-latest"
-          - python-version: "3.12-dev"
-            platform: "ubuntu-latest"
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         id: cache
         with:
           path: tests/data
@@ -69,17 +60,19 @@ jobs:
         run: pytest -v --cov=nd2 --cov-report=xml --cov-report=term
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
 
   benchmarks:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         id: cache
         with:
           path: tests/data
@@ -95,7 +88,7 @@ jobs:
         run: python -m pip install .[test]
 
       - name: Run benchmarks
-        uses: CodSpeedHQ/action@v1
+        uses: CodSpeedHQ/action@v2
         with:
           run: pytest --codspeed -v --color=yes
 
@@ -108,7 +101,7 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.x"
 

.github/workflows/cron.yml

@@ -19,8 +19,6 @@ jobs:
         python-version: ['3.9', '3.10', '3.11']
         platform: [ubuntu-latest, macos-latest, windows-latest]
         include:
-          - python-version: "3.7"
-            platform: "ubuntu-latest"
           - python-version: "3.8"
             platform: "ubuntu-latest"
           - python-version: "3.8"
@@ -30,11 +28,11 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         id: cache
         with:
           path: tests/data

.github/workflows/docs.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3.x
 

.pre-commit-config.yaml

@@ -20,23 +20,23 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.4
+    rev: v0.2.0
     hooks:
       - id: ruff
         args: [--fix]
 
   - repo: https://github.com/psf/black
-    rev: 23.10.1
+    rev: 24.1.1
     hooks:
       - id: black
 
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.15
+    rev: v0.16
     hooks:
       - id: validate-pyproject
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.6.1
+    rev: v1.8.0
     hooks:
       - id: mypy
         files: "^src/"

README.md

@@ -9,7 +9,7 @@
 
 `.nd2` (Nikon NIS Elements) file reader.
 
-This reader provides a pure python implementation the official Nikon ND2 SDK.
+This reader provides a pure python implementation of the Nikon ND2 SDK.
 
 > It _used_ to wrap the official SDK with Cython, but has since been completely
 > rewritten to be pure python (for performance, ease of distribution, and
@@ -73,7 +73,7 @@ import numpy as np
 my_array = nd2.imread('some_file.nd2')                          # read to numpy array
 my_array = nd2.imread('some_file.nd2', dask=True)               # read to dask array
 my_array = nd2.imread('some_file.nd2', xarray=True)             # read to xarray
-my_array = nd2.imread('some_file.nd2', xarray=True, dask=True)  # read file to dask-xarray
+my_array = nd2.imread('some_file.nd2', xarray=True, dask=True)  # read to dask-xarray
 
 # or open a file with nd2.ND2File
 f = nd2.ND2File('some_file.nd2')

pyproject.toml

@@ -7,14 +7,13 @@ build-backend = "hatchling.build"
 name = "nd2"
 description = "Yet another nd2 (Nikon NIS Elements) file reader"
 readme = "README.md"
-requires-python = ">=3.7"
+requires-python = ">=3.8"
 license = { text = "BSD 3-Clause License" }
 authors = [{ email = "[email protected]", name = "Talley Lambert" }]
 classifiers = [
     "Development Status :: 4 - Beta",
     "License :: OSI Approved :: BSD License",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.7",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
@@ -30,7 +29,7 @@ test = [
     "aicsimageio; python_version < '3.12'",
     "dask[array]",
     "imagecodecs",
-    "lxml",
+    "lxml; python_version >= '3.9'",
     "numpy >=1.26; python_version >= '3.12'",
     "numpy; python_version < '3.12'",
     "ome-types",
@@ -69,17 +68,14 @@ documentation = "https://tlambert03.github.io/nd2/"
 [tool.hatch.version]
 source = "vcs"
 
-[tool.hatch.build.hooks.vcs]
-version-file = "src/nd2/_version.py"
-
 [tool.hatch.build.targets.wheel]
 only-include = ["src"]
 sources = ["src"]
 
 # https://beta.ruff.rs/docs/rules/
 [tool.ruff]
 line-length = 88
-target-version = "py37"
+target-version = "py38"
 src = ["src/nd2", "tests"]
 select = [
     "E",      # style errors

scripts/gather.py

@@ -1,4 +1,5 @@
 """gather metadata from all files in test/data with all nd readers."""
+
 import contextlib
 import json
 from pathlib import Path

scripts/nd2_describe.py

@@ -4,6 +4,7 @@
 
     python scripts/nd2_describe.py > tests/samples_metadata.json
 """
+
 import struct
 from dataclasses import asdict
 from pathlib import Path

src/nd2/__init__.py

@@ -1,9 +1,12 @@
 """nd2: A Python library for reading and writing ND2 files."""
 
+from importlib.metadata import PackageNotFoundError, version
+
 try:
-    from ._version import version as __version__
-except ImportError:
+    __version__ = version(__name__)
+except PackageNotFoundError:  # pragma: no cover
     __version__ = "unknown"
+
 __author__ = "Talley Lambert"
 __email__ = "[email protected]"
 __all__ = [

src/nd2/_binary.py

@@ -1,4 +1,5 @@
 """Utilities for binary layers in ND2 files."""
+
 from __future__ import annotations
 
 import io
@@ -131,12 +132,10 @@ def __init__(self, data: list[BinaryLayer]) -> None:
         self._data = data
 
     @overload
-    def __getitem__(self, key: int) -> BinaryLayer:
-        ...
+    def __getitem__(self, key: int) -> BinaryLayer: ...
 
     @overload
-    def __getitem__(self, key: slice) -> list[BinaryLayer]:
-        ...
+    def __getitem__(self, key: slice) -> list[BinaryLayer]: ...
 
     def __getitem__(self, key: int | slice) -> BinaryLayer | list[BinaryLayer]:
         return self._data[key]

src/nd2/_parse/_chunk_decode.py

@@ -1,4 +1,5 @@
 """FIXME: this has a lot of code duplication with _chunkmap.py."""
+
 from __future__ import annotations
 
 import mmap

src/nd2/_parse/_legacy_xml.py

@@ -5,6 +5,7 @@
 all of this logic is duplicated in _clx_xml.py.
 _legacy.py just needs some slight updates to deal with different parsing results.
 """
+
 from __future__ import annotations
 
 import re

src/nd2/_parse/_parse.py

@@ -584,7 +584,7 @@ def load_metadata(raw_meta: RawMetaDict, global_meta: GlobalMetadata) -> strct.M
         if matrix and (matrix.get("Columns") == 2 and matrix.get("Rows") == 2):
             # matrix["Data"] is a list of int64, we need to recast to float
             data = bytearray(matrix["Data"])
-            matrix_data: tuple[float, float, float, float] = tuple(  # type: ignore
+            matrix_data: tuple[float, float, float, float] = tuple(
                 i[0] for i in strctd.iter_unpack(data)
             )
             volume["cameraTransformationMatrix"] = matrix_data
@@ -637,7 +637,8 @@ def load_metadata(raw_meta: RawMetaDict, global_meta: GlobalMetadata) -> strct.M
             channel=channel_meta,
             loops=loops,
             microscope=strct.Microscope(
-                **microscope, modalityFlags=flags  # type: ignore
+                **microscope,
+                modalityFlags=flags,  # type: ignore
             ),
             volume=strct.Volume(
                 **volume,

src/nd2/_sdk_types.py

@@ -1,11 +1,14 @@
 """Various raw dict structures likely to be found in an ND2 file."""
+
 from __future__ import annotations
 
 from enum import IntEnum, auto
-from typing import TYPE_CHECKING, Union
+from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
-    from typing_extensions import Literal, NotRequired, TypeAlias, TypedDict
+    from typing import Literal, TypedDict, Union
+
+    from typing_extensions import NotRequired, TypeAlias
 
     class RawAttributesDict(TypedDict, total=False):
         uiWidth: int

src/nd2/_util.py

@@ -2,18 +2,14 @@
 
 import math
 import re
-import warnings
 from datetime import datetime, timezone
 from itertools import product
 from typing import TYPE_CHECKING, BinaryIO, NamedTuple, cast
 
 if TYPE_CHECKING:
     from os import PathLike
-    from typing import Any, Callable, ClassVar, Mapping, Sequence, Union
+    from typing import Any, Callable, ClassVar, Final, Mapping, Sequence, Union
 
-    from typing_extensions import Final
-
-    from nd2.readers import ND2Reader
     from nd2.structures import ExpLoop
 
     StrOrPath = Union[str, PathLike]
@@ -77,19 +73,6 @@ def is_legacy(path: StrOrPath) -> bool:
         return fh.read(4) == OLD_HEADER_MAGIC
 
 
-def get_reader(
-    path: str, validate_frames: bool = False, search_window: int = 100
-) -> ND2Reader:  # pragma: no cover
-    warnings.warn(
-        "Deprecated, use nd2.readers.ND2Reader.create if you want to "
-        "directly instantiate a reader subclass.",
-        stacklevel=2,
-    )
-    from nd2.readers import ND2Reader
-
-    return ND2Reader.create(path, search_window * 1000 if validate_frames else None)
-
-
 def is_new_format(path: str) -> bool:
     # TODO: this is just for dealing with missing test data
     with open(path, "rb") as fh:
@@ -159,9 +142,6 @@ def parse_time(time_str: str) -> datetime:
     raise ValueError(f"Could not parse {time_str}")  # pragma: no cover
 
 
-# utils for converting records to dicts, in recorded_data method
-
-
 def convert_records_to_dict_of_lists(
     records: ListOfDicts, null_val: Any = float("nan")
 ) -> DictOfLists:

src/nd2/index.py

@@ -7,9 +7,7 @@
 from concurrent.futures import ThreadPoolExecutor
 from datetime import datetime
 from pathlib import Path
-from typing import Any, Iterable, Iterator, Sequence, cast, no_type_check
-
-from typing_extensions import TypedDict
+from typing import Any, Iterable, Iterator, Sequence, TypedDict, cast, no_type_check
 
 import nd2