build: support python 3.12 (#168)

* test: test 3.12

* try pin numpy

* skip aics

* no xarray on py312

* remove deprecated

* fix import

.github/workflows/ci.yml

@@ -38,6 +38,8 @@ jobs:
             platform: "ubuntu-latest"
           - python-version: "3.8"
             platform: "windows-latest"
+          - python-version: "3.12-dev"
+            platform: "ubuntu-latest"
 
     steps:
       - uses: actions/checkout@v4

pyproject.toml

@@ -11,32 +11,35 @@ requires-python = ">=3.7"
 license = { text = "BSD 3-Clause License" }
 authors = [{ email = "[email protected]", name = "Talley Lambert" }]
 classifiers = [
-    "Development Status :: 3 - Alpha",
+    "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",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
 dynamic = ["version"]
 dependencies = ["resource-backed-dask-array", "typing-extensions", "numpy"]
 
 [project.optional-dependencies]
 legacy = ["imagecodecs"]
 test = [
-    "aicsimageio",
+    "aicsimageio; python_version < '3.12'",
     "dask[array]",
     "imagecodecs",
     "lxml",
+    "numpy >=1.26; python_version >= '3.12'",
+    "numpy; python_version < '3.12'",
     "ome-types",
     "psutil",
     "pytest-codspeed",
     "pytest-cov",
     "pytest-pretty",
     "pytest>=6.0",
-    "xarray",
+    "xarray; python_version < '3.12'",
 ]
 dev = [
     "aicsimageio",

src/nd2/_util.py

@@ -3,7 +3,7 @@
 import math
 import re
 import warnings
-from datetime import datetime
+from datetime import datetime, timezone
 from itertools import product
 from typing import TYPE_CHECKING, BinaryIO, NamedTuple, cast
 
@@ -95,12 +95,8 @@ def is_new_format(path: str) -> bool:
         return fh.read(4) == NEW_HEADER_MAGIC
 
 
-def jdn_to_datetime_local(jdn: float) -> datetime:
-    return datetime.fromtimestamp((jdn - 2440587.5) * 86400.0)
-
-
-def jdn_to_datetime_utc(jdn: float) -> datetime:
-    return datetime.utcfromtimestamp((jdn - 2440587.5) * 86400.0)
+def jdn_to_datetime(jdn: float, tz: timezone = timezone.utc) -> datetime:
+    return datetime.fromtimestamp((jdn - 2440587.5) * 86400.0, tz)
 
 
 def rgb_int_to_tuple(rgb: int) -> tuple[int, int, int]:

src/nd2/readers/_modern/modern_reader.py

@@ -545,9 +545,7 @@ def _acquisition_date(self) -> datetime.datetime | str | None:
 
         time = self._cached_global_metadata().get("time", {})
         jdn = time.get("absoluteJulianDayNumber")
-        if jdn:
-            return _util.jdn_to_datetime_utc(jdn)
-        return None
+        return _util.jdn_to_datetime(jdn) if jdn else None
 
     def binary_data(self) -> BinaryLayers | None:
         from nd2._binary import BinaryLayer, BinaryLayers, decode_binary_mask

tests/test_events.py

@@ -1,21 +1,30 @@
 from pathlib import Path
 
 import nd2
-import pandas as pd
+import numpy as np
 import pytest
 
 DATA = Path(__file__).parent / "data"
 
 
+EXPECTED_COORDS = ([0] * 5 + [1000] * 5 + [2000] * 5) * 3
+
+
 @pytest.mark.parametrize("fname", ["t3p3z5c3.nd2", "t3p3c3z5.nd2", "t1t1t1p3c3z5.nd2"])
 def test_events(fname: str) -> None:
     with nd2.ND2File(DATA / fname) as f:
-        events = f.events()
+        events = f.events(orient="list")
+        assert np.array_equal(events["X Coord [µm]"], EXPECTED_COORDS)
+        assert np.array_equal(events["Y Coord [µm]"], EXPECTED_COORDS)
+
 
-        df = pd.DataFrame(events)
-        expected_coords = ([0] * 5 + [1000] * 5 + [2000] * 5) * 3
-        assert all(df["X Coord [µm]"] == expected_coords)
-        assert all(df["Y Coord [µm]"] == expected_coords)
+@pytest.mark.parametrize("fname", ["t3p3z5c3.nd2", "t3p3c3z5.nd2", "t1t1t1p3c3z5.nd2"])
+def test_events_pandas(fname: str) -> None:
+    pd = pytest.importorskip("pandas")
+    with nd2.ND2File(DATA / fname) as f:
+        df = pd.DataFrame(f.events())
+        assert all(df["X Coord [µm]"] == EXPECTED_COORDS)
+        assert all(df["Y Coord [µm]"] == EXPECTED_COORDS)
         assert all(df["Z-Series"] == [-1, -0.5, 0, 0.5, 1] * 9)
         assert all(df["T Index"] == [0] * 15 + [1] * 15 + [2] * 15)
         assert all(df["Z Index"] == [0, 1, 2, 3, 4] * 9)

tests/test_metadata.py

@@ -7,13 +7,17 @@
 
 import dask.array as da
 import pytest
-import xarray as xr
 from nd2 import ND2File, _util, structures
 from nd2._parse._chunk_decode import ND2_FILE_SIGNATURE
 
 sys.path.append(str(Path(__file__).parent.parent / "scripts"))
 from nd2_describe import get_nd2_stats  # noqa: E402
 
+try:
+    import xarray as xr
+except ImportError:
+    xr = None
+
 if TYPE_CHECKING:
     from typing_extensions import Literal
 
@@ -104,9 +108,10 @@ def test_metadata_extraction_legacy(old_nd2):
         assert isinstance(nd.experiment, list)
         assert isinstance(nd.text_info, dict)
         assert isinstance(nd.metadata, structures.Metadata)
-        xarr = nd.to_xarray()
-        assert isinstance(xarr, xr.DataArray)
-        assert isinstance(xarr.data, da.Array)
+        if xr is not None:
+            xarr = nd.to_xarray()
+            assert isinstance(xarr, xr.DataArray)
+            assert isinstance(xarr.data, da.Array)
 
         with pytest.warns(UserWarning, match="not implemented"):
             nd.events()

tests/test_reader.py

@@ -6,7 +6,6 @@
 import dask.array as da
 import numpy as np
 import pytest
-import xarray as xr
 from nd2 import ND2File, imread
 from nd2._parse._chunk_decode import get_version
 from nd2._util import AXIS, is_supported_file
@@ -23,6 +22,7 @@ def test_read_safety(new_nd2: Path):
 
 def test_position(new_nd2: Path):
     """use position to extract a single stage position with asarray."""
+    pytest.importorskip("xarray")
     if new_nd2.stat().st_size > 250_000_000:
         pytest.skip("skipping read on big files")
     with ND2File(new_nd2) as nd:
@@ -53,6 +53,7 @@ def test_dask_closed(single_nd2):
 
 
 def test_full_read(new_nd2):
+    pytest.importorskip("xarray")
     with ND2File(new_nd2) as nd:
         if new_nd2.stat().st_size > 500_000_000:
             pytest.skip("skipping full read on big files")
@@ -82,6 +83,7 @@ def test_full_read_legacy(old_nd2):
 
 
 def test_xarray(new_nd2):
+    xr = pytest.importorskip("xarray")
     with ND2File(new_nd2) as nd:
         xarr = nd.to_xarray()
         assert isinstance(xarr, xr.DataArray)
@@ -90,6 +92,7 @@ def test_xarray(new_nd2):
 
 
 def test_xarray_legacy(old_nd2):
+    xr = pytest.importorskip("xarray")
     with ND2File(old_nd2) as nd:
         xarr = nd.to_xarray()
         assert isinstance(xarr, xr.DataArray)

tests/test_readme.py

@@ -9,6 +9,8 @@
 
 @pytest.mark.skipif(os.name == "nt", reason="paths annoying on windows")
 def test_readme(capsys):
+    pytest.importorskip("xarray")
+
     code = README.read_text().split("```python")[1].split("```")[0]
     code = code.replace("some_file.nd2", str(SAMPLE.absolute()))
     exec(code)