pin tifffile to a newer version to allow unpinning of ome-zarr.

.github/workflows/docs.yml

@@ -22,7 +22,7 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v3
-        with: 
+        with:
           fetch-depth: 0
       - name: Setup Pages
         id: pages

docs/examples/run_coordinate_transform.py

@@ -72,4 +72,4 @@
 
 # %%
 # Clean up
-tmp_dir.cleanup()
+tmp_dir.cleanup()

docs/examples/run_single_fov_ome_zarr.py

@@ -98,4 +98,4 @@
 
 # %%
 # Clean up
-tmp_dir.cleanup()
+tmp_dir.cleanup()

docs/gh-pages-redirect.html

@@ -6,4 +6,4 @@
     <meta http-equiv="refresh" content="0; url=./main/index.html">
     <link rel="canonical" href="./main/index.html">
   </head>
-</html>
+</html>

docs/source/_static/switcher.json

@@ -3,4 +3,4 @@
         "version": "latest",
         "url": "/main/index.html"
     }
-]
+]

docs/source/api.rst

@@ -17,4 +17,4 @@ Index
 -----
 
 * :ref:`genindex`
-* :ref:`search`
+* :ref:`search`

setup.cfg

@@ -34,10 +34,10 @@ setup_requires = setuptools_scm
 install_requires =
     pandas>=1.5.2
     pydantic>=1.10.2, <2
-    tifffile>=2023.2.3, <2023.3.15
+    tifffile>=2023.3.15, <2024.1.30
     natsort>=7.1.1
     ndtiff>=2.2.1
-    zarr>=2.13, <2.16
+    zarr>=2.15.0
     tqdm
     pillow>=9.4.0
     blosc2

tests/clearcontrol/test_clearcontrol.py

@@ -20,25 +20,27 @@ def mock_clear_control_dataset_path(tmp_path: Path) -> Path:
 
 
 def test_blosc_buffer(tmp_path: Path) -> None:
-
     buffer_path = tmp_path / "buffer.blc"
     in_array = np.random.randint(0, 5_000, size=(32, 32))
 
     _array_to_blosc_buffer(in_array, buffer_path)
-    out_array = blosc_buffer_to_array(buffer_path, in_array.shape, in_array.dtype)
+    out_array = blosc_buffer_to_array(
+        buffer_path, in_array.shape, in_array.dtype
+    )
 
     assert np.allclose(in_array, out_array)
 
 
 @pytest.mark.parametrize(
     "key",
-    [1,
-     (slice(None), 1),
-     (0, [1, 2]),
-     (-1, np.asarray([0, 3])),
-     (slice(1), -2),
-     (np.asarray(0),),
-     (0, 0, slice(32)),
+    [
+        1,
+        (slice(None), 1),
+        (0, [1, 2]),
+        (-1, np.asarray([0, 3])),
+        (slice(1), -2),
+        (np.asarray(0),),
+        (0, 0, slice(32)),
     ],
 )
 def test_CCFOV_indexing(
@@ -58,7 +60,13 @@ def test_CCFOV_metadata(
     mock_clear_control_dataset_path: Path,
 ) -> None:
     cc = ClearControlFOV(mock_clear_control_dataset_path)
-    expected_metadata = {"voxel_size_z": 1.0, "voxel_size_y": 0.25, "voxel_size_x": 0.25, "acquisition_type": "NA", "time_delta": 45.0}
+    expected_metadata = {
+        "voxel_size_z": 1.0,
+        "voxel_size_y": 0.25,
+        "voxel_size_x": 0.25,
+        "acquisition_type": "NA",
+        "time_delta": 45.0,
+    }
     metadata = cc.metadata()
     assert metadata == expected_metadata
 
@@ -79,7 +87,7 @@ def test_CCFOV_cache(
     assert np.array_equal(cc._cache_array, array)
 
     new_array = cc[1]
-    assert id(new_array) == id(array)   # same reference, so cache worked
+    assert id(new_array) == id(array)  # same reference, so cache worked
 
     cc.cache = False
     assert cc._cache_key is None

tests/cli/test_cli.py

@@ -95,7 +95,12 @@ def test_cli_info_ome_zarr(setup_test_data, setup_hcs_ref, verbose):
     suppress_health_check=[HealthCheck.function_scoped_fixture], deadline=20000
 )
 def test_cli_convert_ome_tiff(
-    setup_test_data, setup_mm2gamma_ome_tiffs, f, g, s, chk,
+    setup_test_data,
+    setup_mm2gamma_ome_tiffs,
+    f,
+    g,
+    s,
+    chk,
 ):
     _, _, input_dir = setup_mm2gamma_ome_tiffs
     runner = CliRunner()

tests/conftest.py

@@ -96,7 +96,7 @@ def setup_mm2gamma_ome_tiff_hcs():
         f for f in os.listdir(test_data) if os.path.isdir(pjoin(test_data, f))
     ]
     # select datasets with multiple positioons; here they all have 4 positions
-    hcs_subfolders = [f for f in subfolders if '4p' in f]
+    hcs_subfolders = [f for f in subfolders if "4p" in f]
 
     # specific folder
     one_folder = pjoin(test_data, hcs_subfolders[0])

tests/fov/test_fov.py

@@ -67,7 +67,6 @@ def test_missing_axes(axes: list[str], missing: list[int]) -> None:
 
 
 def test_fov_dict() -> None:
-
     good_collection = FOVDict(
         {
             "488": FOV(["y", "x"]),

tests/pyramid/test_pyramid.py

@@ -14,7 +14,6 @@ def _mock_fov(
     shape: tuple[int, ...],
     scale: tuple[float, float, float],
 ) -> Position:
-
     ds_path = tmp_path / "ds.zarr"
     channels = [str(i) for i in range(shape[1])]
 
@@ -47,7 +46,6 @@ def _mock_fov(
 
 @pytest.mark.parametrize("ndim", [2, 5])
 def test_pyramid(tmp_path: Path, ndim: int) -> None:
-
     # not all shapes not divisible by 2
     shape = (2, 2, 67, 115, 128)[-ndim:]
     scale = (2, 0.5, 0.5)[-min(3, ndim) :]

tests/reader/test_multipagetiff.py

@@ -62,7 +62,6 @@ def test_output_dims_mm2gamma_incomplete(
 
 
 def test_get_zarr_mm2gamma(setup_test_data, setup_mm2gamma_ome_tiffs):
-
     _ = setup_test_data
     _, _, rand_folder = setup_mm2gamma_ome_tiffs
     mmr = MicromanagerOmeTiffReader(rand_folder, extract_data=True)
@@ -73,7 +72,6 @@ def test_get_zarr_mm2gamma(setup_test_data, setup_mm2gamma_ome_tiffs):
 
 
 def test_get_array_mm2gamma(setup_test_data, setup_mm2gamma_ome_tiffs):
-
     _ = setup_test_data
     _, _, rand_folder = setup_mm2gamma_ome_tiffs
     mmr = MicromanagerOmeTiffReader(rand_folder, extract_data=True)
@@ -84,7 +82,6 @@ def test_get_array_mm2gamma(setup_test_data, setup_mm2gamma_ome_tiffs):
 
 
 def test_get_num_positions_mm2gamma(setup_test_data, setup_mm2gamma_ome_tiffs):
-
     _ = setup_test_data
     _, _, rand_folder = setup_mm2gamma_ome_tiffs
     mmr = MicromanagerOmeTiffReader(rand_folder, extract_data=True)
@@ -132,7 +129,6 @@ def test_output_dims_mm1422(setup_test_data, setup_mm1422_ome_tiffs):
 
 
 def test_get_zarr_mm1422(setup_test_data, setup_mm1422_ome_tiffs):
-
     _ = setup_test_data
     _, _, rand_folder = setup_mm1422_ome_tiffs
     mmr = MicromanagerOmeTiffReader(rand_folder, extract_data=True)
@@ -143,7 +139,6 @@ def test_get_zarr_mm1422(setup_test_data, setup_mm1422_ome_tiffs):
 
 
 def test_get_array_mm1422(setup_test_data, setup_mm1422_ome_tiffs):
-
     _ = setup_test_data
     _, _, rand_folder = setup_mm1422_ome_tiffs
     mmr = MicromanagerOmeTiffReader(rand_folder, extract_data=True)
@@ -154,7 +149,6 @@ def test_get_array_mm1422(setup_test_data, setup_mm1422_ome_tiffs):
 
 
 def test_get_num_positions_mm1422(setup_test_data, setup_mm1422_ome_tiffs):
-
     _ = setup_test_data
     _, _, rand_folder = setup_mm1422_ome_tiffs
     mmr = MicromanagerOmeTiffReader(rand_folder, extract_data=True)

tests/reader/test_singlepagetiff.py

@@ -65,7 +65,6 @@ def test_output_dims_mm2gamma_incomplete(
 
 
 def test_get_zarr_mm2gamma(setup_test_data, setup_mm2gamma_singlepage_tiffs):
-
     _ = setup_test_data
     _, _, rand_folder = setup_mm2gamma_singlepage_tiffs
     mmr = MicromanagerSequenceReader(rand_folder, extract_data=True)
@@ -76,7 +75,6 @@ def test_get_zarr_mm2gamma(setup_test_data, setup_mm2gamma_singlepage_tiffs):
 
 
 def test_get_array_mm2gamma(setup_test_data, setup_mm2gamma_singlepage_tiffs):
-
     _ = setup_test_data
     _, _, rand_folder = setup_mm2gamma_singlepage_tiffs
     mmr = MicromanagerSequenceReader(rand_folder, extract_data=True)
@@ -89,7 +87,6 @@ def test_get_array_mm2gamma(setup_test_data, setup_mm2gamma_singlepage_tiffs):
 def test_get_num_positions_mm2gamma(
     setup_test_data, setup_mm2gamma_singlepage_tiffs
 ):
-
     _ = setup_test_data
     _, _, rand_folder = setup_mm2gamma_singlepage_tiffs
     mmr = MicromanagerSequenceReader(rand_folder, extract_data=True)
@@ -136,7 +133,6 @@ def test_output_dims_mm1422(setup_test_data, setup_mm1422_singlepage_tiffs):
 
 
 def test_get_zarr_mm1422(setup_test_data, setup_mm1422_singlepage_tiffs):
-
     _ = setup_test_data
     _, _, rand_folder = setup_mm1422_singlepage_tiffs
     mmr = MicromanagerSequenceReader(rand_folder, extract_data=True)
@@ -147,7 +143,6 @@ def test_get_zarr_mm1422(setup_test_data, setup_mm1422_singlepage_tiffs):
 
 
 def test_get_array_mm1422(setup_test_data, setup_mm1422_singlepage_tiffs):
-
     _ = setup_test_data
     _, _, rand_folder = setup_mm1422_singlepage_tiffs
     mmr = MicromanagerSequenceReader(rand_folder, extract_data=True)
@@ -160,7 +155,6 @@ def test_get_array_mm1422(setup_test_data, setup_mm1422_singlepage_tiffs):
 def test_get_num_positions_mm1422(
     setup_test_data, setup_mm1422_singlepage_tiffs
 ):
-
     _ = setup_test_data
     _, _, rand_folder = setup_mm1422_singlepage_tiffs
     mmr = MicromanagerSequenceReader(rand_folder, extract_data=True)

tests/reader/test_zarrfile.py

@@ -59,7 +59,6 @@ def test_output_dims_mm2gamma(setup_test_data, setup_mm2gamma_zarr):
 
 
 def test_get_zarr_mm2gamma(setup_test_data, setup_mm2gamma_zarr):
-
     _ = setup_test_data
     src = setup_mm2gamma_zarr
     mmr = ZarrReader(src)
@@ -70,7 +69,6 @@ def test_get_zarr_mm2gamma(setup_test_data, setup_mm2gamma_zarr):
 
 
 def test_get_array_mm2gamma(setup_test_data, setup_mm2gamma_zarr):
-
     _ = setup_test_data
     src = setup_mm2gamma_zarr
     mmr = ZarrReader(src)
@@ -82,7 +80,6 @@ def test_get_array_mm2gamma(setup_test_data, setup_mm2gamma_zarr):
 
 
 def test_get_image_mm2gamma(setup_test_data, setup_mm2gamma_zarr):
-
     _ = setup_test_data
     src = setup_mm2gamma_zarr
     mmr = ZarrReader(src)
@@ -94,7 +91,6 @@ def test_get_image_mm2gamma(setup_test_data, setup_mm2gamma_zarr):
 
 
 def test_get_num_positions_mm2gamma(setup_test_data, setup_mm2gamma_zarr):
-
     _ = setup_test_data
     src = setup_mm2gamma_zarr
     mmr = ZarrReader(src)