Change the default path type to UPath (#1326)

* changed the default path type to UPath

* remove isinstance check

* lint

* implement feedback

* add Changelog.md

---------

Co-authored-by: valentin-pinkau <[email protected]>

Author: valentin-pinkau

webknossos/Changelog.md

@@ -17,6 +17,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 ### Added
 
 ### Changed
+- Changed the default path type to `UPath` [#1326](https://github.com/scalableminds/webknossos-libs/pull/1326)
 
 ### Fixed
 

webknossos/tests/conftest.py

@@ -1,7 +1,7 @@
 import gc
 import os
 import warnings
-from collections.abc import Generator
+from collections.abc import Generator, Iterator
 from os import makedirs
 from pathlib import Path
 from shutil import rmtree, unpack_archive
@@ -11,6 +11,7 @@
 import httpx
 import pytest
 from hypothesis import strategies as st
+from upath import UPath
 
 import webknossos as wk
 from webknossos.client._upload_dataset import _cached_get_upload_datastore
@@ -19,6 +20,11 @@
 from .constants import TESTDATA_DIR, TESTOUTPUT_DIR
 
 
+@pytest.fixture()
+def tmp_upath(tmp_path: Path) -> Iterator[UPath]:
+    yield UPath(tmp_path)
+
+
 def pytest_make_parametrize_id(config: Any, val: Any, argname: str) -> Any:
     del config
     del argname

webknossos/tests/constants.py

@@ -4,15 +4,14 @@
 import sys
 from collections.abc import Iterator
 from contextlib import contextmanager
-from pathlib import Path
 from time import sleep
 
 from upath import UPath
 
 from webknossos.utils import rmtree
 
-TESTDATA_DIR = Path(__file__).parent.parent / "testdata"
-TESTOUTPUT_DIR = Path(__file__).parent.parent / "testoutput"
+TESTDATA_DIR = UPath(__file__).parent.parent / "testdata"
+TESTOUTPUT_DIR = UPath(__file__).parent.parent / "testoutput"
 
 
 MINIO_ROOT_USER = "TtnuieannGt2rGuie2t8Tt7urarg5nauedRndrur"
@@ -31,7 +30,7 @@
 def use_minio() -> Iterator[None]:
     """Minio is an S3 clone and is used as local test server"""
     if sys.platform == "darwin":
-        minio_path = Path("testoutput_minio")
+        minio_path = UPath("testoutput_minio")
         rmtree(minio_path)
         minio_process = subprocess.Popen(
             shlex.split(f"minio server --address :8000 ./{minio_path}"),

webknossos/tests/dataset/test_attachments.py

@@ -15,7 +15,7 @@
 from webknossos.geometry import BoundingBox
 
 
-def make_dataset(dataset_path: Path) -> tuple[Dataset, SegmentationLayer]:
+def make_dataset(dataset_path: UPath) -> tuple[Dataset, SegmentationLayer]:
     dataset = Dataset(dataset_path / "test_attachments", voxel_size=(10, 10, 10))
     seg_layer = dataset.add_layer(
         "seg",
@@ -26,8 +26,8 @@ def make_dataset(dataset_path: Path) -> tuple[Dataset, SegmentationLayer]:
     return dataset, seg_layer
 
 
-def test_attachments(tmp_path: Path) -> None:
-    dataset, seg_layer = make_dataset(tmp_path)
+def test_attachments(tmp_upath: UPath) -> None:
+    dataset, seg_layer = make_dataset(tmp_upath)
 
     # meshes
     seg_layer.attachments.add_mesh(
@@ -142,14 +142,14 @@ def test_attachments(tmp_path: Path) -> None:
     assert "attachments" not in properties_json["dataLayers"][0]
 
 
-def test_copy_layer(tmp_path: Path) -> None:
-    dataset, seg_layer = make_dataset(tmp_path)
+def test_copy_layer(tmp_upath: UPath) -> None:
+    dataset, seg_layer = make_dataset(tmp_upath)
 
     mesh_path = dataset.path / "seg" / "meshes" / "meshfile.hdf5"
     mesh_path.parent.mkdir(parents=True, exist_ok=True)
     mesh_path.write_text("test")
 
-    agglomerate_path = (tmp_path / "agglomerate_view_15").resolve()
+    agglomerate_path = (tmp_upath / "agglomerate_view_15").resolve()
     agglomerate_path.mkdir(parents=True, exist_ok=True)
     (agglomerate_path / "zarr.json").write_text("test")
 
@@ -164,7 +164,7 @@ def test_copy_layer(tmp_path: Path) -> None:
         data_format=AttachmentDataFormat.Zarr3,
     )
 
-    copy_dataset = Dataset(tmp_path / "test_copy", voxel_size=(10, 10, 10))
+    copy_dataset = Dataset(tmp_upath / "test_copy", voxel_size=(10, 10, 10))
     copy_layer = copy_dataset.add_copy_layer(seg_layer).as_segmentation_layer()
 
     assert (
@@ -189,14 +189,14 @@ def test_copy_layer(tmp_path: Path) -> None:
     )
 
 
-def test_fs_copy_layer(tmp_path: Path) -> None:
-    dataset, seg_layer = make_dataset(tmp_path)
+def test_fs_copy_layer(tmp_upath: UPath) -> None:
+    dataset, seg_layer = make_dataset(tmp_upath)
 
     mesh_path = dataset.path / "seg" / "meshes" / "meshfile.hdf5"
     mesh_path.parent.mkdir(parents=True, exist_ok=True)
     mesh_path.write_text("test")
 
-    agglomerate_path = (tmp_path / "agglomerate_view_15").resolve()
+    agglomerate_path = (tmp_upath / "agglomerate_view_15").resolve()
     agglomerate_path.mkdir(parents=True, exist_ok=True)
     (agglomerate_path / "zarr.json").write_text("test")
 
@@ -212,7 +212,7 @@ def test_fs_copy_layer(tmp_path: Path) -> None:
         data_format=AttachmentDataFormat.Zarr3,
     )
 
-    copy_dataset = Dataset(tmp_path / "test_copy", voxel_size=(10, 10, 10))
+    copy_dataset = Dataset(tmp_upath / "test_copy", voxel_size=(10, 10, 10))
     copy_layer = copy_dataset.add_fs_copy_layer(seg_layer).as_segmentation_layer()
 
     # has been copied
@@ -229,14 +229,14 @@ def test_fs_copy_layer(tmp_path: Path) -> None:
     )
 
 
-def test_symlink_layer(tmp_path: Path) -> None:
-    dataset, seg_layer = make_dataset(tmp_path)
+def test_symlink_layer(tmp_upath: UPath) -> None:
+    dataset, seg_layer = make_dataset(tmp_upath)
 
     mesh_path = dataset.path / "seg" / "meshes" / "meshfile.hdf5"
     mesh_path.parent.mkdir(parents=True, exist_ok=True)
     mesh_path.write_text("test")
 
-    agglomerate_path = (tmp_path / "agglomerate_view_15").resolve()
+    agglomerate_path = (tmp_upath / "agglomerate_view_15").resolve()
     agglomerate_path.mkdir(parents=True, exist_ok=True)
     (agglomerate_path / "zarr.json").write_text("test")
 
@@ -252,7 +252,7 @@ def test_symlink_layer(tmp_path: Path) -> None:
         data_format=AttachmentDataFormat.Zarr3,
     )
 
-    copy_dataset = Dataset(tmp_path / "test_copy", voxel_size=(10, 10, 10))
+    copy_dataset = Dataset(tmp_upath / "test_copy", voxel_size=(10, 10, 10))
     copy_layer = copy_dataset.add_symlink_layer(
         seg_layer, make_relative=True
     ).as_segmentation_layer()
@@ -276,8 +276,8 @@ def test_symlink_layer(tmp_path: Path) -> None:
     )
 
 
-def test_remote_layer(tmp_path: Path) -> None:
-    dataset, seg_layer = make_dataset(tmp_path)
+def test_remote_layer(tmp_upath: UPath) -> None:
+    dataset, seg_layer = make_dataset(tmp_upath)
 
     mesh_path = UPath(
         "s3://bucket/meshfile.zarr",
@@ -290,7 +290,7 @@ def test_remote_layer(tmp_path: Path) -> None:
         data_format=AttachmentDataFormat.Zarr3,
     )
 
-    copy_dataset = Dataset(tmp_path / "test_copy", voxel_size=(10, 10, 10))
+    copy_dataset = Dataset(tmp_upath / "test_copy", voxel_size=(10, 10, 10))
     copy_layer = copy_dataset.add_remote_layer(seg_layer).as_segmentation_layer()
 
     assert copy_layer.attachments.meshes[0].path == mesh_path
@@ -301,8 +301,8 @@ def test_remote_layer(tmp_path: Path) -> None:
     )
 
 
-def test_upload_fail(tmp_path: Path) -> None:
-    dataset, seg_layer = make_dataset(tmp_path)
+def test_upload_fail(tmp_upath: UPath) -> None:
+    dataset, seg_layer = make_dataset(tmp_upath)
     seg_layer.attachments.add_mesh(
         dataset.path / "seg" / "meshfile",
         name="meshfile",
@@ -313,8 +313,8 @@ def test_upload_fail(tmp_path: Path) -> None:
         dataset.upload()
 
 
-def test_unique_attachment_names(tmp_path: Path) -> None:
-    dataset, seg_layer = make_dataset(tmp_path)
+def test_unique_attachment_names(tmp_upath: UPath) -> None:
+    dataset, seg_layer = make_dataset(tmp_upath)
 
     seg_layer.attachments.add_mesh(
         UPath("http://example.com/meshfile.zarr"),
@@ -329,8 +329,8 @@ def test_unique_attachment_names(tmp_path: Path) -> None:
         )
 
 
-def test_acceptable_attachment_names(tmp_path: Path) -> None:
-    dataset, seg_layer = make_dataset(tmp_path)
+def test_acceptable_attachment_names(tmp_upath: UPath) -> None:
+    dataset, seg_layer = make_dataset(tmp_upath)
 
     with pytest.raises(ValueError):
         seg_layer.attachments.add_mesh(
@@ -356,8 +356,8 @@ def test_remote_dataset() -> None:
     assert seg_layer.attachments.meshes[0]._properties.path == "seg/meshes/meshfile"
 
 
-def test_add_attachments(tmp_path: Path) -> None:
-    dataset, seg_layer = make_dataset(tmp_path)
+def test_add_attachments(tmp_upath: UPath) -> None:
+    dataset, seg_layer = make_dataset(tmp_upath)
 
     mesh = MeshAttachment.from_path_and_name(
         dataset.path / "seg" / "meshes" / "meshfile",
@@ -370,11 +370,11 @@ def test_add_attachments(tmp_path: Path) -> None:
     assert seg_layer.attachments.meshes[0].name == "meshfile_4-4-1"
 
 
-def test_add_copy_attachments(tmp_path: Path) -> None:
-    dataset, seg_layer = make_dataset(tmp_path)
+def test_add_copy_attachments(tmp_upath: UPath) -> None:
+    dataset, seg_layer = make_dataset(tmp_upath)
 
     # meshes
-    mesh_path = tmp_path / "meshfile"
+    mesh_path = tmp_upath / "meshfile"
     mesh_path.write_text("test")
 
     mesh = MeshAttachment.from_path_and_name(
@@ -393,7 +393,7 @@ def test_add_copy_attachments(tmp_path: Path) -> None:
     assert mesh_path.exists()
 
     # segment index (has camel-casing)
-    segment_index_path = tmp_path / "segment_index"
+    segment_index_path = tmp_upath / "segment_index"
     segment_index_path.write_text("test")
 
     segment_index = SegmentIndexAttachment.from_path_and_name(
@@ -408,11 +408,11 @@ def test_add_copy_attachments(tmp_path: Path) -> None:
     )
 
 
-def test_add_symlink_attachments(tmp_path: Path) -> None:
-    dataset, seg_layer = make_dataset(tmp_path)
+def test_add_symlink_attachments(tmp_upath: UPath) -> None:
+    dataset, seg_layer = make_dataset(tmp_upath)
 
     # meshes
-    mesh_path = tmp_path.resolve() / "meshfile"
+    mesh_path = tmp_upath.resolve() / "meshfile"
     mesh_path.write_text("test")
 
     mesh = MeshAttachment.from_path_and_name(
@@ -430,7 +430,7 @@ def test_add_symlink_attachments(tmp_path: Path) -> None:
     assert mesh_path.exists()
 
     # segment index (has camel-casing)
-    segment_index_path = tmp_path / "segment_index"
+    segment_index_path = tmp_upath / "segment_index"
     segment_index_path.write_text("test")
 
     segment_index = SegmentIndexAttachment.from_path_and_name(
@@ -450,8 +450,8 @@ def test_add_symlink_attachments(tmp_path: Path) -> None:
     ).resolve() == segment_index_path
 
 
-def test_detect_legacy_attachments(tmp_path: Path) -> None:
-    _, seg_layer = make_dataset(tmp_path)
+def test_detect_legacy_attachments(tmp_upath: UPath) -> None:
+    _, seg_layer = make_dataset(tmp_upath)
 
     # legacy meshes
     mesh_path = seg_layer.path / "meshes" / "meshfile_4-4-1.hdf5"