Correctly parse relative mag paths and add version field (#1288)

* wip

* fixes

* update cassettes

* json

* add test for relative paths

* moar relative paths

* upgrade pylibczirw

* changelog

* fix issue in setup_mag

* Apply suggestions from code review

Co-authored-by: Mark Bader <[email protected]>

* allow metadata-only editing of read-only layers

* Update webknossos/Changelog.md

* fix test_symlink_layer_rename

---------

Co-authored-by: Mark Bader <[email protected]>

Author: normanrz

webknossos/Changelog.md

@@ -15,8 +15,12 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 ### Breaking Changes
 
 ### Added
+- Added a `version` field to the `datasource-properties.json` file, which is always set to `1`, for now. [#1288](https://github.com/scalableminds/webknossos-libs/pull/1288)
 
 ### Changed
+- The `Layer.path` property now always returns `Dataset.path / layer.name`, even if all mags are stored remotely. [#1288](https://github.com/scalableminds/webknossos-libs/pull/1288)
+- `Layer.is_remote_to_dataset` is deprecated in favor of `Layer.is_foreign` and `MagView.is_remote_to_dataset` is deprecated in favor of `MagView.is_foreign`. [#1288](https://github.com/scalableminds/webknossos-libs/pull/1288) 
+- Relative `path` fields in the mag definition of a `datasource-properties.json` file are now interpreted relative to the `Dataset.path`. [#1288](https://github.com/scalableminds/webknossos-libs/pull/1288)
 
 ### Fixed
 

webknossos/pyproject.toml

@@ -68,15 +68,15 @@ Changelog = "https://github.com/scalableminds/webknossos-libs/blob/master/webkno
 tifffile = ["tifffile >=2024.8.24"]
 imagecodecs = ["imagecodecs >=2021.11.20"]
 bioformats = ["JPype1 ~=1.5.0"]
-czi = ["pylibCZIrw ==4.1.3"]
+czi = ["pylibCZIrw ==5.0.0"]
 examples = [
     "fastremap ~=1.15.0",
     "pandas ~=2.2.0",
     "pooch ~=1.5.2",
     "s3fs >=2023.9.0",
     "tabulate >=0.9.0",
     "scikit-learn ~=1.5.1",
-    "scikit-image ~=0.24.0"
+    "scikit-image ~=0.25.0"
 ]
 all = [
     "webknossos[tifffile]",

webknossos/testdata/complex_property_ds/datasource-properties.json

@@ -1,4 +1,5 @@
 {
+  "version": 1,
   "id": {
     "name": "ROI2017_wkw",
     "team": "Connectomics department"
@@ -8,62 +9,34 @@
       "name": "color",
       "category": "color",
       "boundingBox": {
-        "topLeft": [
-          0,
-          0,
-          0
-        ],
+        "topLeft": [0, 0, 0],
         "width": 1024,
         "height": 1024,
         "depth": 1024
       },
       "wkwResolutions": [
         {
-          "resolution": [
-            1,
-            1,
-            1
-          ],
+          "resolution": [1, 1, 1],
           "cubeLength": 1024
         },
         {
-          "resolution": [
-            16,
-            16,
-            16
-          ],
+          "resolution": [16, 16, 16],
           "cubeLength": 64
         },
         {
-          "resolution": [
-            2,
-            2,
-            2
-          ],
+          "resolution": [2, 2, 2],
           "cubeLength": 512
         },
         {
-          "resolution": [
-            32,
-            32,
-            32
-          ],
+          "resolution": [32, 32, 32],
           "cubeLength": 32
         },
         {
-          "resolution": [
-            4,
-            4,
-            4
-          ],
+          "resolution": [4, 4, 4],
           "cubeLength": 256
         },
         {
-          "resolution": [
-            8,
-            8,
-            8
-          ],
+          "resolution": [8, 8, 8],
           "cubeLength": 128
         }
       ],
@@ -73,62 +46,34 @@
     {
       "name": "segmentation",
       "boundingBox": {
-        "topLeft": [
-          0,
-          0,
-          0
-        ],
+        "topLeft": [0, 0, 0],
         "width": 1024,
         "height": 1024,
         "depth": 1024
       },
       "wkwResolutions": [
         {
-          "resolution": [
-            1,
-            1,
-            1
-          ],
+          "resolution": [1, 1, 1],
           "cubeLength": 1024
         },
         {
-          "resolution": [
-            16,
-            16,
-            16
-          ],
+          "resolution": [16, 16, 16],
           "cubeLength": 64
         },
         {
-          "resolution": [
-            2,
-            2,
-            2
-          ],
+          "resolution": [2, 2, 2],
           "cubeLength": 512
         },
         {
-          "resolution": [
-            32,
-            32,
-            32
-          ],
+          "resolution": [32, 32, 32],
           "cubeLength": 32
         },
         {
-          "resolution": [
-            4,
-            4,
-            4
-          ],
+          "resolution": [4, 4, 4],
           "cubeLength": 256
         },
         {
-          "resolution": [
-            8,
-            8,
-            8
-          ],
+          "resolution": [8, 8, 8],
           "cubeLength": 128
         }
       ],
@@ -148,10 +93,6 @@
   ],
   "scale": {
     "unit": "nanometer",
-    "factor": [
-      11.239999771118164,
-      11.239999771118164,
-      28
-    ]
+    "factor": [11.239999771118164, 11.239999771118164, 28.0]
   }
 }

webknossos/testdata/simple_zarr_dataset/color/1/.zarray renamed to webknossos/testdata/simple_zarr_dataset/color/1-1-1/.zarray

@@ -1,39 +1,28 @@
 {
+  "version": 1,
   "id": {
     "name": "test_dataset",
     "team": "<unknown>"
   },
   "scale": {
     "unit": "nanometer",
-    "factor": [
-      11.24,
-      11.24,
-      25.0
-    ]
+    "factor": [11.24, 11.24, 25.0]
   },
   "dataLayers": [
     {
       "name": "tiff",
       "category": "segmentation",
       "boundingBox": {
-        "topLeft": [
-          0,
-          0,
-          0
-        ],
+        "topLeft": [0, 0, 0],
         "width": 265,
         "height": 265,
         "depth": 257
       },
       "elementClass": "uint8",
-      "dataFormat": "zarr",
+      "dataFormat": "zarr3",
       "mags": [
         {
-          "mag": [
-            1,
-            1,
-            1
-          ],
+          "mag": [1, 1, 1],
           "axisOrder": {
             "c": 0,
             "x": 1,