Merge branch 'main' into Xiang

Author: TeunHuijben

.gitignore

@@ -14,6 +14,8 @@ dist-ssr
 
 # Editor directories and files
 .vscode/*
+CLAUDE.md
+python/.vscode/*
 !.vscode/extensions.json
 .idea
 .DS_Store

README.md

@@ -0,0 +1,7 @@
+Supplementary Videos: 
+
+- [video 1:](https://vimeo.com/1019958933/a61cfa4120) inTRACKtive web-viewer
+- [video 2:](https://vimeo.com/1019959289/edfcb4d6a7) Virtual Embryo Zoo website
+- [video 3: ](https://vimeo.com/1037262379/86bd332f4e) Color cell labeling in inTRACKtive based on any attribute
+- [video 4: ](https://vimeo.com/1067871601/b7272b46e3) Visualizing velocity, density, and structure tensor in inTRACKtive
+- [video 5: ](https://vimeo.com/1088515499/483f98cd9d) Using inTRACKtive from the command line, from napari, from a Jupyter notebook, and within a Jupyter notebook

public/docs/videos.md

@@ -26,15 +26,9 @@ repos:
       - id: isort
         args: ["--profile", "black", "--filter-files"]
 
-  # formatting
-  - repo: https://github.com/psf/black
-    rev: 22.3.0
-    hooks:
-      - id: black
-
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.5.7
+    rev: v0.12.5
     hooks:
       # Run the linter.
       - id: ruff
@@ -43,6 +37,7 @@ repos:
       # Run the formatter.
       - id: ruff-format
         types_or: [python, pyi, jupyter]
+        args: [--line-length=88]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0  # You can check for the latest version

python/.pre-commit-config.yaml

@@ -27,7 +27,8 @@ dependencies = [
   "scipy",
   "scikit-image",
   "pandas",
-  "zarr<3",
+  "zarr>=3",
+  "geff>=1",
   "pyarrow",
 ]
 
@@ -45,10 +46,13 @@ intracktive = "intracktive:napari.yaml"
 [tool.hatch.version]
 path = "src/intracktive/__about__.py"
 
+[tool.hatch.metadata]
+allow-direct-references = true
+
 [tool.coverage.run]
 source_pkgs = ["intracktive"]
 branch = true
-parallel = true
+parallel = false
 omit = [
   "src/intracktive/__about__.py",
 ]

python/pyproject.toml

@@ -1 +1 @@
-__version__ = "0.1.0"
+__version__ = "0.1.3"

python/src/intracktive/__about__.py

@@ -0,0 +1,4 @@
+from intracktive.main import main
+
+if __name__ == "__main__":
+    main()

python/src/intracktive/__main__.py

@@ -0,0 +1,79 @@
+{
+    "geff": {
+        "axes": [
+            {
+                "max": 91.0,
+                "min": 0.0,
+                "name": "t",
+                "offset": null,
+                "scale": null,
+                "scaled_unit": null,
+                "type": "time",
+                "unit": null
+            },
+            {
+                "max": 680.0,
+                "min": 4.088235294117647,
+                "name": "y",
+                "offset": null,
+                "scale": null,
+                "scaled_unit": null,
+                "type": "space",
+                "unit": null
+            },
+            {
+                "max": 1079.0,
+                "min": 14.0,
+                "name": "x",
+                "offset": null,
+                "scale": null,
+                "scaled_unit": null,
+                "type": "space",
+                "unit": null
+            }
+        ],
+        "directed": true,
+        "display_hints": null,
+        "edge_props_metadata": {},
+        "ellipsoid": null,
+        "extra": {},
+        "geff_version": "1.0.0.1.1.dev3+g1d804267a.d20250925",
+        "node_props_metadata": {
+            "t": {
+                "description": null,
+                "dtype": "int64",
+                "identifier": "t",
+                "name": null,
+                "unit": null,
+                "varlength": false
+            },
+            "tracklet_id": {
+                "description": null,
+                "dtype": "int64",
+                "identifier": "tracklet_id",
+                "name": null,
+                "unit": null,
+                "varlength": false
+            },
+            "x": {
+                "description": null,
+                "dtype": "float64",
+                "identifier": "x",
+                "name": null,
+                "unit": null,
+                "varlength": false
+            },
+            "y": {
+                "description": null,
+                "dtype": "float64",
+                "identifier": "y",
+                "name": null,
+                "unit": null,
+                "varlength": false
+            }
+        },
+        "related_objects": null,
+        "sphere": null,
+        "track_node_props": null
+    }
+}

python/src/intracktive/_tests/data/ctc_hela_example.geff/.zattrs

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}

python/src/intracktive/_tests/data/ctc_hela_example.geff/.zgroup

@@ -0,0 +1,3 @@
+{
+    "zarr_format": 2
+}