Merge branch 'major-version-2.0' of github.com:scalableminds/webknossos-libs into major-version-2.0

normanrz · normanrz · commit 22859427d568 · 2025-03-03T14:28:51.000+01:00
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -47,7 +47,9 @@ jobs:
       - name: Install uv
         uses: astral-sh/setup-uv@v3
         with:
-          version: "0.5.22"
+          version: "0.6.3"
+          enable-cache: true
+          cache-dependency-glob: "cluster_tools/uv.lock"
       
       - name: Set up Python ${{ matrix.python-version }}
         run: uv python install ${{ matrix.python-version }}
@@ -169,7 +171,9 @@ jobs:
         uses: astral-sh/setup-uv@v3
         with:
           # Install a specific version of uv.
-          version: "0.5.22"
+          version: "0.5.26"
+          enable-cache: true
+          cache-dependency-glob: "webknossos/uv.lock"
 
       - name: Install proxay
         run: npm install -g proxay
@@ -214,7 +218,7 @@ jobs:
         uses: astral-sh/setup-uv@v3
         with:
           # Install a specific version of uv.
-          version: "0.5.22"
+          version: "0.6.3"
       - name: Write version file
         run: |
           pushd webknossos
@@ -291,7 +295,7 @@ jobs:
         uses: astral-sh/setup-uv@v3
         with:
           # Install a specific version of uv.
-          version: "0.5.22"
+          version: "0.6.3"
       - name: Build Docs
         run: |
           cd docs
@@ -343,7 +347,7 @@ jobs:
         uses: astral-sh/setup-uv@v3
         with:
           # Install a specific version of uv.
-          version: "0.5.22"
+          version: "0.6.3"
       - name: Publish python packages
         env:
           UV_PUBLISH_TOKEN: ${{ secrets.PYPI_PASSWORD }}
diff --git a/.github/workflows/nightly.yml b/.github/workflows/nightly.yml
@@ -24,7 +24,7 @@ jobs:
     - name: Install uv
       uses: astral-sh/setup-uv@v3
       with:
-        version: "0.5.22"
+        version: "0.5.26"
 
     - name: Install proxay
       run: npm install -g proxay
diff --git a/.github/workflows/publish_docs.yml b/.github/workflows/publish_docs.yml
@@ -19,7 +19,7 @@ jobs:
       uses: astral-sh/setup-uv@v3
       with:
         # Install a specific version of uv.
-        version: "0.5.22"
+        version: "0.6.3"
 
     - name: Build Docs
       run: |
diff --git a/cluster_tools/Changelog.md b/cluster_tools/Changelog.md
@@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/) `MAJOR.MIN
 For upgrade instructions, please check the respective *Breaking Changes* sections.
 
 ## Unreleased
-[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.16.6...HEAD)
+[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.16.10...HEAD)
 
 ### Breaking Changes
 - The deprecated executor `WrappedProcessPoolExecutor` was removed. Use `MultiprocessingExecutor` instead. [#1244](https://github.com/scalableminds/webknossos-libs/pull/1244)
@@ -21,6 +21,22 @@ For upgrade instructions, please check the respective *Breaking Changes* section
 ### Fixed
 
 
+## [0.16.10](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.16.10) - 2025-02-26
+[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.16.9...v0.16.10)
+
+
+## [0.16.9](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.16.9) - 2025-02-24
+[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.16.8...v0.16.9)
+
+
+## [0.16.8](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.16.8) - 2025-02-04
+[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.16.7...v0.16.8)
+
+
+## [0.16.7](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.16.7) - 2025-02-03
+[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.16.6...v0.16.7)
+
+
 ## [0.16.6](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.16.6) - 2025-02-03
 [Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.16.5...v0.16.6)
 
diff --git a/cluster_tools/pyproject.toml b/cluster_tools/pyproject.toml
@@ -37,6 +37,10 @@ where = ["."]
 include = ["cluster_tools*"]
 exclude = ["cluster_tools.tests"]
 
+# This is a fix for an issue in setuptools. See: https://github.com/pypa/setuptools/issues/4759
+# This shoulde be removed when the issue is resolved.
+[tool.setuptools]
+license-files = []
 
 [tool.ruff]
 # Exclude a variety of commonly ignored directories.
diff --git a/cluster_tools/tests/Dockerfile b/cluster_tools/tests/Dockerfile
@@ -2,7 +2,7 @@ ARG PYTHON_VERSION="3.11"
 
 FROM python:${PYTHON_VERSION}
 
-COPY --from=ghcr.io/astral-sh/uv:0.5.22 /uv /bin/uv
+COPY --from=ghcr.io/astral-sh/uv:0.6.3 /uv /bin/uv
 
 RUN mkdir /cluster_tools
 COPY . /cluster_tools
diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml
@@ -215,7 +215,7 @@ nav:
       - Volume Annotation: webknossos/tutorial_volume_annotation.md
       - Data Sharing: webknossos/tutorial_data_sharing.md
       - Automation: webknossos/tutorial_automation.md
-      # - Today I Learned: webknossos/today_i_learned.md
+      - Today I Learned: webknossos/today_i_learned.md
     - Reference:
       - Frontend Scripting API: https://webknossos.org/assets/docs/frontend-api/index.html" target="_blank
       - Changelog: webknossos/CHANGELOG.released.md
diff --git a/docs/overrides/main.html b/docs/overrides/main.html
@@ -3,6 +3,7 @@
 {% block styles %}
 {{ super() }}
 <link rel="stylesheet" href="{{ base_url }}/css/lists.css">
+<meta name="algolia-site-verification" content="65D883F50DB31A35" />
 <style type="text/css">
 	@font-face {
 		font-family: "Nunito";
diff --git a/webknossos/Changelog.md b/webknossos/Changelog.md
@@ -10,7 +10,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/) `MAJOR.MIN
 For upgrade instructions, please check the respective _Breaking Changes_ sections.
 
 ## Unreleased
-[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.16.6...HEAD)
+[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.16.10...HEAD)
 
 ### Breaking Changes
 
@@ -21,6 +21,30 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 ### Fixed
 
 
+## [0.16.10](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.16.10) - 2025-02-26
+[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.16.9...v0.16.10)
+
+
+## [0.16.9](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.16.9) - 2025-02-24
+[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.16.8...v0.16.9)
+
+### Fixed
+- Fixed opening a renamed dataset via an annotation link. [#1256](https://github.com/scalableminds/webknossos-libs/pull/1256)
+
+
+
+## [0.16.8](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.16.8) - 2025-02-04
+[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.16.7...v0.16.8)
+
+
+## [0.16.7](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.16.7) - 2025-02-03
+[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.16.6...v0.16.7)
+
+### Fixed
+- Fixed a misleading error message when Dataset.open() can't find a valid dataset. [#1246](https://github.com/scalableminds/webknossos-libs/pull/1246)
+
+
+
 ## [0.16.6](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.16.6) - 2025-02-03
 [Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.16.5...v0.16.6)
 
@@ -39,7 +63,6 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 - Fixed a bug with loading metadata lists. [#1247](https://github.com/scalableminds/webknossos-libs/pull/1247)
 
 
-
 ## [0.16.4](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.16.4) - 2025-01-23
 [Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.16.3...v0.16.4)
 
@@ -70,7 +93,6 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 - Fixed an issue when shallow copying datasets with a remote mag. [#1224](https://github.com/scalableminds/webknossos-libs/pull/1224)
 
 
-
 ## [0.16.2](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.16.2) - 2024-12-18
 [Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.16.1...v0.16.2)
 
diff --git a/webknossos/Dockerfile b/webknossos/Dockerfile
@@ -1,6 +1,6 @@
 FROM python:3.12
 
-COPY --from=ghcr.io/astral-sh/uv:0.4.20 /uv /bin/uv
+COPY --from=ghcr.io/astral-sh/uv:0.5.26 /uv /bin/uv
 
 RUN mkdir /webknossos
 COPY webknossos/webknossos /webknossos/webknossos
diff --git a/webknossos/README.md b/webknossos/README.md
@@ -18,11 +18,12 @@ For the WEBKNOSSOS server, please refer to https://github.com/scalableminds/webk
     - up/downsample layers
     - compress layers 
     - add/remove magnifications
-    - execute any of the `wkCuber` operations from your code
+- Command line tool (CLI) for manipulating and creating WEBKNOSSOS datasets
 - manipulation of WEBKNOSSOS skeleton annotations (*.nml) as Python objects
     - access to nodes, comments, trees, bounding boxes, metadata, etc.
     - create new skeleton annotation from Graph structures or Python objects
 - interaction, connection & scripting with your WEBKNOSSOS instance over the REST API
+    - list datastets, annotations, and tasks
     - up- & downloading annotations and datasets
 
 Please refer to [the documentation for further instructions](https://docs.webknossos.org/webknossos-py).
diff --git a/webknossos/pyproject.toml b/webknossos/pyproject.toml
@@ -30,7 +30,7 @@ classifiers = [
     "Programming Language :: Python :: 3.13", 
 ]
 
-requires-python = ">=3.9,<=3.13"
+requires-python = ">=3.9,<3.14"
 
 dependencies = [
     "aiohttp ~=3.10.5",
@@ -97,7 +97,7 @@ dev-dependencies = [
     "mypy ~=1.10.0",
     "pytest ~=8.3.2",
     "pytest-custom-exit-code ~=0.3.0",
-    "pytest-split ~=0.9.0",
+    "pytest-split ~=0.10.0",
     "pytest-sugar ~=1.0.0",
     "pytest-timeout ~=2.3.0",
     "pytest-timestamper ~=0.0.10",
@@ -188,6 +188,11 @@ testpaths = ["tests"]
 requires = ["setuptools>=70.0", "wheel; python_version>='3.12'"]
 build-backend = "setuptools.build_meta"
 
+# This is a fix for an issue in setuptools. See: https://github.com/pypa/setuptools/issues/4759
+# This shoulde be removed when the issue is resolved.
+[tool.setuptools]
+license-files = []
+
 [tool.setuptools.packages.find]
 where = ["."]
 include = ["webknossos*", "webknossos/version.py"]
diff --git a/webknossos/testdata/annotations/l4dense_motta_et_al_demo_v2__explorational__4a6356.zip b/webknossos/testdata/annotations/l4dense_motta_et_al_demo_v2__explorational__4a6356.zip
diff --git a/webknossos/tests/dataset/test_dataset.py b/webknossos/tests/dataset/test_dataset.py
@@ -2802,3 +2802,8 @@ def test_remote_dataset_urls() -> None:
         f"http://localhost:9000/datasets/l4_sample-{dataset_id}/view#2786,4326,1816,0,3"
     )
     assert ds6.url == ds.url
+
+
+def test_dataset_open_wrong_path() -> None:
+    with pytest.raises(FileNotFoundError):
+        Dataset.open("wrong_path")
diff --git a/webknossos/tests/test_annotation.py b/webknossos/tests/test_annotation.py
@@ -21,6 +21,7 @@ def test_annotation_from_wkw_zip_file() -> None:
 
     assert annotation.dataset_name == "l4dense_motta_et_al_demo_v2"
     assert annotation.organization_id == "scalable_minds"
+    assert annotation.dataset_id == "67b7c81b0100004d00f5ab31"
     assert annotation.owner_name == "Philipp Otto"
     assert annotation.annotation_id == "61c20205010000cc004a6356"
     assert "timestamp" in annotation.metadata
@@ -32,6 +33,7 @@ def test_annotation_from_wkw_zip_file() -> None:
 
     assert copied_annotation.dataset_name == "l4dense_motta_et_al_demo_v2"
     assert copied_annotation.organization_id == "scalable_minds"
+    assert copied_annotation.dataset_id == "67b7c81b0100004d00f5ab31"
     assert copied_annotation.owner_name == "Philipp Otto"
     assert copied_annotation.annotation_id == "61c20205010000cc004a6356"
     assert "timestamp" in copied_annotation.metadata
diff --git a/webknossos/uv.lock b/webknossos/uv.lock
diff --git a/webknossos/webknossos/_nml/parameters.py b/webknossos/webknossos/_nml/parameters.py
diff --git a/webknossos/webknossos/annotation/_nml_conversion.py b/webknossos/webknossos/annotation/_nml_conversion.py
diff --git a/webknossos/webknossos/dataset/_array.py b/webknossos/webknossos/dataset/_array.py
diff --git a/webknossos/webknossos/dataset/dataset.py b/webknossos/webknossos/dataset/dataset.py
