diff --git a/webknossos/Changelog.md b/webknossos/Changelog.md index ea647a335..d80dd7a30 100644 --- a/webknossos/Changelog.md +++ b/webknossos/Changelog.md @@ -24,6 +24,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section ### Changed - Removed the proxay request recording/replaying functionality. All requests in the tests are now sent directly to the local WEBKNOSSOS instance. [#1441](https://github.com/scalableminds/webknossos-libs/pull/1441) - Set more comfortable retries for s3 connections in the CLI commands. Call `webknossos.utils.set_s3fs_retry_settings()` for library use. [#1443](https://github.com/scalableminds/webknossos-libs/pull/1443) +- Swapped out `pims` for our fork `scm-pims`, which fixes issues with skimage. A non-user facing change. [#1445](https://github.com/scalableminds/webknossos-libs/pull/1445) ### Fixed diff --git a/webknossos/pyproject.toml b/webknossos/pyproject.toml index ad7a1ac4d..1ed709ba4 100644 --- a/webknossos/pyproject.toml +++ b/webknossos/pyproject.toml @@ -46,7 +46,7 @@ dependencies = [ "networkx ~=3.2.1", "numba ~=0.61", "numpy >=2.0.0,<3.0.0", - "pims ~=0.7.0", + "scm-pims ~=0.7.1", "protobuf<7,>=3.12.0", "google-api-python-client >= 2.0.0", "psutil ~=6.0.0", diff --git a/webknossos/uv.lock b/webknossos/uv.lock index 1d598ff39..49d831ae2 100644 --- a/webknossos/uv.lock +++ b/webknossos/uv.lock @@ -1716,20 +1716,6 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/95/7e/f896623c3c635a90537ac093c6a618ebe1a90d87206e42309cb5d98a1b9e/pillow-12.0.0-pp311-pypy311_pp73-win_amd64.whl", hash = "sha256:b290fd8aa38422444d4b50d579de197557f182ef1068b75f5aa8558638b8d0a5", size = 6997850, upload-time = "2025-10-15T18:24:11.495Z" }, ] -[[package]] -name = "pims" -version = "0.7" -source = { registry = "https://pypi.org/simple" } -dependencies = [ - { name = "imageio" }, - { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" }, - { name = "numpy", version = "2.3.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, - { name = "packaging" }, - { name = "slicerator" }, - { name = "tifffile" }, -] -sdist = { url = "https://files.pythonhosted.org/packages/b8/02/5bf3639f5b77e9b183011c08541c5039ba3d04f5316c70312b48a8e003a9/pims-0.7.tar.gz", hash = "sha256:55907a4c301256086d2aa4e34a5361b9109f24e375c2071e1117b9491e82946b", size = 87779, upload-time = "2024-06-10T19:20:42.842Z" } - [[package]] name = "pluggy" version = "1.6.0" @@ -2443,6 +2429,23 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/8e/f3/d854ff38789aca9b0cc23008d607ced9de4f7ab14fa1ca4329f86b3758ca/scipy-1.16.3-cp313-cp313t-win_arm64.whl", hash = "sha256:0c623a54f7b79dd88ef56da19bc2873afec9673a48f3b85b18e4d402bdd29a5a", size = 25803246, upload-time = "2025-10-28T17:35:42.155Z" }, ] +[[package]] +name = "scm-pims" +version = "0.7.1" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "imageio" }, + { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" }, + { name = "numpy", version = "2.3.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, + { name = "packaging" }, + { name = "slicerator" }, + { name = "tifffile" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/f0/58/621282b94f6c04a28f042921f71cfe15dedcc431b63f16294a3c2d61af3f/scm_pims-0.7.1.tar.gz", hash = "sha256:8bd26c9ec78aba770569314b2480077a74ef79267a4c04505b69615314c3f684", size = 89827, upload-time = "2026-03-30T16:27:53.426Z" } +wheels = [ + { url = "https://files.pythonhosted.org/packages/1e/43/9c5d6df0f420928a70ee29b934872bd023bf738a4ab9dbdab8ff61f27eac/scm_pims-0.7.1-py3-none-any.whl", hash = "sha256:f4f25d7768bfa2d3939de8df832623db5bffa4a14bd6b78376c7ba7e7f65f116", size = 84785, upload-time = "2026-03-30T16:27:52.155Z" }, +] + [[package]] name = "shellingham" version = "1.5.4" @@ -2747,7 +2750,6 @@ dependencies = [ { name = "numba" }, { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" }, { name = "numpy", version = "2.3.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, - { name = "pims" }, { name = "protobuf" }, { name = "psutil" }, { name = "python-dateutil" }, @@ -2755,6 +2757,7 @@ dependencies = [ { name = "rich" }, { name = "scipy", version = "1.15.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" }, { name = "scipy", version = "1.16.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, + { name = "scm-pims" }, { name = "tensorstore", version = "0.1.76", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform == 'win32'" }, { name = "tensorstore", version = "0.1.78", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11' and sys_platform != 'win32'" }, { name = "tensorstore", version = "0.1.79", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11' and sys_platform != 'win32'" }, @@ -2846,7 +2849,6 @@ requires-dist = [ { name = "numba", specifier = "~=0.61" }, { name = "numpy", specifier = ">=2.0.0,<3.0.0" }, { name = "pandas", marker = "extra == 'examples'", specifier = "~=2.2.0" }, - { name = "pims", specifier = "~=0.7.0" }, { name = "pooch", marker = "extra == 'examples'", specifier = "~=1.5.2" }, { name = "protobuf", specifier = ">=3.12.0,<7" }, { name = "psutil", specifier = "~=6.0.0" }, @@ -2858,6 +2860,7 @@ requires-dist = [ { name = "scikit-image", marker = "extra == 'examples'", specifier = "~=0.25.0" }, { name = "scikit-learn", marker = "extra == 'examples'", specifier = "~=1.5.1" }, { name = "scipy", specifier = ">=1.13" }, + { name = "scm-pims", specifier = "~=0.7.1" }, { name = "tabulate", marker = "extra == 'examples'", specifier = ">=0.9.0" }, { name = "tensorstore", marker = "sys_platform != 'win32'", specifier = "~=0.1.78" }, { name = "tensorstore", marker = "sys_platform == 'win32'", specifier = "==0.1.76" },