diff --git a/docs/src/webknossos-py/installation.md b/docs/src/webknossos-py/installation.md index 2a0d6572d..f5edc88a1 100644 --- a/docs/src/webknossos-py/installation.md +++ b/docs/src/webknossos-py/installation.md @@ -17,8 +17,8 @@ For extended file format conversation support it is necessary to install the opt pip install "webknossos[all]" ``` -If you have issues with installing the `pylibczirw` package on macOS, try: +For working with Zeiss CZI microscopy data utilizing the`pylibczirw` package run: ```bash -pip install --extra-index-url https://pypi.scm.io/simple/ "webknossos[all]" +pip install --extra-index-url https://pypi.scm.io/simple/ "webknossos[czi]" ``` diff --git a/webknossos/Changelog.md b/webknossos/Changelog.md index 145ee27cc..c215fb7be 100644 --- a/webknossos/Changelog.md +++ b/webknossos/Changelog.md @@ -17,6 +17,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section ### Added ### Changed +Removed the CZI installation extra from `pip install webknossos[all]` by default. Users need to manually install it with `pip install --extra-index-url https://pypi.scm.io/simple/ webknossos[czi]`. [#1219](https://github.com/scalableminds/webknossos-libs/pull/1219) ### Fixed diff --git a/webknossos/README.md b/webknossos/README.md index 4d1ba435a..281ac7086 100644 --- a/webknossos/README.md +++ b/webknossos/README.md @@ -36,7 +36,9 @@ You can install it from [pypi](https://pypi.org/project/webknossos/), e.g. via p pip install webknossos ``` -To install `webknossos` with the depencies for all examples, support for CZI files, and BioFormats conversions, run: `pip install webknossos[all]`. +To install `webknossos` with the dependencies for all examples, support for more file types, and BioFormats conversions, run: `pip install webknossos[all]`. + +For working with Zeiss CZI microscopy data use `pip install --extra-index-url https://pypi.scm.io/simple/ webknossos[czi]`. By default `webknossos` can only distribute any computations through multiprocessing or Slurm. For Kubernetes or Dask install these additional dependencies: diff --git a/webknossos/pyproject.toml b/webknossos/pyproject.toml index fb705c420..8de3dc9b3 100644 --- a/webknossos/pyproject.toml +++ b/webknossos/pyproject.toml @@ -23,6 +23,10 @@ classifiers = [ "Topic :: Scientific/Engineering :: Visualization", "Topic :: Software Development :: Libraries", "Typing :: Typed", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", ] requires-python = ">=3.9,<3.13" @@ -81,7 +85,6 @@ all = [ "webknossos[tifffile]", "webknossos[imagecodecs]", "webknossos[bioformats]", - "webknossos[czi]", "webknossos[examples]", ] diff --git a/webknossos/webknossos/dataset/_utils/pims_czi_reader.py b/webknossos/webknossos/dataset/_utils/pims_czi_reader.py index f711c700a..da5426925 100644 --- a/webknossos/webknossos/dataset/_utils/pims_czi_reader.py +++ b/webknossos/webknossos/dataset/_utils/pims_czi_reader.py @@ -10,7 +10,7 @@ from pylibCZIrw import czi as pyczi except ImportError as e: raise ImportError( - "Cannot import pylibCZIrw, please install it e.g. using 'webknossos[czi]'" + "Cannot import pylibCZIrw, please install it e.g. using pip install --extra-index-url https://pypi.scm.io/simple/ webknossos[czi]" ) from e PIXEL_TYPE_TO_DTYPE = { diff --git a/webknossos/webknossos/dataset/dataset.py b/webknossos/webknossos/dataset/dataset.py index f6a8c8688..9d8dd1fc7 100644 --- a/webknossos/webknossos/dataset/dataset.py +++ b/webknossos/webknossos/dataset/dataset.py @@ -824,7 +824,7 @@ def from_images( Note: This method needs extra packages like tifffile or pylibczirw. - Install with `python -m pip install "webknossos[all]"`. + Install with `pip install "webknossos[all]"` and `pip install --extra-index-url https://pypi.scm.io/simple/ "webknossos[czi]"`. """ input_upath = UPath(input_path)