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Fix install "all extras" for Python 3.12 #1219

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merged 2 commits into from
Nov 22, 2024
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Fix install "all extras" for Python 3.12 #1219

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a35685a
remove CZI from webknossos[all]
hotzenklotz Nov 22, 2024
97f9519
updated cahngelog
hotzenklotz Nov 22, 2024
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4 changes: 2 additions & 2 deletions docs/src/webknossos-py/installation.md
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Expand Up @@ -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]"
```
1 change: 1 addition & 0 deletions webknossos/Changelog.md
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Expand Up @@ -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

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4 changes: 3 additions & 1 deletion webknossos/README.md
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Expand Up @@ -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:

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5 changes: 4 additions & 1 deletion webknossos/pyproject.toml
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Expand Up @@ -23,6 +23,10 @@ classifiers = [
"Topic :: Scientific/Engineering :: Visualization",
"Topic :: Software Development :: Libraries",
"Typing :: Typed",
"Programming Language :: Python :: 3.9",
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Fixes
Screenshot 2024-11-22 at 13 38 52

Screenshot 2024-11-22 at 13 40 59

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Alternatively, shields.io can somehow parse the requires_python argument from the pyprpoject.toml and display a range instead of each version. However, that would not add this info to Pypi.org website where I typicall find it easier to spot at the first glance.

Code: https://img.shields.io/badge/dynamic/json?query=info.requires_python&label=python&url=https%3A%2F%2Fpypi.org%2Fpypi%2Fwebknossos%2Fjson

"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
]

requires-python = ">=3.9,<3.13"
Expand Down Expand Up @@ -81,7 +85,6 @@ all = [
"webknossos[tifffile]",
"webknossos[imagecodecs]",
"webknossos[bioformats]",
"webknossos[czi]",
"webknossos[examples]",
]

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2 changes: 1 addition & 1 deletion webknossos/webknossos/dataset/_utils/pims_czi_reader.py
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Expand Up @@ -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 = {
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2 changes: 1 addition & 1 deletion webknossos/webknossos/dataset/dataset.py
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Expand Up @@ -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)
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