diff --git a/README.md b/README.md index 394c9d96d..adc99118d 100644 --- a/README.md +++ b/README.md @@ -15,9 +15,9 @@ Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in P - `OME-TIFF` - `TIFF` - `CZI` -- (`pip install aicsimageio[czi]`) - - `LIF` -- (`pip install aicsimageio[lif]`) + - `LIF` -- (`pip install readlif>=0.6.4`) - `PNG`, `GIF`, [etc.](https://github.com/imageio/imageio) -- (`pip install aicsimageio[base-imageio]`) - - Files supported by [Bio-Formats](https://docs.openmicroscopy.org/bio-formats/latest/supported-formats.html) -- (`pip install aicsimageio bioformats_jar`) + - Files supported by [Bio-Formats](https://docs.openmicroscopy.org/bio-formats/latest/supported-formats.html) -- (`pip install aicsimageio bioformats_jar`) - Supports writing metadata and imaging data for: - `OME-TIFF` - `PNG`, `GIF`, [etc.](https://github.com/imageio/imageio) -- (`pip install aicsimageio[base-imageio]`) @@ -49,8 +49,9 @@ optionally installed using `[...]` syntax. - For a single additional supported format (e.g. CZI): `pip install aicsimageio[czi]` - For a single additional supported format (e.g. CZI), development head: `pip install "aicsimageio[czi] @ git+https://github.com/AllenCellModeling/aicsimageio.git"` - For a single additional supported format (e.g. CZI), specific tag (e.g. `v4.0.0.dev6`): `pip install "aicsimageio[czi] @ git+https://github.com/AllenCellModeling/aicsimageio.git@v4.0.0.dev6"` -- For multiple additional supported formats: `pip install aicsimageio[czi,lif]` +- For multiple additional supported formats: `pip install aicsimageio[base-imageio,czi]` - For all additional supported formats: `pip install aicsimageio[all]` +- Due to the GPL license, LIF support is not included with the `[all]` extra, and must be installed manually with `pip install aicsimageio readlif>=0.6.4` - Due to the GPL license, Bio-Formats support is not included with the `[all]` extra, and must be installed manually with `pip install aicsimageio bioformats_jar` ## Documentation @@ -332,4 +333,5 @@ If you find `aicsimageio` useful, please cite this repository as: _Free software: BSD-3-Clause_ +_(The LIF component is licensed under GPLv3 and is not included in this package)_ _(The Bio-Formats component is licensed under GPLv2 and is not included in this package)_ diff --git a/aicsimageio/readers/lif_reader.py b/aicsimageio/readers/lif_reader.py index 189a739f0..ecf23877c 100644 --- a/aicsimageio/readers/lif_reader.py +++ b/aicsimageio/readers/lif_reader.py @@ -28,7 +28,7 @@ except ImportError: raise ImportError( "readlif is required for this reader. " - "Install with `pip install aicsimageio[lif]`" + "Install with `pip install readlif>=0.6.4`" ) ############################################################################### @@ -52,7 +52,9 @@ class LifReader(Reader): Notes ----- - To use this reader, install with: `pip install aicsimageio[lif]`. + To use this reader, install with: `pip install readlif>=0.6.4`. + + readlif is licensed under GPLv3 and is not included in this package. """ @staticmethod diff --git a/setup.py b/setup.py index 791891439..1e0e42cda 100644 --- a/setup.py +++ b/setup.py @@ -27,7 +27,7 @@ def run(self): format_libs: Dict[str, List[str]] = { "base-imageio": ["imageio[ffmpeg]>=2.9.0,<3", "Pillow>=8.2.0,!=8.3.0,<9"], - "lif": ["readlif>=0.6.4"], + # "lif": ["readlif>=0.6.4"], # excluded for licensing reasons "czi": ["aicspylibczi>=3.0.2"], # "bioformats": ["bioformats_jar"], # excluded for licensing reasons } @@ -53,7 +53,8 @@ def run(self): "quilt3", # no pin to avoid pip cycling (boto is really hard to manage) "s3fs[boto3]>=0.4.2", "tox>=3.15.2", - "bioformats_jar", # to test bioformats + "bioformats_jar", # to test bioformats + "readlif>=0.6.4", # to test lif ] dev_requirements = [