admin/remove-lif-from-standard-install (#332)

* Remove from extra installs

* Add license indication to docs

* Add license indication to README

* Swap lif for base-imageio in the multi-support install example

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/[email protected]"`
--   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)_

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

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 = [