admin/include-fsspec-dep-for-czi-in-readme (#433)

* README note the CZI fsspec compat

* Note fsspec install in CZI import error catch

* Wrap lif install with string to have proper lif install

Author: evamaxfield

README.md

@@ -16,7 +16,7 @@ Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in P
     -   `TIFF`
     -   `ND2` -- (`pip install aicsimageio[nd2]`)
     -   `DV` -- (`pip install aicsimageio[dv]`)
-    -   `CZI` -- (`pip install aicspylibczi>=3.0.5`)
+    -   `CZI` -- (`pip install aicspylibczi>=3.0.5 fsspec>=2022.7.1`)
     -   `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`)
@@ -55,7 +55,7 @@ optionally installed using `[...]` syntax.
 -   For multiple additional supported formats: `pip install aicsimageio[base-imageio,nd2]`
 -   For all additional supported (and openly licensed) 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, CZI support is not included with the `[all]` extra, and must be installed manually with `pip install aicsimageio aicspylibczi>=3.0.5`
+-   Due to the GPL license, CZI support is not included with the `[all]` extra, and must be installed manually with `pip install aicsimageio aicspylibczi>=3.0.5 fsspec>=2022.7.1`
 -   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`. **Important!!** Bio-Formats support also requires a `java` executable in the environment. The simplest method is to install `bioformats_jar` from conda: `conda install -c conda-forge bioformats_jar` (which will additionally bring `openjdk`).
 
 ## Documentation

aicsimageio/readers/czi_reader.py

@@ -28,7 +28,7 @@
 except ImportError:
     raise ImportError(
         "aicspylibczi is required for this reader. "
-        "Install with `pip install aicspylibczi>=3.0.5"
+        "Install with `pip install 'aicspylibczi>=3.0.5' 'fsspec>=2022.7.1'`"
     )
 
 ###############################################################################

aicsimageio/readers/lif_reader.py

@@ -28,7 +28,7 @@
 except ImportError:
     raise ImportError(
         "readlif is required for this reader. "
-        "Install with `pip install readlif>=0.6.4`"
+        "Install with `pip install 'readlif>=0.6.4'`"
     )
 
 ###############################################################################

setup.py

@@ -37,7 +37,10 @@ def run(self):
     "nd2": ["nd2[legacy]>=0.2.0"],
     "dv": ["mrc>=0.2.0"],
     "bfio": ["bfio>=2.3.0", "tifffile<2022.4.22"],
-    # "czi": ["aicspylibczi>=3.0.5"],  # excluded for licensing reasons
+    "czi": [
+        "fsspec>=2022.7.1",
+        # "aicspylibczi>=3.0.5",  # excluded for licensing reasons
+    ],
     # "bioformats": ["bioformats_jar"],  # excluded for licensing reasons
     # "lif": ["readlif>=0.6.4"],  # excluded for licensing reasons
 }

tox.ini

@@ -31,7 +31,9 @@ setenv =
     PYTHONPATH = {toxinidir}
 extras =
     test
-deps = aicspylibczi>=3.0.5
+deps = 
+    aicspylibczi>=3.0.5
+    fsspec>=2022.7.1
 commands =
     pytest --basetemp={envtmpdir} --cov-report xml --cov-report html --cov=aicsimageio aicsimageio/tests/readers/extra_readers/test_czi_reader.py {posargs}