Remove affogato as a dependency.

also update README with updated installation instructions.
affogato was removed as a python dependency because there is a different
package on pypi also called affogato that we do not want. This is also
breaking the conda recipe tests since pip check does not recognize the
conda version of affogato as satisfying the dependency

README.md

@@ -23,10 +23,10 @@ https://napari.org/plugins/stable/index.html
 
 ## Installation
 
-Pre-requisites:
-
-    1) Install lsds with: `pip install git+https://github.com/pattonw/lsd.git@no-convenience-imports` (This is necessary since we need lsds but the package name `lsd` is already taken on pypi. While we resolve this the specific lsd version needs to be specified)
+You will need a conda environment for everything to run
+smoothly. Supported python versions are 3.7, 3.8, 3.9.
 
+### pip
 You can install `napari-affinities` via [pip]:
 
     `pip install napari-affinities`
@@ -43,6 +43,15 @@ Install conda requirements:
 
     conda install -c conda-forge affogato
 
+### conda
+
+If you install via conda, there are fewer steps since
+affogato and pytorch will be installed for you.
+
+You can install `napari-affinities` via [conda]:
+
+    `conda install -c conda-forge napari-affinities`
+
 ### Download example model:
 
 #### 2D:

setup.cfg

@@ -39,7 +39,6 @@ install_requires =
     magicgui
     bioimageio.core
     gunpowder
-    affogato
     matplotlib
 
 

src/napari_affinities/widgets/mutex_watershed.py

@@ -3,7 +3,13 @@
 from napari.types import LabelsData, LayerDataTuple
 from napari.layers import Labels, Image
 
-from affogato.segmentation import MWSGridGraph, compute_mws_clustering
+try:
+    from affogato.segmentation import MWSGridGraph, compute_mws_clustering
+except ImportError as e:
+    raise ImportError(
+        "To use mutex watershed please install affogato via: "
+        "conda install -c conda-forge affogato"
+    ) from e
 
 import numpy as np
 from typing import Optional
@@ -13,6 +19,7 @@
 import napari
 from napari.qt.threading import FunctionWorker, thread_worker
 
+
 def toggle_interactivity_callback(widget, interactive_callbacks):
     def callback(live):
         # remove old callbacks
@@ -23,14 +30,17 @@ def callback(live):
         if live:
             # add callback for seed_layer change
             if seed_layer is not None:
+
                 def change(*args, **kwargs):
                     # this sets off the auto run
                     widget.toggle.value = 1 - widget.toggle.value
 
                 cb = seed_layer.events.set_data.connect(change)
                 interactive_callbacks.append(cb)
+
     return callback
 
+
 def add_interactive_callback(widget, interactive_callbacks):
     def callback(seed_layer):
         if seed_layer is not None:
@@ -47,6 +57,7 @@ def change(*args, **kwargs):
                 # add new callback
                 cb = seed_layer.events.set_data.connect(change)
                 interactive_callbacks.append(cb)
+
     return callback