Merge pull request #1202 from MouseLand/docs_update

fix #1180 example not working from docs and update docs for autodoc to work

Author: mrariden

docs/conf.py

@@ -46,6 +46,7 @@
 autodoc_mock_imports = [
     "importlib",
     "torch",
+    "torchvision",
     "numpy",
     "tqdm",
     "scipy",
@@ -57,6 +58,8 @@
     "fastremap",
     "natsort",
     "numba",
+    "segment_anything", 
+    "fill_voids"
 ]
 
 autoapi_dirs = ['../cellpose']

docs/index.rst

@@ -14,6 +14,9 @@ can install it as ``pip install cellpose[gui]``.
 - talk 
 
 
+
+**See details on migrating from Cellpose 3 to 4 in** :ref:`Settings`
+
 Old releases:
 -----------------------------
 

docs/settings.rst

@@ -6,15 +6,19 @@ Settings
 The important settings are described on this page. 
 See the :ref:`cpmclass` for all run options.
 
-Here is an example of calling the Cellpose class and
+.. warning:: 
+    Cellpose 3 used ``models.Cellpose`` class which has been removed in Cellpose 4. Users should
+    now only use the ``models.CellposeModel``` class. 
+
+Here is an example of calling the ``CellposeModel`` class and
 running a list of images for reference:
 
 ::
 
     from cellpose import models
     from cellpose.io import imread
 
-    model = models.Cellpose(gpu=True)
+    model = models.CellposeModel(gpu=True)
 
     files = ['img0.tif', 'img1.tif']
     imgs = [imread(f) for f in files]
@@ -36,7 +40,7 @@ you will want to omit it from the input, or combine it with the cytoplasm channe
     from cellpose import models
     from cellpose.io import imread
 
-    model = models.Cellpose(gpu=True)
+    model = models.CellposeModel(gpu=True)
 
     img = imread("img.tif") # tiff is n x 100 x 100