Merge branch 'cellpose-test' into 'master'

Fix cellpose-gpu build

See merge request !1

cellpose/README.md

@@ -16,6 +16,7 @@ CUDA_VISIBIBLE_DEVICES=0
 ```
 conda env create -f environment_gpu.yaml
 conda activate cellpose-gpu
+pip install --no-deps -r requirements.txt
 ```
 
 ```

cellpose/check_gpu.py

+import os
+os.environ['CUDA_VISIBLE_DEVICES'] = '0'
+print("Imporintg utils")
+from cellpose import utils
+print(utils.use_gpu())

cellpose/environment-gpu.yaml

 name: cellpose-gpu
 dependencies:
+  - cudatoolkit>=10.2,<10.3  # pin to the same version as mxnet
   - python=3.7
   - pip
   - numpy
@@ -8,14 +9,13 @@ dependencies:
   - pyqt
   - scipy
   - matplotlib
+  - natsort
   - jupyter
-  - pip:
-    # this needs to be adapted to your cuda version:
-    # for 10.0 choose 100 etc.
-    - mxnet-cu102
-    - opencv_python
-    - pyqtgraph==0.11.0rc0
-    - natsort
-    - google-cloud-storage
-    - tqdm
-    - cellpose
+  - tqdm
+  - google-cloud-storage
+  - pyqtgraph>=0.11,<0.12
+  - opencv
+  - tifffile
+  # pip in environment.yaml does not support no-deps, see
+  # https://github.com/conda/conda/issues/6805#issuecomment-515680253
+  # so we install the pip requirements separately instead

cellpose/requirements.txt

+cellpose
+mxnet-cu102