Improve installation guide and env files for Napari/Qt and PlantSeg (#85

)

* Update PlantSeg environment files

- Fix typo in environment name
- Update PlantSeg dependencies and channel
- Remove pip dependencies

* Improve installation guides

- Qt is best to be installed in conda via conda-forge
- Users need to install ultrack after env yml in examples

README.md

@@ -24,7 +24,7 @@ Install [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/instal
 Create a conda environment.
 
 ```bash
-conda create --name tracking python=3.10
+conda create --name tracking -c conda-forge python=3.10 pyqt
 ```
 
 And activate it.

docs/source/faq.rst

@@ -3,3 +3,6 @@ FAQ
 
 **Q: What is each configuration parameters for?**
     A: See the `configuration README <https://github.com/royerlab/ultrack/tree/main/ultrack/config>`_.
+
+**Q: What to do when Qt platform plugin cannot be initialized?**
+    A: The solution to try is to install `pyqt` using `conda` from the `-c conda-forge` channel.

examples/README.md

@@ -6,6 +6,7 @@ Therefore, conda environment files are provided, they can be installed using:
 ```
 conda env create -f <environment-file.yml>
 conda activate <your new env>
+pip install git+https://github.com/royerlab/ultrack
 ```
 
 The existing examples are:

examples/neuromast_plantseg/environment_cpu.yml

@@ -1,22 +1,19 @@
-name: ultrack-flow-field
+name: ultrack-plant-seg
 channels:
   - pytorch
   - gurobi
   - rapidsai
   - conda-forge
   - defaults
-  - lcerrone
 dependencies:
   - coin-or-cbc
   - cucim
   - cupy
   - cpuonly
   - gurobi
   - jupyter
-  - pip
-  - plantseg
   - pyqt
   - pytorch
-  - pip:
-    - napari==0.4.18
-    - napari-ome-zarr
+  - plant-seg
+  - napari
+  - napari-ome-zarr

examples/neuromast_plantseg/environment_gpu.yml

@@ -6,18 +6,16 @@ channels:
   - rapidsai
   - conda-forge
   - defaults
-  - lcerrone
 dependencies:
   - coin-or-cbc
   - cucim
   - cupy
   - gurobi
   - jupyter
-  - pip
   - pyqt
   - pytorch
-  - pytorch-cuda
-  - plantseg
-  - pip:
-    - napari==0.4.18
-    - napari-ome-zarr
+  - pytorch-cuda=12.1
+  - cudnn
+  - plant-seg
+  - napari
+  - napari-ome-zarr