Merge pull request #92 from computational-cell-analytics/update-install

Update installation instructions

Author: constantinpape

.github/workflows/run_tests.yaml

@@ -27,7 +27,7 @@ jobs:
       - name: Setup micromamba
         uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: environment_cpu.yaml
+          environment-file: ${{ runner.os == 'Windows' && 'environment_cpu_win.yaml' || 'environment.yaml' }}
           create-args: >-
             python=${{ matrix.python-version }}
 

doc/start_page.md

@@ -18,7 +18,7 @@ Please cite our [bioRxiv preprint](https://www.biorxiv.org/content/10.1101/2024.
 
 ## Requirements & Installation
 
-SynapseNet was developed and tested on Linux. It should be possible to install and use it on Mac or Windows, but we have not tested this.
+SynapseNet was developed and tested on Linux. It is possible to install and use it on Mac or Windows, but we have not extensively tested this.
 Furthermore, SynapseNet requires a GPU for segmentation of 3D volumes.
 
 You need a [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) or [mamba](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html) installation. Follow the instruction at the respective links if you have installed neither. We assume you have `conda` for the rest of the instructions. After installing it, you can use the `conda` command.
@@ -36,6 +36,7 @@ cd synapse-net
 ```bash
 conda env create -f environment.yaml
 ```
+    - If you are using Windows then you have to use a different environment file for the installation: Use `environment_gpu_win.yaml` if you have a GPU and `environment_cpu_win.yaml` without a GPU.
 - You will need to confirm this step. It will take a while. Afterwards you can activate the environment:
 ```bash
 conda activate synapse-net

environment.yaml

@@ -1,6 +1,4 @@
 channels:
-    - pytorch
-    - nvidia
     - conda-forge
 name:
     synapse-net
@@ -13,7 +11,6 @@ dependencies:
     - pyqt
     - python-elf
     - pytorch
-    - pytorch-cuda=12.4
     - tensorboard
     - torch_em
     - torchvision

environment_cpu.yaml renamed to environment_cpu_win.yaml

@@ -1,16 +1,22 @@
 channels:
+    - pytorch
     - conda-forge
 name:
     synapse-net
 dependencies:
+    - cpuonly
     - bioimageio.core
     - kornia
+    # This pin is necessary because later nifty versions have import errors on windows.
+    - nifty =1.2.1=*_4
     - magicgui
     - napari
+    - protobuf <5
     - pip
     - pyqt
     - python-elf
     - pytorch
+    - torchvision
     - tensorboard
     - torch_em
     - trimesh