Merge pull request #62 from multimeric/docs

Docs

README.md

@@ -36,6 +36,7 @@ Check the [Wiki page](https://github.com/BioimageAnalysisCoreWEHI/napari_lattice
 **Key Features**
 
 Apply custom image processing workflows using `napari-workflows`. 
+
 * [Interactive workflow generation (no coding experience needed)](https://github.com/BioimageAnalysisCoreWEHI/napari_lattice/wiki/5.-Workflows-(Interactive:-no-coding)#workflow)
 * [Use custom python functions/modules within workflows](https://github.com/BioimageAnalysisCoreWEHI/napari_lattice/wiki/5.1-Workflows-(Custom-workflow))
 * [How to use Cellpose for cell segmentation](https://github.com/BioimageAnalysisCoreWEHI/napari_lattice/wiki/5.1-Workflows-(Custom-workflow)#cellpose)

core/lls_core/__init__.py

@@ -4,15 +4,12 @@
 from strenum import StrEnum
 from enum import Enum
 from pyclesperanto_prototype._tier8._affine_transform_deskew_3d import DeskewDirection
+from lls_core.models.lattice_data import LatticeData
+from lls_core.models.deconvolution import DeconvolutionParams
+from lls_core.models.lattice_data import CropParams
 
 # Initialize configuration options
 
-#Choice of Deconvolution
-class DeconvolutionChoice(StrEnum):
-    cuda_gpu = "cuda_gpu"
-    opencl_gpu = "opencl_gpu"
-    cpu = "cpu"
-
 #CONFIGURE LOGGING using a dictionary (can also be done with yaml file)
 import logging.config
 LOGGING_CONFIG = {

core/lls_core/cmds/__main__.py

@@ -15,8 +15,9 @@
 from lls_core.models.deconvolution import DeconvolutionParams
 from lls_core.models.output import OutputParams
 from lls_core.models.crop import CropParams
-from lls_core import DeconvolutionChoice
+from lls_core.deconvolution import DeconvolutionChoice
 from typer import Typer, Argument, Option, Context, Exit
+from typer.main import get_command
 
 from lls_core.models.output import SaveFileType
 from pydantic import ValidationError
@@ -227,6 +228,8 @@ def process(
     lattice.save()
     console.print(f"Processing successful. Results can be found in {lattice.save_dir.resolve()}")
 
+# Used by the docs
+click_app = get_command(app)
 
 def main():
     app()