Add script to build the doc

Author: constantinpape

.github/workflows/build_docs.yaml

@@ -0,0 +1,66 @@
+name: Build and Deploy Docs
+
+on:
+  push:
+    paths:
+      - "doc/*.md"   # Trigger on changes to any markdown file
+      - "flamigo_tools/**/*.py"   # Optionally include changes in Python files
+    branches:
+      - main        # Run the workflow only on pushes to the main branch
+  workflow_dispatch:
+
+# security: restrict permissions for CI jobs.
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: Build Documentation
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout Code
+      uses: actions/checkout@v4
+
+    - name: Set up Micromamba
+      uses: mamba-org/setup-micromamba@v2
+      with:
+        micromamba-version: "latest"
+        environment-file: environment.yaml
+        init-shell: bash
+        cache-environment: true
+        post-cleanup: 'all'
+
+    - name: Install package
+      shell: bash -l {0}
+      run: pip install -e .
+
+    - name: Install pdoc
+      shell: bash -l {0}
+      run: pip install pdoc
+
+    - name: Generate Documentation
+      shell: bash -l {0}
+      run: pdoc flamingo_tools/ -d google -o doc/
+
+    - name: Verify Documentation Output
+      run: ls -la doc/
+
+    - name: Upload Documentation Artifact
+      uses: actions/upload-pages-artifact@v3
+      with:
+        path: doc/
+
+  deploy:
+    name: Deploy Documentation
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GiHub Pages
+        uses: actions/deploy-pages@v4

README.md

@@ -1,7 +1,14 @@
-# Flamingo Tools
+# CochleaNet
 
-Data processing for light-sheet microscopy, specifically for data from [Flamingo microscopes](https://huiskenlab.com/flamingo/).
+CochleaNet is a software for the analysis of cochleae imaged in light-sheet microscopy. It is based on deep neural networks for the segmentation of spiral ganglion neurons, inner hair cells, and the detection of ribbon synapses.
+It was developed for imaging data from (clear-tissue) [flamingo microscopes](https://huiskenlab.com/flamingo/) and is also applicable to data from commercial microscopes.
 
+In addition to the analysis functionality, CochleaNet implements data pre-processing to convert data from flamingo microscopes into a format compatible with [BigStitcher](https://imagej.net/plugins/bigstitcher/) and to export image data and segmentation results to [ome.zarr](https://www.nature.com/articles/s41592-021-01326-w) and [MoBIE](https://mobie.github.io/).
+This functionality is applicable to any imaging data from flamingo microscopes, not only clear-tissue data or cochleae. We aim to also extend the segmentation and analysis functionality to other kinds of samples imaged in the flamingo in the future.
+
+For installation and usage instructions, check out [the documentation](TODO). For more details on the underlying methodology check out [our preprint](TODO).
+
+<!---
 The `flamingo_tools` library implements functionality for:
 - converting the lightsheet data into a format compatible with [BigDataViewer](https://imagej.net/plugins/bdv/) and [BigStitcher](https://imagej.net/plugins/bigstitcher/).
 - Cell / nucleus segmentation via a 3D U-net.
@@ -48,3 +55,4 @@ You can also check out the following example scripts:
 - `load_data.py`: Example script for how to load sub-regions from the converted data into python.
 
 For advanced examples to segment data with a U-Net, check out the `scripts` folder.
+--->

doc/documentation.md

@@ -49,10 +49,20 @@ conda install -c conda-forge napari pyqt
 
 ## Usage
 
+TODO
+
 ### Napari Plugin
 
+TODO
+
 ### Command Line Interface
 
+TODO
+
 ### Available Models
 
+TODO
+
 ### Python Library
+
+TODO