Update docs using MkDocs (#21)

* added basic docs and config

* added docs worflow

.github/workflows/build_docs.yml

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+name: mkdocs
+on:
+  push:
+    branches:
+      - main
+permissions:
+  contents: write
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV 
+      - uses: actions/cache@v4
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+      - run: pip install mkdocs-material 
+      - run: mkdocs gh-deploy --force

docs/index.md

@@ -1,18 +1,16 @@
-# Documentation
 ---
+title: Welcome
+---
+
+# Welcome to Feature Forest Documentation
+
+Feature Forest (**FF**) is a *[napari]* plugin for creating image annotations with less manual work, utilizing image embeddings (*features*) of vision transformer models like *[SAM2]* and training a *Random Forest* model using a little scribble labels provided by the user.
+
+### Overview
+![figure 1](assets/fig1.png)
 
-## How to use the plugin
-This plugin provides four widgets; one for extracting the SAM embeddings and three for segmentation using different methods:
-- [SAM Embedding Extractor](./widgets.md#sam-embedding-extractor-widget)
-- [SAM-RF Widget](./widgets.md#sam-rf-widget)
-    - [Notes](./widgets.md#notes)
-- [SAM Prompt Segmentation Widget](./widgets.md#sam-prompt-segmentation-widget)
-- [SAM Predictor Widget](./widgets.md#sam-predictor-widget)
-<br><br>
 
-## Overview of SAM-RF Segmentation
-![extraction process](images/extract_process.jpg)
 
-![training process](images/training_process.jpg)
 
-![prediction process](images/prediction_process.jpg)
+[napari]: https://napari.org/
+[SAM2]: https://ai.meta.com/sam2/

docs/install.md

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+---
+title: Installation
+---
+
+## Easy Way!
+To install this plugin you need to use [mamba] or [conda] to create a environment and install the requirements. Use the commands below to create the environment and install the plugin:
+```bash
+# for GPU
+mamba env create -f ./env_gpu.yml
+```
+```bash
+# if you don't have a GPU
+mamba env create -f ./env_cpu.yml
+```
+
+### Note 
+You need to install `sam-2` which can be installed easily using mamba (or conda). To install `sam-2` using `pip` please refer to the official [sam-2](https://github.com/facebookresearch/sam2) repository.
+
+## Requirements
+- `python >= 3.10`
+- `numpy==1.24.4`
+- `opencv-python`
+- `scikit-learn`
+- `scikit-image`
+- `matplotlib`
+- `pyqt`
+- `magicgui`
+- `qtpy`
+- `napari`
+- `h5py`
+- `pytorch=2.3.1`
+- `torchvision=0.18.1`
+- `timm=1.0.9`
+- `pynrrd`
+- `segment-anything`
+- `sam-2`
+
+If you want to install the plugin manually using GPU, please follow the pytorch installation instruction [here](https://pytorch.org/get-started/locally/).  
+For detailed napari installation see [here](https://napari.org/stable/tutorials/fundamentals/installation).  
+
+## Installing Only The Plugin
+If you use the provided conda environment yaml files, the plugin will be installed automatically. But in case you already have the environment setup, 
+you can just install the plugin. First clone the repository:
+```bash
+git clone https://github.com/juglab/featureforest
+```
+Then run the following commands:
+```bash
+cd ./featureforest
+pip install .
+```
+
+[PyPI]: https://pypi.org/
+[conda]: https://conda.io/projects/conda/en/latest/index.html
+[mamba]: https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html

docs/stylesheets/extra.css

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+.md-typeset code {
+    font-size: 90%;
+    font-weight: 600;
+}

mkdocs.yml

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+site_name: Feature Forest Documents
+site_url: https://juglab.github.io/featureforest
+extra_css:
+  - stylesheets/extra.css
+theme:
+  name: material
+  features:
+    - navigation.footer
+    - navigation.sections
+    - navigation.instant
+    - navigation.instant.progress
+    - content.code.copy
+  # logo: assets/logo.png
+  # favicon: images/favicon.png
+  icon:
+    repo: fontawesome/brands/git-alt
+  font:
+    text: Parkinsans
+    code: Fira Code
+  palette:
+    # Palette toggle for dark mode
+    - scheme: slate
+      primary: green
+      accent: cyan
+      toggle:
+        icon: material/brightness-4
+        name: Switch to light mode
+
+    # Palette toggle for light mode
+    - scheme: default
+      primary: green
+      accent: cyan
+      toggle:
+        icon: material/brightness-7 
+        name: Switch to dark mode
+
+extra:
+  version:
+      provider: mike
+  social:
+    - icon: fontawesome/brands/github-alt
+      link: https://github.com/juglab/featureforest
+
+repo_url: https://github.com/juglab/featureforest
+repo_name: juglab/featureforest
+
+markdown_extensions:
+  - pymdownx.highlight:
+      anchor_linenums: true
+      line_spans: __span
+      pygments_lang_class: true
+  - pymdownx.inlinehilite
+  - pymdownx.snippets
+  - pymdownx.superfences