Merge PR #364 | fix and promote PlantSeg v1 installation

docs/chapters/getting_started/index.md

@@ -17,7 +17,7 @@ then, start the plantseg in napari
 plantseg --napari
 ```
 
-A more in depth guide can be found in our [documentation (GUI)](https://hci-unihd.github.io/plant-seg/chapters/plantseg_interactive_napari/).
+A more in depth guide can be found in our [documentation (GUI)](../plantseg_interactive_napari/index.md).
 
 ## Command Line PlantSeg
 
@@ -36,13 +36,13 @@ plantseg --config CONFIG_PATH
 ```
 
 where `CONFIG_PATH` is the path to the `YAML` configuration file. See [config.yaml](https://github.com/kreshuklab/plant-seg/blob/master/examples/config.yaml) for a sample configuration
-file and our [documentation (CLI)](https://hci-unihd.github.io/plant-seg/chapters/plantseg_classic_cli/) for a
+file and our [documentation (CLI)](../plantseg_legacy/plantseg_classic_cli/index.md) for a
 detailed description of the parameters.
 
 ## PlantSeg with Legacy GUI
 
 !!! failure "Deprecated"
-    This interface is deprecated and has been removed from PlantSeg v2. Please use the Napari viewer or the command line interface instead, or install PlantSeg v1.
+    This interface is deprecated and has been removed from PlantSeg v2. Please use the Napari viewer or the command line interface instead, or [install PlantSeg v1](../plantseg_legacy/installation.md).
 
 PlantSeg app can also be started in a GUI mode, where basic user interface allows to configure and run the pipeline.
 First, activate the newly created conda environment with:
@@ -57,4 +57,4 @@ then, run the GUI by simply typing:
 plantseg --gui
 ```
 
-A more in depth guide can be found in our [documentation (Classic GUI)](https://hci-unihd.github.io/plant-seg/chapters/plantseg_classic_gui/).
+A more in depth guide can be found in our [documentation (Classic GUI)](../plantseg_legacy/plantseg_classic_gui/index.md).

docs/chapters/getting_started/installation.md

@@ -1,5 +1,7 @@
 # Installation
 
+This is the installation guide for the latest PlantSeg. Please check the installation guide for PlantSeg v1 at [PlantSeg Legacy Installation](../plantseg_legacy/installation.md).
+
 ## Prerequisites for Conda package
 
 * Linux, Windows, macOS (not all features are available on macOS)
@@ -105,3 +107,7 @@ If you plan to use SimpleITK-based watershed segmentation, you will need to inst
 conda activate plant-seg
 pip install SimpleITK
 ```
+
+## Installing PlantSeg v1
+
+Please check the installation guide for PlantSeg v1 at [PlantSeg Legacy Installation](../plantseg_legacy/installation.md).

docs/chapters/plantseg_legacy/installation.md

@@ -41,47 +41,47 @@ PlantSeg can be installed directly by executing in the terminal (or PowerShell o
     * NVIDIA GPU version, CUDA=12.x
 
         ```bash
-        mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch pytorch-cuda=12.1 plant-seg=1.8.1 biomagecore.io --no-channel-priority
+        mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch pytorch-cuda=12.1 plant-seg=1.8.1 bioimageio.core --no-channel-priority
         ```
 
     * NVIDIA GPU version, CUDA=11.x
 
         ```bash
-        mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch pytorch-cuda=11.8 plant-seg=1.8.1 biomagecore.io --no-channel-priority
+        mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch pytorch-cuda=11.8 plant-seg=1.8.1 bioimageio.core --no-channel-priority
         ```
 
     * CPU version
 
         ```bash
-        mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch cpuonly plant-seg=1.8.1 biomagecore.io --no-channel-priority
+        mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch cpuonly plant-seg=1.8.1 bioimageio.core --no-channel-priority
         ```
 
 === "Windows"
 
     * NVIDIA GPU version, CUDA=12.x
 
         ```bash
-        mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch pytorch-cuda=12.1 nifty=1.2.1=*_4 plant-seg=1.8.1 biomagecore.io --no-channel-priority
+        mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch pytorch-cuda=12.1 nifty=1.2.1=*_4 plant-seg=1.8.1 bioimageio.core --no-channel-priority
         ```
 
     * NVIDIA GPU version, CUDA=11.x
 
         ```bash
-        mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch pytorch-cuda=11.8 nifty=1.2.1=*_4 plant-seg=1.8.1 biomagecore.io --no-channel-priority
+        mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch pytorch-cuda=11.8 nifty=1.2.1=*_4 plant-seg=1.8.1 bioimageio.core --no-channel-priority
         ```
 
     * CPU version
 
         ```bash
-        mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch cpuonly nifty=1.2.1=*_4 plant-seg=1.8.1 biomagecore.io --no-channel-priority
+        mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch cpuonly nifty=1.2.1=*_4 plant-seg=1.8.1 bioimageio.core --no-channel-priority
         ```
 
 === "macOS"
 
     * Apple silicon version
 
         ```bash
-        mamba create -n plant-seg -c pytorch -c conda-forge python=3.11 pytorch::pytorch plant-seg=1.8.1 biomagecore.io --no-channel-priority
+        mamba create -n plant-seg -c pytorch -c conda-forge python=3.11 pytorch::pytorch plant-seg=1.8.1 bioimageio.core --no-channel-priority
         ```
 
 If you used older versions of PlantSeg, please delete the old config files in `~/.plantseg_models/configs/` after installing new PlantSeg.

mkdocs.yml

@@ -116,26 +116,24 @@ nav:
       - Training: chapters/plantseg_models/training.md
 
   - API:
-      # - chapters/python_api/index.md
       - tasks:
         - plantseg.tasks.io_tasks: chapters/python_api/tasks/io_tasks.md
         - plantseg.tasks.dataprocessing_tasks: chapters/python_api/tasks/dataprocessing_tasks.md
         - plantseg.tasks.segmentation_tasks: chapters/python_api/tasks/segmentation_tasks.md
         - plantseg.tasks.prediction_tasks: chapters/python_api/tasks/prediction_tasks.md
-
       - functionals:
         - plantseg.io: chapters/python_api/functionals/io.md
         - plantseg.functionals.dataprocessing: chapters/python_api/functionals/data_processing.md
         - plantseg.functionals.prediction: chapters/python_api/functionals/cnn_prediction.md
         - plantseg.functionals.segmentation: chapters/python_api/functionals/segmentation.md
-  
-  - PlantSeg Legacy: 
+
+  - PlantSeg v1:
       - chapters/plantseg_legacy/installation.md
-      - PlantSeg Classic GUI:
+      - Classic GUI:
           - chapters/plantseg_legacy/plantseg_classic_gui/index.md
           - Data Processing: chapters/plantseg_legacy/plantseg_classic_gui/data_processing.md
           - Prediction: chapters/plantseg_legacy/plantseg_classic_gui/cnn_prediction.md
           - Segmentation: chapters/plantseg_legacy/plantseg_classic_gui/segmentation.md
 
       - Classic CLI:
-          - chapters/plantseg_legacy/plantseg_classic_cli/index.md
+          - chapters/plantseg_legacy/plantseg_classic_cli/index.md