fix: installation documentation

kreshuklab · Oct 21, 2024 · d031d78 · d031d78
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diff --git a/docs/chapters/plantseg_legacy/installation.md b/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 --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 biomagecore.io --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 --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 biomagecore.io --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 --no-channel-priority
+        mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch cpuonly plant-seg=1.8.1 biomagecore.io --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 --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 biomagecore.io --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 --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 biomagecore.io --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 --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 biomagecore.io --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 --no-channel-priority
+        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
         ```
 
 If you used older versions of PlantSeg, please delete the old config files in `~/.plantseg_models/configs/` after installing new PlantSeg.

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -115,18 +115,27 @@ nav:
       - Custom Datasets: chapters/plantseg_models/custom_datasets.md
       - Training: chapters/plantseg_models/training.md
 
-  - Classic GUI:
-      - chapters/plantseg_classic_gui/index.md
-      - Data Processing: chapters/plantseg_classic_gui/data_processing.md
-      - Prediction: chapters/plantseg_classic_gui/cnn_prediction.md
-      - Segmentation: chapters/plantseg_classic_gui/segmentation.md
-
-  - Classic CLI:
-      - chapters/plantseg_classic_cli/index.md
-
   - API:
       # - chapters/python_api/index.md
-      - plantseg.io: chapters/python_api/io.md
-      - plantseg.dataprocessing: chapters/python_api/data_processing.md
-      - plantseg.prediction: chapters/python_api/cnn_prediction.md
-      - plantseg.segmentation: chapters/python_api/segmentation.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: 
+      - chapters/plantseg_legacy/installation.md
+      - PlantSeg 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