corrected broken links and broken references (#46)

* corrected broken links and broken references

* Update README.md

- putting /conda only works for linux users so please do not add that @yeshaokai

* Update README.md

- always add full links; in external docs or on pypi these are also broken links @yeshaokai

* Update amadesuGPT.yml

- keep amadeusgpt as a dependency ...

---------

Co-authored-by: Mackenzie Mathis <[email protected]>

Author: yeshaokai

README.md

@@ -72,12 +72,12 @@ You can git clone (or download) this repo to grab a copy and go. We provide exam
 
 ### Here are a few demos that could fuel your own work, so please check them out!
 
-1) [Draw a region of interest (ROI) and ask, "when is the animal in the ROI?"](notebook/EPM_demo.ipynb)
-2) [Use a DeepLabCut SuperAnimal pose model to do video inference](notebook/custom_mouse_demo.ipynb) - (make sure you use a GPU if you don't have corresponding DeepLabCut keypoint files already!
-3) [Write you own integration modules and use them](notebook/Horse_demo.ipynb). Bonus: [source code](amadeusgpt/integration_modules). Make sure you delete the cached modules_embedding.pickle if you add new modules!
-4) [Multi-Animal social interactions](notebook/MABe_demo.ipynb)
-5) [Reuse the task program generated by LLM and run it on different videos](notebook/MABe_demo.ipynb)
-7) You can ask one query across multiple videos. Put your keypoint files and video files (pairs) in the same folder and specify the `data_folder` as shown in this [Demo](notebook/custom_mouse_video.ipynb). Make sure your video file and keypoint file follows the normal DeepLabCut convention, i.e., `prefix.mp4` `prefix*.h5`.
+1) [Draw a region of interest (ROI) and ask, "when is the animal in the ROI?"](https://github.com/AdaptiveMotorControlLab/AmadeusGPT/tree/main/notebooks/EPM_demo.ipynb)
+2) [Use a DeepLabCut SuperAnimal pose model to do video inference](https://github.com/AdaptiveMotorControlLab/AmadeusGPT/tree/main/notebooks/custom_mouse_demo.ipynb) - (make sure you use a GPU if you don't have corresponding DeepLabCut keypoint files already!
+3) [Write you own integration modules and use them](https://github.com/AdaptiveMotorControlLab/AmadeusGPT/tree/main/notebooks/Horse_demo.ipynb). Bonus: [source code](amadeusgpt/integration_modules). Make sure you delete the cached modules_embedding.pickle if you add new modules!
+4) [Multi-Animal social interactions](https://github.com/AdaptiveMotorControlLab/AmadeusGPT/tree/main/notebooks/MABe_demo.ipynb)
+5) [Reuse the task program generated by LLM and run it on different videos](https://github.com/AdaptiveMotorControlLab/AmadeusGPT/tree/main/notebooks/MABe_demo.ipynb)
+7) You can ask one query across multiple videos. Put your keypoint files and video files (pairs) in the same folder and specify the `data_folder` as shown in this [Demo](https://github.com/AdaptiveMotorControlLab/AmadeusGPT/tree/main/notebooks/custom_mouse_video.ipynb). Make sure your video file and keypoint file follows the normal DeepLabCut convention, i.e., `prefix.mp4` `prefix*.h5`.
 
 ### Minimal example
 

conda/amadesuGPT.yml

@@ -6,6 +6,6 @@ dependencies:
     - python==3.10
     - pytables==3.8.0
     - hdf5
-    - pip
     - jupyter
-    - amadeusGPT
+    - pip:
+      - amadeusgpt

conda/install_cpu.sh

@@ -1,10 +1,10 @@
 #!/bin/bash
 source /Users/shaokaiye/miniforge3/bin/activate
-conda env create -f conda/amadesuGPT-cpu.yml
-conda activate amadeusgpt-cpu
+conda env create -f conda/amadesuGPT.yml
+conda activate amadeusgpt
 conda install pytorch torchvision cpuonly -c pytorch
 pip install "git+https://github.com/DeepLabCut/DeepLabCut.git@pytorch_dlc#egg=deeplabcut"
 pip install pycocotools
 pip install -e .[streamlit]
 # install the python kernel
-python -m ipykernel install --user --name amadeusgpt-cpu --display-name "amadeusgpt-cpu"
+python -m ipykernel install --user --name amadeusgpt --display-name "amadeusgpt"

conda/install_gpu.sh

@@ -1,11 +1,11 @@
 #!/bin/bash
 source /mnt/md0/shaokai/miniconda3/bin/activate
-conda env create -f conda/amadesuGPT-gpu.yml
-conda activate amadeusgpt-gpu
+conda env create -f conda/amadesuGPT.yml
+conda activate amadeusgpt
 # adjust this line according to your cuda version
 conda install pytorch torchvision torchaudio pytorch-cuda=12.1 -c pytorch -c nvidia
 pip install "git+https://github.com/DeepLabCut/DeepLabCut.git@pytorch_dlc#egg=deeplabcut"
 pip install pycocotools
 pip install -e .[streamlit]
 # install the python kernel
-python -m ipykernel install --user --name amadeusgpt-gpu --display-name "amadeusgpt-gpu"
+python -m ipykernel install --user --name amadeusgpt --display-name "amadeusgpt"

conda/install_minimal.sh

@@ -1,8 +1,8 @@
 #!/bin/bash
 # change this to your own miniconda / miniforge path
 source /Users/shaokaiye/miniforge3/bin/activate
-conda env create -f conda/amadesuGPT-minimal.yml
-conda activate amadeusgpt-minimal
+conda env create -f conda/amadesuGPT.yml
+conda activate amadeusgpt
 pip install pycocotools
 pip install -e .[streamlit]
-python -m ipykernel install --user --name amadeusgpt-minimal --display-name "amadeusgpt-minimal"
+python -m ipykernel install --user --name amadeusgpt --display-name "amadeusgpt"