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Create conda yaml file, and update readme accordingly
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benlansdell committed Jan 29, 2024
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11 changes: 11 additions & 0 deletions README.md
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Expand Up @@ -30,6 +30,17 @@ pip install ethome-ml

`ethome` has been tested with Python 3.7 and 3.8.

### Conda environment

Note that dependencies have tried to be kept to a minimum so that `ethome` can work easily alongside other programs that may be part of your behavior analysis pipeline (e.g. `DeepLabCut`) -- thus you can try running the `pip install` line above in an existing virtual environment.

That said, you may want a separate environment for running `ethome`. A conda environment can be created with the following steps:

1. Download the conda environment yaml file [ethome-conda.yaml](www.google.com)
2. (From the location you downloaded the yaml file) Create the environment: `conda env create -f ethome-conda.yaml`
3. Run `conda activate ethome`
3. And finally `pip install ethome-ml`

## Quickstart

It's easiest to start with an NWB file, which has metadata already connected to the pose data.
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23 changes: 23 additions & 0 deletions conda/ethome-conda.yaml
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name: ethome
channels:
- defaults
- conda-forge
dependencies:
- python=3.8
- setuptools>=42
- wheel
- numpy
- pandas>=1.5.0
- scikit-learn
- tqdm
- protobuf
- tensorflow==2.9.0
- typeguard
- tensorflow-addons
- typing
- matplotlib
- umap-learn
- scikit-image
- dill
- pynwb
- ipywidgets

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