OpenSoundscape¶

OpenSoundscape is a utility library for analyzing bioacoustic data. It consists of command line scripts for tasks such as preprocessing audio data, training machine learning models to classify vocalizations, estimating the spatial location of sounds, identifying which species’ sounds are present in acoustic data, and more.

These utilities can be strung together to create data analysis pipelines. OpenSoundscape is designed to be run on any scale of computer: laptop, desktop, or computing cluster.

OpenSoundscape is currently in active development. If you find a bug, please submit an issue. If you have another question about OpenSoundscape, please email Sam Lapp (sam.lapp at pitt.edu) or Tessa Rhinehart (tessa.rhinehart at pitt.edu).

For examples of some of the utilities offered, please see the “Tutorials” section of the documentation. Included are instructions on how to download and use a pretrained machine learning model from our publicly available set of models. We plan to add additional tutorials soon.

Installation¶

OpenSoundscape can be installed either via pip (for users) or poetry (for developers contributing to the code). Either way, Python 3.7 or higher is required.

Installation via pip (most users)¶

Just give me the pip command!¶

Already familiar with installing python packages via pip? The pip command to install OpenSoundscape is pip install opensoundscape==0.4.5.

Detailed instructions¶

Python 3.7 is required to run OpenSoundscape. Download it from this website.

We recommend installing OpenSoundscape in a virtual environment to prevent dependency conflicts. Below are instructions for installation with Python’s included virtual environment manager, venv, but feel free to use another virtual environment manager (e.g. conda, virtualenvwrapper) if desired.

Run the following commands in your bash terminal:

Check that you have installed Python 3.7._: python3 --version
Change directories to where you wish to store the environment: cd [path for environments folder]
- Tip: You can use this folder to store virtual environments for other projects as well, so put it somewhere that makes sense for you, e.g. in your home directory.
Make a directory for virtual environments and cd into it: mkdir .venv && cd .venv
Create an environment called opensoundscape in the directory: python3 -m venv opensoundscape
For Windows computers: activate/use the environment: opensoundscape\Scripts\activate.bat
For Mac computers: activate/use the environment source opensoundscape/bin/activate
Install OpenSoundscape in the environment: pip install opensoundscape==0.4.5
Once you are done with OpenSoundscape, deactivate the environment: deactivate
To use the environment again, you will have to refer to absolute path of the virtual environments folder. For instance, if I were on a Mac and created .venv inside a directory /Users/MyFiles/Code I would activate the virtual environment using: source /Users/MyFiles/Code/.venv/opensoundscape/bin/activate

For some of our functions, you will need a version of ffmpeg >= 0.4.1. On Mac machines, ffmpeg can be installed via brew.

Installation via poetry (contributors and advanced users)¶

Poetry installation allows direct use of the most recent version of the code. This workflow allows advanced users to use the newest features in OpenSoundscape, and allows developers/contributors to build and test their contributions.

To install via poetry, do the following:

Download poetry
Download virtualenvwrapper

Link poetry and virtualenvwrapper:

Figure out where the virtualenvwrapper.sh file is: which virtualenvwrapper.sh

Add the following to your ~/.bashrc and source it. .. code-block:

# virtualenvwrapper + poetry
export PATH=~/.local/bin:$PATH
export WORKON_HOME=~/Library/Caches/pypoetry/virtualenvs
source [insert path to virtualenvwrapper.sh, e.g. ~/.local/bin/virtualenvwrapper_lazy.sh]

Users: clone this github repository to your machine: git clone https://github.com/kitzeslab/opensoundscape.git
Contributors: fork this github repository and clone the fork to your machine
Ensure you are in the top-level directory of the clone
Switch to the development branch of OpenSoundscape: git checkout develop
Build the virtual environment for opensoundscape: poetry install
- If poetry install outputs the following error, make sure to download Python 3.7: .. code-block:
```
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
opensoundscape requires Python '>=3.7,<4.0' but the running Python is 3.6.10
```
  If you are using conda, install Python 3.7 using conda install python==3.7
- If you are on a Mac and poetry install fails to install numba, contact one of the developers for help troubleshooting your issues.
Activate the virtual environment with the name provided at install e.g.: workon opensoundscape-dxMTH98s-py3.7 or poetry shell
Check that OpenSoundscape runs: opensoundscape -h
Run tests (from the top-level directory): poetry run pytest
Go back to your system’s Python when you are done: deactivate

Jupyter¶

To use OpenSoundscape within JupyterLab, you will have to make an ipykernel for the OpenSoundscape virtual environment.

Activate poetry virtual environment, e.g.: workon opensoundscape-dxMTH98s-py3.7
- Use poetry env list if you’re not sure what the name of the environment is
Create ipython kernel: python -m ipykernel install --user --name=[name of poetry environment] --display-name=OpenSoundscape
Now when you make a new document on JupyterLab, you should see a Python kernel available called OpenSoundscape.
Contributors: if you include Jupyter’s autoreload, any changes you make to the source code installed via poetry will be reflected whenever you run the %autoreload line magic in a cell: .. code-block:
```
%load_ext autoreload
%autoreload
```

Contributing to code¶

Make contributions by editing the code in your fork. Create branches for features using git checkout -b feature_branch_name and push these changes to remote using git push -u origin feature_branch_name. To merge a feature branch into the development branch, use the GitHub web interface to create a merge request.

When contributions in your fork are complete, open a pull request using the GitHub web interface. Before opening a PR, do the following to ensure the code is consistent with the rest of the package:

Run tests: poetry run pytest
Format the code with black style (from the top level of the repo): poetry run black .
- To automatically handle this, poetry run pre-commit install
Additional libraries to be installed should be installed with poetry add, but in most cases contributors should not add libraries.

Contributing to documentation¶

Build the documentation using either poetry or sphinx-build

With poetry: poetry run build_docs
With sphinx-build: sphinx-build doc doc/_build