opensoundscape 0.4.1

Open source, scalable acoustic classification for ecology and conservation

OpenSoundscape

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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 documentation website. We plan to add more vignettes and documentation 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 is pip install opensoundscape==0.4.1

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==0.4.1
• 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

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.

    # 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:

    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:

  %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): black .
• 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

Publish the documentation with the following commands:

rm -rf /tmp/gh-pages
cp -r doc/_build /tmp/gh-pages
git checkout gh-pages
rm -rf *
cp -r /tmp/gh-pages/* .
git add .
git commit -m "Updated gh-pages"
git push
git checkout master