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Next Steps for ndx-biosample Extension for NWB

Creating Your Extension

  1. In a terminal, change directory into the new ndx-biosample directory.

  2. Add any packages required by your extension to requirements.txt and setup.py.

  3. Run python -m pip install -r requirements.txt -r requirements-dev.txt to install the pynwb package and any other packages required to install, develop, and document your extension.

  4. Modify src/spec/create_extension_spec.py to define your extension.

  5. Run python src/spec/create_extension_spec.py to generate the spec/ndx-biosample.namespace.yaml and spec/ndx-biosample.extensions.yaml files.

  6. Define API classes for your new extension data types.

    • As a starting point, src/pynwb/__init__.py includes an example for how to use the pynwb.get_class to get a basic Python class for your new extension data type. This class contains a constructor and properties for the new data type.
    • Instead of using pynwb.get_class, you can define your own custom class for the new type, which will allow you to customize the class methods, customize the object mapping, and create convenience functions. See https://pynwb.readthedocs.io/en/stable/tutorials/general/extensions.html for more details.

  7. Define tests for your new extension data types in src/pynwb/tests or src/matnwb/tests. A test for the example TetrodeSeries data type is provided as a reference and should be replaced or removed.

    • Python tests should be runnable by executing pytest from the root of the extension directory. Use of PyNWB testing infrastructure from pynwb.testing is encouraged (see documentation).
    • Creating both unit tests (e.g., testing initialization of new data type classes and new functions) and integration tests (e.g., write the new data types to file, read the file, and confirm the read data types are equal to the written data types) is highly encouraged.

  8. You may need to modify setup.py and re-run python setup.py install if you use any dependencies.

Documenting and Publishing Your Extension to the Community

  1. Install the latest release of hdmf_docutils: python -m pip install hdmf-docutils

  2. Start a git repository for your extension directory ndx-biosample and push it to GitHub. You will need a GitHub account.

  3. Change directory into docs.

  4. Run make html to generate documentation for your extension based on the YAML files.

  5. Read docs/README.md for instructions on how to customize documentation for your extension.

  6. Modify README.md to describe this extension for interested developers.

  7. Add a license file. Permissive licenses should be used if possible. A BSD license is recommended.

  8. Make a release for the extension on GitHub with the version number specified. e.g. if version is 0.1.0, then this page should exist: https://github.com/bendichter/ndx-biosample/releases/tag/0.1.0 . For instructions on how to make a release on GitHub see here.

  9. Publish your updated extension on PyPI.

    Once your GitHub release and setup.py are ready, publishing on PyPI:

    python setup.py sdist bdist_wheel
twine upload dist/*

  10. Go to https://github.com/nwb-extensions/staged-extensions and fork the repository.

  11. Clone the fork onto your local filesystem.

  12. Copy the directory staged-extensions/example to a new directory staged-extensions/ndx-biosample:

    cp -r staged-extensions/example staged-extensions/ndx-biosample

  13. Edit staged-extensions/ndx-biosample/ndx-meta.yaml with information on where to find your NWB extension.

    • The YAML file MUST contain a dict with the following keys:

      • name: extension namespace name
      • version: extension version
      • src: URL for the main page of the public repository (e.g. on GitHub, BitBucket, GitLab) that contains the sources of the extension
      • pip: URL for the main page of the extension on PyPI
      • license: name of the license of the extension
      • maintainers: list of GitHub usernames of those who will reliably maintain the extension

    • You may copy and modify the following YAML that was auto-generated:

      name: ndx-biosample
version: 0.1.0
src: https://github.com/bendichter/ndx-biosample
pip: https://pypi.org/project/ndx-biosample/
license: BSD-3
maintainers: 
  - bendichter

  14. Edit staged-extensions/ndx-biosample/README.md to add information about your extension. You may copy it from ndx-biosample/README.md.

cp ndx-biosample/README.md staged-extensions/ndx-biosample/README.md
  1. Add and commit your changes to Git and push your changes to GitHub.
cd staged-extensions
git add ndx-biosample
git commit -m "Add new catalog entry for ndx-biosample" .
git push

  1. Open a pull request. Building of your extension will be tested on Windows, Mac, and Linux. The technical team will review your extension shortly after and provide feedback and request changes, if any.

  2. When your pull request is merged, a new repository, called ndx-biosample-record will be created in the nwb-extensions GitHub organization and you will be added as a maintainer for that repository.

Updating Your Published Extension

  1. Update your ndx-biosample GitHub repository.

  2. Publish your updated extension on PyPI.

  3. Fork the ndx-biosample-record repository on GitHub.

  4. Open a pull request to test the changes automatically. The technical team will review your changes shortly after and provide feedback and request changes, if any.

  5. Your updated extension is approved.