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Contributing

When contributing to this repository, please first discuss the change you wish to make via issue, email, or any other method with the owners of this repository before making a change.

Please note we have a code of conduct, please follow it in all your interactions with the project.

How to contribute

Reporting bugs or feature requests

You can use Sage Bionetwork's FAIR Data service desk to create bug and feature requests. Providing enough details to the developers to verify and troubleshoot your issue is paramount:

  • Provide a clear and descriptive title as well as a concise summary of the issue to identify the problem.
  • Describe the exact steps which reproduce the problem in as many details as possible.
  • Describe the behavior you observed after following the steps and point out what exactly is the problem with that behavior.
  • Explain which behavior you expected to see instead and why.
  • Provide screenshots of the expected or actual behaviour where applicable.

General contribution instructions

  1. Follow the Github docs to make a copy (a fork) of the repository to your own Github account.
  2. Clone the forked repository to your local machine so you can begin making changes.
  3. Make sure this repository is set as the upstream remote repository so you are able to fetch the latest commits.
  4. Push all your changes to the develop branch of the forked repository.

Note: Make sure you have you have the latest version of the develop branch on your local machine.

git checkout develop
git pull upstream develop
  1. Create pull requests to the upstream repository.

The development lifecycle

  1. Pull the latest content from the develop branch of this central repository (not your fork).
  2. Create a branch off the develop branch. Name the branch appropriately, either briefly summarizing the bug (ex., spatil/add-restapi-layer) or feature or simply use the issue number in the name (ex., spatil/issue-414-fix).
  3. After completing work and testing locally, push the code to the appropriate branch on your fork.
  4. In Github, create a pull request from the bug/feature branch of your fork to the develop branch of the central repository.

A Sage Bionetworks engineer must review and accept your pull request. A code review (which happens with both the contributor and the reviewer present) is required for contributing.

Development environment setup

  1. Install package dependencies.
  2. Clone the schematic package repository.
git clone https://github.com/Sage-Bionetworks/schematic.git
  1. Create and activate a virtual environment.
  2. Run the following commands to build schematic and install the package along with all of its dependencies:
cd schematic  # change directory to schematic
git checkout develop  # switch to develop branch of schematic
poetry build # build source and wheel archives
pip install dist/schematicpy-x.y.z-py3-none-any.whl  # install wheel file

Note: Use the appropriate version number (based on the version of the codebase you are pulling) while installing the wheel file above.

  1. Obtain appropriate Google credentials file(s).
  2. Obtain and Fill in the config.yml file and the .synapseConfig file as well as described in the Fill in Configuration File(s) part of the documentation.
  3. Run the test suite.

Note: To ensure that all tests run successfully, contact your DCC liason and request to be added to the schematic-dev team on Synapse.

  1. To test new changes made to any of the modules within schematic, do the following:
# make changes to any files or modules
pip uninstall schematicpy  # uninstall package
poetry build
pip install dist/schematicpy-x.y.z-py3-none-any.whl  # install wheel file

Release process

Once the code has been merged into the develop branch on this repo, there are two processes that need to be completed to ensure a release is complete.

  • You should create a GitHub tag, with the appropriate version number. Typically, from v21.06 onwards all tags are created following the Linux Ubuntu versioning convention which is the YY.MM format where Y is the year and M is the month of that year when that release was created.
  • You should push the package to PyPI. Schematic is on PyPI as schematicpy. You can go through the following two sections for that.

Release to Test PyPI (optional)

The purpose of this section is to verify that the package looks and works as intended, by viewing it on Test PyPI and installing the test version in a separate virtual environment.

poetry build   # build the package
poetry config repositories.testpypi https://test.pypi.org/legacy/   # add Test PyPI as an alternate package repository
poetry publish -r testpypi   # publish the package to Test PyPI

Installing:

pip install --index-url https://test.pypi.org/simple/

Release to PyPI (mandatory)

If the package looks great on Test PyPI and works well, the next step is to publish the package to PyPI:

poetry publish  # publish the package to PyPI

You'll need to register for a PyPI account before uploading packages to the package index. Similarly for Test PyPI as well.

Testing

All code added to the client must have tests. The Python client uses pytest to run tests. The test code is located in the tests subdirectory.

You can run the test suite in the following way:

pytest -vs tests/

Updating Synapse test resources

  1. Duplicate the entity being updated (or folder if applicable).
  2. Edit the duplicates (e.g. annotations, contents, name).
  3. Update the test suite in your branch to use these duplicates, including the expected values in the test assertions.
  4. Open a PR as per the usual process (see above).
  5. Once the PR is merged, leave the original copies on Synapse to maintain support for feature branches that were forked from develop before your update.
    • If the old copies are problematic and need to be removed immediately (e.g. contain sensitive data), proceed with the deletion and alert the other contributors that they need to merge the latest develop branch into their feature branches for their tests to work.

Code style

  • Please consult the Google Python style guide prior to contributing code to this project.
  • Be consistent and follow existing code conventions and spirit.