Maintaining SPRAS

Go dependency

The yamlfmt tool requires Go, which must be installed manually.

Naming conventions

SPRAS wrappers try to follow the naming conventions of the algorithms they wrap. This includes their name and their required_inputs: when sensible, we preserve the file name of inputs required by the internal algorithm.

For example, Maximum Edge Orientation calls a network edges, while PathLinker calls a network network. Therefore, we say edges in MEO when referring to a network.

Reviewing pull requests

Contributors may help review pull requests from other contributors. Part of the review process includes running the updated code locally. This requires checking out a branch from the other contributor’s fork.

We’ll use pull request #170 as an example from the ntalluri fork with branch implement-eval. First, you need to add the ntalluri fork as a git remote from the command line so that you can pull branches from it.

git remote add ntalluri https://github.com/ntalluri/spras.git

The first ntalluri is the name we give to the new remote. It doesn’t have to match the GitHub user name, but that is a convenient convention.

Then, confirm the new remote was added

git remote -v

You should see the new remote along with your origin remote and any others you added previously. Now you can pull and fetch branches from any of these remotes and push to any remotes where you have permissions.

To checkout the branch in the pull request locally run

git fetch ntalluri
git checkout implement-eval

Optionally run

git log

To confirm that the most recent commit matches the most recent commit in the pull request. Now your local version of SPRAS matches the code in the pull request and you can test the code to confirm it runs as expected.

.test_durations

To regenerate the .test_durations file, use pytest --store-durations. A clean docker cache is recommended to best split up the test runs. .test_durations is used to split the testing CI (with pytest-splti) into several evenly-sized groups for parallelization. Because of this, .test_durations should be regenerated for every few algorithms or analysis tools added, to make sure the CI works as fast as it can.