Contribution Guide

This guide is intended for developers or administrators who want to contribute a new feature or bugfix to SSAPy. It assumes that you have at least some familiarity with Git and GitHub. The guide will show a few examples of contributing workflows and discuss the granularity of pull-requests (PRs). It will also discuss the tests your PR must pass in order to be accepted into SSAPy.

First, what is a PR? Quoting Bitbucket’s tutorials:

Pull requests are a mechanism for a developer to notify team members that they have completed a feature. The pull request is more than just a notification—it’s a dedicated forum for discussing the proposed feature.

The emphasis is on a completed feature. The changes one proposes in a PR should correspond to one feature/bugfix/extension/etc. One can create PRs with changes relevant to different ideas, however reviewing such PRs becomes tedious and error prone. If possible, try to follow the one-PR-one-feature rule.

Branches

SSAPy’s main branch has the latest contributions. Nearly all pull requests should start from main and target main.

There is a branch for each major release series. Release branches originate from main and have tags for each point release in the series. For example, releases/v0.14 might have tags for 0.14.0, 0.14.1, 0.14.2, etc. versions of SSAPy. We backport important bug fixes to these branches, but we do not advance the package versions or make other changes that would change the way SSAPy concretizes dependencies. Currently, the maintainers manage these branches by cherry-picking from main. See releases for more information.

Continuous Integration

SSAPy uses Github Actions for Continuous Integration testing. This means that every time you submit a pull request, a series of tests will be run to make sure you didn’t accidentally introduce any bugs into SSAPy. Your PR will not be accepted until it passes all of these tests. While you can certainly wait for the results of these tests after submitting a PR, we recommend that you run them locally to speed up the review process.

Note

Oftentimes, CI will fail for reasons other than a problem with your PR. For example, apt-get, pip, or homebrew will fail to download one of the dependencies for the test suite, or a transient bug will cause the unit tests to timeout. If any job fails, click the “Details” link and click on the test(s) that is failing. If it doesn’t look like it is failing for reasons related to your PR, you have two options. If you have write permissions for the SSAPy repository, you should see a “Restart workflow” button on the right-hand side. If not, you can close and reopen your PR to rerun all of the tests. If the same test keeps failing, there may be a problem with your PR. If you notice that every recent PR is failing with the same error message, it may be that an issue occurred with the CI infrastructure or one of SSAPy’s dependencies put out a new release that is causing problems. If this is the case, please file an issue.

We currently test against Python 3.10 on both macOS and Linux and perform 3 types of tests:

Unit Tests

Unit tests ensure that core SSAPy features like fetching or spec resolution are working as expected. If your PR only adds new packages or modifies existing ones, there’s very little chance that your changes could cause the unit tests to fail. However, if you make changes to SSAPy’s core libraries, you should run the unit tests to make sure you didn’t break anything.

Since they test things like fetching from VCS repos, the unit tests require git, mercurial, and subversion to run. Make sure these are installed on your system and can be found in your PATH. All of these can be installed with SSAPy or with your system package manager.

To run all of the unit tests, use:

$ ssapy unit-test

These tests may take several minutes to complete. If you know you are only modifying a single SSAPy feature, you can run subsets of tests at a time. For example, this would run all the tests in tests/*.py:

$ ssapy unit-test tests/*.py

This allows you to develop iteratively: make a change, test that change, make another change, test that change, etc. We use pytest as our tests framework, and these types of arguments are just passed to the pytest command underneath. See the pytest docs for more details on test selection syntax.

By default, pytest captures the output of all unit tests, and it will print any captured output for failed tests. Sometimes it’s helpful to see your output interactively, while the tests run (e.g., if you add print statements to a unit tests). To see the output live, use the -s argument to pytest:

$ ssapy unit-test -s --list-long tests/architecture.py::test_platform

Unit tests are crucial to making sure bugs aren’t introduced into SSAPy. If you are modifying core SSAPy libraries or adding new functionality, please add new unit tests for your feature, and consider strengthening existing tests. You will likely be asked to do this if you submit a pull request to the SSAPy project on GitHub. Check out the pytest docs and feel free to ask for guidance on how to write tests!

Style Tests

SSAPy uses Flake8 to test for PEP 8 conformance and mypy <https://mypy.readthedocs.io/en/stable/> for type checking. PEP 8 is a series of style guides for Python that provide suggestions for everything from variable naming to indentation. In order to limit the number of PRs that were mostly style changes, we decided to enforce PEP 8 conformance. Your PR needs to comply with PEP 8 in order to be accepted, and if it modifies the ssapy library it needs to successfully type-check with mypy as well.

Testing for compliance with ssapy’s style is easy. Simply run the ssapy style command:

$ ssapy style

ssapy style has a couple advantages over running the tools by hand:

It only tests files that you have modified since branching off of main.
It works regardless of what directory you are in.
It automatically adds approved exemptions from the flake8 checks. For example, URLs are often longer than 80 characters, so we exempt them from line length checks. We also exempt lines that start with “homepage”, “url”, “version”, “variant”, “depends_on”, and “extends” in package.py files. This is now also possible when directly running flake8 if you can use the ssapy formatter plugin included with ssapy.

More approved flake8 exemptions can be found here.

If all is well, you’ll see something like this:

$ run-flake8-tests
Dependencies found.
=======================================================
flake8: running flake8 code checks on SSAPy.

Modified files:

  var/ssapy/repos/builtin/packages/hdf5/package.py
  var/ssapy/repos/builtin/packages/hdf/package.py
  var/ssapy/repos/builtin/packages/netcdf/package.py
=======================================================
Flake8 checks were clean.

However, if you aren’t compliant with PEP 8, flake8 will complain:

var/ssapy/repos/builtin/packages/netcdf/package.py:26: [F401] 'os' imported but unused
var/ssapy/repos/builtin/packages/netcdf/package.py:61: [E303] too many blank lines (2)
var/ssapy/repos/builtin/packages/netcdf/package.py:106: [E501] line too long (92 > 79 characters)
Flake8 found errors.

Most of the error messages are straightforward, but if you don’t understand what they mean, just ask questions about them when you submit your PR. The line numbers will change if you add or delete lines, so simply run ssapy style again to update them.

Tip

Try fixing flake8 errors in reverse order. This eliminates the need for multiple runs of ssapy style just to re-compute line numbers and makes it much easier to fix errors directly off of the CI output.

Documentation Tests

SSAPy uses Sphinx to build its documentation. In order to prevent things like broken links and missing imports, we added documentation tests that build the documentation and fail if there are any warning or error messages.

Building the documentation requires several dependencies:

docutils
sphinx
sphinx-rtd-theme
sphinx-copybutton
sphinx-autobuild
sphinx-tabs
sphinx-automodapi
myst-parser
graphviz

All of these can be installed with Pip, e.g.

$ python3 -m pip install docutils sphinx, sphinx-rtd-theme sphinx-copybutton sphinx-autobuild sphinx-tabs sphinx-automodapi myst-parser graphviz

Once all of the dependencies are installed, you can try building the documentation:

$ cd path/to/ssapy/docs/
$ make clean
$ make

If you see any warning or error messages, you will have to correct those before your PR is accepted. If you are editing the documentation, you should be running the documentation tests to make sure there are no errors. Documentation changes can result in some obfuscated warning messages. If you don’t understand what they mean, feel free to ask when you submit your PR.

Coverage

SSAPy uses Codecov to generate and report unit test coverage. This helps us tell what percentage of lines of code in SSAPy are covered by unit tests. Although code covered by unit tests can still contain bugs, it is much less error prone than code that is not covered by unit tests.

Codecov provides browser extensions for Google Chrome and Firefox. These extensions integrate with GitHub and allow you to see coverage line-by-line when viewing the SSAPy repository. If you are new to SSAPy, a great way to get started is to write unit tests to increase coverage!

Unlike with CI on Github Actions Codecov tests are not required to pass in order for your PR to be merged. If you modify core SSAPy libraries, we would greatly appreciate unit tests that cover these changed lines. Otherwise, we have no way of knowing whether or not your changes introduce a bug. If you make substantial changes to the core, we may request unit tests to increase coverage.

Note

You may notice that the Codecov tests fail even though you didn’t modify any core files. This means that SSAPy’s overall coverage has increased since you branched off of main. This is a good thing! If you really want to get the Codecov tests to pass, you can rebase off of the latest main, but again, this is not required.

Git Workflows

SSAPy is still in the beta stages of development. Most of our users run off of the main branch, and fixes and new features are constantly being merged. So how do you keep up-to-date with upstream while maintaining your own local differences and contributing PRs to SSAPy?

Branching

The easiest way to contribute a pull request is to make all of your changes on new branches. Make sure your main is up-to-date and create a new branch off of it:

$ git checkout main
$ git pull upstream main
$ git branch <descriptive_branch_name>
$ git checkout <descriptive_branch_name>

Here we assume that the local main branch tracks the upstream main branch of SSAPy. This is not a requirement and you could also do the same with remote branches. But for some it is more convenient to have a local branch that tracks upstream.

Normally we prefer that commits pertaining to a package <package-name> have a message <package-name>: descriptive message. It is important to add descriptive message so that others, who might be looking at your changes later (in a year or maybe two), would understand the rationale behind them.

Now, you can make your changes while keeping the main branch pure. Edit a few files and commit them by running:

$ git add <files_to_be_part_of_the_commit>
$ git commit --message <descriptive_message_of_this_particular_commit>

Next, push it to your remote fork and create a PR:

$ git push origin <descriptive_branch_name> --set-upstream

GitHub provides a tutorial on how to file a pull request. When you send the request, make main the destination branch.

If you need this change immediately and don’t have time to wait for your PR to be merged, you can always work on this branch. But if you have multiple PRs, another option is to maintain a Frankenstein branch that combines all of your other branches:

$ git checkout main
$ git branch <your_modified_main_branch>
$ git checkout <your_modified_main_branch>
$ git merge <descriptive_branch_name>

This can be done with each new PR you submit. Just make sure to keep this local branch up-to-date with upstream main too.

Cherry-Picking

What if you made some changes to your local modified main branch and already committed them, but later decided to contribute them to SSAPy? You can use cherry-picking to create a new branch with only these commits.

First, check out your local modified main branch:

$ git checkout <your_modified_main_branch>

Now, get the hashes of the commits you want from the output of:

$ git log

Next, create a new branch off of upstream main and copy the commits that you want in your PR:

$ git checkout main
$ git pull upstream main
$ git branch <descriptive_branch_name>
$ git checkout <descriptive_branch_name>
$ git cherry-pick <hash>
$ git push origin <descriptive_branch_name> --set-upstream

Now you can create a PR from the web-interface of GitHub. The net result is as follows:

You patched your local version of SSAPy and can use it further.
You “cherry-picked” these changes in a stand-alone branch and submitted it as a PR upstream.

Should you have several commits to contribute, you could follow the same procedure by getting hashes of all of them and cherry-picking to the PR branch.

Note

It is important that whenever you change something that might be of importance upstream, create a pull request as soon as possible. Do not wait for weeks/months to do this, because:

you might forget why you modified certain files
it could get difficult to isolate this change into a stand-alone clean PR.

Rebasing

Other developers are constantly making contributions to SSAPy, possibly on the same files that your PR changed. If their PR is merged before yours, it can create a merge conflict. This means that your PR can no longer be automatically merged without a chance of breaking your changes. In this case, you will be asked to rebase on top of the latest upstream main.

First, make sure your main branch is up-to-date:

$ git checkout main
$ git pull upstream main

Now, we need to switch to the branch you submitted for your PR and rebase it on top of main:

$ git checkout <descriptive_branch_name>
$ git rebase main

Git will likely ask you to resolve conflicts. Edit the file that it says can’t be merged automatically and resolve the conflict. Then, run:

$ git add <file_that_could_not_be_merged>
$ git rebase --continue

You may have to repeat this process multiple times until all conflicts are resolved. Once this is done, simply force push your rebased branch to your remote fork:

$ git push --force origin <descriptive_branch_name>

Rebasing with cherry-pick

You can also perform a rebase using cherry-pick. First, create a temporary backup branch:

$ git checkout <descriptive_branch_name>
$ git branch tmp

If anything goes wrong, you can always go back to your tmp branch. Now, look at the logs and save the hashes of any commits you would like to keep:

$ git log

Next, go back to the original branch and reset it to main. Before doing so, make sure that you local main branch is up-to-date with upstream:

$ git checkout main
$ git pull upstream main
$ git checkout <descriptive_branch_name>
$ git reset --hard main

Now you can cherry-pick relevant commits:

$ git cherry-pick <hash1>
$ git cherry-pick <hash2>

Push the modified branch to your fork:

$ git push --force origin <descriptive_branch_name>

If everything looks good, delete the backup branch:

$ git branch --delete --force tmp

Re-writing History

Sometimes you may end up on a branch that has diverged so much from main that it cannot easily be rebased. If the current commits history is more of an experimental nature and only the net result is important, you may rewrite the history.

First, merge upstream main and reset you branch to it. On the branch in question, run:

$ git merge main
$ git reset main

At this point your branch will point to the same commit as main and thereby the two are indistinguishable. However, all the files that were previously modified will stay as such. In other words, you do not lose the changes you made. Changes can be reviewed by looking at diffs:

$ git status
$ git diff

The next step is to rewrite the history by adding files and creating commits:

$ git add <files_to_be_part_of_commit>
$ git commit --message <descriptive_message>

After all changed files are committed, you can push the branch to your fork and create a PR:

$ git push origin --set-upstream