Developing#

Developer Environment#

To develop, we suggest using Python virtual environments together with pip and steered by nox. Once the virtual environment is activated and you have SSH keys setup with GitHub, clone the repo from GitHub

git clone git@github.com:scikit-hep/pyhf

and install all necessary packages for development

python -m pip install --upgrade --editable '.[develop]'

Then setup the Git pre-commit hooks by running

pre-commit install

inside of the virtual environment. pre-commit.ci keeps the pre-commit hooks updated through time, so pre-commit will automatically update itself when you run it locally after the hooks were updated.

It is then suggested that you use nox to actually run all development operations in “sessions” defined in noxfile.py. To list all of the available sessions run

nox --list

Linting#

Linting and code formatting is handled by pre-commit. To run the linting either run pre-commit

pre-commit run --all-files

or use nox

nox --session lint

Testing#

Writing tests#

Data Files#

A function-scoped fixture called datadir exists for a given test module which will automatically copy files from the associated test modules data directory into a temporary directory for the given test execution. That is, for example, if a test was defined in test_schema.py, then data files located in test_schema/ will be copied to a temporary directory whose path is made available by the datadir fixture. Therefore, one can do:

def test_patchset(datadir):
    data_file = open(datadir.join("test.txt"), encoding="utf-8")
    ...

which will load the copy of text.txt in the temporary directory. This also works for parameterizations as this will effectively sandbox the file modifications made.

Running with pytest#

To run the test suite in full, from the top level of the repository run

pytest

More practically for most local testing you will not want to test the benchmarks, contrib module, or notebooks, and so instead to test the core codebase a developer can run

nox --session tests --python 3.12

Contrib module matplotlib image tests#

To run the visualization tests for the contrib module with the pytest-mpl pytest plugin run

nox --session tests --python 3.12 -- contrib

If the image files need to be regenerated, run the tests with the --mpl-generate-path=tests/contrib/baseline option or just run

nox --session regenerate

Doctest#

pyhf’s configuration of pytest will automatically run doctest on all the modules when the full test suite is run. To run doctest on an individual module or file just run pytest on its path. For example, to run doctest on the JAX backend run

pytest src/pyhf/tensor/jax_backend.py

Coverage#

To measure coverage for the codebase run the tests under coverage with

coverage run --module pytest

or pass coverage as a positional argument to the nox tests session

nox --session tests --python 3.12 -- coverage

Coverage Report#

To generate a coverage report after running the tests under coverage run

coverage

or to also generate XML and HTML versions of the report run the coverage nox session

nox --session coverage

Documentation#

To build the docs run

nox --session docs

To view the built docs locally, open the resulting docs/_build/html/index.html file in a web browser or run

nox --session docs -- serve

Publishing#

Publishing to TestPyPI and PyPI is automated through the PyPA’s PyPI publish GitHub Action and the pyhf bump version GitHub Actions workflow.

Release Checklist#

As part of the release process a checklist is required to be completed to make sure steps aren’t missed. There is a GitHub Issue template for this that the maintainer in charge of the release should step through and update if needed.

Release Tags#

A release tag can be created by a maintainer by using the bump version GitHub Actions workflow through workflow dispatch. The maintainer needs to:

  • Select the semantic versioning (SemVer) type (major, minor, patch) of the release tag.

  • Select if the release tag is a release candidate or not.

  • Input the SemVer version number of the release tag.

  • Select the branch to push the new release tag to.

  • Select if to override the SemVer compatibility of the previous options (default is to run checks).

  • Select if a dry run should be performed (default is to do a dry run to avoid accidental release tags).

The maintainer should do a dry run first to make sure everything looks reasonable. Once they have done that, they can run the bump version GitHub Actions workflow which will produce a new tag, bump the version of all files defined in tbump.toml, and then commit and push these changes and the tag back to the main branch.

Deployment#

The push of a tag to the repository will trigger a build of a sdist and wheel, and then the deployment of them to TestPyPI.

TestPyPI#

pyhf tests packaging and distribution by publishing to TestPyPI in advance of releases. Installation of the latest test release from TestPyPI can be tested by first installing pyhf normally, to ensure all dependencies are installed from PyPI, and then upgrading pyhf to a test release from TestPyPI

python -m pip install pyhf
python -m pip install --upgrade --extra-index-url https://test.pypi.org/simple/ --pre pyhf

Note

This adds TestPyPI as an additional package index to search when installing. PyPI will still be the default package index pip will attempt to install from for all dependencies, but if a package has a release on TestPyPI that is a more recent release then the package will be installed from TestPyPI instead. Note that dev releases are considered pre-releases, so 0.1.2 is a “newer” release than 0.1.2.dev3.

PyPI#

Once the TestPyPI deployment has been examined, installed, and tested locally by the maintainers final deployment to PyPI can be done by creating a GitHub Release:

  1. From the pyhf GitHub releases page select the “Draft a new release” button.

  2. Select the release tag that was just pushed, and set the release title to be the tag (e.g. v1.2.3).

  3. Use the “Auto-generate release notes” button to generate a skeleton of the release notes and then augment them with the preprepared release notes the release maintainer has written.

  4. Select “This is a pre-release” if the release is a release candidate.

  5. Select “Create a discussion for this release” if the release is a stable release.

  6. Select “Publish release”.

Once the release has been published to GitHub, the publishing workflow will build a sdist and wheel, and then deploy them to PyPI.

Context Files and Archive Metadata#

The .zenodo.json file has the version number automatically updated through tbump, though its additional metadata should be checked periodically by the dev team (probably every release).

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