Pyhf

Notes

This is the first `v0.7.0` release candidate and contains a **known** bugs related to `staterror` (Issue 1720) and `shapesys` correlation (Issue 1908) that were introduced after `v0.6.3`. While this is suitable for API testing, please wait for `v0.7.0rc2` before testing correctness or performance.

To install the release candidate you can either use [pip install's --pre flag](https://pip.pypa.io/en/stable/cli/pip_install/#cmdoption-pre)


python -m pip install --upgrade --pre pyhf


or specify the version number exactly


python -m pip install --upgrade 'pyhf==0.7.0rc1'


What's Changed
* fix: Update notebooks to use `include_auxdata` kwarg for `pyhf.Workspace.data` by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1588
* ci: Skip doctest for 'Minimum supported dependencies' workflow by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1589
* chore: [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1593
* docs: Correct v0.6.3 release notes to note `pyhf.pdf._ModelConfig.channels` is a list by RhnSharma in https://github.com/scikit-hep/pyhf/pull/1592
* ci: Add Python 3.9 to 'Current Release' workflow tests by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1596
* docs: Update maintainer release checklist with v0.6.3 notes by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1597
* ci: Use `jupyter-black` pre-commit hook over `nbqa-black` by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1598
* docs: Add use citation from publishing statistical models white paper by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1600
* docs: Add `uproot4` writing speedup to v0.6.3 release notes by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1601
* docs: Add use citation from collider signatures of coannihilating dark matter paper by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1604
* fix: Use MLEs of NPs to create sampling distributions in ToyCalculator by masonproffitt in https://github.com/scikit-hep/pyhf/pull/1610
* docs: Add use citation from simplified likelihoods ATLAS PUB note by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1614
* docs: Use sphinxcontrib-bibtex style 'unsrt' to sort citations in reverse chronological order by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1615
* chore: [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1616
* docs: Use sphinx-copybutton prompt regex to fully capture examples by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1617
* ci: Allow reporting of coverage on PRs from forks by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1622
* ci: Update codecov-action to v2 API by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1623
* ci: Report coverage to Codecov without token by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1628
* feat: Add hypotest kwargs to pyhf.infer.intervals.upperlimit by aryan26roy in https://github.com/scikit-hep/pyhf/pull/1613
* feat: Expose fitted parameter values of implicit fits in test statistic calls by lhenkelm in https://github.com/scikit-hep/pyhf/pull/1554
* ci: Add absolufy-imports pre-commit hook by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1635
* feat: Add setup for custom modifiers by lukasheinrich in https://github.com/scikit-hep/pyhf/pull/1625
* feat: Allow POI-less models via Workspace.model by kratsg in https://github.com/scikit-hep/pyhf/pull/1636
* fix: Fix bug in impact plot visualization by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1642
* feat: Add POI-less specification support by kratsg in https://github.com/scikit-hep/pyhf/pull/1638
* docs: Add and apply codespell as a pre-commit hook by alexander-held in https://github.com/scikit-hep/pyhf/pull/1645
* fix: custom modifier / new parameter support and test by lukasheinrich in https://github.com/scikit-hep/pyhf/pull/1644
* test: Use netlocs that are known to not exist or give known return by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1651
* feat: Add support for arrayful JSON by lukasheinrich in https://github.com/scikit-hep/pyhf/pull/1647
* test: Remove 'src' from pytest test testpaths to allow for non-editable install in CI by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1467
* feat: Allow zero rate Poisson by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1657
* ci: Add release candidates to HEAD of dependencies workflow by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1660
* feat: Configurable default backend by kratsg in https://github.com/scikit-hep/pyhf/pull/1646
* refactor: Simplified parameters by lukasheinrich in https://github.com/scikit-hep/pyhf/pull/1639
* ci: Turn off PyPI release tests on pull requests by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1664
* build: Set lower bound of scipy v1.1.0 by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1661
* build: Update lower bound on jax to v0.2.10 by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1666
* feat: Remove pyhf.simplemodels.hepdata_like from API by aryan26roy in https://github.com/scikit-hep/pyhf/pull/1670
* docs: Update 2021 published ATLAS probability models by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1671
* chore: [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1679
* refactor: Pass `Accept` header to requests in `contrib.utils.download` by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1673
* fix: Use https protocol as unauthenticated git protocol is no longer supported by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1680
* docs: Add ATLAS top group probability model records through June 2021 by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1681
* docs: Add ATLAS third-generation scalar leptoquarks search statistical model record by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1682
* fix: Speed-up readxml by caching key lookup instead of using try/except by kratsg in https://github.com/scikit-hep/pyhf/pull/1691
* feat: Add percentile function to tensorlib by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/817
* docs: only lists are accepted when specifying objects to prune by alexander-held in https://github.com/scikit-hep/pyhf/pull/1692
* feat: Add transpose function to tensorlib by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1696
* refactor: Use jax.numpy for JAX backend tensorlib.tolist by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1138
* refactor: Use tensorlib.percentile in calculators by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1694
* test: Use xfail for tests that fail for upstream problems by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1702
* build: Set only lower bounds on backend dependencies by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1698
* docs: Ensure docstring examples are contiguous by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1703
* refactor: Make contrib.utils.download robust to archive file types by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1697
* fix: Accept tar and zip headers in contrib.utils.download requests by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1704
* fix: Ensure `_ModelConfig.suggested_fixed` list contains only booleans for all modifiers by alexander-held in https://github.com/scikit-hep/pyhf/pull/1706
* ci: Quote GitHub Action python-version number as YAML strings by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1707
* feat: Raise exception if bin-wise modifier data length doesn't match sample data by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1708
* feat: Catch unexpected keyword arguments in workspace construction by alexander-held in https://github.com/scikit-hep/pyhf/pull/1709
* test: Use scikit-hep-testdata to provide probability models for regression tests by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1711
* fix: Skip doctest of `pyhf.contrib.utils.download` by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1715
* chore: Use constraints.txt for lower bound testing by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1713
* docs: Fix download method of probability models archive in impact plot notebook by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1721
* chore: [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1723
* docs: Fix download method of probability models archive in pull plot notebook by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1724
* feat: Allow skipping validation when constructing workspaces by alexander-held in https://github.com/scikit-hep/pyhf/pull/1710
* test: Make fail_backend markers add pytest.mark.xfail and remove fail_jax marker on percentile tests by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1730
* ci: Publish to TestPyPI on tag or by workflow dispatch trigger by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1727
* docs: Truncate floating point docstring examples to 8 decimal places by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1726
* docs: Add GitHub Release Radar check to release checklist by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1733
* docs: Update citation references publication status by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1738
* docs: Add milestone for 1000 project commits to README by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1739
* fix: Disallow nbsphinx v0.8.8 to avoid empty "raw" directive bug by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1742
* chore: [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1741
* docs: Note shapesys and staterror modifier set to 1 for modifier data of 0 by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1740
* ci: Limit concurrent workflow jobs to one per workflow per branch by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1632
* ci: Update gh-action-pypi-publish to use print_hash by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1743
* docs: Add use citation from revisiting mono-tau tails at the LHC paper by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1744
* fix: Accept ValueError for JAX backend `tolist` fallback by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1746
* ci: Launch tmate session if pytest fails on workflow dispatch run by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1748
* chore: Update black to first stable release v22.1.0 by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1754
* test: Avoid tensorflow macOS floating point deviation with pytest.approx by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1761
* ci: Add macos-latest to dependency release candidates testing by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1760
* docs: Update scipy intersphinx url to drop 'reference' by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1767
* chore: [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1765
* test: Add html coverage reports from pytest by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1771
* test: Consolidate and update pytest options in pyproject.toml by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1773
* docs: fix link to TRExFitter documentation by alexander-held in https://github.com/scikit-hep/pyhf/pull/1777
* docs: Add citation from 'HL-LHC Computing Review Stage 2' paper by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1779
* build: Require setuptools v42.0.0+ for stability by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1783
* build: Remove wheel and attrs from build-system requires by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1788
* docs: Add section for tutorial and docs to README by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1789
* feat: Use tbump over bump2version by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1790
* docs: Add general citation from MadJAX paper by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1799
* docs: Update Lukas's affiliation to Technical University of Munich by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1798
* docs: Add use citation from ATLAS UEH MS displaced jet paper by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1800
* docs: Correct Giordon's affiliation to SCIPP in CITATON.cff by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1801
* docs: Add use citation from ATLAS UEH displaced jets CalRatio paper by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1802
* docs: Fix tiny typo in MC Stat Error documentation by kratsg in https://github.com/scikit-hep/pyhf/pull/1803
* chore: [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1805
* refactor: Clarify exception message applies only to profile likelihood ratio by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1806
* ci: Add CPython 3.10 to testing by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1808
* build: Add support for Python 3.10 across all backends by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1809
* docs: Add use citation from neos paper by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1812
* docs: Update JAX backend normal docstring to jax v0.3.2 returns by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1813
* feat: Alternative Schema Locations by kratsg in https://github.com/scikit-hep/pyhf/pull/1753
* ci: Report coverage for oldest and newest Python tested by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1817
* fix: writexml handles missing parameter configs for normfactor by kratsg in https://github.com/scikit-hep/pyhf/pull/1819
* feat: Add contextlib support to pyhf.schema API by kratsg in https://github.com/scikit-hep/pyhf/pull/1818
* test: Assert exported StatError has no name attribute by kratsg in https://github.com/scikit-hep/pyhf/pull/1821
* fix: Disallow Jinja2 v3.1.0 to avoid nbsphinx triggering attribute error by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1824
* docs: Add JupyterLite REPL for interactive pyhf in docs by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1820
* fix: bump black to 22.3.0 due to click 8.1 release by henryiii in https://github.com/scikit-hep/pyhf/pull/1827
* ci: Use actions/setup-python v3 by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1828
* fix: Add filterwarnings ignore for Pillow DeprecationWarning by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1834
* ci: Update GitHub Actions to next stable version by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1833
* ci: Add matplotlib nightly wheels to HEAD of dependencies testing by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1835
* ci: Add concurrency group to HEAD of dependencies workflow by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1836
* revert: Remove Jinja2 restrictions given nbconvert v6.4.5 by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1837
* chore: [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1839
* fix: Override error on filterwarnings to pass notebook tests by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1841
* docs: Add general use citation from SimpleAnalysis ATLAS PUB note by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1842
* docs: Add general use citation from End-to-End Optimization paper by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1843
* docs: Add general use citation from Survey of Open Data Concepts paper by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1844
* ci: Add bump version workflow for release tags by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1846
* refactor: Deprecate distutils in favor of setuptools._distutils by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1849
* docs: Update developer documentation by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1847
* docs: Deprecate use of git.io URL shortener by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1851
* docs: Fix broken links identified by Sphinx linkcheck by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1854
* ci: Add sphinx linkcheck builder to docs build workflow by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1855
* chore: [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1859
* ci: Update ReadTheDocs build to Ubuntu 22.04 by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1860
* docs: Add use citation from strange quark probe Snowmass paper by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1861
* docs: Add use citation from ATLAS dE/dX long-lived particle paper by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1863
* feat: Allow readxml to demote validation exception to warning by kratsg in https://github.com/scikit-hep/pyhf/pull/1865
* docs: Clarify staterror modifier specification by Moelf in https://github.com/scikit-hep/pyhf/pull/1856
* test: Ignore LHEP DOI URLs during Sphinx linkcheck by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1866
* ci: Add semantic PR check GHA workflow by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1868
* test: Ignore EPJ Web of Conferences DOI URLs during Sphinx linkcheck by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1870
* test: Restrict tf dependency protobuf to ABI compatible releases by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1869
* build: Update lower bound on tensorflow to v2.6.5 by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1874
* fix: Allow for true_divide or divide `RuntimeWarning` from NumPy by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1873
* docs: Set English as language for Sphinx by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1875
* docs: Update Matthew's affiliation to University of Wisconsin-Madison by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1876
* ci: Add 'name-tests-test' to pre-commit hooks by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1877
* chore: [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1878
* ci: Use `github.workflow` property to ensure unique concurrency group by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1879
* build: Use `find_namespace:` to ensure discovery of package data by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1881
* build: Use `license_files` in setup.cfg by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1883
* feat: Allow for clipping negative yields in the main model by kratsg in https://github.com/scikit-hep/pyhf/pull/1845
* ci: Use '--pytest-test-first' option for naming clarity by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1892
* build: Update lower bound on iminuit to v2.7.0 by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1895
* docs: Add use citation from Audrey Kvam's Ph.D. thesis by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1896
* docs: Update use citations published in journals in June 2022 by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1897
* chore: Use actions/setup-python v4 by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1898
* ci: Enable Dependabot version updates for GitHub Actions by henryiii in https://github.com/scikit-hep/pyhf/pull/1900
* chore: Update Docker GitHub Actions to Dependabot bumped versions by matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1906
* build(deps): bump codecov/codecov-action from 2 to 3 by dependabot in https://github.com/scikit-hep/pyhf/pull/1903

New Contributors
* RhnSharma made their first contribution in https://github.com/scikit-hep/pyhf/pull/1592
* masonproffitt made their first contribution in https://github.com/scikit-hep/pyhf/pull/1610
* aryan26roy made their first contribution in https://github.com/scikit-hep/pyhf/pull/1613
* lhenkelm made their first contribution in https://github.com/scikit-hep/pyhf/pull/1554
* Moelf made their first contribution in https://github.com/scikit-hep/pyhf/pull/1856

**Full Changelog**: https://github.com/scikit-hep/pyhf/compare/v0.6.3...v0.7.0rc1

This is a patch release from `v0.6.2` → `v0.6.3`.

Important Notes

* With the addition of writing ROOT files in [`uproot` `v4.1.0`](https://github.com/scikit-hep/uproot4/releases/tag/4.1.0) the `xmlio` extra no longer requires `uproot3` and all dependencies on `uproot3` and `uproot3-methods` have been dropped. (PR #1567). `uproot4` additionally brings large speedups to writing, which results in an order of magnitude faster conversion time for most workspace conversions from JSON back to XML + ROOT with [`pyhf json2xml`](https://pyhf.readthedocs.io/en/v0.6.3/cli.html#pyhf-json2xml).
* All backends are now fully compatible and tested with [Python 3.9](https://www.python.org/dev/peps/pep-0596/). (PR #1574)
* The TensorFlow backend now supports compatibility with TensorFlow `v2.2.1` and later and TensorFlow Probability `v0.10.1` and later. (PR 1001)
* The [`pyhf.workspace.Workspace.data()`][pyhf.workspace.Workspace.data] `with_aux` keyword arg has been renamed to `include_auxdata` to improve API consistency. (PR 1562)

Fixes

* The weakref bug with Click `v8.0+` was resolved. `pyhf` is now fully compatible with Click `v7` and `v8` releases. (PR 1530)

Features

Python API

* Model parameter names are now propagated to optimizers through addition of the [`pyhf.pdf._ModelConfig.par_names()`][pyhf.pdf._ModelConfig.par_names] API. [`pyhf.pdf._ModelConfig.par_names()`][pyhf.pdf._ModelConfig.par_names] also handles non-scalar modifiers with 1 parameter. (PRs 1536, 1560)

python
>>> import pyhf
>>> model = pyhf.simplemodels.uncorrelated_background(
... signal=[12.0, 11.0], bkg=[50.0, 52.0], bkg_uncertainty=[3.0, 7.0]
... )
>>> model.config.parameters
['mu', 'uncorr_bkguncrt']
>>> model.config.npars
3
>>> model.config.par_names()
['mu', 'uncorr_bkguncrt[0]', 'uncorr_bkguncrt[1]']


* The [`pyhf.pdf._ModelConfig`][pyhf.pdf._ModelConfig] `channel_nbins` dict is now sorted by keys to match the order of the `channels` list. (PR 1546)

* The [`pyhf.workspace.Workspace.data()`][pyhf.workspace.Workspace.data] `with_aux` keyword arg has been renamed to `include_auxdata` to improve API consistency. (PR 1562)

[pyhf.workspace.Workspace.data]: https://pyhf.readthedocs.io/en/v0.6.3/_generated/pyhf.workspace.Workspace.html#pyhf.workspace.Workspace.data
[pyhf.pdf._ModelConfig.par_names]: https://pyhf.readthedocs.io/en/v0.6.3/_generated/pyhf.pdf._ModelConfig.html#pyhf.pdf._ModelConfig.par_names
[pyhf.pdf._ModelConfig]: https://pyhf.readthedocs.io/en/v0.6.3/_generated/pyhf.pdf._ModelConfig.html#pyhf.pdf._ModelConfig

Changes

* docs: Add v0.6.3 release notes (1583)
* docs: Update JAX backend poisson docstring to jax v0.2.20 returns (1584)
* docs: Fix links to existing issues for 'docs' and 'feat' labels (1582)
* docs: Use GitHub Issue forms as Issue templates (1576)
* feat: Add support for Python 3.9 across all backends (1574)
* fix: Ensure TensorFlow backend Poisson compatibility with other backends (1001)
* ci: Use Google Cloud Storage buckets for long term JAX wheel stability (1579)
* docs: Add use citations from vCHEP 2021 (1572)
* chore: Remove unnecessary str conversions of pathlib.Path objects (1568)
* feat: Drop uproot3 for uproot4 for writing ROOT files (1567)
* fix: Remove .dockerignore to give clean working tree during Docker build (1569)
* style: Update validation scripts to be more Pythonic (1565)
* feat: Rename kwarg with_aux to include_auxdata in pyhf.Workspace.data API (1562)
* ci: Check sdist and wheel listed contents with python -m CLI (1563)
* feat: par_names handles non-scalar modifiers with 1 parameter (1560)
* docs: Promote comments to docstring examples for pyhf.event (1556)
* fix: Remove WeakList in favor of built-ins (1530)
* chore: Define OS in base image tag of Dockerfile (1552)
* docs: Add CITATION.cff Citation File Format file (1551)
* refactor: Use absolute imports over explicit relative imports (1539)
* feat: Sort `_ChannelSummaryMixin.channel_nbins` by keys to match `channels` order (1546)
* docs: Separate citations into 'use' and 'general' (1540)
* chore: [pre-commit.ci] pre-commit autoupdate (1542)
* docs: Add citation from heavy neutral leptons neutrino oscillation model paper (1537)
* docs: Add project origin summary (1415)
* feat: Propagate model parameter names to optimizers (1536)
* fix: Use nightly SciPy wheels from Anaconda in HEAD of dependencies testing (1533)
* test: Temporarily move to testing against SciPy pre-releases (1532)
* fix: Unrestrict jaxlib upper bound and exclude jaxlib v0.1.68 (524)
* test: Remove tests of deprecated simplemodels.hepdata_like API (1521)
* chore: [pre-commit.ci] pre-commit autoupdate (1520)
* docs: Update citation for 'Charged Lepton Flavor Violation at the EIC' paper (1518)
* docs: Add release notes URL to PyPI project urls metadata (1512)
* test: Remove 32b test_minimize tests from optim tests (1504)
* fix: Temporarily restrict jaxlib to below v0.1.68 (1502)

* Alexander Held (alexander-held)

Changes:
- chore: Update codemeta softwareRequirements to match setup.cfg (1498)
- docs: Add v0.6.2 release notes (1495)
- docs: Add developer release checklist Issue template (1493)
- docs: Improve badge layout and fix broken Docker badge (1497)
- docs: Add squarks and gluinos search statistical model record (1496)
- ci: Remove distribution options to enable default build v0.5.0 behavior (1492)
- chore: Update pre-commit hooks versions and run order (1490)
- feat: Allow strings in patch values for patchset (1488)
- chore: Use tmpdir fixture over datadir in pyhf contrib download tests (1487)
- docs: Add use citation from ATLAS SUSY 3L+compressed combination paper (1483)
- chore: Add default virtual environment on PATH for Docker image (1484)
- chore: Use _version.py to follow setuptools_scm recommendations (1480)
- feat: Add 'contrib' extra to Docker images (1479)
- docs: Add use citation from Belle II in Moriond EW 2021 contribution (1475)
- chore: Use newer setuptools_scm for versioning (1450)
- fix: Do not configure logging in contrib.utils (1460)
- ci: Don't login to Docker container registries on PRs (1463)
- chore: Trial pip in-tree-build before release in pip 21.3 (1453)
- fix: Update to mathjax3_config to support math rendering in Sphinx v4.x+ (1457)
- build: Revise MANIFEST.in strategy to properly use prune (1449)
- feat: ROOT parameter name compatibility module (1439)
- ci: Publish Docker images to GitHub Container Registry (1444)
- ci: Set pre-commit.ci autoupdate schedule to monthly (1440)
- chore: [pre-commit.ci] pre-commit autoupdate (1445)
- refactor: Deprecate simplemodels.hepdata_like API for uncorrelated_background (1438)
- fix: Remove load option from Docker workflow publish steps (1442)
- ci: Update Docker workflow to build-push-action v2 (1441)
- fix: Remove trailing spaces in parameter names (1436)
- feat: Add correlated_background API to simplemodels (1435)
- ci: Add custom commit message for pre-commit.ci autoupdate (1432)
- docs: Add CERN Courier article to media listing (1429)
- chore: [pre-commit.ci] pre-commit autoupdate (1428)
- chore: Use module level __dir__ to restrict public API views (1403)
- docs: Add docstrings to _ModelConfig methods (1420)
- docs: Update software citation URL to Zenodo DOI (1424)
- docs: Add utils.citation to Python API docs (1419)
- docs: Add use citation from Belle II B⁺→ K⁺νν̅ decays search paper (1421)
- feat: Add CLs component plotting kwargs to contrib.viz.brazil.plot_results (1377)
- chore: Update Black to release v21.4b1 (1418)
- chore: Update Black to release v21.4b0 (1417)
- docs: Add use citation from single leptoquark B-physics anomalies paper (1416)
- feat: `pyhf patchset inspect` (1412)
- chore: Update flake8 and nbQA in pre-commit (1411)
- fix: check POIs floating (1409)
- chore: Update to pyupgrade v2.12.0 in pre-commit (1404)
- refactor: Set default precision to 64b (1400)
- fix: Ensure tensorlib precision used throughout TensorFlow backend (1399)
- fix: Stricter schema definitions for histosys and normsys (1388)
- chore: Update to nbQA v0.6.0 in pre-commit (1395)
- fix: Loosen iminuit tolerances for optimization tests (1306)
- feat: Use PyYAML's safe_load for better security (1383)
- build: Set only lower bounds on core dependencies (1382)
- ci: Simplify CodeQL scan setup (1384)
- chore: Ignore JAX tensor type in doctest (1379)
- ci: Upload coverage to Codecov in flagged stages for complete coverage report (1380)
- fix: Correct JAX tensor type in docstring (1375)
- fix: Set precision for ones and zeros through dtype arg (1369)
- chore: Update to pyupgrade 2.11.0 in pre-commit (1370)
- fix: Adjust sbottom region A regression test tolerance for GHA runner change (1364)
- chore: Update to flake8 3.9.0 in pre-commit (1363)

This is a patch release from `v0.6.0` → `v0.6.1`.

Important Notes

* As a result of changes to the default behavior of `torch.distributions` in PyTorch `v1.8.0`, accommodating changes have been made in the underlying implementations for [`pyhf.tensor.pytorch_backend.pytorch_backend`](https://pyhf.readthedocs.io/en/v0.6.1/_generated/pyhf.tensor.pytorch_backend.pytorch_backend.html#pyhf.tensor.pytorch_backend.pytorch_backend). These changes require a new lower bound of `torch` `v1.8.0` for use of the PyTorch backend.

Fixes

* In the PyTorch backend the `validate_args` kwarg is used with `torch.distributions` to ensure a continuous approximation of the Poisson distribution in `torch` `v1.8.0+`.

Features

Python API

* The `solver_options` kwarg can be passed to the [`pyhf.optimize.opt_scipy.scipy_optimizer`](https://pyhf.readthedocs.io/en/v0.6.1/_generated/pyhf.optimize.opt_scipy.scipy_optimizer.html#pyhf.optimize.opt_scipy.scipy_optimizer) optimizer for additional configuration of the minimization. See [`scipy.optimize.show_options`](https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.show_options.html#scipy.optimize.show_options) for additional options of optimization solvers.
* The `torch` API is now used to provide the implementations of the `ravel`, `tile`, and `outer` tensorlib methods for the PyTorch backend.

Changes

- docs: Add v0.6.1 release notes (1357)
- test: Test lower bounds of dependencies (1355)
- refactor: Use torch APIs for ravel, tile, and outer tensorlib methods (1354)
- ci: Run docs CI on push events only from PR merges (1353)
- docs: Add use citation for Artificial Proto-Modelling paper (1347)
- fix: Retain continuous approximation of Poisson in torch v1.8.0 (1351)
- docs: Add and apply blacken-docs as a pre-commit hook (1345)
- docs: Clarify and harmonize docstrings for fit parameters (1344)
- docs: Add record for published ATLAS likelihoods from November 2020 (1343)
- docs: Add use citation for wino and higgsino dark matter at muon collider (1340)
- feat: Solver options for scipy (1337)
- docs: Drop modifierclass and improve autosummary (1338)
- chore: Update to nbQA 0.5.9 in pre-commit (1333)
- docs: Update CONTRIBUTING.md to disincentivize 'drive by PRs' (1332)
- docs: Fix typo in Using Calculator learn notebook (1331)
- docs: Update ATLAS 3G tt 2L citation (1330)
- chore: Apply minor code quality revisions (1325)
- docs: Add use citations for QCD instantons and charged lepton flavor violation (1329)
- docs: Add CPython implementation and Python 3 only metadata (1324)
- docs: Update Zenodo BibTeX author field in citation in docs (1323)
- docs: Use more flexible BibTeX syntax for Zenodo DOI (1322)
- docs: Add dropping of Python 3.6 support to v0.6.0 release notes (1317)
- chore: Update codemeta to include v0.6.0 software requirements (1318)
- docs: Correct typos in v0.6.0 release notes (1316)

* Alexander Held
* Marco Gorelli
* Pradyumna Rahul K
* Eric Schanet
* Henry Schreiner

Changes:
- docs: Add v0.6.0 release notes (1314)
- docs: Update API in notebooks to v0.6.0 (1312)
- fix: Make p-value-like values 0-d tensors (1311)
- feat: Add kwarg for AsymptoticCalculator base distribution (993)
- docs: Add release notes to website (1304)
- fix: Restrict iminuit to compatible releases below 2.4.0 (1307)
- build: Drop support for Python 3.6 (1272)
- build: Update minimum required tqdm release to avoid repr crash (1302)
- docs: Add syntax highlighting for bash snippets (1300)
- ci: Update PyPI publish GitHub Action to v1.4.2 (1299)
- chore: Update to pyupgrade 2.10.0 in pre-commit (1298)
- docs: Add use citation from MadAnalysis 5 workshop (1297)
- fix: Make wheel naming indicate wheels are not Python 2 compatible (1295)
- docs: Widen the content box of docs (1292)
- docs: Add JOSS paper to preferred citation and DOI Badge (1291)
- ci: Drop GESIS from Binder trigger (1293)
- docs: Make 'Statement of Need' explicit section in JOSS paper (1290)
- docs: Correct TestPyPI install instructions (1289)
- docs: Add warning banners for dev versions on docs (1288)
- docs: Make docs badge link to latest stable version on ReadTheDocs (1287)
- docs: Redirect questions to GitHub Discussions (1283)
- chore: Update to pyupgrade 2.9.0 and nbQA v0.5.7 in pre-commit (1282)
- docs: Explicitly give version number in JOSS paper (1280)
- feat: Provide support for returning correlations from minuit (988)
- fix: Model.spec should be self-consistent and reproducible (1281)
- ci: Add pre-commit hooks from pre-commit-hooks recommended by Scikit-HEP (1276)
- docs: Add JOSS paper (1089)
- docs: Add commas to infer.mle.fixed_poi_fit docstring for clarity (1273)
- fix: Report expected p-values based on their quantiles under background hypotheses (1162)
- docs: Update README to address JOSS reviewer changes (1266)
- feat: Add discovery p0 test statistic (1232)
- docs: Add Symmetry Magazine article on likelihood publication (1263)
- docs: Add learn notebook on using calculators (1258)
- chore: Remove duplicated and unused dependencies (1261)
- docs: Build docs with sphinx-build via Sphinx Makefile (1257)
- docs: Use sphinxcontrib-bibtex v2.1 and bibtex_bibfiles setting (1221)
- docs: Add talks and use citations from 2020 (1254)
- fix: Don't use exact assert for test_probability.py (1252)
- docs: Fix data ordering bug in ShapeFactor (1245)
- docs: Fix math mode syntax in contrib.viz.brazil.plot_results docstring (1243)
- docs: Add readxml and writexml (1242)
- build: Begin move to uproot4 (1002)
- feat: Add to_numpy API to tensorlib (1226)
- feat: Use iminuit v2.0 API (1208)
- chore: Update to nbQA v0.5.6 in pre-commit (1240)
- feat: Test statistic specified by string instead of using qtilde kwarg (1231)
- refactor: Clean up docstrings and remove qtilde from hypotest (1230)
- build: Use compatible release syntax to give ranges for install_requires (1229)
- fix: Control utils.py docstring example with .bumpversion.cfg (1218)
- ci: Uninstall dependencies before installed HEAD versions (1227)
- chore: Update to nbQA v0.5.5 in pre-commit (1222)
- fix: Ensure pytest.approx only compares floats (1220)
- docs: Link to conda-forge feedstock and link banner to repo (1217)
- chore: Use exc_info in log.error, re-raise last exceptions (1209)
- feat: Add utility to get software citation and CLI interface (1210)
- chore: Update nbQA in pre-commit (1207)
- fix: Update JAX DeviceArray type in docstrings for doctest (1206)
- ci: Test only latest Python runtime on MacOS (1203)
- feat: Use iminuit v1.5.X API (1202)
- docs: Correct spelling of continuous (1201)
- chore: Specify exceptions to remove inline ignores of E722 (1194)
- chore: Update nbQA in pre-commit (1199)
- fix: Use uproot3-methods with uproot3 (1200)
- test: Verify NLL values and Minuit parameter uncertainties (1197)
- chore: Use flake8 for linting (1191)
- fix: Use uproot3 namespace (1192)
- chore: Update nbQA in pre-commit (1190)
- refactor: Drop 'modifier' from parameter set requirements (1189)
- fix: Isolate pyhf contrib commands from rest of CLI (1186)
- feat: Configurable optimizer tolerance for termination (1184)
- docs: Add CHEP 2019 proceedings use citation (1185)
- feat: Set minuit strategy automatically for gradient/non-gradient mode (1183)
- docs: Add ATLAS SUSY+Exotics Tutorial (1181)
- fix: Ensure float-like values used in division in writexml (1179)
- chore: Update pyupgrade and nbQA in pre-commit (1178)
- feat: Add default axis labels to contrib.viz.brazil.plot_results (1176)
- fix: Pin additional dependencies in pre-commit hooks (1167)
- feat: Add nbQA to pre-commit hooks (1165)
- chore: Run pyupgrade on codebase (3.6+) (1164)
- feat: Add toy calculator, empirical distribution, and toy example notebook (790)
- feat: Update model and inference defaults (1114)
- feat: Tensorlib ravel functionality (1147)

uproot 4.0.0
uproot3 3.14.1