v0.7.0rc1

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

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

New Contributors

• @RhnSharma made their first contribution in #1592
• @masonproffitt made their first contribution in #1610
• @aryan26roy made their first contribution in #1613
• @lhenkelm made their first contribution in #1554
• @Moelf made their first contribution in #1856

Full Changelog: v0.6.3...v0.7.0rc1