v0.7.0

[matthewfeickert]

This is a minor release from v0.6.3 → v0.7.0.

Important Notes

• Please note this release has API breaking changes and carefully read these notes while updating your code to the v0.7.0 API.

• All backends are now fully compatible and tested with Python 3.10. (PR build: Add support for Python 3.10 across all backends #1809)

• The pyhf.tensorlib.poisson API now allows for the expected rate parameter lam to be 0 in the case that the observed events n is 0 given that the limit $$\lim_{\lambda \to 0} ,\mathrm{Pois}(n | \lambda)$$ is well defined. (PR feat: Allow zero rate Poisson  #1657)

• pyhf.readxml.parse now supports reading of XML configurations with absolute paths. To support this, pyhf xlm2json now has a -v/--mount option. (PR feat: Handle absolute paths in XML config files (xml2json / readxml) #1909)

• Support for model specifications without a parameter of interest defined is added. (PRs feat: Add POI-less specification support #1638, feat: Allow POI-less models via Workspace.model #1636)

• The pyhf.parameters.paramsets classes suggested_fixed attribute behavior has been updated. To access the behavior used in pyhf v0.6.x use the suggested_fixed_as_bool attribute. (PR refactor: Simplified parameters #1639)

• pyhf.pdf._ModelConfig.par_names is changed to be a property attribute. (PR feat: Make par_names a _ModelConfig property attribute #2027)

• The order of model parameters is now sorted by model parameter name. (PR feat: Add setup for custom modifiers #1625)

• Support for writing user custom modifiers is added. (PRs feat: Add setup for custom modifiers #1625, fix: custom modifier / new parameter support and test #1644)

• Performance in pyhf.readxml is increased by improvements to pyhf.readxml.import_root_histogram. (PR fix: Speed-up readxml by caching key lookup instead of using try/except #1691)

• pyhf.contrib.utils.download is now more robust to different target file types. (PRs refactor: Make contrib.utils.download robust to archive file types #1697, fix: Accept tar and zip headers in contrib.utils.download requests #1704)

• A pyhf.default_backend has been added that is configurable through a default kwarg in pyhf.set_backend. (PR feat: Configurable default backend #1646) This is part of work to make pyhf fully automatic differentiable. (Issue Making pyhf differentiable #882)

• Schema validation now allows for both list and pyhf.tensorlib objects to exist in the model specification. (PR feat: Add support for arrayful JSON #1647)

• The minimum required dependencies have been updated to support added features:

  • scipy>=1.2.0 (PR feat: Add autoscan for upper limit using TOMS Algorithm 748 #1274)
  • click>=8.0.0 (PRs feat: Handle absolute paths in XML config files (xml2json / readxml) #1909, build: Update lower bound of click to v8.0.0 #1958)
  • jsonschema>=4.15.0 (PRs fix: Base URI for jsonschema.RefResolver has better behavior #1976, build: Update lower bounds to jsonschema v4.15.0, importlib-resources v1.4.0 #1979)
  • importlib_resources>=1.4.0 (for Python 3.7, 3.8) (PR build: Update lower bounds to jsonschema v4.15.0, importlib-resources v1.4.0 #1979)
  • typing_extensions>=3.7.4.3 (for Python 3.7 only) (PRs feat: Add typehints to pyhf.tensor #1940, build: Update lower bound of typing-extensions to v3.7.4.3 #1961)

• The minimum required backend versions have been updated to support added features:

  • JAX backend requires jax>=0.2.10, jaxlib>=0.1.61 (PR build: Update lower bounds to tensorflow v2.7.0, jaxlib v0.1.61 #1962)
  • PyTorch backend requires torch>=1.10.0 (PR feat: Allow zero rate Poisson  #1657)
  • TensorFlow backend requires tensorflow>=2.7.0, tensorflow-probability>=0.11.0 (PRs build: Update lower bounds to tensorflow v2.7.0, jaxlib v0.1.61 #1962, feat: Allow zero rate Poisson  #1657)
  • iminuit optimizer requires iminuit>=2.7.0 (PR build: Update lower bound on iminuit to v2.7.0  #1895)
  • 'xmlio' extra requires uproot>=4.1.1 (PR feat: Drop uproot3 for uproot4 for writing ROOT files #1567)

Fixes

• Use improvements to jsonschema.RefResolver to avoid jsonschema.exceptions.RefResolutionError. (PR fix: Base URI for jsonschema.RefResolver has better behavior #1976)

• Use the conditional maximum likelihood estimators of the nuisance parameters to create the sampling distributions for pyhf.infer.calculators.ToyCalculator. (PR fix: Use MLEs of NPs to create sampling distributions in ToyCalculator #1610) This follows the joint recommendations of the ATLAS and CMS experiments in Procedure for the LHC Higgs boson search combination in Summer 2011.

Features

Python API

• The following functions have been added to the pyhf.tensorlib API:

  • pyhf.tensorlib.transpose (PR feat: Add transpose function to tensorlib #1696)
  • pyhf.tensorlib.percentile (PR feat: Add percentile function to tensorlib #817)

• pyhf.readxml.parse now supports reading of XML configurations with absolute paths with the addition of the mounts optional argument. (PR feat: Handle absolute paths in XML config files (xml2json / readxml) #1909)

• Support for overriding the paths for finding schemas is added, using the pyhf installed location as a base via pyhf.utils.schemas. (PRs feat: Alternative Schema Locations #1753, feat: Add contextlib support to pyhf.schema API #1818)

    >>> from pathlib import Path
    >>> import pyhf.schema
    >>> current_schema_path = pyhf.schema.path
    >>> current_schema_path
    PosixPath('/path/to/your/venv/lib/python3.X/site-packages/pyhf/schemas')
    >>> custom_schema_path = Path("/path/to/custom/pyhf/schema")
    >>> with pyhf.schema(custom_schema_path):
    ...     print(repr(pyhf.schema.path))
    ...
    PosixPath('/path/to/custom/pyhf/schema')
    >>> pyhf.schema.path
    PosixPath('/path/to/your/venv/lib/python3.X/site-packages/pyhf/schemas')

• In pyhf.workspace.Workspace.model the parameter of interest specified in the measurement may now be overridden using the added poi_name kwarg. (PR feat: Allow POI-less models via Workspace.model #1636)

• The pyhf.parameters.paramsets classes suggested_fixed attribute behavior has been updated to return a list of bool of length n_parameters. To access the behavior used in pyhf v0.6.x use the suggested_fixed_as_bool attribute. (PR refactor: Simplified parameters #1639)

• pyhf.pdf._ModelConfig.par_names is changed to be a property attribute. (PR feat: Make par_names a _ModelConfig property attribute #2027)

• The order of model parameters is now sorted by model parameter name. (PR feat: Add setup for custom modifiers #1625)

    >>> import pyhf
    >>> model = pyhf.simplemodels.correlated_background(
    ...     signal=[12.0, 11.0],
    ...     bkg=[50.0, 52.0],
    ...     bkg_up=[45.0, 57.0],
    ...     bkg_down=[55.0, 47.0],
    ... )
    >>> model.config.par_order
    ['correlated_bkg_uncertainty', 'mu']
    >>> model.config.par_names
    ['correlated_bkg_uncertainty', 'mu']

• Support for writing user custom modifiers is added.
  (PRs feat: Add setup for custom modifiers #1625, fix: custom modifier / new parameter support and test #1644) This is still in the stage where it is targeted at expert users.

• {modifier}_builder classes are added for all modifiers. (PRs feat: Add setup for custom modifiers #1625) For example, pyhf.modifiers.histosys.histosys_builder.

• When using pyhf.writexml and the normfactor parameter config is missing inits or bounds, fall back to using default values. (PRs fix: writexml handles missing parameter configs for normfactor #1819)

• Supported options for pyhf.infer.hypotest can now be passed as kwargs through the pyhf.infer.intervals.upper_limits.upper_limit API. (PR feat: Add hypotest kwargs to pyhf.infer.intervals.upperlimit #1613) This now enables things like using pyhf.infer.calculators.ToyCalculator as the calculator used for the hypothesis test scan:

    >>> import numpy as np
    >>> import pyhf
    >>> pyhf.set_backend("jax")
    >>> model = pyhf.simplemodels.uncorrelated_background(
    ...     signal=[12.0, 11.0], bkg=[50.0, 52.0], bkg_uncertainty=[3.0, 7.0]
    ... )
    >>> observations = [51, 48]
    >>> data = pyhf.tensorlib.astensor(observations + model.config.auxdata)
    >>> scan = np.linspace(0, 5, 21)
    >>> obs_limit, exp_limits, (scan, results) = pyhf.infer.intervals.upper_limits.upper_limit(
    ...     data, model, scan, return_results=True, calctype="toybased", ntoys=3000
    ... )

• Allow for fit parameter values from required fits in pyhf.infer.test_statistics functions to be returned by use of return_fitted_pars kwarg with the pyhf.infer.test_statistics functions and return_calculator kwarg with pyhf.infer.hypotest. (PR feat: Expose fitted parameter values of implicit fits in test statistic calls #1554)

• A validate kwarg has been added to pyhf.workspace.Workspace and
  pyhf.pdf.Model to allow skipping validation. (PR feat: Configurable default backend #1646) This should only be used by expert users who understand the risks.

• A pyhf.default_backend has been added that is configurable through a default kwarg in pyhf.set_backend. (PR feat: Configurable default backend #1646) This allows setting the pyhf.default_backend to be different from the value of pyhf.tensorlib returned by pyhf.get_backend, which can be useful in situations where differentiable model construction is needed.

    >>> import jax
    >>> import pyhf
    >>> pyhf.set_backend("jax", default=True)
    >>> pyhf.set_backend("numpy")
    >>> pyhf.get_backend()
    (<pyhf.tensor.numpy_backend.numpy_backend object at 0x...>, <pyhf.optimize.scipy_optimizer object at 0x...>)
    >>> pyhf.default_backend
    <pyhf.tensor.jax_backend.jax_backend object at 0x...>
    >>> def example_op(x):
    ...     return 2 * pyhf.default_backend.power(pyhf.default_backend.astensor(x), 3)
    ...
    >>> example_op([2.0])
    DeviceArray([16.], dtype=float64)
    >>> jax.jacrev(jax.jit(example_op))([2.0])
    [DeviceArray([24.], dtype=float64, weak_type=True)]

• Schema validation now allows for both list and pyhf.tensorlib objects to exist in the model specification. (PR feat: Add support for arrayful JSON #1647)

      >>> import pyhf
      >>> signal = pyhf.tensorlib.astensor([12.0, 11.0])
      >>> background = pyhf.tensorlib.astensor([50.0, 52.0])
      >>> background_uncertainty = pyhf.tensorlib.astensor([3.0, 7.0])
      >>> model = pyhf.simplemodels.uncorrelated_background(
      ...     signal=signal, bkg=background, bkg_uncertainty=background_uncertainty
      ... )

CLI API

• The pyhf xlm2json CLI API now has a -v/--mount option to support reading XML configurations with absolute paths. (PR feat: Handle absolute paths in XML config files (xml2json / readxml) #1909) Similar to Docker volume mounts, the options allows a user to pass two fields separated by a colon (:). The first field is a local path and the second field is the absolute path specified in the XML configuration to be substituted. Without the -v/--mount` option a user would have to manually edit the absolute path in each XML file it appeared in!

  pyhf xml2json \
      --mount /local/path/to/workspace:/absolute/path/to/replace/inside/xml \
      --output-file workspace.json \
      workspace/analysis_config.xml

Deprecations

Python API

• The pyhf.infer.intervals.upperlimit API has been deprecated in favor of
  pyhf.infer.intervals.upper_limits.upper_limit.
  The pyhf.infer.intervals.upperlimit API will removed in pyhf v0.9.0.
  (PR feat: Add autoscan for upper limit using TOMS Algorithm 748 #1274)

Removals

Python API

• The pyhf.simplemodels.hepdata_like API, deprecated since pyhf
v0.6.2, has been removed.
  (PR feat: Remove pyhf.simplemodels.hepdata_like from API #1670)
  Use the pyhf.simplemodels.uncorrelated_background API instead.

• pyhf.workspace.Workspace's parameters attribute is removed in favor of
  using pyhf.pdf._ModelConfig's parameters.
  (PR feat: Add setup for custom modifiers #1625)

• pyhf.workspace.Workspace.get_measurement has the poi_name kwarg removed.
  (PR feat: Allow POI-less models via Workspace.model #1636)

Contributors

v0.7.0 benefited from contributions from:

• Alexander Held
• Mason Proffitt
• Lars Henkelmann
• Aryan Roy
• Graeme Watt
• Jerry Ling
• Nathan Simpson
• Beojan Stanislaus

Changes

• fix: Update notebooks to use include_auxdata kwarg for pyhf.Workspace.data by @matthewfeickert in fix: Update notebooks to use include_auxdata kwarg for pyhf.Workspace.data #1588
• ci: Skip doctest for 'Minimum supported dependencies' workflow by @matthewfeickert in ci: Skip doctest for 'Minimum supported dependencies' workflow #1589
• chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in chore: [pre-commit.ci] pre-commit autoupdate #1593
• docs: Correct v0.6.3 release notes to note pyhf.pdf._ModelConfig.channels is a list by @RhnSharma in docs: Correct v0.6.3 release notes to note pyhf.pdf._ModelConfig.channels is a list #1592
• ci: Add Python 3.9 to 'Current Release' workflow tests by @matthewfeickert in ci: Add Python 3.9 to 'Current Release' workflow tests #1596
• docs: Update maintainer release checklist with v0.6.3 notes by @matthewfeickert in docs: Update maintainer release checklist with v0.6.3 notes #1597
• ci: Use jupyter-black pre-commit hook over nbqa-black by @matthewfeickert in ci: Use jupyter-black pre-commit hook over nbqa-black #1598
• docs: Add use citation from publishing statistical models white paper by @matthewfeickert in docs: Add use citation from publishing statistical models white paper #1600
• docs: Add uproot4 writing speedup to v0.6.3 release notes by @matthewfeickert in docs: Add uproot4 writing speedup to v0.6.3 release notes #1601
• docs: Add use citation from collider signatures of coannihilating dark matter paper by @matthewfeickert in docs: Add use citation from collider signatures of coannihilating dark matter paper #1604
• fix: Use MLEs of NPs to create sampling distributions in ToyCalculator by @masonproffitt in fix: Use MLEs of NPs to create sampling distributions in ToyCalculator #1610
• docs: Add use citation from simplified likelihoods ATLAS PUB note by @matthewfeickert in docs: Add use citation from simplified likelihoods ATLAS PUB note #1614
• docs: Use sphinxcontrib-bibtex style 'unsrt' to sort citations in reverse chronological order by @matthewfeickert in docs: Use sphinxcontrib-bibtex style 'unsrt' to sort citations in reverse chronological order #1615
• chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in chore: [pre-commit.ci] pre-commit autoupdate #1616
• docs: Use sphinx-copybutton prompt regex to fully capture examples by @matthewfeickert in docs: Use sphinx-copybutton prompt regex to fully capture examples #1617
• ci: Allow reporting of coverage on PRs from forks by @matthewfeickert in ci: Allow reporting of coverage on PRs from forks #1622
• ci: Update codecov-action to v2 API by @matthewfeickert in ci: Update codecov-action to v2 API #1623
• ci: Report coverage to Codecov without token by @matthewfeickert in ci: Report coverage to Codecov without token #1628
• feat: Add hypotest kwargs to pyhf.infer.intervals.upperlimit by @aryan26roy in feat: Add hypotest kwargs to pyhf.infer.intervals.upperlimit #1613
• feat: Expose fitted parameter values of implicit fits in test statistic calls by @lhenkelm in feat: Expose fitted parameter values of implicit fits in test statistic calls #1554
• ci: Add absolufy-imports pre-commit hook by @matthewfeickert in ci: Add absolufy-imports pre-commit hook #1635
• feat: Add setup for custom modifiers by @lukasheinrich in feat: Add setup for custom modifiers #1625
• feat: Allow POI-less models via Workspace.model by @kratsg in feat: Allow POI-less models via Workspace.model #1636
• fix: Fix bug in impact plot visualization by @matthewfeickert in fix: Fix bug in impact plot visualization #1642
• feat: Add POI-less specification support by @kratsg in feat: Add POI-less specification support #1638
• docs: Add and apply codespell as a pre-commit hook by @alexander-held in docs: Add and apply codespell as a pre-commit hook #1645
• fix: custom modifier / new parameter support and test by @lukasheinrich in fix: custom modifier / new parameter support and test #1644
• test: Use netlocs that are known to not exist or give known return by @matthewfeickert in test: Use netlocs that are known to not exist or give known return #1651
• feat: Add support for arrayful JSON by @lukasheinrich in feat: Add support for arrayful JSON #1647
• test: Remove 'src' from pytest test testpaths to allow for non-editable install in CI by @matthewfeickert in test: Remove 'src' from pytest test testpaths to allow for non-editable install in CI #1467
• feat: Allow zero rate Poisson by @matthewfeickert in feat: Allow zero rate Poisson  #1657
• ci: Add release candidates to HEAD of dependencies workflow by @matthewfeickert in ci: Add release candidates to HEAD of dependencies workflow #1660
• feat: Configurable default backend by @kratsg in feat: Configurable default backend #1646
• refactor: Simplified parameters by @lukasheinrich in refactor: Simplified parameters #1639
• ci: Turn off PyPI release tests on pull requests by @matthewfeickert in ci: Turn off PyPI release tests on pull requests #1664
• build: Set lower bound of scipy v1.1.0 by @matthewfeickert in build: Set lower bound of scipy v1.1.0 #1661
• build: Update lower bound on jax to v0.2.10 by @matthewfeickert in build: Update lower bound on jax to v0.2.10 #1666
• feat: Remove pyhf.simplemodels.hepdata_like from API by @aryan26roy in feat: Remove pyhf.simplemodels.hepdata_like from API #1670
• docs: Update 2021 published ATLAS probability models by @matthewfeickert in docs: Update 2021 published ATLAS probability models #1671
• chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in chore: [pre-commit.ci] pre-commit autoupdate #1679
• refactor: Pass Accept header to requests in contrib.utils.download by @matthewfeickert in refactor: Pass Accept header to requests in contrib.utils.download #1673
• fix: Use https protocol as unauthenticated git protocol is no longer supported by @matthewfeickert in fix: Use https protocol as unauthenticated git protocol is no longer supported #1680
• docs: Add ATLAS top group probability model records through June 2021 by @matthewfeickert in docs: Add ATLAS top group probability model records through June 2021 #1681
• docs: Add ATLAS third-generation scalar leptoquarks search statistical model record by @matthewfeickert in docs: Add ATLAS third-generation scalar leptoquarks search statistical model record #1682
• fix: Speed-up readxml by caching key lookup instead of using try/except by @kratsg in fix: Speed-up readxml by caching key lookup instead of using try/except #1691
• feat: Add percentile function to tensorlib by @matthewfeickert in feat: Add percentile function to tensorlib #817
• docs: only lists are accepted when specifying objects to prune by @alexander-held in docs: only lists are accepted when specifying objects to prune #1692
• feat: Add transpose function to tensorlib by @matthewfeickert in feat: Add transpose function to tensorlib #1696
• refactor: Use jax.numpy for JAX backend tensorlib.tolist by @matthewfeickert in refactor: Use jax.numpy for JAX backend tensorlib.tolist #1138
• refactor: Use tensorlib.percentile in calculators by @matthewfeickert in refactor: Use tensorlib.percentile in calculators #1694
• test: Use xfail for tests that fail for upstream problems by @matthewfeickert in test: Use xfail for tests that fail for upstream problems #1702
• build: Set only lower bounds on backend dependencies by @matthewfeickert in build: Set only lower bounds on backend dependencies #1698
• docs: Ensure docstring examples are contiguous by @matthewfeickert in docs: Ensure docstring examples are contiguous #1703
• refactor: Make contrib.utils.download robust to archive file types by @matthewfeickert in refactor: Make contrib.utils.download robust to archive file types #1697
• fix: Accept tar and zip headers in contrib.utils.download requests by @matthewfeickert in fix: Accept tar and zip headers in contrib.utils.download requests #1704
• fix: Ensure _ModelConfig.suggested_fixed list contains only booleans for all modifiers by @alexander-held in fix: Ensure _ModelConfig.suggested_fixed list contains only booleans for all modifiers #1706
• ci: Quote GitHub Action python-version number as YAML strings by @matthewfeickert in ci: Quote GitHub Action python-version number as YAML strings #1707
• feat: Raise exception if bin-wise modifier data length doesn't match sample data by @matthewfeickert in feat: Raise exception if bin-wise modifier data length doesn't match sample data #1708
• feat: Catch unexpected keyword arguments in workspace construction by @alexander-held in feat: Catch unexpected keyword arguments in workspace construction #1709
• test: Use scikit-hep-testdata to provide probability models for regression tests by @matthewfeickert in test: Use scikit-hep-testdata to provide probability models for regression tests #1711
• fix: Skip doctest of pyhf.contrib.utils.download by @matthewfeickert in fix: Skip doctest of pyhf.contrib.utils.download #1715
• chore: Use constraints.txt for lower bound testing by @matthewfeickert in chore: Use constraints.txt for lower bound testing #1713
• docs: Fix download method of probability models archive in impact plot notebook by @matthewfeickert in docs: Fix download method of probability models archive in impact plot notebook #1721
• chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in chore: [pre-commit.ci] pre-commit autoupdate #1723
• docs: Fix download method of probability models archive in pull plot notebook by @matthewfeickert in docs: Fix download method of probability models archive in pull plot notebook #1724
• feat: Allow skipping validation when constructing workspaces by @alexander-held in feat: Allow skipping validation when constructing workspaces #1710
• test: Make fail_backend markers add pytest.mark.xfail and remove fail_jax marker on percentile tests by @matthewfeickert in test: Make fail_backend markers add pytest.mark.xfail and remove fail_jax marker on percentile tests #1730
• ci: Publish to TestPyPI on tag or by workflow dispatch trigger by @matthewfeickert in ci: Publish to TestPyPI on tag or by workflow dispatch trigger #1727
• docs: Truncate floating point docstring examples to 8 decimal places by @matthewfeickert in docs: Truncate floating point docstring examples to 8 decimal places #1726
• docs: Add GitHub Release Radar check to release checklist by @matthewfeickert in docs: Add GitHub Release Radar check to release checklist #1733
• docs: Update citation references publication status by @matthewfeickert in docs: Update citation references publication status #1738
• docs: Add milestone for 1000 project commits to README by @matthewfeickert in docs: Add milestone for 1000 project commits to README #1739
• fix: Disallow nbsphinx v0.8.8 to avoid empty "raw" directive bug by @matthewfeickert in fix: Disallow nbsphinx v0.8.8 to avoid empty "raw" directive bug #1742
• chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in chore: [pre-commit.ci] pre-commit autoupdate #1741
• docs: Note shapesys and staterror modifier set to 1 for modifier data of 0 by @matthewfeickert in docs: Note shapesys and staterror modifier set to 1 for modifier data of 0 #1740
• ci: Limit concurrent workflow jobs to one per workflow per branch by @matthewfeickert in ci: Limit concurrent workflow jobs to one per workflow per branch #1632
• ci: Update gh-action-pypi-publish to use print_hash by @matthewfeickert in ci: Update gh-action-pypi-publish to use print_hash #1743
• docs: Add use citation from revisiting mono-tau tails at the LHC paper by @matthewfeickert in docs: Add use citation from revisiting mono-tau tails at the LHC paper #1744
• fix: Accept ValueError for JAX backend tolist fallback by @matthewfeickert in fix: Accept ValueError for JAX backend tolist fallback #1746
• ci: Launch tmate session if pytest fails on workflow dispatch run by @matthewfeickert in ci: Launch tmate session if pytest fails on workflow dispatch run #1748
• chore: Update black to first stable release v22.1.0 by @matthewfeickert in chore: Update black to first stable release v22.1.0 #1754
• test: Avoid tensorflow macOS floating point deviation with pytest.approx by @matthewfeickert in test: Avoid tensorflow macOS floating point deviation with pytest.approx #1761
• ci: Add macos-latest to dependency release candidates testing by @matthewfeickert in ci: Add macos-latest to dependency release candidates testing #1760
• docs: Update scipy intersphinx url to drop 'reference' by @matthewfeickert in docs: Update scipy intersphinx url to drop 'reference' #1767
• chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in chore: [pre-commit.ci] pre-commit autoupdate #1765
• test: Add html coverage reports from pytest by @matthewfeickert in test: Add html coverage reports from pytest #1771
• test: Consolidate and update pytest options in pyproject.toml by @matthewfeickert in test: Consolidate and update pytest options in pyproject.toml #1773
• docs: fix link to TRExFitter documentation by @alexander-held in docs: fix link to TRExFitter documentation #1777
• docs: Add citation from 'HL-LHC Computing Review Stage 2' paper by @matthewfeickert in docs: Add citation from 'HL-LHC Computing Review Stage 2' paper #1779
• build: Require setuptools v42.0.0+ for stability by @matthewfeickert in build: Require setuptools v42.0.0+ for stability #1783
• build: Remove wheel and attrs from build-system requires by @matthewfeickert in build: Remove wheel and attrs from build-system requires #1788
• docs: Add section for tutorial and docs to README by @matthewfeickert in docs: Add section for tutorial and docs to README #1789
• feat: Use tbump over bump2version by @matthewfeickert in feat: Use tbump over bump2version #1790
• docs: Add general citation from MadJAX paper by @matthewfeickert in docs: Add general citation from MadJAX paper #1799
• docs: Update Lukas's affiliation to Technical University of Munich by @matthewfeickert in docs: Update Lukas's affiliation to Technical University of Munich #1798
• docs: Add use citation from ATLAS UEH MS displaced jet paper by @matthewfeickert in docs: Add use citation from ATLAS UEH MS displaced jet paper #1800
• docs: Correct Giordon's affiliation to SCIPP in CITATON.cff by @matthewfeickert in docs: Correct Giordon's affiliation to SCIPP in CITATON.cff #1801
• docs: Add use citation from ATLAS UEH displaced jets CalRatio paper by @matthewfeickert in docs: Add use citation from ATLAS UEH displaced jets CalRatio paper #1802
• docs: Fix tiny typo in MC Stat Error documentation by @kratsg in docs: Fix tiny typo in MC Stat Error documentation #1803
• chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in chore: [pre-commit.ci] pre-commit autoupdate #1805
• refactor: Clarify exception message applies only to profile likelihood ratio by @matthewfeickert in refactor: Clarify exception message applies only to profile likelihood ratio #1806
• ci: Add CPython 3.10 to testing by @matthewfeickert in ci: Add CPython 3.10 to testing #1808
• build: Add support for Python 3.10 across all backends by @matthewfeickert in build: Add support for Python 3.10 across all backends #1809
• docs: Add use citation from neos paper by @matthewfeickert in docs: Add use citation from neos paper #1812
• docs: Update JAX backend normal docstring to jax v0.3.2 returns by @matthewfeickert in docs: Update JAX backend normal docstring to jax v0.3.2 returns #1813
• feat: Alternative Schema Locations by @kratsg in feat: Alternative Schema Locations #1753
• ci: Report coverage for oldest and newest Python tested by @matthewfeickert in ci: Report coverage for oldest and newest Python tested #1817
• fix: writexml handles missing parameter configs for normfactor by @kratsg in fix: writexml handles missing parameter configs for normfactor #1819
• feat: Add contextlib support to pyhf.schema API by @kratsg in feat: Add contextlib support to pyhf.schema API #1818
• test: Assert exported StatError has no name attribute by @kratsg in test: Assert exported StatError has no name attribute #1821
• fix: Disallow Jinja2 v3.1.0 to avoid nbsphinx triggering attribute error by @matthewfeickert in fix: Disallow Jinja2 v3.1.0 to avoid nbsphinx triggering attribute error #1824
• docs: Add JupyterLite REPL for interactive pyhf in docs by @matthewfeickert in docs: Add JupyterLite REPL for interactive pyhf in docs #1820
• fix: bump black to 22.3.0 due to click 8.1 release by @henryiii in fix: bump black to 22.3.0 due to click 8.1 release #1827
• ci: Use actions/setup-python v3 by @matthewfeickert in ci: Use actions/setup-python v3 #1828
• fix: Add filterwarnings ignore for Pillow DeprecationWarning by @matthewfeickert in fix: Add filterwarnings ignore for Pillow DeprecationWarning #1834
• ci: Update GitHub Actions to next stable version by @matthewfeickert in ci: Update GitHub Actions to next stable version #1833
• ci: Add matplotlib nightly wheels to HEAD of dependencies testing by @matthewfeickert in ci: Add matplotlib nightly wheels to HEAD of dependencies testing #1835
• ci: Add concurrency group to HEAD of dependencies workflow by @matthewfeickert in ci: Add concurrency group to HEAD of dependencies workflow #1836
• revert: Remove Jinja2 restrictions given nbconvert v6.4.5 by @matthewfeickert in revert: Remove Jinja2 restrictions given nbconvert v6.4.5 #1837
• chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in chore: [pre-commit.ci] pre-commit autoupdate #1839
• fix: Override error on filterwarnings to pass notebook tests by @matthewfeickert in fix: Override error on filterwarnings to pass notebook tests #1841
• docs: Add general use citation from SimpleAnalysis ATLAS PUB note by @matthewfeickert in docs: Add general use citation from SimpleAnalysis ATLAS PUB note #1842
• docs: Add general use citation from End-to-End Optimization paper by @matthewfeickert in docs: Add general use citation from End-to-End Optimization paper #1843
• docs: Add general use citation from Survey of Open Data Concepts paper by @matthewfeickert in docs: Add general use citation from Survey of Open Data Concepts paper #1844
• ci: Add bump version workflow for release tags by @matthewfeickert in ci: Add bump version workflow for release tags #1846
• refactor: Deprecate distutils in favor of setuptools._distutils by @matthewfeickert in refactor: Deprecate distutils in favor of setuptools._distutils #1849
• docs: Update developer documentation by @matthewfeickert in docs: Update developer documentation #1847
• docs: Deprecate use of git.io URL shortener by @matthewfeickert in docs: Deprecate use of git.io URL shortener #1851
• docs: Fix broken links identified by Sphinx linkcheck by @matthewfeickert in docs: Fix broken links identified by Sphinx linkcheck #1854
• ci: Add sphinx linkcheck builder to docs build workflow by @matthewfeickert in ci: Add sphinx linkcheck builder to docs build workflow #1855
• chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in chore: [pre-commit.ci] pre-commit autoupdate #1859
• ci: Update ReadTheDocs build to Ubuntu 22.04 by @matthewfeickert in ci: Update ReadTheDocs build to Ubuntu 22.04 #1860
• docs: Add use citation from strange quark probe Snowmass paper by @matthewfeickert in docs: Add use citation from strange quark probe Snowmass paper #1861
• docs: Add use citation from ATLAS dE/dX long-lived particle paper by @matthewfeickert in docs: Add use citation from ATLAS dE/dX long-lived particle paper #1863
• feat: Allow readxml to demote validation exception to warning by @kratsg in feat: Allow readxml to demote validation exception to warning #1865
• docs: Clarify staterror modifier specification by @Moelf in docs: Clarify staterror modifier specification #1856
• test: Ignore LHEP DOI URLs during Sphinx linkcheck by @matthewfeickert in test: Ignore LHEP DOI URLs during Sphinx linkcheck #1866
• ci: Add semantic PR check GHA workflow by @matthewfeickert in ci: Add semantic PR check GHA workflow #1868
• test: Ignore EPJ Web of Conferences DOI URLs during Sphinx linkcheck by @matthewfeickert in test: Ignore EPJ Web of Conferences DOI URLs during Sphinx linkcheck #1870
• test: Restrict tf dependency protobuf to ABI compatible releases by @matthewfeickert in test: Restrict tf dependency protobuf to ABI compatible releases #1869
• build: Update lower bound on tensorflow to v2.6.5 by @matthewfeickert in build: Update lower bound on tensorflow to v2.6.5 #1874
• fix: Allow for true_divide or divide RuntimeWarning from NumPy by @matthewfeickert in fix: Allow for true_divide or divide RuntimeWarning from NumPy #1873
• docs: Set English as language for Sphinx by @matthewfeickert in docs: Set English as language for Sphinx #1875
• docs: Update Matthew's affiliation to University of Wisconsin-Madison by @matthewfeickert in docs: Update Matthew's affiliation to University of Wisconsin-Madison #1876
• ci: Add 'name-tests-test' to pre-commit hooks by @matthewfeickert in ci: Add 'name-tests-test' to pre-commit hooks #1877
• chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in chore: [pre-commit.ci] pre-commit autoupdate #1878
• ci: Use github.workflow property to ensure unique concurrency group by @matthewfeickert in ci: Use github.workflow property to ensure unique concurrency group #1879
• build: Use find_namespace: to ensure discovery of package data by @matthewfeickert in build: Use find_namespace: to ensure discovery of package data #1881
• build: Use license_files in setup.cfg by @matthewfeickert in build: Use license_files in setup.cfg #1883
• feat: Allow for clipping negative yields in the main model by @kratsg in feat: Allow for clipping negative yields in the main model #1845
• ci: Use '--pytest-test-first' option for naming clarity by @matthewfeickert in ci: Use '--pytest-test-first' option for naming clarity #1892
• build: Update lower bound on iminuit to v2.7.0 by @matthewfeickert in build: Update lower bound on iminuit to v2.7.0  #1895
• docs: Add use citation from Audrey Kvam's Ph.D. thesis by @matthewfeickert in docs: Add use citation from Audrey Kvam's Ph.D. thesis #1896
• docs: Update use citations published in journals in June 2022 by @matthewfeickert in docs: Update use citations published in journals in June 2022 #1897
• chore: Use actions/setup-python v4 by @matthewfeickert in chore: Use actions/setup-python v4 #1898
• ci: Enable Dependabot version updates for GitHub Actions by @henryiii in ci: Enable Dependabot version updates for GitHub Actions #1900
• chore: Update Docker GitHub Actions to Dependabot bumped versions by @matthewfeickert in chore: Update Docker GitHub Actions to Dependabot bumped versions #1906
• build(deps): bump codecov/codecov-action from 2 to 3 by @dependabot in build(deps): bump codecov/codecov-action from 2 to 3 #1903
• chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in chore: [pre-commit.ci] pre-commit autoupdate #1913
• fix: Disallow Sphinx v5.1.0 to avoid 'exception: pop from an empty deque' by @matthewfeickert in fix: Disallow Sphinx v5.1.0 to avoid 'exception: pop from an empty deque' #1925
• build(deps): bump pypa/gh-action-pypi-publish from 1.5.0 to 1.5.1 by @dependabot in build(deps): bump pypa/gh-action-pypi-publish from 1.5.0 to 1.5.1 #1924
• chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in chore: [pre-commit.ci] pre-commit autoupdate #1927
• docs: Update lower bound on Sphinx to v5.1.1 by @matthewfeickert in docs: Update lower bound on Sphinx to v5.1.1 #1926
• fix: Manually set uncertainties for fixed parameters to 0 by @matthewfeickert in fix: Manually set uncertainties for fixed parameters to 0 #1919
• docs: Add July 2022 use citations by @matthewfeickert in docs: Add July 2022 use citations #1929
• docs: Add use citation from Lucas Santiago Borgna's Ph.D. thesis by @matthewfeickert in docs: Add use citation from Lucas Santiago Borgna's Ph.D. thesis #1930
• ci: Add yesqa pre-commit hook by @matthewfeickert in ci: Add yesqa pre-commit hook #1932
• fix: Coverage for importing XML channels with no data by @kratsg in fix: Coverage for importing XML channels with no data #1931
• fix: Handle importing XML measurements with no POI attribute by @kratsg in fix: Handle importing XML measurements with no POI attribute #1933
• feat: Handle absolute paths in XML config files (xml2json / readxml) by @kratsg in feat: Handle absolute paths in XML config files (xml2json / readxml) #1909
• ci: Report coverage for all Python versions by @matthewfeickert in ci: Report coverage for all Python versions #1936
• feat: Enable typehints in pre-commit and add typehints to readxml by @kratsg in feat: Enable typehints in pre-commit and add typehints to readxml #1934
• test: Ignore TYPE_CHECKING for coverage by @kratsg in test: Ignore TYPE_CHECKING for coverage #1937
• build: Set lower bound of typing-extensions to v3.7.4 by @matthewfeickert in build: Set lower bound of typing-extensions to v3.7.4 #1938
• ci: Make build error on warnings by @matthewfeickert in ci: Make build error on warnings #1887
• chore: Remove 'lint' extra from setup.py by @matthewfeickert in chore: Remove 'lint' extra from setup.py #1943
• refactor: Use string literal types of generic builtins for type checking by @matthewfeickert in refactor: Use string literal types of generic builtins for type checking #1942
• build: Update git archival options to support auto versioning by @matthewfeickert in build: Update git archival options to support auto versioning #1951
• ci: Use 'strict' option for twine check by @matthewfeickert in ci: Use 'strict' option for twine check #1954
• feat: Validate workspace specification before accessing parts of it by @alexander-held in feat: Validate workspace specification before accessing parts of it #1953
• ci: Deploy GitHub Pages docs directly using GitHub Actions by @matthewfeickert in ci: Deploy GitHub Pages docs directly using GitHub Actions #1955
• fix: Populate the schema cache with local defs.json again by @lhenkelm in fix: Populate the schema cache with local defs.json again #1917
• feat: Add typehints to pyhf.tensor by @kratsg in feat: Add typehints to pyhf.tensor #1940
• build: Update lower bound of click to v8.0.0 by @matthewfeickert in build: Update lower bound of click to v8.0.0 #1958
• build: Update lower bound of typing-extensions to v3.7.4.3 by @matthewfeickert in build: Update lower bound of typing-extensions to v3.7.4.3 #1961
• build: Update lower bounds to tensorflow v2.7.0, jaxlib v0.1.61 by @matthewfeickert in build: Update lower bounds to tensorflow v2.7.0, jaxlib v0.1.61 #1962
• ci: Restrict deployments of environments to PR merges by @matthewfeickert in ci: Restrict deployments of environments to PR merges #1960
• docs: Add link to public-probability-models website by @matthewfeickert in docs: Add link to public-probability-models website #1956
• fix: Keep staterror from affecting multiple samples by @lukasheinrich in fix: Keep staterror from affecting multiple samples #1965
• ci: Publish to PyPI on publish of GitHub release by @matthewfeickert in ci: Publish to PyPI on publish of GitHub release #1968
• docs: Add typehint aliases by @kratsg in docs: Add typehint aliases #1969
• fix: Base URI for jsonschema.RefResolver has better behavior by @kratsg in fix: Base URI for jsonschema.RefResolver has better behavior #1976
• build: Update lower bounds to jsonschema v4.15.0, importlib-resources v1.4.0 by @matthewfeickert in build: Update lower bounds to jsonschema v4.15.0, importlib-resources v1.4.0 #1979
• fix: Add PR number to Semantic PR Title Check concurrency group by @kratsg in fix: Add PR number to Semantic PR Title Check concurrency group #1981
• feat: Promote validate kwarg to top-level functions in pyhf.simplemodels by @phinate in feat: Promote validate kwarg to top-level functions in pyhf.simplemodels #1858
• docs: Clarify absolute/relative for histosys by @kratsg in docs: Clarify absolute/relative for histosys #1971
• docs: Document Channel Summary Mixin by @kratsg in docs: Document Channel Summary Mixin #1972
• docs: Harmonize docstring for test_stat in ToyCalculator by @kratsg in docs: Harmonize docstring for test_stat in ToyCalculator #1970
• feat: Add support for _ModelConfig.set_poi(None) to unset model POI by @kratsg in feat: Add support for _ModelConfig.set_poi(None) to unset model POI #1985
• chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in chore: [pre-commit.ci] pre-commit autoupdate #1989
• fix: Add guards against shared shapesys paramsets by @kratsg in fix: Add guards against shared shapesys paramsets #1977
• feat: Add type hints for tensor manager by @kratsg in feat: Add type hints for tensor manager #1963
• fix: Form data through loop over channels for multichannel coupled histo notebook by @kratsg in fix: Form data through loop over channels for multichannel coupled histo notebook #1974
• feat: Allow schema validation with tensor types by @kratsg in feat: Allow schema validation with tensor types #1665
• fix: Guard against nan in test stat calculation by @matthewfeickert in fix: Guard against nan in test stat calculation #1993
• fix: Pin codemetapy to v0.3.5 for --no-extras functionality by @matthewfeickert in fix: Pin codemetapy to v0.3.5 for --no-extras functionality #1995
• ci: Install release candidates for 'current release' test workflow by @matthewfeickert in ci: Install release candidates for 'current release' test workflow #1996
• refactor: Use urllib.parse.urlsplit over urlparse by @matthewfeickert in refactor: Use urllib.parse.urlsplit over urlparse #1997
• docs: Add Binder Python runtime environment specification by @matthewfeickert in docs: Add Binder Python runtime environment specification #1998
• fix: Update codemeta lower bounds for jsonschema, importlib-resources by @matthewfeickert in fix: Update codemeta lower bounds for jsonschema, importlib-resources #2000
• docs: Add milestone for 2000 project GitHub items by @matthewfeickert in docs: Add milestone for 2000 project GitHub items #2001
• fix: Use codemetapy v2.2.2+ API by @matthewfeickert in fix: Use codemetapy v2.2.2+ API #2002
• fix: Add filterwarnings ignore for protobuf DeprecationWarning by @matthewfeickert in fix: Add filterwarnings ignore for protobuf DeprecationWarning #2005
• fix: Specify encoding as utf-8 to enforce PEP 597 by @matthewfeickert in fix: Specify encoding as utf-8 to enforce PEP 597 #2007
• docs: Add FAQ on reasons for need to downgrade dependencies by @matthewfeickert in docs: Add FAQ on reasons for need to downgrade dependencies #1529
• test: Update test_plot_results_no_axis baseline image by @matthewfeickert in test: Update test_plot_results_no_axis baseline image #2009
• feat: Add internal API to warn of deprecation and future removal by @matthewfeickert in feat: Add internal API to warn of deprecation and future removal #2012
• fix: Use function scope to avoid altering hypotest_args fixture by @matthewfeickert in fix: Use function scope to avoid altering hypotest_args fixture #2011
• test: Discover pytest fixtures during doctest by @matthewfeickert in test: Discover pytest fixtures during doctest #2017
• feat: Add autoscan for upper limit using TOMS Algorithm 748 by @beojan in feat: Add autoscan for upper limit using TOMS Algorithm 748 #1274
• ci: Ignore Dependabot PRs to update tests/constraints.txt by @matthewfeickert in ci: Ignore Dependabot PRs to update tests/constraints.txt  #2010
• chore: Update references to default branch to 'main' by @matthewfeickert in chore: Update references to default branch to 'main' #2019
• docs: Remove requests install from JupyterLite REPL setup by @matthewfeickert in docs: Remove requests install from JupyterLite REPL setup #2020
• docs: Update list of statistical models for 2022 by @matthewfeickert in docs: Update list of statistical models for 2022 #2018
• docs: Update release checklist notes for Conda-forge and LCG views by @matthewfeickert in docs: Update release checklist notes for Conda-forge and LCG views #2021
• chore: Update codemeta.json for scipy lower bounds by @matthewfeickert in chore: Update codemeta.json for scipy lower bounds #2023
• docs: Add versionadded to new tensorlib methods by @kratsg in docs: Add versionadded to new tensorlib methods #2025
• docs: Update use citations and general citations to latest distribution by @matthewfeickert in docs: Update use citations and general citations to latest distribution #2026
• feat: Make par_names a _ModelConfig property attribute by @matthewfeickert in feat: Make par_names a _ModelConfig property attribute #2027
• docs: Add v0.7.0 release notes by @matthewfeickert in docs: Add v0.7.0 release notes #1705

New Contributors

• @RhnSharma made their first contribution in docs: Correct v0.6.3 release notes to note pyhf.pdf._ModelConfig.channels is a list #1592
• @masonproffitt made their first contribution in fix: Use MLEs of NPs to create sampling distributions in ToyCalculator #1610
• @aryan26roy made their first contribution in feat: Add hypotest kwargs to pyhf.infer.intervals.upperlimit #1613
• @lhenkelm made their first contribution in feat: Expose fitted parameter values of implicit fits in test statistic calls #1554
• @Moelf made their first contribution in docs: Clarify staterror modifier specification #1856
• @phinate made their first contribution in feat: Promote validate kwarg to top-level functions in pyhf.simplemodels #1858
• @beojan made their first contribution in feat: Add autoscan for upper limit using TOMS Algorithm 748 #1274

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

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This discussion was created from the release v0.7.0.