v0.7.0 #2030

matthewfeickert · 2022-09-24T19:10:38Z

matthewfeickert
Sep 24, 2022
Maintainer

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

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v0.7.0 #2030

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v0.7.0 #2030

matthewfeickert Sep 24, 2022 Maintainer

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matthewfeickert
Sep 24, 2022
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