Recent Releases of pyhf

pyhf - v0.7.6

This is a patch release from v0.7.5 → v0.7.6.

Fixes

For the JAX backend access jax.config from the jax top level API to avoid support issues with jax and jaxlib v0.4.20+. (PR #2376)
Add information in the warnings for pyhf.infer.test_statistics.qmu and pyhf.infer.test_statistics.qmu_tilde that provides users with the higher level pyhf.infer APIs kwarg to set the correct test statistic. (PR #2390)
Correct the variable assignment for the one-sigma and two-sigma limit band artists in pyhf.contrib.viz.brazil.plot_brazil_band to match the stated return structure. (PR #2411)
In the pyhf.infer module, correct the fixed_params type in the docs to be to tuple or list. (PR #2420)

Contributors

v0.7.6 benefited from contributions from:

Lorenz Gaertner (@lorenzennio)

What's Changed

ci(backport): Update GitHub Actions by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2421
ci: Use --find-links to install jax and jaxlib on Python 3.7 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2422
fix(backport): Access jax.config from jax by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2423
chore(backport): Update pre-commit hooks by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2424
docs(backport): Update citations and README by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2425
feat(backport): Improve warnings for qmu and qmu_tilde for the set POI bounds by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2426
fix(backport): Correct variable assignment for limit band artists by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2427
docs(backport): Correct fixed_params type to tuple or list by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2428
docs: Add v0.7.6 release notes by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2430

Full Changelog: https://github.com/scikit-hep/pyhf/compare/v0.7.5...v0.7.6

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert almost 2 years ago

pyhf - v0.7.5

This is a patch release from v0.7.4 → v0.7.5.

Fixes

Remove operating system dependent components of schema validation to allow for validation on Windows. (PR #2357)

What's Changed

chore(backport): Update GitHub Actions and pre-commit hooks by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2359
docs(backport): Update citations and docs by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2360
fix(backport): Remove os-dependent pieces of schema validation by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2361
docs: Add v0.7.5 release notes by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2362
docs(backport): Update citations references with journal pubs through 2023-10 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2368

Full Changelog: https://github.com/scikit-hep/pyhf/compare/v0.7.4...v0.7.5

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert about 2 years ago

pyhf - v0.7.4

This is a patch release from v0.7.3 → v0.7.4.

Fixes

Skip callbacks with dead weakrefs while iterating over callbacks in pyhf events, like pyhf.set_backend, to avoid the possibility of accessing dead weakrefs before they could be garbage collected. (PR #2310)

The fixed bug was subtle and occurred nondeterministically when the pyhf.tensorlib was changed repeatedly causing dead weakrefs to be accessed before Python's garbage collection could remove them. Most users should be unaffected.

Contributors

v0.7.4 benefited from contributions from:

Daniel Werner
Jonas Rembser

What's Changed

chore(backport): Update pre-commit hooks by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2317
ci(backport): Update GitHub Actions by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2318
docs(backport): Update docs requirements and use citations by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2320
fix(backport): Skip callbacks with dead weakrefs while iterating over callbacks by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2321
docs: Add v0.7.4 release notes by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2322
docs(backport): Update citations references and model records by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2325

Full Changelog: https://github.com/scikit-hep/pyhf/compare/v0.7.3...v0.7.4

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert over 2 years ago

pyhf - v0.7.3

This is a patch release from v0.7.2 → v0.7.3.

Fixes

Use np.prod API over np.product as np.product is deprecated as of NumPy v1.25.0. (PR #2242)
Guard pyhf.optimize.opt_minuit.minuit_optimizer optimizer strategy from None to ensure iminuit.Minuit.strategy strategies are correctly handled. (PRs #2277, #2278)

The fixed bug was subtle and only occurred for specific configurations of settings and arguments where do_grad=False was used (either explicitly by provided kwarg or implicitly through defaults). To determine if you might have been affected by it, check your code for setups like the following.

```python # Bug is backend independent. JAX is selected as an example where # dograd=False might be selected in response to the backend's value of # pyhf.tensorlib.defaultdograd being True. pyhf.setbackend("jax", pyhf.optimize.minuit_optimizer(strategy=0))

...

fitresult, optresult = pyhf.infer.mle.fit( data, model, returnresultobj=True, dograd=False ) assert optresult.minuit.strategy.strategy == 0 # fails for pyhf v0.7.2 ```

Full example that fails in pyhf v0.7.2:

```python import pyhf

pyhf.setbackend("jax", pyhf.optimize.minuitoptimizer(strategy=0))

model = pyhf.simplemodels.uncorrelatedbackground( signal=[12.0, 11.0], bkg=[50.0, 52.0], bkguncertainty=[3.0, 7.0] ) data = [51, 48] + model.config.auxdata

# passing with strategy kwarg explicitly given fitresult, optresult = pyhf.infer.mle.fit( data, model, returnresultobj=True, dograd=False, strategy=0 ) minuitstrategy = optresult.minuit.strategy.strategy print(f"# Minuit minimization strategy: {minuitstrategy}") assert minuit_strategy == 0

# strategy kwarg not given fitresult, optresult = pyhf.infer.mle.fit( data, model, returnresultobj=True, dograd=False ) minuitstrategy = optresult.minuit.strategy.strategy print(f"# Minuit minimization strategy: {minuitstrategy}") assert minuit_strategy == 0 # fails for pyhf v0.7.2 ```

Contributors

v0.7.3 benefited from contributions from:

Alexander Held
Daniel Werner

What's Changed

fix(backport): Pass script_runner commands as a single sequence by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2222
docs(backport): Add sphinxrtdtheme to extensions by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2223
ci(backport): Update GitHub Actions workflows by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2279
fix: Support JAX array API before and after JAX v0.4.1 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2280
docs(backport): Update docs build requirements by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2281
chore(backport): Move to using Ruff for pre-commit by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2282
chore(backport): Update pre-commit hooks by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2283
fix(backport): Replace deprecated np.product by np.prod by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2284
docs(backport): Update use citations by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2285
docs(backport): Use SVG version of logo for docs by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2286
feat(backport): Use non-root default user for Docker image by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2287
fix(backport): Guard Minuit optimizer against provided strategy of None by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2288
docs: Add v0.7.3 release notes by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2290
docs(backport): Update models and journal publication citations by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2295
docs: Add v0.7.2 failing example to v0.7.3 release notes by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2294

Full Changelog: https://github.com/scikit-hep/pyhf/compare/v0.7.2...v0.7.3

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert over 2 years ago

pyhf - v0.7.2

This is a patch release from v0.7.1 → v0.7.2.

Important Notes

pyhf became a NumFOCUS Affiliated Project on 2022-12-19. v0.7.1 is the first release to appear in a NumFOCUS Newsletter and v0.7.2 is the first release to appear as part of the Affiliated Projects page. (PR #2179)

Fixes

If a multiple component parameter of interest is used raise pyhf.exceptions.InvalidModel. This guards against modifiers like shapefactor, shapesys, and staterror from being used as POIs. (PR #2197)
Use typing.TYPE_CHECKING guard to avoid causing a ModuleNotFoundError when the version of NumPy installed is older than v1.21.0, which is the first NumPy release to include numpy.typing. (PR #2208)

Contributors

v0.7.2 benefited from contributions from:

Alexander Held

What's Changed

ci(backport): Use gh-action-pypi-publish v1.7.0+ APIs by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2178
docs(backport): Add NumFOCUS Affiliated Project to README by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2180
docs(backport): Use Plausible for page visit statistics by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2188
docs(backport): Add use citations through April 2023 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2202
fix: Disallow TensorFlow Probability v0.20.0 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2203
ci(backport): Update CI workflows and use Trusted Publishers by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2204
docs(backport): Use jupyterlite-sphinx to embed JupyterLite in docs by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2205
docs(backport): Add dev instructions and fix typos by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2206
docs(backport): Update talk list and release checklist by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2211
fix(backport): Catch use of multi-component parameters as POI by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2212
fix(backport): Add TYPE_CHECKING guard for numpy.typing by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2213
docs: Add v0.7.2 release notes by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2214

Full Changelog: https://github.com/scikit-hep/pyhf/compare/v0.7.1...v0.7.2

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert over 2 years ago

pyhf - v0.7.1

This is a patch release from v0.7.0 → v0.7.1.

Important Notes

All backends are now fully compatible and tested with Python 3.11. (PR #2145)
The tensorflow extra ('pyhf[tensorflow]') now automatically installs tensorflow-macos for Apple silicon machines. (PR #2119)

Fixes

Raise NotImplementedError when attempting to convert a XML workspace that contains no data. (PR #2109)

Contributors

v0.7.1 benefited from contributions from:

Alexander Held

What's Changed

fix: Skip ReadTheDocs verions during Sphinx link check by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2031
fix: Use jax.errors API as jax._src removed from public namespace by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2034
build(backport): Switch to using Hatchling as build backend by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2148
chore(backport): Update pre-commit hooks by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2150
ci: Run CI and packaging workflows on release branch PRs by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2151
docs(backport): Update JAX backend docstring types to jax.Array by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2152
ci(backport): Add workflow input for bump version branch by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2157
chore(backport): Update pre-commit hooks and dependabot updates by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2163
docs(backport): Add use citations and general citations by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2164
test(backport): Use pytest.raises match argument to check Error messages by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2165
fix(backport): Raise error when converting xml workspaces without data by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2166
docs: Add v0.7.1 release notes by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2168
docs(backport): Add ATLAS search for gluinos in multi-b final states statistical model record by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2170
docs(backport): Update use citations references to include journal publications by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2172
chore: Update codemeta by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2173

Full Changelog: https://github.com/scikit-hep/pyhf/compare/v0.7.0...v0.7.1

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert over 2 years ago

pyhf - v0.7.0

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 #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 #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 #1909)
Support for model specifications without a parameter of interest defined is added. (PRs #1638, #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 #1639)
pyhf.pdf._ModelConfig.par_names is changed to be a property attribute. (PR #2027)
The order of model parameters is now sorted by model parameter name. (PR #1625)
Support for writing user custom modifiers is added. (PRs #1625, #1644)
Performance in pyhf.readxml is increased by improvements to pyhf.readxml.import_root_histogram. (PR #1691)
pyhf.contrib.utils.download is now more robust to different target file types. (PRs #1697, #1704)
A pyhf.default_backend has been added that is configurable through a default kwarg in pyhf.set_backend. (PR #1646) This is part of work to make pyhf fully automatic differentiable. (Issue #882)
Schema validation now allows for both list and pyhf.tensorlib objects to exist in the model specification. (PR #1647)
The minimum required dependencies have been updated to support added features:
- scipy>=1.2.0 (PR #1274)
- click>=8.0.0 (PRs #1909, #1958)
- jsonschema>=4.15.0 (PRs #1976, #1979)
- importlib_resources>=1.4.0 (for Python 3.7, 3.8) (PR #1979)
- typing_extensions>=3.7.4.3 (for Python 3.7 only) (PRs #1940, #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 #1962)
- PyTorch backend requires torch>=1.10.0 (PR #1657)
- TensorFlow backend requires tensorflow>=2.7.0, tensorflow-probability>=0.11.0 (PRs #1962, #1657)
- iminuit optimizer requires iminuit>=2.7.0 (PR #1895)
- 'xmlio' extra requires uproot>=4.1.1 (PR #1567)

Fixes

Use improvements to jsonschema.RefResolver to avoid jsonschema.exceptions.RefResolutionError. (PR #1976)
Use the conditional maximum likelihood estimators of the nuisance parameters to create the sampling distributions for pyhf.infer.calculators.ToyCalculator. (PR #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 #1696)
- pyhf.tensorlib.percentile (PR #817)
pyhf.readxml.parse now supports reading of XML configurations with absolute paths with the addition of the mounts optional argument. (PR #1909)
Support for overriding the paths for finding schemas is added, using the pyhf installed location as a base via pyhf.utils.schemas. (PRs #1753, #1818)

```pycon

from pathlib import Path import pyhf.schema currentschemapath = pyhf.schema.path currentschemapath PosixPath('/path/to/your/venv/lib/python3.X/site-packages/pyhf/schemas') customschemapath = Path("/path/to/custom/pyhf/schema") with pyhf.schema(customschemapath): ... 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 #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 #1639)
pyhf.pdf._ModelConfig.par_names is changed to be a property attribute. (PR #2027)
The order of model parameters is now sorted by model parameter name. (PR #1625)

```pycon

import pyhf model = pyhf.simplemodels.correlatedbackground( ... signal=[12.0, 11.0], ... bkg=[50.0, 52.0], ... bkgup=[45.0, 57.0], ... bkgdown=[55.0, 47.0], ... ) model.config.parorder ['correlatedbkguncertainty', 'mu'] model.config.parnames ['correlatedbkg_uncertainty', 'mu'] ```
Support for writing user custom modifiers is added. (PRs #1625, #1644) This is still in the stage where it is targeted at expert users.
{modifier}_builder classes are added for all modifiers. (PRs #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 #1819)
Supported options for pyhf.infer.hypotest can now be passed as kwargs through the pyhf.infer.intervals.upper_limits.upper_limit API. (PR #1613) This now enables things like using pyhf.infer.calculators.ToyCalculator as the calculator used for the hypothesis test scan:

```pycon

import numpy as np import pyhf pyhf.setbackend("jax") model = pyhf.simplemodels.uncorrelatedbackground( ... signal=[12.0, 11.0], bkg=[50.0, 52.0], bkguncertainty=[3.0, 7.0] ... ) observations = [51, 48] data = pyhf.tensorlib.astensor(observations + model.config.auxdata) scan = np.linspace(0, 5, 21) obslimit, explimits, (scan, results) = pyhf.infer.intervals.upperlimits.upperlimit( ... data, model, scan, returnresults=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 #1554)
A validate kwarg has been added to pyhf.workspace.Workspace and pyhf.pdf.Model to allow skipping validation. (PR #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 #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.

```pycon

import jax import pyhf pyhf.setbackend("jax", default=True) pyhf.setbackend("numpy") pyhf.getbackend() (<pyhf.tensor.numpybackend.numpybackend object at 0x...>, <pyhf.optimize.scipyoptimizer object at 0x...>) pyhf.defaultbackend <pyhf.tensor.jaxbackend.jaxbackend object at 0x...> def exampleop(x): ... return 2 * pyhf.defaultbackend.power(pyhf.defaultbackend.astensor(x), 3) ... exampleop([2.0]) DeviceArray([16.], dtype=float64) jax.jacrev(jax.jit(exampleop))([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 #1647)

pycon >>> 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 #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!

console 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 #1274)

Removals

Python API

The pyhf.simplemodels.hepdata_like API, deprecated since pyhf v0.6.2, has been removed. (PR #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 #1625)
pyhf.workspace.Workspace.get_measurement has the poi_name kwarg removed. (PR #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 https://github.com/scikit-hep/pyhf/pull/1588
ci: Skip doctest for 'Minimum supported dependencies' workflow by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1589
chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1593
docs: Correct v0.6.3 release notes to note pyhf.pdf._ModelConfig.channels is a list by @RhnSharma in https://github.com/scikit-hep/pyhf/pull/1592
ci: Add Python 3.9 to 'Current Release' workflow tests by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1596
docs: Update maintainer release checklist with v0.6.3 notes by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1597
ci: Use jupyter-black pre-commit hook over nbqa-black by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1598
docs: Add use citation from publishing statistical models white paper by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1600
docs: Add uproot4 writing speedup to v0.6.3 release notes by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1601
docs: Add use citation from collider signatures of coannihilating dark matter paper by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1604
fix: Use MLEs of NPs to create sampling distributions in ToyCalculator by @masonproffitt in https://github.com/scikit-hep/pyhf/pull/1610
docs: Add use citation from simplified likelihoods ATLAS PUB note by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1614
docs: Use sphinxcontrib-bibtex style 'unsrt' to sort citations in reverse chronological order by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1615
chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1616
docs: Use sphinx-copybutton prompt regex to fully capture examples by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1617
ci: Allow reporting of coverage on PRs from forks by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1622
ci: Update codecov-action to v2 API by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1623
ci: Report coverage to Codecov without token by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1628
feat: Add hypotest kwargs to pyhf.infer.intervals.upperlimit by @aryan26roy in https://github.com/scikit-hep/pyhf/pull/1613
feat: Expose fitted parameter values of implicit fits in test statistic calls by @lhenkelm in https://github.com/scikit-hep/pyhf/pull/1554
ci: Add absolufy-imports pre-commit hook by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1635
feat: Add setup for custom modifiers by @lukasheinrich in https://github.com/scikit-hep/pyhf/pull/1625
feat: Allow POI-less models via Workspace.model by @kratsg in https://github.com/scikit-hep/pyhf/pull/1636
fix: Fix bug in impact plot visualization by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1642
feat: Add POI-less specification support by @kratsg in https://github.com/scikit-hep/pyhf/pull/1638
docs: Add and apply codespell as a pre-commit hook by @alexander-held in https://github.com/scikit-hep/pyhf/pull/1645
fix: custom modifier / new parameter support and test by @lukasheinrich in https://github.com/scikit-hep/pyhf/pull/1644
test: Use netlocs that are known to not exist or give known return by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1651
feat: Add support for arrayful JSON by @lukasheinrich in https://github.com/scikit-hep/pyhf/pull/1647
test: Remove 'src' from pytest test testpaths to allow for non-editable install in CI by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1467
feat: Allow zero rate Poisson by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1657
ci: Add release candidates to HEAD of dependencies workflow by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1660
feat: Configurable default backend by @kratsg in https://github.com/scikit-hep/pyhf/pull/1646
refactor: Simplified parameters by @lukasheinrich in https://github.com/scikit-hep/pyhf/pull/1639
ci: Turn off PyPI release tests on pull requests by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1664
build: Set lower bound of scipy v1.1.0 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1661
build: Update lower bound on jax to v0.2.10 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1666
feat: Remove pyhf.simplemodels.hepdata_like from API by @aryan26roy in https://github.com/scikit-hep/pyhf/pull/1670
docs: Update 2021 published ATLAS probability models by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1671
chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1679
refactor: Pass Accept header to requests in contrib.utils.download by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1673
fix: Use https protocol as unauthenticated git protocol is no longer supported by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1680
docs: Add ATLAS top group probability model records through June 2021 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1681
docs: Add ATLAS third-generation scalar leptoquarks search statistical model record by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1682
fix: Speed-up readxml by caching key lookup instead of using try/except by @kratsg in https://github.com/scikit-hep/pyhf/pull/1691
feat: Add percentile function to tensorlib by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/817
docs: only lists are accepted when specifying objects to prune by @alexander-held in https://github.com/scikit-hep/pyhf/pull/1692
feat: Add transpose function to tensorlib by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1696
refactor: Use jax.numpy for JAX backend tensorlib.tolist by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1138
refactor: Use tensorlib.percentile in calculators by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1694
test: Use xfail for tests that fail for upstream problems by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1702
build: Set only lower bounds on backend dependencies by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1698
docs: Ensure docstring examples are contiguous by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1703
refactor: Make contrib.utils.download robust to archive file types by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1697
fix: Accept tar and zip headers in contrib.utils.download requests by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1704
fix: Ensure _ModelConfig.suggested_fixed list contains only booleans for all modifiers by @alexander-held in https://github.com/scikit-hep/pyhf/pull/1706
ci: Quote GitHub Action python-version number as YAML strings by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1707
feat: Raise exception if bin-wise modifier data length doesn't match sample data by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1708
feat: Catch unexpected keyword arguments in workspace construction by @alexander-held in https://github.com/scikit-hep/pyhf/pull/1709
test: Use scikit-hep-testdata to provide probability models for regression tests by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1711
fix: Skip doctest of pyhf.contrib.utils.download by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1715
chore: Use constraints.txt for lower bound testing by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1713
docs: Fix download method of probability models archive in impact plot notebook by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1721
chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1723
docs: Fix download method of probability models archive in pull plot notebook by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1724
feat: Allow skipping validation when constructing workspaces by @alexander-held in https://github.com/scikit-hep/pyhf/pull/1710
test: Make failbackend markers add pytest.mark.xfail and remove failjax marker on percentile tests by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1730
ci: Publish to TestPyPI on tag or by workflow dispatch trigger by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1727
docs: Truncate floating point docstring examples to 8 decimal places by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1726
docs: Add GitHub Release Radar check to release checklist by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1733
docs: Update citation references publication status by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1738
docs: Add milestone for 1000 project commits to README by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1739
fix: Disallow nbsphinx v0.8.8 to avoid empty "raw" directive bug by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1742
chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1741
docs: Note shapesys and staterror modifier set to 1 for modifier data of 0 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1740
ci: Limit concurrent workflow jobs to one per workflow per branch by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1632
ci: Update gh-action-pypi-publish to use print_hash by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1743
docs: Add use citation from revisiting mono-tau tails at the LHC paper by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1744
fix: Accept ValueError for JAX backend tolist fallback by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1746
ci: Launch tmate session if pytest fails on workflow dispatch run by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1748
chore: Update black to first stable release v22.1.0 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1754
test: Avoid tensorflow macOS floating point deviation with pytest.approx by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1761
ci: Add macos-latest to dependency release candidates testing by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1760
docs: Update scipy intersphinx url to drop 'reference' by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1767
chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1765
test: Add html coverage reports from pytest by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1771
test: Consolidate and update pytest options in pyproject.toml by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1773
docs: fix link to TRExFitter documentation by @alexander-held in https://github.com/scikit-hep/pyhf/pull/1777
docs: Add citation from 'HL-LHC Computing Review Stage 2' paper by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1779
build: Require setuptools v42.0.0+ for stability by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1783
build: Remove wheel and attrs from build-system requires by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1788
docs: Add section for tutorial and docs to README by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1789
feat: Use tbump over bump2version by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1790
docs: Add general citation from MadJAX paper by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1799
docs: Update Lukas's affiliation to Technical University of Munich by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1798
docs: Add use citation from ATLAS UEH MS displaced jet paper by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1800
docs: Correct Giordon's affiliation to SCIPP in CITATON.cff by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1801
docs: Add use citation from ATLAS UEH displaced jets CalRatio paper by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1802
docs: Fix tiny typo in MC Stat Error documentation by @kratsg in https://github.com/scikit-hep/pyhf/pull/1803
chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1805
refactor: Clarify exception message applies only to profile likelihood ratio by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1806
ci: Add CPython 3.10 to testing by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1808
build: Add support for Python 3.10 across all backends by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1809
docs: Add use citation from neos paper by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1812
docs: Update JAX backend normal docstring to jax v0.3.2 returns by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1813
feat: Alternative Schema Locations by @kratsg in https://github.com/scikit-hep/pyhf/pull/1753
ci: Report coverage for oldest and newest Python tested by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1817
fix: writexml handles missing parameter configs for normfactor by @kratsg in https://github.com/scikit-hep/pyhf/pull/1819
feat: Add contextlib support to pyhf.schema API by @kratsg in https://github.com/scikit-hep/pyhf/pull/1818
test: Assert exported StatError has no name attribute by @kratsg in https://github.com/scikit-hep/pyhf/pull/1821
fix: Disallow Jinja2 v3.1.0 to avoid nbsphinx triggering attribute error by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1824
docs: Add JupyterLite REPL for interactive pyhf in docs by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1820
fix: bump black to 22.3.0 due to click 8.1 release by @henryiii in https://github.com/scikit-hep/pyhf/pull/1827
ci: Use actions/setup-python v3 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1828
fix: Add filterwarnings ignore for Pillow DeprecationWarning by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1834
ci: Update GitHub Actions to next stable version by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1833
ci: Add matplotlib nightly wheels to HEAD of dependencies testing by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1835
ci: Add concurrency group to HEAD of dependencies workflow by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1836
revert: Remove Jinja2 restrictions given nbconvert v6.4.5 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1837
chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1839
fix: Override error on filterwarnings to pass notebook tests by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1841
docs: Add general use citation from SimpleAnalysis ATLAS PUB note by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1842
docs: Add general use citation from End-to-End Optimization paper by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1843
docs: Add general use citation from Survey of Open Data Concepts paper by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1844
ci: Add bump version workflow for release tags by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1846
refactor: Deprecate distutils in favor of setuptools._distutils by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1849
docs: Update developer documentation by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1847
docs: Deprecate use of git.io URL shortener by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1851
docs: Fix broken links identified by Sphinx linkcheck by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1854
ci: Add sphinx linkcheck builder to docs build workflow by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1855
chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1859
ci: Update ReadTheDocs build to Ubuntu 22.04 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1860
docs: Add use citation from strange quark probe Snowmass paper by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1861
docs: Add use citation from ATLAS dE/dX long-lived particle paper by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1863
feat: Allow readxml to demote validation exception to warning by @kratsg in https://github.com/scikit-hep/pyhf/pull/1865
docs: Clarify staterror modifier specification by @Moelf in https://github.com/scikit-hep/pyhf/pull/1856
test: Ignore LHEP DOI URLs during Sphinx linkcheck by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1866
ci: Add semantic PR check GHA workflow by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1868
test: Ignore EPJ Web of Conferences DOI URLs during Sphinx linkcheck by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1870
test: Restrict tf dependency protobuf to ABI compatible releases by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1869
build: Update lower bound on tensorflow to v2.6.5 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1874
fix: Allow for true_divide or divide RuntimeWarning from NumPy by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1873
docs: Set English as language for Sphinx by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1875
docs: Update Matthew's affiliation to University of Wisconsin-Madison by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1876
ci: Add 'name-tests-test' to pre-commit hooks by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1877
chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1878
ci: Use github.workflow property to ensure unique concurrency group by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1879
build: Use find_namespace: to ensure discovery of package data by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1881
build: Use license_files in setup.cfg by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1883
feat: Allow for clipping negative yields in the main model by @kratsg in https://github.com/scikit-hep/pyhf/pull/1845
ci: Use '--pytest-test-first' option for naming clarity by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1892
build: Update lower bound on iminuit to v2.7.0 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1895
docs: Add use citation from Audrey Kvam's Ph.D. thesis by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1896
docs: Update use citations published in journals in June 2022 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1897
chore: Use actions/setup-python v4 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1898
ci: Enable Dependabot version updates for GitHub Actions by @henryiii in https://github.com/scikit-hep/pyhf/pull/1900
chore: Update Docker GitHub Actions to Dependabot bumped versions by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1906
build(deps): bump codecov/codecov-action from 2 to 3 by @dependabot in https://github.com/scikit-hep/pyhf/pull/1903
chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1913
fix: Disallow Sphinx v5.1.0 to avoid 'exception: pop from an empty deque' by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1925
build(deps): bump pypa/gh-action-pypi-publish from 1.5.0 to 1.5.1 by @dependabot in https://github.com/scikit-hep/pyhf/pull/1924
chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1927
docs: Update lower bound on Sphinx to v5.1.1 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1926
fix: Manually set uncertainties for fixed parameters to 0 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1919
docs: Add July 2022 use citations by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1929
docs: Add use citation from Lucas Santiago Borgna's Ph.D. thesis by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1930
ci: Add yesqa pre-commit hook by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1932
fix: Coverage for importing XML channels with no data by @kratsg in https://github.com/scikit-hep/pyhf/pull/1931
fix: Handle importing XML measurements with no POI attribute by @kratsg in https://github.com/scikit-hep/pyhf/pull/1933
feat: Handle absolute paths in XML config files (xml2json / readxml) by @kratsg in https://github.com/scikit-hep/pyhf/pull/1909
ci: Report coverage for all Python versions by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1936
feat: Enable typehints in pre-commit and add typehints to readxml by @kratsg in https://github.com/scikit-hep/pyhf/pull/1934
test: Ignore TYPE_CHECKING for coverage by @kratsg in https://github.com/scikit-hep/pyhf/pull/1937
build: Set lower bound of typing-extensions to v3.7.4 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1938
ci: Make build error on warnings by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1887
chore: Remove 'lint' extra from setup.py by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1943
refactor: Use string literal types of generic builtins for type checking by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1942
build: Update git archival options to support auto versioning by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1951
ci: Use 'strict' option for twine check by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1954
feat: Validate workspace specification before accessing parts of it by @alexander-held in https://github.com/scikit-hep/pyhf/pull/1953
ci: Deploy GitHub Pages docs directly using GitHub Actions by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1955
fix: Populate the schema cache with local defs.json again by @lhenkelm in https://github.com/scikit-hep/pyhf/pull/1917
feat: Add typehints to pyhf.tensor by @kratsg in https://github.com/scikit-hep/pyhf/pull/1940
build: Update lower bound of click to v8.0.0 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1958
build: Update lower bound of typing-extensions to v3.7.4.3 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1961
build: Update lower bounds to tensorflow v2.7.0, jaxlib v0.1.61 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1962
ci: Restrict deployments of environments to PR merges by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1960
docs: Add link to public-probability-models website by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1956
fix: Keep staterror from affecting multiple samples by @lukasheinrich in https://github.com/scikit-hep/pyhf/pull/1965
ci: Publish to PyPI on publish of GitHub release by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1968
docs: Add typehint aliases by @kratsg in https://github.com/scikit-hep/pyhf/pull/1969
fix: Base URI for jsonschema.RefResolver has better behavior by @kratsg in https://github.com/scikit-hep/pyhf/pull/1976
build: Update lower bounds to jsonschema v4.15.0, importlib-resources v1.4.0 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1979
fix: Add PR number to Semantic PR Title Check concurrency group by @kratsg in https://github.com/scikit-hep/pyhf/pull/1981
feat: Promote validate kwarg to top-level functions in pyhf.simplemodels by @phinate in https://github.com/scikit-hep/pyhf/pull/1858
docs: Clarify absolute/relative for histosys by @kratsg in https://github.com/scikit-hep/pyhf/pull/1971
docs: Document Channel Summary Mixin by @kratsg in https://github.com/scikit-hep/pyhf/pull/1972
docs: Harmonize docstring for test_stat in ToyCalculator by @kratsg in https://github.com/scikit-hep/pyhf/pull/1970
feat: Add support for _ModelConfig.set_poi(None) to unset model POI by @kratsg in https://github.com/scikit-hep/pyhf/pull/1985
chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1989
fix: Add guards against shared shapesys paramsets by @kratsg in https://github.com/scikit-hep/pyhf/pull/1977
feat: Add type hints for tensor manager by @kratsg in https://github.com/scikit-hep/pyhf/pull/1963
fix: Form data through loop over channels for multichannel coupled histo notebook by @kratsg in https://github.com/scikit-hep/pyhf/pull/1974
feat: Allow schema validation with tensor types by @kratsg in https://github.com/scikit-hep/pyhf/pull/1665
fix: Guard against nan in test stat calculation by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1993
fix: Pin codemetapy to v0.3.5 for --no-extras functionality by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1995
ci: Install release candidates for 'current release' test workflow by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1996
refactor: Use urllib.parse.urlsplit over urlparse by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1997
docs: Add Binder Python runtime environment specification by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1998
fix: Update codemeta lower bounds for jsonschema, importlib-resources by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2000
docs: Add milestone for 2000 project GitHub items by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2001
fix: Use codemetapy v2.2.2+ API by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2002
fix: Add filterwarnings ignore for protobuf DeprecationWarning by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2005
fix: Specify encoding as utf-8 to enforce PEP 597 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2007
docs: Add FAQ on reasons for need to downgrade dependencies by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1529
test: Update testplotresultsnoaxis baseline image by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2009
feat: Add internal API to warn of deprecation and future removal by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2012
fix: Use function scope to avoid altering hypotest_args fixture by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2011
test: Discover pytest fixtures during doctest by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2017
feat: Add autoscan for upper limit using TOMS Algorithm 748 by @beojan in https://github.com/scikit-hep/pyhf/pull/1274
ci: Ignore Dependabot PRs to update tests/constraints.txt by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2010
chore: Update references to default branch to 'main' by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2019
docs: Remove requests install from JupyterLite REPL setup by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2020
docs: Update list of statistical models for 2022 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2018
docs: Update release checklist notes for Conda-forge and LCG views by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2021
chore: Update codemeta.json for scipy lower bounds by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2023
docs: Add versionadded to new tensorlib methods by @kratsg in https://github.com/scikit-hep/pyhf/pull/2025
docs: Update use citations and general citations to latest distribution by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2026
feat: Make par_names a _ModelConfig property attribute by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/2027
docs: Add v0.7.0 release notes by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1705

New Contributors

@RhnSharma made their first contribution in https://github.com/scikit-hep/pyhf/pull/1592
@masonproffitt made their first contribution in https://github.com/scikit-hep/pyhf/pull/1610
@aryan26roy made their first contribution in https://github.com/scikit-hep/pyhf/pull/1613
@lhenkelm made their first contribution in https://github.com/scikit-hep/pyhf/pull/1554
@Moelf made their first contribution in https://github.com/scikit-hep/pyhf/pull/1856
@phinate made their first contribution in https://github.com/scikit-hep/pyhf/pull/1858
@beojan made their first contribution in https://github.com/scikit-hep/pyhf/pull/1274

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

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert over 3 years ago

pyhf - v0.7.0rc4

Notes

This is the fourth v0.7.0 release candidate. Please use this for API testing, and for testing correctness or performance for v0.7.0.

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==0.7.0rc4'

What's Changed

docs: Document Channel Summary Mixin by @kratsg in https://github.com/scikit-hep/pyhf/pull/1972
docs: Harmonize docstring for test_stat in ToyCalculator by @kratsg in https://github.com/scikit-hep/pyhf/pull/1970
feat: Add support for _ModelConfig.set_poi(None) to unset model POI by @kratsg in https://github.com/scikit-hep/pyhf/pull/1985
chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1989
fix: Add guards against shared shapesys paramsets by @kratsg in https://github.com/scikit-hep/pyhf/pull/1977
feat: Add type hints for tensor manager by @kratsg in https://github.com/scikit-hep/pyhf/pull/1963
fix: Form data through loop over channels for multichannel coupled histo notebook by @kratsg in https://github.com/scikit-hep/pyhf/pull/1974
feat: Allow schema validation with tensor types by @kratsg in https://github.com/scikit-hep/pyhf/pull/1665
fix: Guard against nan in test stat calculation by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1993
fix: Pin codemetapy to v0.3.5 for --no-extras functionality by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1995
ci: Install release candidates for 'current release' test workflow by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1996
refactor: Use urllib.parse.urlsplit over urlparse by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1997

Full Changelog: https://github.com/scikit-hep/pyhf/compare/v0.7.0rc3...v0.7.0rc4

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert over 3 years ago

pyhf - v0.7.0rc3

Notes

This is the third v0.7.0 release candidate. Please use this for API testing, and for testing correctness or performance for v0.7.0.

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==0.7.0rc3'

What's Changed

docs: Add typehint aliases by @kratsg in https://github.com/scikit-hep/pyhf/pull/1969
fix: Base URI for jsonschema.RefResolver has better behavior by @kratsg in https://github.com/scikit-hep/pyhf/pull/1976
build: Update lower bounds to jsonschema v4.15.0, importlib-resources v1.4.0 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1979
fix: Add PR number to Semantic PR Title Check concurrency group by @kratsg in https://github.com/scikit-hep/pyhf/pull/1981
feat: Promote validate kwarg to top-level functions in pyhf.simplemodels by @phinate in https://github.com/scikit-hep/pyhf/pull/1858
docs: Clarify absolute/relative for histosys by @kratsg in https://github.com/scikit-hep/pyhf/pull/1971

New Contributors

@phinate made their first contribution in https://github.com/scikit-hep/pyhf/pull/1858

Full Changelog: https://github.com/scikit-hep/pyhf/compare/v0.7.0rc2...v0.7.0rc3

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert over 3 years ago

pyhf - v0.7.0rc2

Notes

This is the second v0.7.0 release candidate. Please use this for API testing, and for testing correctness or performance for v0.7.0.

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==0.7.0rc2'

What's Changed

chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1913
fix: Disallow Sphinx v5.1.0 to avoid 'exception: pop from an empty deque' by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1925
build(deps): bump pypa/gh-action-pypi-publish from 1.5.0 to 1.5.1 by @dependabot in https://github.com/scikit-hep/pyhf/pull/1924
chore: [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/scikit-hep/pyhf/pull/1927
docs: Update lower bound on Sphinx to v5.1.1 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1926
fix: Manually set uncertainties for fixed parameters to 0 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1919
docs: Add July 2022 use citations by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1929
docs: Add use citation from Lucas Santiago Borgna's Ph.D. thesis by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1930
ci: Add yesqa pre-commit hook by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1932
fix: Coverage for importing XML channels with no data by @kratsg in https://github.com/scikit-hep/pyhf/pull/1931
fix: Handle importing XML measurements with no POI attribute by @kratsg in https://github.com/scikit-hep/pyhf/pull/1933
feat: Handle absolute paths in XML config files (xml2json / readxml) by @kratsg in https://github.com/scikit-hep/pyhf/pull/1909
ci: Report coverage for all Python versions by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1936
feat: Enable typehints in pre-commit and add typehints to readxml by @kratsg in https://github.com/scikit-hep/pyhf/pull/1934
test: Ignore TYPE_CHECKING for coverage by @kratsg in https://github.com/scikit-hep/pyhf/pull/1937
build: Set lower bound of typing-extensions to v3.7.4 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1938
ci: Make build error on warnings by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1887
chore: Remove 'lint' extra from setup.py by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1943
refactor: Use string literal types of generic builtins for type checking by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1942
build: Update git archival options to support auto versioning by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1951
ci: Use 'strict' option for twine check by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1954
feat: Validate workspace specification before accessing parts of it by @alexander-held in https://github.com/scikit-hep/pyhf/pull/1953
ci: Deploy GitHub Pages docs directly using GitHub Actions by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1955
fix: Populate the schema cache with local defs.json again by @lhenkelm in https://github.com/scikit-hep/pyhf/pull/1917
feat: Add typehints to pyhf.tensor by @kratsg in https://github.com/scikit-hep/pyhf/pull/1940
build: Update lower bound of click to v8.0.0 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1958
build: Update lower bound of typing-extensions to v3.7.4.3 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1961
build: Update lower bounds to tensorflow v2.7.0, jaxlib v0.1.61 by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1962
ci: Restrict deployments of environments to PR merges by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1960
docs: Add link to public-probability-models website by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1956
fix: Keep staterror from affecting multiple samples by @lukasheinrich in https://github.com/scikit-hep/pyhf/pull/1965
ci: Publish to PyPI on publish of GitHub release by @matthewfeickert in https://github.com/scikit-hep/pyhf/pull/1968

Full Changelog: https://github.com/scikit-hep/pyhf/compare/v0.7.0rc1...v0.7.0rc2

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert over 3 years ago

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

New Contributors

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

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

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert over 3 years ago

pyhf - v0.6.3

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

Important Notes

With the addition of writing ROOT files in uproot v4.1.0 the xmlio extra no longer requires uproot3 and all dependencies on uproot3 and uproot3-methods have been dropped. (PR #1567). uproot4 additionally brings large speedups to writing, which results in an order of magnitude faster conversion time for most workspace conversions from JSON back to XML + ROOT with pyhf json2xml.
All backends are now fully compatible and tested with Python 3.9. (PR #1574)
The TensorFlow backend now supports compatibility with TensorFlow v2.2.1 and later and TensorFlow Probability v0.10.1 and later. (PR #1001)
The pyhf.workspace.Workspace.data() with_aux keyword arg has been renamed to include_auxdata to improve API consistency. (PR #1562)

Fixes

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

Features

Python API

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

```python

import pyhf model = pyhf.simplemodels.uncorrelatedbackground( ... signal=[12.0, 11.0], bkg=[50.0, 52.0], bkguncertainty=[3.0, 7.0] ... ) model.config.parameters ['mu', 'uncorrbkguncrt'] model.config.npars 3 model.config.parnames() ['mu', 'uncorrbkguncrt[0]', 'uncorrbkguncrt[1]'] ```

The pyhf.pdf._ModelConfig channel_nbins dict is now sorted by keys to match the order of the channels list. (PR #1546)
The pyhf.workspace.Workspace.data() with_aux keyword arg has been renamed to include_auxdata to improve API consistency. (PR #1562)

Changes

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

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert over 4 years ago

pyhf - v0.6.2

This is a patch release from v0.6.1 → v0.6.2.

Important Notes

The pyhf.simplemodels.hepdata_like() API has been deprecated in favor of pyhf.simplemodels.uncorrelated_background(). The pyhf.simplemodels.hepdata_like() API will be removed in pyhf v0.7.0. (PR #1438)
There is a small breaking API change for pyhf.contrib.viz.brazil.plot_results(). See the Python API changes section for more information.
The pyhf.patchset.PatchSet schema now allows string types for patch values in patchsets. (PR #1488)
Only lower bounds on core dependencies are now set. This allows for greater developer freedom and reduces the risk of breaking user’s applications by unnecessarily constraining libraries. This also means that users will be responsible for ensuring that their installed dependencies do not conflict with or break pyhf. c.f. Hynek Schlawack’s blog post Semantic Versioning Will Not Save You for more in-depth coverage on this topic. For most users nothing should change. This mainly affects developers of other libraries in which pyhf is a dependency. (PR #1382)
Calling dir() on any pyhf module or trying to tab complete an API will now provide a more helpfully restricted view of the available APIs. This should help provide better exploration of the pyhf API. (PR #1403) python >>> import pyhf >>> pyhf. # Tab complete pyhf.Model( pyhf.Workspace( pyhf.exceptions pyhf.infer pyhf.modifiers pyhf.parameters pyhf.pdf pyhf.set_backend( pyhf.tensor pyhf.utils pyhf.PatchSet( pyhf.compat pyhf.get_backend( pyhf.interpolators pyhf.optimizer pyhf.patchset pyhf.probability pyhf.simplemodels pyhf.tensorlib pyhf.workspace
Docker images of releases are now published to both Docker Hub and to the GitHub Container Registry. (PR #1444)
CUDA enabled Docker images are now available for release v0.6.1 and later on Docker Hub and the GitHub Container Registry. Visit https://github.com/pyhf/cuda-images for more information.

Fixes

Allow for precision to be properly set for the tensorlib ones and zeros methods through a dtype argument. This allows for precision to be properly set through the pyhf.set_backend() precision argument. (PR #1369)
The default precision for all backends is now 64b. (PR #1400)
Add check to ensure that POIs are not fixed during a fit. (PR #1409)
Parameter name strings are now normalized to remove trailing spaces. (PR #1436)
The logging level is now not automatically set in pyhf.contrib.utils. (PR #1460)

Features

Python API

The pyhf.simplemodels.hepdata_like() API has been deprecated in favor of pyhf.simplemodels.uncorrelated_background(). The pyhf.simplemodels.hepdata_like() API will be removed in pyhf v0.7.0. (PR #1438)
The pyhf.simplemodels.correlated_background() API has been added to provide an example model with a single channel with a correlated background uncertainty. (PR #1435)
Add CLs component plotting kwargs to pyhf.contrib.viz.brazil.plot_results(). This allows CLs+b and CLb components of the CLs ratio to be plotted as well. To be more consistent with the matplotlib API, pyhf.contrib.viz.brazil.plot_results() now returns a lists of the artists drawn on the axis and moves the ax arguments to the to the last argument. (PR #1377)

api_example

The pyhf.compat module has been added to aid in translating to and from ROOT names. (PR #1439)

CLI API

The CLI API now supports a patchset inspect API to list the individual patches in a PatchSet. (PR #1412)

console pyhf patchset inspect [OPTIONS] [PATCHSET]

Contributors

v0.6.2 benefited from contributions from:

Alexander Held (@alexander-held)

Changes:

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

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert over 4 years ago

pyhf - v0.6.1

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

Important Notes

As a result of changes to the default behavior of torch.distributions in PyTorch v1.8.0, accommodating changes have been made in the underlying implementations for pyhf.tensor.pytorch_backend.pytorch_backend. These changes require a new lower bound of torch v1.8.0 for use of the PyTorch backend.

Fixes

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

Features

Python API

The solver_options kwarg can be passed to the pyhf.optimize.opt_scipy.scipy_optimizer optimizer for additional configuration of the minimization. See scipy.optimize.show_options for additional options of optimization solvers.
The torch API is now used to provide the implementations of the ravel, tile, and outer tensorlib methods for the PyTorch backend.

Changes

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

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert almost 5 years ago

pyhf - v0.6.0

This is a minor release from v0.5.4 → v0.6.0.

Important Notes

Please note this release has API breaking changes and carefully read these notes while updating your code to the v0.6.0 API. Perhaps most relevant is the changes to the pyhf.infer.hypotest API, which now uses a calctype argument to differentiate between using an asymptotic calculator or a toy calculator, and a test_stat kwarg to specify which test statistic the calculator should use, with 'qtilde', corresponding to pyhf.infer.test_statistics.qmu_tilde, now the default option. It also relies more heavily on using kwargs to pass options through to the optimizer.
Following the recommendations of NEP 29 — Recommend Python and NumPy version support as a community policy standard pyhf v0.6.0 drops support for Python 3.6. PEP 494 -- Python 3.6 Release Schedule also notes that Python 3.6 will be end of life in December 2021, so pyhf is moving forward with a minimum required runtime of Python 3.7.
Support for the discovery test statistic, q0, has now been added through the pyhf.infer.test_statistics.q0 API.
Support for pseudoexperiments (toys) has been added through the pyhf.infer.calculators.ToyCalculator API. Please see the corresponding example notebook for more detailed exploration of the API.
The minuit extra, python -m pip install pyhf[minuit], now uses and requires the iminuit v2.X release series and API. Note that iminuit v2.X can result in slight differences in minimization results from iminuit v1.X.
The documentation will now be versioned with releases on ReadTheDocs. Please use pyhf.readthedocs.io to access the documentation for the latest stable release of pyhf.
pyhf is transitioning away from Stack Overflow to GitHub Discussions for resolving user questions not covered in the documentation. Please check the GitHub Discussions page to search for discussions addressing your questions and to open up a new discussion if your question is not covered.
pyhf has published a paper in the Journal of Open Source Software. Please make sure to include the paper reference in all citations of pyhf, as documented in the Use and Citations section of the documentation.

Fixes

Fix bug where all extras triggered warning for installation of the contrib extra.
float-like values are used in division for pyhf.writexml.
Model.spec now supports building new models from existing models.
p-values are now reported based on their quantiles, instead of interpolating test statistics and converting to p-values.
Namespace collisions between uproot3 and uproot/uproot4 have been fixed for the xmlio extra.
The normsys modifier now uses the pyhf.interpolators.code4 interpolation method by default.
The histosys modifier now uses the pyhf.interpolators.code4p interpolation method by default.

Features

Python API

The tensorlib API now supports a tensorlib.to_numpy and tensorlib.ravel API.
The pyhf.infer.calculators.ToyCalculator API has been added to support pseudoexperiments (toys).
The empirical test statistic distribution API has been added to help support the ToyCalculator API.
Add a tolerance kwarg to the optimizer API to set a float value as a tolerance for termination of the fit.
The pyhf.optimize.opt_minuit.minuit_optimizer optimizer now can return correlations of the fitted parameters through use of the return_correlation Boolean kwarg.
Add the pyhf.utils.citation API to get a str of the preferred BibTeX entry for citation of the version of pyhf installed. See the example for the CLI API for more information.
The pyhf.infer.hypotest API now uses a calctype argument to differentiate between using an asymptotic calculator or a toy calculator, and a test_stat kwarg to specify which test statistic to use. It also relies more heavily on using kwargs to pass options through to the optimizer.
The default test_stat kwarg for pyhf.infer.hypotest and the calculator APIs is 'qtilde', which corresponds to the alternative test statistic pyhf.infer.test_statistics.qmu_tilde.
The return type of p-value like functions is now a 0-dimensional tensor (with shape ()) instead of a float. This is required to support end-to-end automatic differentiation in future releases.

CLI API

The CLI API now supports a --citation or --cite option to print the preferred BibTeX entry for citation of the version of pyhf installed.

```shell $ pyhf --citation @software{pyhf, author = {Lukas Heinrich and Matthew Feickert and Giordon Stark}, title = "{pyhf: v0.6.0}", version = {0.6.0}, doi = {10.5281/zenodo.1169739}, url = {https://github.com/scikit-hep/pyhf}, }

@article{pyhf_joss, doi = {10.21105/joss.02823}, url = {https://doi.org/10.21105/joss.02823}, year = {2021}, publisher = {The Open Journal}, volume = {6}, number = {58}, pages = {2823}, author = {Lukas Heinrich and Matthew Feickert and Giordon Stark and Kyle Cranmer}, title = {pyhf: pure-Python implementation of HistFactory statistical models}, journal = {Journal of Open Source Software} } ```

Contributors

v0.6.0 benefited from contributions from:

Alexander Held
Marco Gorelli
Pradyumna Rahul K
Eric Schanet
Henry Schreiner

Changes:

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

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert almost 5 years ago

pyhf - v0.5.4

This is a patch release from v0.5.3 → v0.5.4.

Fixes

Require uproot3 instead of uproot v3.X releases to avoid conflicts when uproot4 is installed in an environment with uproot v3.X installed and namespace conflicts with uproot-methods. Adoption of uproot3 in v0.5.4 will ensure v0.5.4 works far into the future if XML and ROOT I/O through uproot is required.

Example:

Without the v0.5.4 patch release there is a regression in using uproot v3.X and uproot4 in the same environment (which was swiftly identified and patched by the fantastic uproot team)

$ python -m pip install "pyhf[xmlio]<0.5.4" $ python -m pip list | grep "pyhf\|uproot" pyhf 0.5.3 uproot 3.13.1 uproot-methods 0.8.0 $ python -m pip install uproot4 $ python -m pip list | grep "pyhf\|uproot" pyhf 0.5.3 uproot 4.0.0 uproot-methods 0.8.0 uproot4 4.0.0

this is resolved in v0.5.4 with the requirement of uproot3

$ python -m pip install "pyhf[xmlio]>=0.5.4" $ python -m pip list | grep "pyhf\|uproot" pyhf 0.5.4 uproot3 3.14.1 uproot3-methods 0.10.0 $ python -m pip install uproot4 # or uproot $ python -m pip list | grep "pyhf\|uproot" pyhf 0.5.4 uproot 4.0.0 uproot3 3.14.1 uproot3-methods 0.10.0 uproot4 4.0.0

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert about 5 years ago

pyhf - v0.5.3

This is a patch release from v0.5.2 → v0.5.3.

Fixes

Workspaces are now immutable
ShapeFactor support added to XML reading and writing
An error is raised if a fit initialization parameter is outside of its bounds (preventing hypotest with POI outside of bounds)

Features

Python API

Inverting hypothesis tests to get upper limits now has an API with pyhf.infer.intervals.upperlimit
Building workspaces from a model and data added with pyhf.workspace.build

CLI API

Added CLI API for pyhf.infer.fit: pyhf fit
pyhf combine now allows for merging channels: pyhf combine --merge-channels --join <join option>
Added utility to download archived pyhf pallets (workspaces + patchsets) to contrib module: pyhf contrib download

Changes

chore: Migrate to new way to set environment variables in GHA (#1139)
feat: Support ShapeFactor for import/export (#1136)
style: Adopt new JAX style of np and jnp (#1135)
docs: Add ss3L hepdata likelihood record (#1133)
fix: Use JAX v0.2.4+ API (#1134)
chore: Add file types for diff to .gitattributes (#1130)
fix: Fixed parameter naming for compatibility with ROOT import/export (#1125)
fix: Make workspaces immutable (#1132)
fix: Logic bug for outer joins of merge channels (#1128)
fix: Validate fit initialization parameters (#1126)
fix: Use functools.wraps with events.register to render docstrings (#1124)
docs: Use sphinx obj scope in docs by default (#1122)
feat: Merge channel functionality in pyhf combine (#1088)
ci: Make docs separate workflow (#1120)
refactor: Migrate contrib download to contrib module (#1119)
docs: Add importance of Issues to CONTRIBUTING.md (#1113)
refactor: Rename paramset.fixed to paramset.suggested_fixed (#1110)
feat: Add pyhf.workspace.build (#1101)
fix: Import all infer submodules (#1104)
docs: Use 1Lbb DOI in contrib download docstring (#1109)
fix: Remove improper defaults for contrib download (#1105)
docs: Add JSON example to README (#1102)
docs: Add CodeMeta JSON-LD Context File (#1091)
feat: Add API to download likelihood patchset archives (#1046)
fix: Avoid deprecation warnings due to invalid escape sequences (#1047)
docs: Add contributors to website (#1095)
docs: Remove fixed parameters caveat for TRexFitter in babel (#1093)
feat: Add test inversion / interval inference API (#953)
ci: Add code scanning CodeQL workflow (#1085)
test: Ensure continuous approximation of Poisson implemented (#1084)
chore: Migrate from bumpversion to bump2version (#1083)
docs: Add citations from 2019 and 2020 papers (#1081)
docs: Add information on announcement mailing list (#1079)
ci: Add workflow for nightly tests of notebooks (#1078)
ci: Add workflow dispatch support (#1076)
chore: Update GitHub Action releases and Python runtimes in CI (#1074)
ci: Add nightly tests using HEAD of dependencies (#1071)
fix: Restrict iminuit to v1.4.X releases (#1070)
chore: Migrate from pep517 to python-build (#1066)
refactor: Remove unused fixtures, refactor validation tests (#1063)
feat: Add fit to infer CLI API (#1060)
feat: Add erf and erfinv to tensorlib (#1061)
feat: Bump to modern pytest (6.0+) (#1049)

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert about 5 years ago

pyhf - v0.5.2

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert over 5 years ago

pyhf - v0.5.1

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert over 5 years ago

pyhf - v0.5.0

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert over 5 years ago

pyhf - v0.4.4

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert over 5 years ago

pyhf - v0.4.3

Scientific Software - Peer-reviewed - Python
Published by matthewfeickert over 5 years ago