pyhf 0.6.0

Hello World

This is how you use the pyhf Python API to build a statistical model and run basic inference:

>>> import pyhf
>>> model = pyhf.simplemodels.hepdata_like(signal_data=[12.0, 11.0], bkg_data=[50.0, 52.0], bkg_uncerts=[3.0, 7.0])
>>> data = [51, 48] + model.config.auxdata
>>> test_mu = 1.0
>>> CLs_obs, CLs_exp = pyhf.infer.hypotest(test_mu, data, model, test_stat="qtilde", return_expected=True)
>>> print(f"Observed: {CLs_obs}, Expected: {CLs_exp}")
Observed: 0.05251497423736956, Expected: 0.06445320535890459

Alternatively the statistical model and observational data can be read from its serialized JSON representation (see next section).

>>> import pyhf
>>> import requests
>>> wspace = pyhf.Workspace(requests.get('https://git.io/JJYDE').json())
>>> model = wspace.model()
>>> data = wspace.data(model)
>>> test_mu = 1.0
>>> CLs_obs, CLs_exp = pyhf.infer.hypotest(test_mu, data, model, test_stat="qtilde", return_expected=True)
>>> print(f"Observed: {CLs_obs}, Expected: {CLs_exp}")
Observed: 0.3599840922126626, Expected: 0.3599840922126626

Finally, you can also use the command line interface that pyhf provides

$ cat << EOF  | tee likelihood.json | pyhf cls
{
    "channels": [
        { "name": "singlechannel",
          "samples": [
            { "name": "signal",
              "data": [12.0, 11.0],
              "modifiers": [ { "name": "mu", "type": "normfactor", "data": null} ]
            },
            { "name": "background",
              "data": [50.0, 52.0],
              "modifiers": [ {"name": "uncorr_bkguncrt", "type": "shapesys", "data": [3.0, 7.0]} ]
            }
          ]
        }
    ],
    "observations": [
        { "name": "singlechannel", "data": [51.0, 48.0] }
    ],
    "measurements": [
        { "name": "Measurement", "config": {"poi": "mu", "parameters": []} }
    ],
    "version": "1.0.0"
}
EOF

which should produce the following JSON output:

{
   "CLs_exp": [
      0.0026062609501074576,
      0.01382005356161206,
      0.06445320535890459,
      0.23525643861460702,
      0.573036205919389
   ],
   "CLs_obs": 0.05251497423736956
}

What does it support

Implemented variations:

• ☑ HistoSys

• ☑ OverallSys

• ☑ ShapeSys

• ☑ NormFactor

• ☑ Multiple Channels

• ☑ Import from XML + ROOT via uproot

• ☑ ShapeFactor

• ☑ StatError

• ☑ Lumi Uncertainty

• ☑ Non-asymptotic calculators

Computational Backends:

• ☑ NumPy

• ☑ PyTorch

• ☑ TensorFlow

• ☑ JAX

Optimizers:

• ☑ SciPy (scipy.optimize)

• ☑ MINUIT (iminuit)

All backends can be used in combination with all optimizers. Custom user backends and optimizers can be used as well.

Todo

• ☐ StatConfig

results obtained from this package are validated against output computed from HistFactory workspaces

A one bin example

import pyhf
import numpy as np
import matplotlib.pyplot as plt
import pyhf.contrib.viz.brazil

pyhf.set_backend("numpy")
model = pyhf.simplemodels.hepdata_like(
    signal_data=[10.0], bkg_data=[50.0], bkg_uncerts=[7.0]
)
data = [55.0] + model.config.auxdata

poi_vals = np.linspace(0, 5, 41)
results = [
    pyhf.infer.hypotest(
        test_poi, data, model, test_stat="qtilde", return_expected_set=True
    )
    for test_poi in poi_vals
]

fig, ax = plt.subplots()
fig.set_size_inches(7, 5)
ax.set_xlabel(r"$\mu$ (POI)")
ax.set_ylabel(r"$\mathrm{CL}_{s}$")
pyhf.contrib.viz.brazil.plot_results(ax, poi_vals, results)
fig.show()

pyhf

ROOT

A two bin example

import pyhf
import numpy as np
import matplotlib.pyplot as plt
import pyhf.contrib.viz.brazil

pyhf.set_backend("numpy")
model = pyhf.simplemodels.hepdata_like(
    signal_data=[30.0, 45.0], bkg_data=[100.0, 150.0], bkg_uncerts=[15.0, 20.0]
)
data = [100.0, 145.0] + model.config.auxdata

poi_vals = np.linspace(0, 5, 41)
results = [
    pyhf.infer.hypotest(
        test_poi, data, model, test_stat="qtilde", return_expected_set=True
    )
    for test_poi in poi_vals
]

fig, ax = plt.subplots()
fig.set_size_inches(7, 5)
ax.set_xlabel(r"$\mu$ (POI)")
ax.set_ylabel(r"$\mathrm{CL}_{s}$")
pyhf.contrib.viz.brazil.plot_results(ax, poi_vals, results)
fig.show()

pyhf

ROOT

Installation

To install pyhf from PyPI with the NumPy backend run

python -m pip install pyhf

and to install pyhf with all additional backends run

python -m pip install pyhf[backends]

or a subset of the options.

To uninstall run

python -m pip uninstall pyhf

Questions

If you have a question about the use of pyhf not covered in the documentation, please ask a question on the GitHub Discussions.

If you believe you have found a bug in pyhf, please report it in the GitHub Issues. If you’re interested in getting updates from the pyhf dev team and release announcements you can join the pyhf-announcements mailing list.

Citation

As noted in Use and Citations, the preferred BibTeX entry for citation of pyhf includes both the Zenodo archive and the JOSS paper:

@software{pyhf,
  author = "{Heinrich, Lukas and Feickert, Matthew and Stark, Giordon}",
  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}
}

Authors

pyhf is openly developed by Lukas Heinrich, Matthew Feickert, and Giordon Stark.

Please check the contribution statistics for a list of contributors.

Milestones

• 2020-07-28: 1000 GitHub issues and pull requests. (See PR #1000)

Acknowledgements

Matthew Feickert has received support to work on pyhf provided by NSF cooperative agreement OAC-1836650 (IRIS-HEP) and grant OAC-1450377 (DIANA/HEP).