Merge branch 'master' into prefill-schema-cache

.pre-commit-config.yaml

@@ -48,10 +48,16 @@ repos:
     - id: blacken-docs
       additional_dependencies: [black==22.6.0]
 
+-   repo: https://github.com/asottile/yesqa
+    rev: v1.4.0
+    hooks:
+    - id: yesqa
+
 -   repo: https://github.com/PyCQA/flake8
     rev: 5.0.2
     hooks:
     - id: flake8
+      args: ["--count", "--statistics"]
 
 -   repo: https://github.com/nbQA-dev/nbQA
     rev: 1.4.0

docs/bib/use_citations.bib

@@ -1,3 +1,42 @@
+% 2022-07-21
+@article{Allwicher:2022mcg,
+    author = "Allwicher, Lukas and Faroughy, Darius. A. and Jaffredo, Florentin and Sumensari, Olcyr and Wilsch, Felix",
+    title = "{HighPT: A Tool for high-$p_T$ Drell-Yan Tails Beyond the Standard Model}",
+    eprint = "2207.10756",
+    archivePrefix = "arXiv",
+    primaryClass = "hep-ph",
+    reportNumber = "ZU-TH-29/22",
+    month = "7",
+    year = "2022",
+    journal = ""
+}
+
+% 2022-07-15
+@article{Belle:2022gbl,
+    author = "{Belle Collaboration}",
+    title = "{Search for a dark leptophilic scalar produced in association with $\tau^+\tau^-$ pair in $e^+e^-$ annihilation at center-of-mass energies near 10.58 GeV}",
+    eprint = "2207.07476",
+    archivePrefix = "arXiv",
+    primaryClass = "hep-ex",
+    reportNumber = "BELLE-CONF-2201",
+    month = "7",
+    year = "2022",
+    journal = ""
+}
+
+% 2022-06-29
+@article{Alguero:2022gwm,
+    author = {Alguero, Ga\"el and Araz, Jack Y. and Fuks, Benjamin and Kraml, Sabine},
+    title = "{Signal region combination with full and simplified likelihoods in MadAnalysis 5}",
+    eprint = "2206.14870",
+    archivePrefix = "arXiv",
+    primaryClass = "hep-ph",
+    reportNumber = "IPPP/22/41",
+    month = "6",
+    year = "2022",
+    journal = ""
+}
+
 % 2022-04-19
 @phdthesis{Kvam:2022vgy,
     author = "Kvam, Audrey",
@@ -20,6 +59,15 @@ @article{ATLAS:2022pib
     journal = ""
 }
 
+% 2022-03-28
+@phdthesis{Borgna:2022zoi,
+    author = "Borgna, Lucas Santiago",
+    title = "{Search for pair production of Higgs Bosons decaying to four bottom quarks with data collected by the ATLAS detector}",
+    school = "University Coll. London",
+    year = "2022",
+    url = "https://cds.cern.ch/record/2812193"
+}
+
 % 2022-03-14
 @inproceedings{Albert:2022mpk,
     author = "Albert, Alexander and others",

setup.cfg

@@ -56,5 +56,3 @@ console_scripts =
 # E501: line too long
 extend-ignore = E203, E402, E501
 max-line-length = 88
-count = True
-statistics = True

src/pyhf/cli/rootio.py

@@ -6,6 +6,7 @@
 import os
 from pathlib import Path
 import jsonpatch
+from pyhf.utils import VolumeMountPath
 
 log = logging.getLogger(__name__)
 
@@ -23,14 +24,24 @@ def cli():
     type=click.Path(exists=True),
     default=Path.cwd(),
 )
+@click.option(
+    '-v',
+    '--mount',
+    help='Consists of two fields, separated by a colon character ( : ). The first field is the local path to where files are located, the second field is the path where the file or directory are saved in the XML configuration. This is similar in spirit to docker.',
+    type=VolumeMountPath(exists=True, resolve_path=True, path_type=Path),
+    default=None,
+    multiple=True,
+)
 @click.option(
     '--output-file',
     help='The location of the output json file. If not specified, prints to screen.',
     default=None,
 )
 @click.option('--track-progress/--hide-progress', default=True)
 @click.option('--validation-as-error/--validation-as-warning', default=True)
-def xml2json(entrypoint_xml, basedir, output_file, track_progress, validation_as_error):
+def xml2json(
+    entrypoint_xml, basedir, mount, output_file, track_progress, validation_as_error
+):
     """Entrypoint XML: The top-level XML file for the PDF definition."""
     try:
         import uproot
@@ -47,6 +58,7 @@ def xml2json(entrypoint_xml, basedir, output_file, track_progress, validation_as
     spec = readxml.parse(
         entrypoint_xml,
         basedir,
+        mounts=mount,
         track_progress=track_progress,
         validation_as_error=validation_as_error,
     )

src/pyhf/infer/__init__.py

@@ -204,7 +204,7 @@ def hypotest(
     return tuple(_returns) if len(_returns) > 1 else _returns[0]
 
 
-from pyhf.infer import intervals  # noqa: F401
+from pyhf.infer import intervals
 
 __all__ = ["hypotest", "calculators", "intervals", "mle", "test_statistics", "utils"]
 

src/pyhf/optimize/mixins.py

@@ -1,9 +1,11 @@
 """Helper Classes for use of automatic differentiation."""
-from pyhf.tensor.manager import get_backend
+import logging
+
+import numpy as np
+
 from pyhf import exceptions
 from pyhf.optimize.common import shim
-
-import logging
+from pyhf.tensor.manager import get_backend
 
 log = logging.getLogger(__name__)
 
@@ -82,6 +84,13 @@ def _internal_postprocess(self, fitresult, stitch_pars, return_uncertainties=Fal
         if uncertainties is not None:
             # extract number of fixed parameters
             num_fixed_pars = len(fitted_pars) - len(fitresult.x)
+
+            # FIXME: Set uncertainties for fixed parameters to 0 manually
+            # https://github.com/scikit-hep/iminuit/issues/762
+            # https://github.com/scikit-hep/pyhf/issues/1918
+            # https://github.com/scikit-hep/cabinetry/pull/346
+            uncertainties = np.where(fitresult.minuit.fixed, 0.0, uncertainties)
+
             # stitch in zero-uncertainty for fixed values
             uncertainties = stitch_pars(
                 tensorlib.astensor(uncertainties),

src/pyhf/optimize/opt_minuit.py

@@ -50,14 +50,12 @@ def _get_minimizer(
         par_names=None,
     ):
 
-        step_sizes = [(b[1] - b[0]) / float(self.steps) for b in init_bounds]
         fixed_vals = fixed_vals or []
         # Minuit wants True/False for each parameter
         fixed_bools = [False] * len(init_pars)
         for index, val in fixed_vals:
             fixed_bools[index] = True
             init_pars[index] = val
-            step_sizes[index] = 0.0
 
         # Minuit requires jac=callable
         if do_grad:
@@ -68,7 +66,6 @@ def _get_minimizer(
             jac = None
 
         minuit = iminuit.Minuit(wrapped_objective, init_pars, grad=jac, name=par_names)
-        minuit.errors = step_sizes
         minuit.limits = init_bounds
         minuit.fixed = fixed_bools
         minuit.print_level = self.verbose