Merge branch 'master' into correct_ndof

.flake8

@@ -0,0 +1,13 @@
+[flake8]
+max-complexity = 18
+max-line-length = 88
+exclude = docs/conf.py
+count = True
+statistics = True
+import-order-style = google
+application-import-names = cabinetry, utils
+# ignore whitespace before ':'
+extend-ignore = E203
+# ignore print statements in example
+per-file-ignores =
+    example.py: T

.github/workflows/test-package.yml

@@ -24,16 +24,12 @@ jobs:
       with:
         python-version: '3.x'
 
-    - name: Install python-build, check-manifest, and twine
+    - name: Install python-build and twine
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip install build check-manifest twine
+        python -m pip install build twine
         python -m pip list
 
-    - name: Check MANIFEST
-      run: |
-        check-manifest --verbose
-
     - name: Build a wheel and a sdist
       run: |
         python -m build --outdir dist/ .

.pre-commit-config.yaml

@@ -1,34 +1,28 @@
 repos:
 -   repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.3.0
+    rev: 25.1.0
     hooks:
     -   id: black
--   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.9.0
-    hooks:
-    -   id: mypy
-        name: mypy with Python 3.9
-        files: src/cabinetry
-        additional_dependencies: ["numpy>=1.22", "boost-histogram>=1.0.1", "click>=8", "types-tabulate", "types-PyYAML", "hist>=2.3.0"]
-        # numpy 1.25 is no longer compatible with Python 3.8, so use Python >=3.9 for type checking
-        args: ["--python-version=3.9"]
-    -   id: mypy
-        name: mypy with Python 3.12
-        files: src/cabinetry
-        additional_dependencies: ["numpy>=1.22", "boost-histogram>=1.0.1", "click>=8", "types-tabulate", "types-PyYAML", "hist>=2.3.0"]
-        args: ["--python-version=3.12"]
+# -   repo: https://github.com/pre-commit/mirrors-mypy
+#     rev: v1.14.1
+#     hooks:
+#     -   id: mypy
+#         name: mypy with Python 3.12
+#         files: src/cabinetry
+#         additional_dependencies: ["numpy>=1.22", "boost-histogram>=1.0.1", "click>=8", "types-tabulate", "types-PyYAML", "hist>=2.3.0"]
+#         args: ["--python-version=3.12"]
 -   repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
+    rev: 7.1.1
     hooks:
     -   id: flake8
         additional_dependencies: [flake8-bugbear, flake8-import-order, flake8-print]
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.1
+    rev: v3.19.1
     hooks:
     -   id: pyupgrade
         args: ["--py38-plus"]
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
     -   id: check-added-large-files
         args: ["--maxkb=100"]
@@ -40,7 +34,7 @@ repos:
         # configuration duplicated in setup.cfg
         args: ["--match=(?!setup|example).*\\.py'", "--match-dir='^(?!(tests|utils|docs)).*'", "--convention=google"]
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.4.1
     hooks:
     -   id: codespell
         args: ["-L", "hist", "src", "tests", "utils", "docs/*rst"]

CITATION.cff

@@ -0,0 +1,51 @@
+cff-version: 1.2.0
+message: "Please cite the following works when using this software."
+type: software
+authors:
+- family-names: "Held"
+  given-names: "Alexander"
+  orcid: "https://orcid.org/0000-0002-8924-5885"
+  affiliation: "University of Wisconsin-Madison"
+title: "cabinetry: v0.6.0"
+version: 0.6.0
+doi: 10.5281/zenodo.4742752
+repository-code: "https://github.com/scikit-hep/cabinetry/releases/tag/v0.6.0"
+url: "https://cabinetry.readthedocs.io/"
+keywords:
+  - python
+  - fitting
+  - physics
+  - profile likelihood
+license: "BSD-3-Clause"
+abstract: |
+  Statistical models in [HistFactory](https://cds.cern.ch/record/1456844)
+  format can be built by `cabinetry` from instructions in a declarative
+  configuration.
+  `cabinetry` makes heavy use of [`pyhf`](https://pyhf.readthedocs.io/) for
+  statistical inference, and provides additional utilities to help study and
+  disseminate fit results.
+  This includes commonly used visualizations.
+  Due to its modular approach, analyzers are free to use all of `cabinetry`'s
+  functionality or only some pieces.
+  `cabinetry` can be used for inference and visualization with any
+  `pyhf`-compatible model, whether it was built with `cabinetry` or not.
+references:
+  - type: article
+    authors:
+    - family-names: "Held"
+      given-names: "Alexander"
+      orcid: "https://orcid.org/0000-0002-8924-5885"
+      affiliation: "New York University"
+    - family-names: "Cranmer"
+      given-names: "Kyle"
+      orcid: "https://orcid.org/0000-0002-5769-7094"
+      affiliation: "New York University"
+    title: "Building and steering binned template fits with cabinetry"
+    doi: 10.1051/epjconf/202125103067
+    url: "https://doi.org/10.1051/epjconf/202125103067"
+    year: 2021
+    publisher:
+      name: "EDP Sciences"
+    volume: 251
+    pages: 03067
+    journal: EPJ Web of Web of Conferences

README.md

@@ -72,8 +72,7 @@ It requires additional dependencies obtained with `pip install cabinetry[contrib
 ## Documentation
 
 Find more information in the [documentation](https://cabinetry.readthedocs.io/) and tutorial material in the [cabinetry-tutorials](https://github.com/cabinetry/cabinetry-tutorials) repository.
-`cabinetry` is also described in a paper submitted to vCHEP 2021: [10.5281/zenodo.4627037](https://doi.org/10.5281/zenodo.4627037).
-
+`cabinetry` is also described in a paper submitted to vCHEP 2021: [10.1051/epjconf/202125103067](https://doi.org/10.1051/epjconf/202125103067).
 
 ## Acknowledgements
 

pyproject.toml

@@ -1,6 +1,115 @@
 [build-system]
-requires = ["setuptools>=42"]
-build-backend = "setuptools.build_meta"
+requires = [
+    "hatchling>=1.13.0",
+]
+build-backend = "hatchling.build"
+
+[project]
+name = "cabinetry"
+version = "0.6.0"
+description = "design and steer profile likelihood fits"
+readme = "README.md"
+license = { text = "BSD-3-Clause" }  # SPDX short identifier
+requires-python = ">=3.8"
+authors = [
+    { name = "Alexander Held", email = "[email protected]" },
+]
+maintainers = [ {name = "The Scikit-HEP admins", email = "[email protected]"} ]
+keywords = [
+    "fitting",
+    "physics",
+    "profile likelihood",
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Physics",
+]
+dependencies = [
+    "pyhf[minuit]~=0.7.0",  # model.config.suggested_fixed / .par_names API changes, set_poi(None)
+    "boost_histogram>=1.0.0",  # subclassing with family, 1.02 for stdev scaling fix (currently not needed)
+    "hist>=2.5.0",  # hist.intervals.poisson_interval
+    "tabulate>=0.8.1",  # multiline text
+    "matplotlib>=3.5.0",  # layout kwarg for subplots
+    # below are direct dependencies of cabinetry, which are also included via pyhf[iminuit]
+    "numpy",
+    "pyyaml",
+    "iminuit",
+    "jsonschema",
+    "click",
+    "scipy",
+    "packaging",  # for version parsing
+]
+
+[project.scripts]
+cabinetry = "cabinetry.cli:cabinetry"
+
+[project.urls]
+Documentation = "https://cabinetry.readthedocs.io/"
+Homepage = "https://github.com/scikit-hep/cabinetry"
+"Issue Tracker" = "https://github.com/scikit-hep/cabinetry/issues"
+"Releases" = "https://github.com/scikit-hep/cabinetry/releases"
+"Source Code" = "https://github.com/scikit-hep/cabinetry"
+
+[project.optional-dependencies]
+contrib = ["uproot>=4.1.5"]  # file writing bug-fixes
+pyhf_backends = ["pyhf[backends]"]
+
+# Developer extras
+test = [
+    "cabinetry[contrib]",
+    "pytest",
+    "pytest-cov>=2.6.1",  # no_cover support
+    "pydocstyle",
+    "check-manifest",
+    "flake8",
+    "flake8-bugbear",
+    "flake8-import-order",
+    "flake8-print",
+    "mypy",
+    "types-tabulate",
+    "types-PyYAML",
+    "typeguard>=4.0.0",  # cabinetry#391
+    "black",
+]
+docs = [
+    "sphinx!=5.2.0.post0",  # broken due to version parsing in RTD theme
+    "sphinx-click",
+    "sphinx-copybutton",
+    "sphinx-jsonschema",
+    "sphinx-rtd-theme>=1.2",  # Sphinx 7 compatibility
+]
+develop = [
+    "cabinetry[test,docs]",
+    "pre-commit",
+    "twine",
+]
+complete = [
+    "cabinetry[develop]",
+    "cabinetry[pyhf_backends]",
+]
+
+[tool.hatch.build.targets.sdist]
+# hatchling always includes:
+# pyproject.toml, .gitignore, any README, any LICENSE, AUTHORS
+only-include = [
+    "/src",
+    "/tests",
+    "/utils",
+]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/cabinetry"]
 
 [tool.black]
 target-version = ['py38']
@@ -13,6 +122,19 @@ exclude = '''
 )/
 '''
 
+[tool.pytest.ini_options]
+# running typeguard can result in lower coverage https://github.com/agronholm/typeguard/issues/356
+addopts = "--cov=cabinetry --cov-report html --cov-report term-missing --cov-branch -rsx --typeguard-packages=cabinetry"
+
+[tool.pytype]
+inputs = "src/cabinetry"
+
+[tool.pydocstyle]
+# configuration duplicated in pre-commit config
+match = "(?!setup|example).*\\.py"
+match_dir = "^(?!(tests|utils|docs)).*"
+convention = "google"
+
 [tool.mypy]
 files = "src/cabinetry"
 pretty = true