Merge remote-tracking branch 'upstream/master'

.github/workflows/pr_tests.yml

@@ -3,66 +3,55 @@ name: PR Tests
 on:
   pull_request:
     branches:
-    - master
+      - master
 
 jobs:
-  linter:
-    name: Linter
+  pre-commit:
+    name: Format
     runs-on: ubuntu-latest
-
     steps:
-      - name: Check out Git repository
-        uses: actions/checkout@v2
-
-      - name: Set up Python
-        uses: actions/setup-python@v1
+      - uses: actions/checkout@v4
         with:
-          python-version: 3.9
-
-      - name: Install Python dependencies
-        run: pip install black flake8
-
-      - name: Run black
-        uses: wearerequired/lint-action@v2
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - uses: pre-commit/action@v3.0.1
         with:
-          auto_fix: true
-          black: true
-          black_auto_fix: true
-
-      - name: Lint with flake8
-        run: flake8 rhalphalib --count --show-source --statistics
+          extra_args: --hook-stage manual --all-files
 
   test:
-    name: Run pytest (Python ${{ matrix.python-version }}, ROOT ${{ matrix.root-version }})
-    needs: linter
+    name:
+      Run pytest (Python ${{ matrix.python-version }}, ROOT ${{
+      matrix.root-version }})
+    needs: pre-commit
     runs-on: ubuntu-latest
     strategy:
       max-parallel: 4
       fail-fast: true
       matrix:
-        python-version: [3.7]
-        root-version: [6.16, 6.22]
+        python-version: ["3.10"]
+        root-version: ["6.30.04", "6.32.10"]
+        include:
+          - python-version: "3.9"
+            root-version: "6.22.8"
 
     steps:
-    - uses: actions/checkout@v1
-    - name: Set up Conda
-      uses: conda-incubator/setup-miniconda@v2.2.0
-      with:
-        python-version: ${{ matrix.python-version }}
-        miniforge-variant: Mambaforge
-        channels: conda-forge,defaults
-        channel-priority: true
-        activate-environment: condaenv
-    - name: Install ROOT ${{ matrix.root-version }}
-      shell: bash -l {0}
-      run: |
-        mamba install -c conda-forge numpy scipy nomkl root==${{ matrix.root-version }}
-    - name: Install package
-      shell: bash -l {0}
-      run: |
-        pip install -e .
-    - name: Test with pytest
-      shell: bash -l {0}
-      run: |
-        pip install pytest
-        pytest tests
+      - uses: actions/checkout@v1
+      - name: Set up Conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+          miniforge-version: latest
+      - name: Install ROOT ${{ matrix.root-version }}
+        shell: bash -l {0}
+        run: |
+          mamba install -c conda-forge numpy scipy nomkl root==${{ matrix.root-version }}
+      - name: Install package
+        shell: bash -l {0}
+        run: |
+          pip install .[test]
+      - name: Test with pytest
+        shell: bash -l {0}
+        run: |
+          pytest tests

.github/workflows/pythonpublish.yml

@@ -8,19 +8,19 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v1
-    - name: Set up Python
-      uses: actions/setup-python@v1
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: __token__
-        TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
-      run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+      - uses: actions/checkout@v1
+      - name: Set up Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools wheel twine
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+        run: |
+          python setup.py sdist bdist_wheel
+          twine upload dist/*

.gitignore

@@ -5,4 +5,4 @@ __pycache__
 *.egg-info
 build
 dist
-.vscode
+.vscode

.pre-commit-config.yaml

@@ -1,9 +1,80 @@
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
+exclude: ^.cruft.json|.copier-answers.yml$
+
 repos:
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "1.19.1"
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==24.*]
+
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.0.0
+    rev: "v5.0.0"
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: "v1.10.0"
+    hooks:
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: "v3.4.2"
+    hooks:
+      - id: prettier
+        types_or: [yaml, markdown, html, css, scss, javascript, json]
+        args: [--prose-wrap=always]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.9.2"
+    hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
+      - id: ruff-format
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.3.0"
+    hooks:
+      - id: codespell
+
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: "v0.10.0.1"
+    hooks:
+      - id: shellcheck
+
+  - repo: local
+    hooks:
+      - id: disallow-caps
+        name: Disallow improper capitalization
+        language: pygrep
+        entry: PyBind|Numpy|Cmake|CCache|Github|PyTest
+        exclude: .pre-commit-config.yaml
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: "v0.23"
     hooks:
-    - id: flake8
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: "23.10.1"
+      - id: validate-pyproject
+        additional_dependencies: ["validate-pyproject-schema-store[all]"]
+
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: "0.31.0"
     hooks:
-      - id: black-jupyter
+      - id: check-dependabot
+      - id: check-github-workflows
+      - id: check-readthedocs

README.md

@@ -6,10 +6,15 @@
 
 ## Quickstart
 
-First, install [Combine v9](https://cms-analysis.github.io/HiggsAnalysis-CombinedLimit/#installation-instructions) using
-your choice of installation instructions (with CMSSW, using LCG, or inside a Conda environment), then in that environment, run:
+First, install
+[Combine v9](https://cms-analysis.github.io/HiggsAnalysis-CombinedLimit/#installation-instructions)
+using your choice of installation instructions (with CMSSW, using LCG, or inside
+a Conda environment), then in that environment, run:
+
 ```bash
 python3 -m pip install --user https://github.com/nsmith-/rhalphalib/archive/master.zip
 ```
-Take a look at [test_rhalphalib.py](https://github.com/nsmith-/rhalphalib/blob/master/tests/test_rhalphalib.py)
+
+Take a look at
+[test_rhalphalib.py](https://github.com/nsmith-/rhalphalib/blob/master/tests/test_rhalphalib.py)
 for examples of how to use the package.

pyproject.toml

@@ -1,2 +1,58 @@
-[tool.black]
-line-length = 199
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "rhalphalib"
+dynamic = ["version"]
+authors = [
+    {name = "Nick Smith", email = "nick.smith@cern.ch"},
+]
+maintainers = [
+    {name = "Nick Smith", email = "nick.smith@cern.ch"},
+]
+description = "A binned fit intermediate representation library"
+readme = "README.md"
+license = {text = "BSD-3-Clause"}
+# keywords = []
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Physics",
+]
+requires-python = ">=3.8"
+dependencies = [
+  "numpy >=1.14",
+  "scipy",
+  "mplhep",
+]
+
+[project.optional-dependencies]
+test = [
+  "pytest",
+]
+dev = [
+  "pre-commit",
+]
+docs = [
+  "sphinx>=7.0",
+  "myst_parser>=0.13",
+  "sphinx_copybutton",
+  "sphinx_autodoc_typehints",
+  "furo>=2023.08.17",
+]
+
+[project.urls]
+Homepage = "https://github.com/nsmith-/rhalphalib"
+
+[tool.setuptools_scm]
+write_to = "src/rhalphalib/version.py"
+
+[tool.ruff]
+line-length = 199
+
+[tool.codespell]
+ignore-words-list = "fpt"

setup.py

@@ -1,49 +1,3 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-import sys
-import os.path
-from setuptools import (
-    setup,
-    find_packages,
-)
+from setuptools import setup
 
-
-about = {}
-with open(os.path.join("rhalphalib", "version.py")) as f:
-    exec(f.read(), about)
-
-
-needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv)
-pytest_runner = ["pytest-runner"] if needs_pytest else []
-
-setup(
-    name="rhalphalib",
-    version=about["__version__"],
-    packages=find_packages(),
-    scripts=[],
-    include_package_data=True,
-    description="A binned fit intermediate representation library",
-    long_description=open("README.md", "rb").read().decode("utf8", "ignore"),
-    long_description_content_type="text/markdown",
-    maintainer="Nick Smith",
-    maintainer_email="nick.smith@cern.ch",
-    url="https://github.com/nsmith-/rhalphalib",
-    download_url="https://github.com/nsmith-/rhalphalib/releases",
-    license="BSD 3-clause",
-    test_suite="tests",
-    install_requires=[
-        "numpy>=1.14",
-        "scipy",
-    ],
-    setup_requires=["flake8"] + pytest_runner,
-    classifiers=[
-        "Development Status :: 4 - Beta",
-        "Intended Audience :: Science/Research",
-        "License :: OSI Approved :: BSD License",
-        "Programming Language :: Python",
-        "Programming Language :: Python :: 2.7",
-        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: 3.7",
-        "Topic :: Scientific/Engineering :: Physics",
-    ],
-)
+setup()

rhalphalib/model.py → src/rhalphalib/model.py

@@ -99,8 +99,13 @@ def renderRoofit(self, workspace):
 
             workspace.add(rooSimul)
             rooObservable = ROOT.RooArgList(channel.observable.renderRoofit(workspace))
-            # that's right I don't need no CombDataSetFactory
-            rooData = ROOT.RooDataHist(self.name + "_observation", "Combined observation", rooObservable, channelCat, obsmap)
+            rooData = ROOT.RooDataHist(
+                self.name + "_observation",
+                "Combined observation",
+                rooObservable,
+                ROOT.RooFit.Index(channelCat),
+                ROOT.RooFit.Import(obsmap),
+            )
             workspace.add(rooData)
         elif rooSimul == None or rooData == None:  # noqa: E711
             raise RuntimeError("Model %r has a pdf or dataset already embedded in workspace %r" % (self, workspace))
@@ -168,7 +173,7 @@ def addSample(self, sample):
         if sample.name in self._samples:
             raise ValueError("Channel %r already has a sample named %s" % (self, sample.name))
         if sample.name[: sample.name.find("_")] != self.name:
-            raise ValueError("Naming convention requires begining of sample %r name to be %s" % (sample, self.name))
+            raise ValueError("Naming convention requires beginning of sample %r name to be %s" % (sample, self.name))
         if self._observable is not None:
             if not sample.observable == self._observable:
                 raise ValueError("Sample %r has an incompatible observable with channel %r" % (sample, self))