Merge branch 'master' into pre-commit-ci-update-config

.github/workflows/main.yml

@@ -31,19 +31,17 @@ jobs:
         os:
           - ubuntu-latest
         python-version:
-          - "3.8"
           - "3.9"
           - "3.10"
           - "3.11"
+          - "3.12"
         include:
           - os: windows-latest
-            python-version: "3.8"
-          - os: windows-latest
-            python-version: "3.11"
-          - os: macos-latest
-            python-version: "3.8"
+            python-version: "3.9"
           - os: macos-latest
-            python-version: "3.11"
+            python-version: "3.9"
+          - os: macos-14
+            python-version: "3.12"  # old versions not supported
     name: Check Python ${{ matrix.python-version }} ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
@@ -68,14 +66,15 @@ jobs:
             ${{ runner.os }}-pip-
 
       - name: Install package
-        run: python -m pip install -e .[test] pytest-xdist   # for multiprocessing
-
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[test] pytest-xdist   # for multiprocessing
 
       - name: Test package
-        run: python -m pytest --doctest-modules --cov=hepstats --cov-report=xml -n3
+        run: python -m pytest --doctest-modules --cov=hepstats --cov-report=xml -n auto
 
       - name: Upload coverage to Codecov
-        if: matrix.python-version == '3.11' && matrix.os == 'ubuntu-latest'
+        if: matrix.python-version == '3.12' && matrix.os == 'ubuntu-latest'
         uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}  # technically not needed, but prevents failures: https://community.codecov.com/t/upload-issues-unable-to-locate-build-via-github-actions-api/3954

.pre-commit-config.yaml

@@ -1,8 +1,4 @@
 repos:
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.4.0
-    hooks:
-      - id: black
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0
     hooks:
@@ -25,7 +21,7 @@ repos:
     hooks:
       - id: check-manifest
         args: [ --update, --no-build-isolation ]
-        additional_dependencies: [ setuptools-scm ]
+        additional_dependencies: [ setuptools-scm, setuptools-scm-git-archive ]
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.9.0
     hooks:
@@ -62,11 +58,9 @@ repos:
   - repo: https://github.com/nbQA-dev/nbQA
     rev: 1.8.5
     hooks:
-      - id: nbqa-isort
-        additional_dependencies: [ isort==5.6.4 ]
 
       - id: nbqa-pyupgrade
-        additional_dependencies: [ pyupgrade==2.7.4 ]
+        additional_dependencies: [ pyupgrade ]
         args: [ --py38-plus ]
 
 
@@ -94,3 +88,18 @@ repos:
       - id: check-github-actions
       - id: check-dependabot
       - id: check-readthedocs
+
+  - repo: https://github.com/MarcoGorelli/auto-walrus
+    rev: 0.3.3
+    hooks:
+      - id: auto-walrus
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.3.7"
+    hooks:
+      - id: ruff
+        types_or: [ python, pyi, jupyter ]
+        args: [ --fix, --unsafe-fixes, --show-fixes , --line-length=120]
+      # Run the formatter.
+      - id: ruff-format
+        types_or: [ python, pyi, jupyter ]

CHANGELOG.rst

@@ -1,9 +1,14 @@
 Changelog
 =========
 
-master
+main
 ******
 
+* Add support for Python 3.12, drop support for Python 3.8
+* Improved support for zfit 0.20+
+
+Thanks to @MoritzNeuberger for finding and proposing a hypothesis test fix.
+
 Version 0.7.0
 *************
 

docs/conf.py

@@ -5,9 +5,11 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
 # -- Path setup --------------------------------------------------------------
+from __future__ import annotations
 
 import sys
 from pathlib import Path
+
 from hepstats import __version__ as version
 
 project_dir = Path(__file__).parents[1]

docs/getting_started/hypotests.rst

@@ -73,7 +73,7 @@ The background plus signal can then be fitted to the data.
 Parameters
 
 +--------+--------+---------------+-----------+
-| name   |  value |  minuit_hesse |  at limit |
+| name   |  value |  hesse |  at limit |
 +========+========+===============+===========+
 | Nsig   |  4.518 |  +/-     5.8  |  False    |
 +--------+--------+---------------+-----------+

environment.yml

@@ -6,11 +6,10 @@ dependencies:
   - numpy
   - scipy
   - iminuit
-  - tensorflow>=2.4
   - tensorflow-probability
-  #- zfit
+  #- zfit  # todo: conda-forge is 0.18.1, we need 0.20.0
   - asdf
   - matplotlib
   - pip:
     - .
-    - zfit >=0.6.4
+    - zfit >=0.20.0

notebooks/hypotests/FC_interval_asy.ipynb

@@ -23,23 +23,19 @@
    },
    "outputs": [],
    "source": [
-    "import os\n",
-    "import time\n",
+    "from __future__ import annotations\n",
     "\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "import zfit\n",
-    "from zfit.loss import UnbinnedNLL\n",
-    "from zfit.minimize import Minuit\n",
-    "\n",
-    "zfit.settings.set_seed(10)\n",
-    "\n",
-    "from utils import one_minus_cl_plot, plotfitresult, pltdist\n",
-    "\n",
     "from hepstats.hypotests import ConfidenceInterval\n",
     "from hepstats.hypotests.calculators import AsymptoticCalculator\n",
     "from hepstats.hypotests.exceptions import POIRangeError\n",
-    "from hepstats.hypotests.parameters import POIarray"
+    "from hepstats.hypotests.parameters import POIarray\n",
+    "from zfit.loss import UnbinnedNLL\n",
+    "from zfit.minimize import Minuit\n",
+    "\n",
+    "zfit.settings.set_seed(10)"
    ]
   },
   {
@@ -66,7 +62,7 @@
    "outputs": [],
    "source": [
     "bounds = (-10, 10)\n",
-    "obs = zfit.Space('x', limits=bounds)\n",
+    "obs = zfit.Space(\"x\", limits=bounds)\n",
     "\n",
     "mean = zfit.Parameter(\"mean\", 0)\n",
     "sigma = zfit.Parameter(\"sigma\", 1.0)\n",
@@ -98,17 +94,16 @@
    "outputs": [],
    "source": [
     "# Create the negative log likelihood\n",
-    "nll = UnbinnedNLL(model=model, data=data) \n",
+    "nll = UnbinnedNLL(model=model, data=data)\n",
     "\n",
     "# Instantiate a minuit minimizer\n",
     "minimizer = Minuit(verbosity=0)\n",
     "\n",
     "# minimisation of the loss function\n",
     "minimum = minimizer.minimize(loss=nll)\n",
-    "minimum.hesse();\n",
-    "print(minimum)\n",
+    "minimum.hesse()\n",
     "\n",
-    "x_err = minimum.params[mean][\"minuit_hesse\"][\"error\"]"
+    "x_err = minimum.params[mean][\"hesse\"][\"error\"]"
    ]
   },
   {
@@ -154,61 +149,60 @@
    "outputs": [],
    "source": [
     "for n in np.arange(-6, 7, 1.0):\n",
-    "        \n",
     "    x = n * x_err\n",
-    "    \n",
+    "\n",
     "    if n not in results:\n",
-    "        \n",
     "        zfit.settings.set_seed(5)\n",
-    "    \n",
+    "\n",
     "        data.resample(param_values={mean: x})\n",
-    "    \n",
+    "\n",
     "        minimum = minimizer.minimize(loss=nll)\n",
-    "        minimum.hesse(); \n",
-    "        \n",
+    "        minimum.hesse()\n",
+    "\n",
     "        results_n = {}\n",
     "        results_n[\"x\"] = minimum.params[mean][\"value\"]\n",
-    "        results_n[\"x_err\"] = minimum.params[mean][\"minuit_hesse\"][\"error\"]\n",
-    "    \n",
+    "        results_n[\"x_err\"] = minimum.params[mean][\"hesse\"][\"error\"]\n",
+    "\n",
     "        calculator = AsymptoticCalculator(minimum, minimizer)\n",
-    "        \n",
-    "        x_min = results_n[\"x\"] - results_n[\"x_err\"]*3\n",
-    "        x_max = results_n[\"x\"] + results_n[\"x_err\"]*3\n",
-    "        \n",
+    "\n",
+    "        x_min = results_n[\"x\"] - results_n[\"x_err\"] * 3\n",
+    "        x_max = results_n[\"x\"] + results_n[\"x_err\"] * 3\n",
+    "\n",
     "        if n < -1:\n",
     "            x_max = max(0.5 * results_n[\"x_err\"], x_max)\n",
-    "        \n",
+    "\n",
     "        poinull = POIarray(mean, np.linspace(x_min, x_max, 50))\n",
-    "      \n",
+    "\n",
     "        results_n[\"calculator\"] = calculator\n",
     "        results_n[\"poinull\"] = poinull\n",
-    "        \n",
+    "\n",
     "    else:\n",
     "        results_n = results[n]\n",
     "        calculator = results_n[\"calculator\"]\n",
     "        poinull = results_n[\"poinull\"]\n",
     "\n",
     "    if \"mu_lower\" not in results_n:\n",
-    "             \n",
     "        for qtilde in [True, False]:\n",
-    "    \n",
     "            while True:\n",
     "                try:\n",
     "                    ci = ConfidenceInterval(calculator, poinull, qtilde=qtilde)\n",
     "                    interval = ci.interval(alpha=0.05, printlevel=0)\n",
     "                    break\n",
     "                except POIRangeError:\n",
     "                    values = poinull.values\n",
-    "                    poinull = POIarray(mean, np.concatenate([values, [values[-1] + np.diff(values)[0]]]))\n",
+    "                    poinull = POIarray(\n",
+    "                        mean,\n",
+    "                        np.concatenate([values, [values[-1] + np.diff(values)[0]]]),\n",
+    "                    )\n",
     "                    results_n[\"poinull\"] = poinull\n",
-    "    \n",
+    "\n",
     "            if qtilde:\n",
     "                results_n[\"mu_lower\"] = interval[\"lower\"]\n",
     "                results_n[\"mu_upper\"] = interval[\"upper\"]\n",
     "            else:\n",
     "                results_n[\"mu_lower_unbound\"] = interval[\"lower\"]\n",
     "                results_n[\"mu_upper_unbound\"] = interval[\"upper\"]\n",
-    "    \n",
+    "\n",
     "        results[n] = results_n"
    ]
   },
@@ -235,15 +229,31 @@
    "source": [
     "f = plt.figure(figsize=(9, 8))\n",
     "\n",
-    "plt.plot([v[\"x\"]/v[\"x_err\"]  for v in results.values()], \n",
-    "         [v[\"mu_upper_unbound\"]/v[\"x_err\"]  for v in results.values()], color=\"black\", label=\"90 % CL, no boundaries\")\n",
-    "plt.plot([v[\"x\"]/v[\"x_err\"]  for v in results.values()], \n",
-    "         [v[\"mu_lower_unbound\"]/v[\"x_err\"]  for v in results.values()], color=\"black\")\n",
-    "plt.plot([v[\"x\"]/v[\"x_err\"]  for v in results.values()], \n",
-    "         [v[\"mu_upper\"]/v[\"x_err\"]  for v in results.values()], \"--\", color=\"crimson\", label=r\"90 % CL, $\\mu > 0$\")\n",
-    "plt.plot([v[\"x\"]/v[\"x_err\"]  for v in results.values()], \n",
-    "         [v[\"mu_lower\"]/v[\"x_err\"]  for v in results.values()], \"--\", color=\"crimson\")\n",
-    "plt.ylim(0.)\n",
+    "plt.plot(\n",
+    "    [v[\"x\"] / v[\"x_err\"] for v in results.values()],\n",
+    "    [v[\"mu_upper_unbound\"] / v[\"x_err\"] for v in results.values()],\n",
+    "    color=\"black\",\n",
+    "    label=\"90 % CL, no boundaries\",\n",
+    ")\n",
+    "plt.plot(\n",
+    "    [v[\"x\"] / v[\"x_err\"] for v in results.values()],\n",
+    "    [v[\"mu_lower_unbound\"] / v[\"x_err\"] for v in results.values()],\n",
+    "    color=\"black\",\n",
+    ")\n",
+    "plt.plot(\n",
+    "    [v[\"x\"] / v[\"x_err\"] for v in results.values()],\n",
+    "    [v[\"mu_upper\"] / v[\"x_err\"] for v in results.values()],\n",
+    "    \"--\",\n",
+    "    color=\"crimson\",\n",
+    "    label=r\"90 % CL, $\\mu > 0$\",\n",
+    ")\n",
+    "plt.plot(\n",
+    "    [v[\"x\"] / v[\"x_err\"] for v in results.values()],\n",
+    "    [v[\"mu_lower\"] / v[\"x_err\"] for v in results.values()],\n",
+    "    \"--\",\n",
+    "    color=\"crimson\",\n",
+    ")\n",
+    "plt.ylim(0.0)\n",
     "plt.legend(fontsize=15)\n",
     "plt.ylabel(r\"Mean $\\mu$\", fontsize=15)\n",
     "plt.xlabel(\"Measured mean $x$\", fontsize=15);"