Merge pull request #18 from SpeysideHEP/update-v0.2

Adapt to the latest spey version

.github/workflows/check+build+deploy.yaml

@@ -0,0 +1,81 @@
+name: Check/Build/Deploy
+
+on:
+  release:
+    types: [published]
+  push:
+    branches: ["releases/**"]
+  workflow_dispatch:
+
+jobs:
+    # check:
+    #     name: OS ${{ matrix.os }}, Python ${{ matrix.python-version }}
+    #     runs-on: ${{ matrix.os }}
+
+    #     strategy:
+    #       fail-fast: false
+    #       matrix:
+    #         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+    #         os: [ubuntu-latest, macos-latest]
+
+    #     steps:
+    #     - uses: actions/checkout@v3
+    #     - name: Set up Python ${{ matrix.python-version }}
+    #       uses: actions/setup-python@v3
+    #       with:
+    #         python-version: ${{ matrix.python-version }}
+    #     - name: Install dependencies
+    #       run: |
+    #         python -m pip install --upgrade pip
+    #         python -m pip install pytest pytest-cov
+    #         python -m pip install -e .
+    #     - name: Test with pytest
+    #       run: |
+    #         python -c 'import spey;spey.about()'
+    #         pytest --cov=spey tests/*py #--cov-fail-under 99
+
+    build:
+        name: Build wheel
+        runs-on: ubuntu-latest
+        # needs: check
+        steps:
+          - name: Checkout git repository
+            uses: actions/checkout@v4
+
+          - name: Build Spey wheel
+            run: |
+              python -m pip install --upgrade pip
+              python -m pip install wheel
+              python setup.py bdist_wheel
+
+          - name: Upload wheels as artifacts
+            uses: actions/upload-artifact@v4
+            with:
+              name: wheel
+              path: ./dist/*.whl
+
+    deploy:
+        if:  ${{ !github.event.release.prerelease && !contains(github.ref, '-rc') && !contains(github.ref, '-beta') && !contains(github.ref, '-alpha') }}
+        runs-on: ubuntu-latest
+        needs: build
+        environment:
+          name: pypi
+          url: https://pypi.org/project/spey-pyhf/
+        permissions:
+          id-token: write
+        steps:
+          - uses: actions/download-artifact@v4
+            with:
+              pattern: wheel
+              merge-multiple: true
+              path: dist
+
+          - name: Debug
+            run: ls -l dist
+
+          - name: Publish package distributions to PyPI
+            uses: pypa/gh-action-pypi-publish@v1.4.2
+            with:
+              user:     ${{ secrets.TWINE_USERNAME }}
+              password: ${{ secrets.TWINE_PSSWRD }}
+              verbose: true

.zenodo.json

@@ -1,8 +1,8 @@
 {
     "description": "pyhf plug-in for spey package",
     "license": "MIT",
-    "title": "SpeysideHEP/spey-pyhf: v0.1.10",
-    "version": "v0.1.10",
+    "title": "SpeysideHEP/spey-pyhf: v0.2.0",
+    "version": "v0.2.0",
     "upload_type": "software",
     "creators": [
         {
@@ -29,7 +29,7 @@
         },
         {
             "scheme": "url",
-            "identifier": "https://github.com/SpeysideHEP/spey-pyhf/tree/v0.1.10",
+            "identifier": "https://github.com/SpeysideHEP/spey-pyhf/tree/v0.2.0",
             "relation": "isSupplementTo"
         },
         {

CITATIONS.bib

@@ -1,15 +1,16 @@
-@article{10.21468/SciPostPhys.16.1.032,
-    author     = {Jack Y. Araz},
-    doi        = {10.21468/SciPostPhys.16.1.032},
-    journal    = {SciPost Phys.},
-    pages      = {032},
-    publisher  = {SciPost},
-    title      = {{Spey: Smooth inference for reinterpretation studies}},
-    url        = {https://scipost.org/10.21468/SciPostPhys.16.1.032},
-    volume     = {16},
-    year       = {2024},
-    bdsk-url-1 = {https://scipost.org/10.21468/SciPostPhys.16.1.032},
-    bdsk-url-2 = {https://doi.org/10.21468/SciPostPhys.16.1.032}
+@article{Araz:2023bwx,
+    author        = {Araz, Jack Y.},
+    title         = {{Spey: Smooth inference for reinterpretation studies}},
+    eprint        = {2307.06996},
+    archiveprefix = {arXiv},
+    primaryclass  = {hep-ph},
+    reportnumber  = {IPPP/23/34},
+    doi           = {10.21468/SciPostPhys.16.1.032},
+    journal       = {SciPost Phys.},
+    volume        = {16},
+    number        = {1},
+    pages         = {032},
+    year          = {2024}
 }
 
 @software{spey_pyhf_zenodo,

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2024 Jack Y. Araz
+Copyright (c) 2025 Jack Y. Araz
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

docs/conf.py

@@ -16,7 +16,7 @@
 sys.path.insert(0, str(Path("./ext").resolve()))
 
 project = "spey-pyhf"
-copyright = "2024, Jack Y. Araz"
+copyright = "2025, Jack Y. Araz"
 author = "Jack Y. Araz"
 release = get_distribution("spey_pyhf").version
 version = ".".join(release.split(".")[:3])

setup.py

@@ -6,7 +6,7 @@
 with open("src/spey_pyhf/_version.py", encoding="UTF-8") as f:
     version = f.readlines()[-1].split()[-1].strip("\"'")
 
-requirements = ["pyhf==0.7.6", "spey>=0.1.11"]
+requirements = ["pyhf==0.7.6", "spey>=0.2.1"]
 
 docs = [
     "sphinx==6.2.1",
@@ -49,7 +49,7 @@
         ]
     },
     install_requires=requirements,
-    python_requires=">=3.8",
+    python_requires=">=3.8, <3.13",
     classifiers=[
         "Intended Audience :: Science/Research",
         "License :: OSI Approved :: MIT License",

src/spey_pyhf/_version.py

@@ -1,3 +1,3 @@
 """Version of the spey - pyhf plugin"""
 
-__version__ = "0.1.10"
+__version__ = "0.2.0-beta"

src/spey_pyhf/helper_functions.py

@@ -2,6 +2,8 @@
 import logging
 from typing import Dict, Iterator, List, Optional, Tuple, Union
 
+from spey import log_once
+
 __all__ = ["WorkspaceInterpreter"]
 
 
@@ -114,15 +116,12 @@ def expected_background_yields(self) -> Dict[str, List[float]]:
                 if channel["name"] not in self._signal_dict:
                     undefined_channels.append(channel["name"])
         if len(undefined_channels) > 0:
-            log.warning(
+            log_once(
                 "Some of the channels are not defined in the patch set, "
                 "these channels will be kept in the statistical model. "
-            )
-            log.warning(
-                "If these channels are meant to be removed, please indicate them in the patch set."
-            )
-            log.warning(
-                "Please check the following channel(s): " + ", ".join(undefined_channels)
+                "If these channels are meant to be removed, please indicate them in the patch set. "
+                "Please check the following channel(s): " + ", ".join(undefined_channels),
+                log_type="warning",
             )
         return yields
 

src/spey_pyhf/interface.py

@@ -2,7 +2,7 @@
 
 import copy
 import warnings
-from typing import Callable, Dict, List, Optional, Text, Tuple, Union
+from typing import Callable, Dict, List, Optional, Tuple, Union
 
 import numpy as np
 from spey.base import ModelConfig
@@ -73,7 +73,7 @@ class PyhfInterface(BackendBase):
     """Version of the backend"""
     author: str = "SpeysideHEP"
     """Author of the backend"""
-    spey_requires: str = ">=0.1.9,<0.2.0"
+    spey_requires: str = ">=0.2.0, <0.3.0"
     """Spey version required for the backend"""
     doi: List[str] = ["10.5281/zenodo.1169739", "10.21105/joss.02823"]
     """Citable DOI for the backend"""

src/spey_pyhf/manager.py

@@ -5,14 +5,21 @@
 
 from spey.system.exceptions import MethodNotAvailable
 
+log = logging.getLogger("Spey")
+
 
 class PyhfManager:
     """Manager to unify the usage of pyhf through out the package"""
 
     pyhf = importlib.import_module("pyhf")
 
     def __init__(self):
-        PyhfManager.pyhf.set_backend("numpy", precision="64b")
+        if importlib.util.find_spec("jax") is not None:
+            PyhfManager.pyhf.set_backend("jax", precision="64b")
+            log.debug("pyhf backend set to Jax")
+        else:
+            PyhfManager.pyhf.set_backend("numpy", precision="64b")
+            log.debug("pyhf backend set to NumPy")
 
         PyhfManager.pyhf.pdf.log.setLevel(logging.CRITICAL)
         PyhfManager.pyhf.workspace.log.setLevel(logging.CRITICAL)
@@ -61,6 +68,7 @@ def backend(self, backend: str) -> None:
         """
         if backend not in self.available_backends:
             raise MethodNotAvailable(f"{backend} backend currently not available.")
+        log.debug(f"setting pyhf backend to {backend}")
         PyhfManager.pyhf.set_backend(backend)
 
     @property

src/spey_pyhf/simplify.py

@@ -4,7 +4,7 @@
 import warnings
 from contextlib import contextmanager
 from pathlib import Path
-from typing import Callable, List, Literal, Optional, Text, Union
+from typing import Callable, List, Literal, Optional, Union
 
 import numpy as np
 import spey
@@ -170,7 +170,7 @@ class Simplify(spey.ConverterBase):
     """Version of the backend"""
     author: str = "SpeysideHEP"
     """Author of the backend"""
-    spey_requires: str = ">=0.1.5,<0.2.0"
+    spey_requires: str = ">=0.2.0,<0.3.0"
     """Spey version required for the backend"""
 
     def __call__(
@@ -340,15 +340,18 @@ def __call__(
                             # if the initial value is NaN continue search
                             continue
                         current_fit_opts["constraints"] += constraints
-                        with warnings.catch_warnings(record=True) as w:
+                        with warnings.catch_warnings(record=True) as warnings_list:
                             _, new_params = fit(
                                 **current_fit_opts,
                                 initial_parameters=init_params.tolist(),
                                 bounds=current_fit_opts[
                                     "model_configuration"
                                 ].suggested_bounds,
                             )
-                            warnings_list += w
+                            for warning in warnings_list:
+                                log.debug(
+                                    f"{warning.message} (file: {warning.filename}, L:{warning.lineno})"
+                                )
 
                 try:
                     current_sample = statistical_model.backend.get_sampler(
@@ -366,12 +369,6 @@ def __call__(
                     )
                     continue
 
-        if len(warnings_list) > 0:
-            log.warning(
-                f"{len(warnings_list)} warning(s) generated during sampling."
-                " This might be due to edge cases in nuisance parameter sampling."
-            )
-
         samples = np.vstack(samples)
 
         covariance_matrix = np.cov(samples, rowvar=0)