add precommit

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -9,7 +9,7 @@ body:
       value: |
         ## Before posting a feature request
         Search existing [GitHub issues](https://github.com/SpeysideHEP/spey-pyhf/issues) to make sure the issue does not already exist.
-        
+
         * **Please use [Markdown syntax](https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax).**
   - type: textarea
     id: system
@@ -49,4 +49,3 @@ body:
       label: Additional information
       description: |
         Add any other context about the problem here.
-

.github/ISSUE_TEMPLATE/question.yml

@@ -10,9 +10,9 @@ body:
         ## Before posting a question
 
         Search existing [GitHub issues](https://github.com/SpeysideHEP/spey-pyhf/issues) to make sure the issue does not already exist.
-          
+
         If your question involves software issues, please include your system settings as shown below;
-        
+
         **System Settings:**
         Please copy and paste the output of `spey.about()` function. If you are working on a specific branch please add the name of the branch and last commit ID. The abbreviated commit ID can be found via `git log -n1 --format="%h"` command. To retreive the branch name please use `git rev-parse --abbrev-ref HEAD` command.)
   - type: textarea
@@ -21,7 +21,7 @@ body:
       label: Question
       description: |
         How can we help?
-        
+
         * **Please use [Markdown syntax](https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax).**
     validations:
       required: true

.github/workflows/black.yml

@@ -22,4 +22,4 @@ jobs:
         id: action_black
         with:
           options: "-l 100"
-          src: "./src"
+          src: "./src"

.pre-commit-config.yaml

@@ -17,7 +17,8 @@ repos:
     rev: v3.3.1
     hooks:
       - id: pyupgrade
-        args: [--py310-plus]
+        args: [--py38-plus]
+        language_version: python3.8
 
   - repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.10.0
@@ -30,5 +31,5 @@ repos:
     rev: 22.6.0
     hooks:
       - id: black
-        args: [--line-length=90]
-        language_version: python3.10
+        args: ["--line-length=90", "--target-version=py38"]
+        language_version: python3.8

.readthedocs.yaml

@@ -23,4 +23,4 @@ python:
   install:
     - requirements: docs/requirements.txt
     - method: pip
-      path: .
+      path: .

.zenodo.json

@@ -43,4 +43,4 @@
             "relation": "requires"
         }
     ]
-}
+}

CITATIONS.bib

@@ -49,4 +49,4 @@ @article{pyhf_joss
     author    = {Lukas Heinrich and Matthew Feickert and Giordon Stark and Kyle Cranmer},
     title     = {pyhf: pure-Python implementation of HistFactory statistical models},
     journal   = {Journal of Open Source Software}
-}
+}

Makefile

@@ -31,8 +31,3 @@ testpypi:
 .PHONY: pypi
 pypi:
 	twine --repository spey-pyhf upload dist/*
-
-
-
-
-

docs/Makefile

@@ -1,4 +1,4 @@
-# Makefile for Sphinx documentation 
+# Makefile for Sphinx documentation
 
 SPHINXOPTS    = -W --keep-going #-n
 SPHINXBUILD   = sphinx-build
@@ -78,4 +78,4 @@ latex:
 	@echo
 	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
 	@echo "Run \`make' in that directory to run these through (pdf)latex" \
-	      "(use \`make latexpdf' here to do that automatically)."
+	      "(use \`make latexpdf' here to do that automatically)."

docs/_static/css/custom.css

@@ -87,4 +87,4 @@ span.label {
     background-color: var(--pst-color-surface);
     color: var(--pst-color-text-base);
     border: 1px solid var(--pst-color-border);
-}
+}

docs/api.rst

@@ -12,7 +12,7 @@ Managers
 
 .. currentmodule:: spey_pyhf
 
-.. autosummary:: 
+.. autosummary::
     :toctree: _generated/
 
     manager.PyhfManager
@@ -63,4 +63,4 @@ Helper functions
 
 .. autoclass:: spey_pyhf.WorkspaceInterpreter
     :members:
-    :undoc-members:
+    :undoc-members:

docs/bib/references.bib

@@ -1,10 +1,10 @@
 %% This BibTeX bibliography file was created using BibDesk.
 %% https://bibdesk.sourceforge.io/
 
-%% Created for Jack Araz at 2023-04-01 8:42:56 am +0100 
+%% Created for Jack Araz at 2023-04-01 8:42:56 am +0100
 
 
-%% Saved with string encoding Unicode (UTF-8) 
+%% Saved with string encoding Unicode (UTF-8)
 
 
 

docs/citations.rst

@@ -38,4 +38,4 @@ This plug-in uses ``pyhf`` internally; thus, please also cite the following
         year = {2021},
         bdsk-url-1 = {https://doi.org/10.21105/joss.02823}}
 
-.. include:: ZENODO-PYHF.rst
+.. include:: ZENODO-PYHF.rst

docs/quick_start.rst

@@ -20,7 +20,7 @@ Installation
 Python >=3.8 is required. This will also automatically install ``pyhf`` since it is a requirement.
 For Gradient and Hessian implementations in likelihood optimisation, we recommend also installing ``Jax``.
 
-Once this package is installed, ``spey`` can automatically detect it, which can be tested using 
+Once this package is installed, ``spey`` can automatically detect it, which can be tested using
 :func:`~spey.AvailableBackends` function;
 
 .. code-block:: python3
@@ -99,7 +99,7 @@ descriptions within ``spey``;
 
     >>> statistical_model.exclusion_confidence_level() # [0.9474850259721279]
 
-For the rest of the functionalities, please refer to the ``spey`` documentation, which can be found 
+For the rest of the functionalities, please refer to the ``spey`` documentation, which can be found
 `in this link <https://speysidehep.github.io/spey/>`_. Due to Spey's fully
 backend agnostic structure, all the functionalities of the :class:`~spey.StatisticalModel` class also
 applies to ``pyhf`` plug-in.
@@ -109,13 +109,13 @@ applies to ``pyhf`` plug-in.
  * ``background_only_model``: This background-only model dictionary includes information about
    background yields, uncertainties and observations. Details on constructing these dictionaries can be
    found in `pyhf's online documentation <https://pyhf.readthedocs.io/en/v0.7.2/likelihood.html>`_.
- * ``signal_patch``: This signal patch includes dictionaries describing which regions will be added or 
+ * ``signal_patch``: This signal patch includes dictionaries describing which regions will be added or
    removed from the statistical model.
  * ``analysis`` (optional): Unique identifier for the analysis.
  * ``xsection`` (optional): Cross-section value for the signal hypothesis. Units determined by the user.
 
 
-Additionally, this plug-in is shipped with simple uncorrelated background-attachment which accesses 
+Additionally, this plug-in is shipped with simple uncorrelated background-attachment which accesses
 ``pyhf``'s ``uncorrelated_backgound`` function can be accessed through spey with the following function
 
 .. code-block:: python3
@@ -152,7 +152,7 @@ Additionally, this plug-in is shipped with simple uncorrelated background-attach
 
 .. note::
 
-    ``pyhf`` offers an interface to combine the likelihoods that are described as JSON serialised 
+    ``pyhf`` offers an interface to combine the likelihoods that are described as JSON serialised
     files. This has been exploited in ``spey`` interface via :func:`combine` `function <https://speysidehep.github.io/spey/api.html#spey.StatisticalModel.combine>`_.
     This function combines ``pyhf`` workspaces and adjusts the signal structure accordingly. For more information
-    about how ``pyhf`` handles the workspace combination `see the dedicated tutorial here <https://pyhf.github.io/pyhf-tutorial/Combinations.html>`_.
+    about how ``pyhf`` handles the workspace combination `see the dedicated tutorial here <https://pyhf.github.io/pyhf-tutorial/Combinations.html>`_.

docs/release_notes.rst

@@ -4,4 +4,4 @@ Release Notes
 .. toctree::
    :maxdepth: 2
 
-   releases/changelog-v0.1
+   releases/changelog-v0.1

docs/requirements.txt

@@ -8,4 +8,4 @@ sphinx-togglebutton>=0.3.0
 myst-parser
 sphinx-rtd-size
 sphinx-book-theme
-myst-nb
+myst-nb