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/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
@@ -63,4 +63,3 @@ body:
       options:
         - label: I have searched existing GitHub issues to make sure the issue does not already exist.
           required: true
-

.github/ISSUE_TEMPLATE/question.yml

@@ -10,9 +10,9 @@ body:
         ## Before posting a question
 
         Search existing [GitHub issues](https://github.com/SpeysideHEP/spey/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/docs.yml

@@ -33,7 +33,7 @@ jobs:
         uses: actions/setup-python@v3
         with:
           python-version: ${{ matrix.python-version }}
-      
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
@@ -44,7 +44,7 @@ jobs:
       - name: Compile Docs
         run: |
           cd docs; make clean; make html; cd ..
-      
+
       - name: Fix permissions if needed
         run: |
           chmod -c -R +rX "docs/_build/html/" | while read line; do
@@ -77,4 +77,4 @@ jobs:
 
     - name: Deploy to GitHub Pages
       id: deployment
-      uses: actions/deploy-pages@v2
+      uses: actions/deploy-pages@v2

.github/workflows/pre-commit.yaml

@@ -0,0 +1,17 @@
+on:
+  pull_request:
+    branches: ["main", "releases/**"]
+  push:
+    branches: ["main", "releases/**", "testing"]
+
+name: Check if pre-commit checks pass
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.8"
+      - uses: pre-commit/[email protected]

.pre-commit-config.yaml

@@ -0,0 +1,34 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-added-large-files
+        args: ["--maxkb=1024"]
+      - id: check-ast
+      - id: check-docstring-first
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: forbid-submodules
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.3.1
+    hooks:
+      - id: pyupgrade
+        args: [--py38-plus]
+        language_version: python3.8
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+
+  - repo: https://github.com/psf/black
+    rev: 22.6.0
+    hooks:
+      - id: black
+        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

@@ -40,4 +40,4 @@
             "relation": "isDocumentedBy"
         }
     ]
-}
+}

CITATIONS.bib

@@ -22,4 +22,4 @@ @software{spey_zenodo
     version   = {v0.1.11},
     doi       = {10.5281/zenodo.14071351},
     url       = {https://doi.org/10.5281/zenodo.14071351}
-}
+}

Makefile

@@ -31,8 +31,3 @@ testpypi:
 .PHONY: pypi
 pypi:
 	python3 -m twine upload -r pypi dist/*
-
-
-
-
-

data/path_finder/example_data.json

@@ -2942,4 +2942,4 @@
             ]
         }
     ]
-}
+}

docs/Makefile

@@ -1,4 +1,4 @@
-# Makefile for Sphinx documentation 
+# Makefile for Sphinx documentation
 
 SPHINXOPTS    = -W --keep-going #-n
 SPHINXBUILD   = sphinx-build

docs/_static/css/custom.css

@@ -45,4 +45,4 @@ span#release {
     width: 200px;
     margin-right: 50px;
     line-height: 22px;
-}
+}

docs/api.rst

@@ -11,7 +11,7 @@ Top-Level
 
 .. currentmodule:: spey
 
-.. autosummary:: 
+.. autosummary::
     :toctree: _generated/
 
     version
@@ -68,7 +68,7 @@ Hypothesis testing
 
 .. currentmodule:: spey.hypothesis_testing
 
-.. autosummary:: 
+.. autosummary::
     :toctree: _generated/
 
     test_statistics.qmu
@@ -91,7 +91,7 @@ Gradient Tools
 
 .. currentmodule:: spey.math
 
-.. autosummary:: 
+.. autosummary::
     :toctree: _generated/
 
     value_and_grad
@@ -105,7 +105,7 @@ Distributions
 
 .. currentmodule:: spey.backends.distributions
 
-.. autosummary:: 
+.. autosummary::
     :toctree: _generated/
 
     Poisson
@@ -119,7 +119,7 @@ Default PDFs
 
 .. currentmodule:: spey.backends.default_pdf
 
-.. autosummary:: 
+.. autosummary::
     :toctree: _generated/
 
     DefaultPDFBase
@@ -133,7 +133,7 @@ Default PDFs
 Simple PDFs
 ~~~~~~~~~~~
 
-.. autosummary:: 
+.. autosummary::
     :toctree: _generated/
 
     simple_pdf.Poisson
@@ -146,7 +146,7 @@ Exceptions
 
 .. currentmodule:: spey.system.exceptions
 
-.. autosummary:: 
+.. autosummary::
     :toctree: _generated/
     :nosignatures:
 

docs/bib/references.bib

@@ -193,4 +193,4 @@ @article{Araz:2023bwx
     reportnumber  = {IPPP/23/34},
     month         = {7},
     year          = {2023}
-}
+}

docs/bibliography.rst

@@ -1,4 +1,4 @@
 Bibliography
 ============
 
-.. bibliography:: bib/references.bib
+.. bibliography:: bib/references.bib

docs/citations.rst

@@ -11,8 +11,8 @@ The BibTeX entry for citing ``spey`` including latest zenodo archive:
     .. note::
 
         To retrieve the latest BibTeX information one can also use :func:`~spey.cite` function.
-        This function pulls the publication information from Inspire-HEP and uses the repository 
-        identification to pull the latest Zenodo archive information. 
+        This function pulls the publication information from Inspire-HEP and uses the repository
+        identification to pull the latest Zenodo archive information.
 
 .. code-block:: bibtex
 
@@ -40,4 +40,4 @@ An up-to-date list can be found on `Inspire-HEP <https://inspirehep.net/literatu
 .. bibliography:: bib/cited.bib
     :all:
     :style: unsrtalpha
-    :list: enumerated
+    :list: enumerated

docs/comb.rst

@@ -7,21 +7,21 @@ Combining Statistical Models
     :property=og:image: https://spey.readthedocs.io/en/main/_static/spey-logo.png
     :property=og:url: https://spey.readthedocs.io/en/main/comb.html
 
-In this section, we will provide a simple statistical model combination example using 
-`Path Finder algorithm <https://github.com/J-Yellen/PathFinder>`_ 
+In this section, we will provide a simple statistical model combination example using
+`Path Finder algorithm <https://github.com/J-Yellen/PathFinder>`_
 (For details, see :cite:`Araz:2022vtr`).
 
 The data, necessary to complete this exercise, has been provided under the ``data/path_finder`` folder of
 `spey's GitHub repository <https://github.com/SpeysideHEP/spey>`_. Here, one will find ``example_data.json``
-and ``overlap_matrix.csv`` files. Both files are generated using MadAnalysis 5 recast of ATLAS-SUSY-2018-31 
-:cite:`ATLAS:2019gdh, DVN/IHALED_2020, Araz:2020stn` 
+and ``overlap_matrix.csv`` files. Both files are generated using MadAnalysis 5 recast of ATLAS-SUSY-2018-31
+:cite:`ATLAS:2019gdh, DVN/IHALED_2020, Araz:2020stn`
 and CMS-SUS-19-006 :cite:`CMS:2019zmd, Mrowietz:2020ztq` analyses.
 
 * ``example_data.json``: Includes cross section and signal, background, and observed yield information
   for this example.
 * ``overlap_matrix.csv``: Includes overlap matrix that the PathFinder algorithm needs to find the best combination.
 
-Let us first import all the necessary packages and construct the data (please add the Pathfinder path to 
+Let us first import all the necessary packages and construct the data (please add the Pathfinder path to
 ``sys.path`` list if needed)
 
 .. code-block:: python3
@@ -35,12 +35,12 @@ Let us first import all the necessary packages and construct the data (please ad
     >>> with open("example_data.json", "r") as f:
     >>>     example_data = json.load(f)
 
-    
+
     >>> models = {}
     >>> # loop overall data
     >>> for data in example_data["data"]:
     >>>     pdf_wrapper = spey.get_backend("default_pdf.uncorrelated_background")
-    
+
     >>>     stat_model = pdf_wrapper(
     ...         signal_yields=data["signal_yields"],
     ...         background_yields=data["background_yields"],
@@ -49,23 +49,23 @@ Let us first import all the necessary packages and construct the data (please ad
     ...         analysis=data["region"],
     ...         xsection=example_data["xsec"],
     ...     )
-    
+
     >>>     llhr = stat_model.chi2(
     ...         poi_test=1.0, poi_test_denominator=0.0, expected=spey.ExpectationType.apriori
     ...     ) / 2.0
-    
+
     >>>     models.update({data["region"]: {"stat_model": stat_model, "llhr": llhr}})
 
-``example_data`` has two main section which are ``"data"`` including all the information about regions 
+``example_data`` has two main section which are ``"data"`` including all the information about regions
 and ``"xsec"`` including cross section value in pb. Using the information provided for each region we construct
 an uncorrelated background-based statistical model. ``llhr`` is the log-likelihood ratio of signal+background and
 background-only statistical models given as
 
-.. math:: 
+.. math::
 
     {\rm llhr} = -\log\frac{\mathcal{L}(1,\theta_1)}{\mathcal{L}(0,\theta_0)}\ .
 
-Finally, the dictionary called ``models`` is just a container to collect all the models. In the next, let us 
+Finally, the dictionary called ``models`` is just a container to collect all the models. In the next, let us
 construct a Binary acceptance matrix and compute the best possible paths
 
 .. code-block:: python3
@@ -80,7 +80,7 @@ construct a Binary acceptance matrix and compute the best possible paths
     >>> plot_results.plot(bam, whdfs)
 
 In the first three lines, we read the overlap matrix, extracted the corresponding weights (``llhr``), and fed these
-into the ``pf.BinaryAcceptance`` function. We use the ``WHDFS`` algorithm to compute the top 5 combinations and plot the 
+into the ``pf.BinaryAcceptance`` function. We use the ``WHDFS`` algorithm to compute the top 5 combinations and plot the
 resulting binary acceptance matrix with the paths.
 
 .. image:: ./figs/bam.png
@@ -90,11 +90,11 @@ resulting binary acceptance matrix with the paths.
 
 Each column and row corresponds to ``overlap_matrix.columns``, and the coloured lines are the chosen paths
 where the best path can be seen via ``whdfs.best.path``. In this case we find ``"atlas_susy_2018_31::SRA_H"``,
-``"cms_sus_19_006::SR25_Njet23_Nb2_HT6001200_MHT350600"`` and ``'cms_sus_19_006::AGGSR7_Njet2_Nb2_HT600_MHT600'`` 
-regions as best regions to be combined. For the combination, we will use :obj:`~spey.UnCorrStatisticsCombiner` 
+``"cms_sus_19_006::SR25_Njet23_Nb2_HT6001200_MHT350600"`` and ``'cms_sus_19_006::AGGSR7_Njet2_Nb2_HT600_MHT600'``
+regions as best regions to be combined. For the combination, we will use :obj:`~spey.UnCorrStatisticsCombiner`
 and feed the statistical models as input.
 
-.. code-block:: 
+.. code-block::
 
     >>> regions = [
     ...      "atlas_susy_2018_31::SRA_H",
@@ -105,7 +105,7 @@ and feed the statistical models as input.
     >>> combined.exclusion_confidence_level(expected=spey.ExpectationType.aposteriori)[2]
     >>> # 0.9858284831278277
 
-.. note:: 
+.. note::
 
     :obj:`~spey.UnCorrStatisticsCombiner` can be used for any backend retrieved via :func:`spey.get_backend`
     function, which wraps the likelihood prescription with :obj:`~spey.StatisticalModel`.
@@ -117,7 +117,7 @@ the stack, which can be found via
 .. code-block:: python3
 
     >>> poiUL = np.array([models[reg]["stat_model"].poi_upper_limit(expected=spey.ExpectationType.aposteriori) for reg in models.keys()])
-    
+
 
 In our case, the minimum value that we found was from ``"atlas_susy_2018_31::SRA_H"`` where the expected exclusion
 limit can be computed via
@@ -127,7 +127,7 @@ limit can be computed via
     >>> models["atlas_susy_2018_31::SRA_H"]["stat_model"].exclusion_confidence_level(expected=spey.ExpectationType.aposteriori)[2]
     >>> # 0.9445409288935508
 
-Finally, we can compare the likelihood distribution of the two 
+Finally, we can compare the likelihood distribution of the two
 
 .. code-block:: python3
     :linenos:
@@ -154,7 +154,7 @@ which gives us the following result:
     :scale: 20
     :alt: Binary Acceptance Matrix
 
-.. attention:: 
+.. attention::
 
     The results can vary between scipy versions and the versions of its compilers due to their effect on
     optimisation algorithm.