Extend sampler

.github/workflows/black.yml

@@ -1,4 +1,4 @@
-name: black-action
+name: Lint
 
 on:
   push:
@@ -13,25 +13,13 @@ on:
   workflow_dispatch:
 
 jobs:
-  linter_name:
+  lint:
     name: runner / black
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - name: Check files using the black formatter
-        uses: rickstaa/action-black@v1
+      - uses: actions/checkout@v3
+      - uses: psf/black@stable
         id: action_black
         with:
-          black_args: "-l 100 ./src/*"
-      - name: Create Pull Request
-        if: steps.action_black.outputs.is_formatted == 'true'
-        uses: peter-evans/create-pull-request@v3
-        with:
-          token: ${{ secrets.GITHUB_TOKEN }}
-          title: "Format Python code with psf/black push"
-          commit-message: ":art: Format Python code with psf/black"
-          body: |
-            There appear to be some python formatting errors in ${{ github.sha }}. This pull request
-            uses the [psf/black](https://github.com/psf/black) formatter to fix these issues.
-          base: ${{ github.head_ref }} # Creates pull request onto pull request or commit branch
-          branch: actions/black
+          options: "-l 100"
+          src: "./src"

.github/workflows/docs.yml

@@ -1,10 +1,9 @@
 name: Build Documentation
 
 on:
-  pull_request:
-    branches: [ "main" ]
   push:
     branches: ["main"]
+    paths: ["**.rst"]
   workflow_dispatch:
 
 # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages

docs/api.rst

@@ -12,6 +12,7 @@ Managers
     manager.PyhfManager
     interface.ModelNotDefined
     interface.CombinationError
+    simplify.ConversionError
 
 Interface
 ---------
@@ -26,4 +27,34 @@ Interface
     :members:
     :undoc-members:
     :show-inheritance:
-    :inherited-members:
+    :inherited-members:
+
+.. autoclass:: spey_pyhf.simplify.Simplify
+    :members:
+    :undoc-members:
+
+Data classes
+------------
+
+.. autoclass:: spey_pyhf.data.Base
+    :members:
+    :undoc-members:
+
+.. autoclass:: spey_pyhf.data.FullStatisticalModelData
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+.. autoclass:: spey_pyhf.data.SimpleModelData
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:
+
+Helper functions
+----------------
+
+.. autoclass:: spey_pyhf.WorkspaceInterpreter
+    :members:
+    :undoc-members:

docs/citations.rst

@@ -16,7 +16,7 @@ The BibTeX entry for citing ``spey`` is
         year = "2023"
     }
 
-This plug-in uses ``pyhf`` internally, thus please also cite the following
+This plug-in uses ``pyhf`` internally; thus, please also cite the following
 
 .. code-block:: BibTeX
 

docs/conf.py

@@ -35,14 +35,19 @@
     "sphinxcontrib.bibtex",
     "sphinx.ext.napoleon",
     "sphinx_click.ext",
+    # "sphinx_toolbox.collapse", # requires sphinx_toolbox to be installed
     "nbsphinx",
     "sphinx_issues",
     "sphinx_copybutton",
     "sphinx_togglebutton",
+    "sphinx_rtd_size",
     "xref",
     "myst_parser",
 ]
 
+# set the width of the page
+sphinx_rtd_size_width = "75%"
+
 # external links
 xref_links = {
     "1007.1727": ("[arXiv:1007.1727]", "https://doi.org/10.48550/arXiv.1007.1727"),

docs/index.rst

@@ -11,14 +11,9 @@ Welcome to the documentation of ``pyhf`` plugin for spey interface
    :caption: Contents:
 
    quick_start
+   simplify
    api
    citations
-
-
-
-Indices and tables
-==================
+   releases/changelog-dev
 
 * :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`

docs/quick_start.rst

@@ -8,10 +8,10 @@ Installation
     >>> pip install spey-pyhf
 
 
-Python >=3.8 is required. This will automatically install ``pyhf`` as well since it is a requirement.
-For Gradient and Hessian implementations in likelihood optimisation we recomend also installing ``Jax``.
+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
@@ -25,13 +25,15 @@ Once this package is installed, ``spey`` can automatically detect it which can b
     >>> #  'pyhf',
     >>> #  'pyhf.uncorrelated_background']
 
+.. _sec_quick_start:
+
 Quick Start
 ===========
 
 ``"pyhf"`` accessor enables user to access all ``pyhf``'s likelihood building capabilities.
-The function of this accessor accepts a background only statistical model dictionary as described
-in `pyhf's online documentation <https://pyhf.readthedocs.io/en/v0.7.2/likelihood.html>`_. Additinally,
-signal patch sample needs to be provided. An example for these two can be found below.
+The function of this accessor accepts a background-only statistical model dictionary as described
+in `pyhf's online documentation <https://pyhf.readthedocs.io/en/v0.7.2/likelihood.html>`_. Additionally,
+a signal patch sample needs to be provided. An example of these two can be found below.
 
 .. code-block:: python3
 
@@ -71,8 +73,8 @@ signal patch sample needs to be provided. An example for these two can be found
     ...     }
     ... ]
 
-where ``background_only`` dictionary refers to the statistical model that encapsulates only the background
-and ``signal`` includes the signal only patch set. In the following we demonstrate the usage of these
+The ``background_only`` dictionary refers to the statistical model that encapsulates only the background
+, and the ``signal`` includes the signal-only patch set. In the following, we demonstrate the usage of these
 descriptions within ``spey``;
 
 .. code-block:: python3
@@ -88,23 +90,24 @@ descriptions within ``spey``;
 
     >>> statistical_model.exclusion_confidence_level() # [0.9474850259721279]
 
-For the rest of the functionalities please refer to the ``spey`` documentation. Due to spey's fully
-backend agnostic structure all the functionalities of the :class:`~spey.StatisticalModel` class also
+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.
 
 **Arguments:**
 
- * ``background_only_model``: This is background-only model dictionary which includes information about
-   background yields, uncertainties and observations. Details on how to construct these dictionaries can be
+ * ``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 is signal patch which includes dictionaries describing which regions are going
-   to be added or removed from the statistical model.
+ * ``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.
+ * ``xsection`` (optional): Cross-section value for the signal hypothesis. Units determined by the user.
 
 
-Additionally this plug-in is shiped with simple uncorrelated background attachment which accesses 
-``pyhf``'s ``uncorrelated_backgound`` function which can be accessed through spey with following function
+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
 
@@ -135,12 +138,12 @@ Additionally this plug-in is shiped with simple uncorrelated background attachme
  * ``data``: observations as a list.
  * ``absolute_uncertainties``: uncertainties on the background as a list.
  * ``analysis`` (optional): Unique identifier for the analysis.
- * ``xsection`` (optional): Cross section value for the signal hypothesis. Units determined by the user.
+ * ``xsection`` (optional): Cross-section value for the signal hypothesis. Units determined by the user.
 
 
 .. note::
 
     ``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 adjust the signal structure accordingly. For more information
+    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>`_.

docs/releases/changelog-v0.1.1.md

@@ -0,0 +1,28 @@
+# Release notes v0.1.1
+
+## New features since last release
+
+* A mapping functionality has been developed between ``pyhf``'s full
+  statistical models and simplified likelihoods framework. Methodology
+  and usage can be found in the online documentation.
+  ([#2](https://github.com/SpeysideHEP/spey-pyhf/pull/2))
+
+## Improvements
+
+* Sampler functionality has been extended to isolate auxiliary data.
+  ([#3](https://github.com/SpeysideHEP/spey-pyhf/pull/3))
+
+* Fixed parameters have been added to the constraints list.
+  ([#2](https://github.com/SpeysideHEP/spey-pyhf/pull/2))
+
+## Bug fixes
+
+* Bugfix in apriori likelihood computation for full likelihoods mentioned in
+  [#5](https://github.com/SpeysideHEP/spey-pyhf/issues/5).
+  ([#2](https://github.com/SpeysideHEP/spey-pyhf/pull/2))
+
+## Contributors
+
+This release contains contributions from (in alphabetical order):
+
+* [Jack Araz](https://github.com/jackaraz)