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feat: Add tutorial skeleton from LHC Reinterpretation Forum Workshop 2021 (#1)
* Copy tutorial structure from LHC Reinterpretation Forum Workshop 2021 tutorial * Use pyhf v0.6.1 * Add pre-commit hooks and linting
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‎.github/workflows/deploy-jupyter-book.yml‎

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name: Deploy Jupyter Book
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on:
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push:
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branches:
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- main
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pull_request:
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workflow_dispatch:
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jobs:
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deploy-book:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python 3.8
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uses: actions/setup-python@v2
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with:
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python-version: 3.8
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip setuptools wheel
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python -m pip install --no-cache-dir -r binder/requirements.txt
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python -m pip install --no-cache-dir -r book/requirements.txt
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- name: Build the book
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run: |
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jupyter-book build book/
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- name: Deploy Jupyter book to GitHub pages
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if: success() && github.event_name == 'push' && github.ref == 'refs/heads/main'
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uses: peaceiris/actions-gh-pages@v3
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: book/_build/html
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force_orphan: true
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user_name: 'github-actions[bot]'
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user_email: 'github-actions[bot]@users.noreply.github.com'
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commit_message: Deploy to GitHub pages

‎.github/workflows/lint.yml‎

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name: Lint
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on:
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push:
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branches:
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- main
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pull_request:
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workflow_dispatch:
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jobs:
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lint:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [ '3.8' ]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip setuptools wheel
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python -m pip install pre-commit
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pre-commit install
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- name: Lint with pre-commit
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run: |
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pre-commit run --all-files

‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/psf/black
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rev: 20.8b1
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hooks:
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- id: black
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- repo: https://github.com/asottile/pyupgrade
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rev: v2.11.0
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hooks:
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- id: pyupgrade
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- repo: https://github.com/nbQA-dev/nbQA
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rev: 0.5.9
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hooks:
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- id: nbqa-black
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additional_dependencies: [black==20.8b1]
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- id: nbqa-pyupgrade
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additional_dependencies: [pyupgrade==2.11.0]

‎Makefile‎

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all: build
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defualt: build
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build:
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jupyter-book build book/
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clean: book/_build
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rm -rf book/_build

‎README.md‎

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# pyhf-tutorial
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Updating tutorial on pyhf
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# `pyhf` Tutorial
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Tutorial last given at the [March 2021 PyHEP topical meeting](https://indico.cern.ch/event/985425/).
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**The tutorial is based off of [`pyhf` `v0.6.1`](https://pypi.org/project/pyhf/0.6.1/)**
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[![Deploy Jupyter Book](https://github.com/pyhf/pyhf-tutorial/workflows/Deploy%20Jupyter%20Book/badge.svg?branch=main)](https://pyhf.github.io/pyhf-tutorial/)
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[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/pyhf/pyhf-tutorial/main)
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## Setup
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In a Python virtual environment run the following
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```
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python -m pip install -r binder/requirements.txt
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python -m pip install -r book/requirements.txt
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```
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## Build
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To build the book after setup simply run
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```
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make build
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```
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## Past tutorials
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- [LHC Reinterpretation Forum Workshop 2021](https://indico.cern.ch/event/982553/contributions/4219487/)

‎binder/apt.txt‎

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jq

‎binder/requirements.txt‎

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pyhf[xmlio,minuit,contrib]==0.6.1
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# visualization
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ipywidgets~=7.5
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pandas~=1.0
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altair~=4.1

‎book/Combinations.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Performing a Combination\n",
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"\n",
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"We'll demonstrate how a combination works by combining everything we've learned so far.\n",
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"\n",
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"## Loading the Workspace\n",
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"\n",
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"To do so, we'll use a simple workspace to demonstrate functionality of combinations."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"import json\n",
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"import pyhf"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"with open(\"data/2-bin_1-channel.json\") as serialized:\n",
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" spec = json.load(serialized)\n",
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"\n",
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"workspace = pyhf.Workspace(spec)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Combine Workspaces\n",
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"\n",
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"Let's just try to combine naively right now."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"tags": [
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"raises-exception"
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]
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},
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"outputs": [],
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"source": [
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"pyhf.Workspace.combine(workspace, workspace)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"As we can see, we can't just combine a workspace with itself if it has some channel names in common. We try very hard in `pyhf` to make sure a combination \"makes sense\".\n",
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"\n",
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"Let's go ahead and rename the channel (as well as the measurement). Then try to combine."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"other_workspace = workspace.rename(\n",
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" channels={\"singlechannel\": \"othersinglechannel\"},\n",
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" modifiers={\"uncorr_bkguncrt\": \"otheruncorr_bkguncrt\"},\n",
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" measurements={\"Measurement\": \"OtherMeasurement\"},\n",
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")\n",
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"\n",
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"combined_workspace = pyhf.Workspace.combine(workspace, other_workspace)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"And did we combine?"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"print(f\" channels: {combined_workspace.channels}\")\n",
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"print(f\" nbins: {combined_workspace.channel_nbins}\")\n",
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"print(f\" samples: {combined_workspace.samples}\")\n",
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"print(f\" modifiers: {combined_workspace.modifiers}\")\n",
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"print(f\" parameters: {combined_workspace.parameters}\")\n",
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"print(f\"measurements: {combined_workspace.measurement_names}\")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Indeed. And at this point, we can just use all the same functionality we expect of pyhf, such as performing a fit:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"model = workspace.model()\n",
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"data = workspace.data(model)\n",
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"test_poi = 1.0\n",
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"\n",
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"pyhf.infer.hypotest(test_poi, data, model, test_stat=\"qtilde\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"other_model = other_workspace.model()\n",
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"other_data = other_workspace.data(other_model)\n",
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"\n",
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"pyhf.infer.hypotest(test_poi, other_data, other_model, test_stat=\"qtilde\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"combined_model = combined_workspace.model()\n",
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"combined_data = combined_workspace.data(combined_model)\n",
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"\n",
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"pyhf.infer.hypotest(test_poi, combined_data, combined_model, test_stat=\"qtilde\")"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.8.7"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 4
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}

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